-- dump date 20140619_025603 -- class Genbank::misc_feature -- table misc_feature_note -- id note 860228000001 Methyltransferase domain; Region: Methyltransf_23; pfam13489 860228000002 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 860228000003 S-adenosylmethionine binding site [chemical binding]; other site 860228000004 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 860228000005 LysE type translocator; Region: LysE; cl00565 860228000006 Bacterial PH domain; Region: DUF304; pfam03703 860228000007 Bacterial PH domain; Region: DUF304; pfam03703 860228000008 Bacterial PH domain; Region: DUF304; pfam03703 860228000009 Bacterial PH domain; Region: DUF304; cl01348 860228000010 Fic family protein [Function unknown]; Region: COG3177 860228000011 Fic/DOC family; Region: Fic; pfam02661 860228000012 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; cl17531 860228000013 Abi-like protein; Region: Abi_2; pfam07751 860228000014 ribonuclease R; Region: RNase_R; TIGR02063 860228000015 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 860228000016 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 860228000017 RNB domain; Region: RNB; pfam00773 860228000018 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 860228000019 RNA binding site [nucleotide binding]; other site 860228000020 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 860228000021 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228000022 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 860228000023 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228000024 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228000025 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 860228000026 starch binding outer membrane protein SusD; Region: SusD; cd08977 860228000027 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 860228000028 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 860228000029 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 860228000030 Beta-lactamase; Region: Beta-lactamase; pfam00144 860228000031 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 860228000032 active site 860228000033 catalytic site [active] 860228000034 substrate binding site [chemical binding]; other site 860228000035 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 860228000036 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 860228000037 Walker A/P-loop; other site 860228000038 ATP binding site [chemical binding]; other site 860228000039 Q-loop/lid; other site 860228000040 ABC transporter signature motif; other site 860228000041 Walker B; other site 860228000042 D-loop; other site 860228000043 H-loop/switch region; other site 860228000044 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 860228000045 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 860228000046 Walker A/P-loop; other site 860228000047 ATP binding site [chemical binding]; other site 860228000048 Q-loop/lid; other site 860228000049 ABC transporter signature motif; other site 860228000050 Walker B; other site 860228000051 D-loop; other site 860228000052 H-loop/switch region; other site 860228000053 Predicted methyltransferases [General function prediction only]; Region: COG0313 860228000054 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 860228000055 putative SAM binding site [chemical binding]; other site 860228000056 putative homodimer interface [polypeptide binding]; other site 860228000057 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 860228000058 Glycoprotease family; Region: Peptidase_M22; pfam00814 860228000059 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 860228000060 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 860228000061 putative substrate translocation pore; other site 860228000062 YtxH-like protein; Region: YtxH; pfam12732 860228000063 Domain of unknown function (DUF1851); Region: DUF1851; pfam08906 860228000064 AIPR protein; Region: AIPR; pfam10592 860228000065 Domain of unknown function (DUF4420); Region: DUF4420; pfam14390 860228000066 Z1 domain; Region: Z1; pfam10593 860228000067 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c_3; pfam13589 860228000068 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 860228000069 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 860228000070 cofactor binding site; other site 860228000071 DNA binding site [nucleotide binding] 860228000072 substrate interaction site [chemical binding]; other site 860228000073 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 860228000074 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502 860228000075 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 860228000076 putative active site [active] 860228000077 catalytic residue [active] 860228000078 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 860228000079 active site residue [active] 860228000080 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 860228000081 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 860228000082 active site 860228000083 homotetramer interface [polypeptide binding]; other site 860228000084 homodimer interface [polypeptide binding]; other site 860228000085 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 860228000086 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228000087 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 860228000088 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228000089 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 860228000090 starch binding outer membrane protein SusD; Region: SusD; cl17845 860228000091 Domain of unknown function (DUF4302); Region: DUF4302; pfam14135 860228000092 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 860228000093 putative protease; Provisional; Region: PRK15452 860228000094 Peptidase family U32; Region: Peptidase_U32; pfam01136 860228000095 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228000096 AAA domain; Region: AAA_21; pfam13304 860228000097 Walker A/P-loop; other site 860228000098 ATP binding site [chemical binding]; other site 860228000099 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228000100 von Willebrand factor; Region: vWF_A; pfam12450 860228000101 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 860228000102 VWA subgroup: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b...; Region: vWA_subgroup; cd01465 860228000103 metal ion-dependent adhesion site (MIDAS); other site 860228000104 Domain of unknown function (DUF3520); Region: DUF3520; pfam12034 860228000105 camphor resistance protein CrcB; Provisional; Region: PRK14195 860228000106 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 860228000107 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 860228000108 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1755 860228000109 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u1; cd11477 860228000110 Na binding site [ion binding]; other site 860228000111 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 860228000112 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 860228000113 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 860228000114 HlyD family secretion protein; Region: HlyD_3; pfam13437 860228000115 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 860228000116 Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; Region: 2-Hacid_dh_14; cd12179 860228000117 putative ligand binding site [chemical binding]; other site 860228000118 putative NAD binding site [chemical binding]; other site 860228000119 catalytic site [active] 860228000120 C-terminal domain of CHU protein family; Region: CHU_C; pfam13585 860228000121 Protein of unknown function (DUF3308); Region: DUF3308; pfam11751 860228000122 TPR repeat; Region: TPR_11; pfam13414 860228000123 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 860228000124 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 860228000125 ligand binding site [chemical binding]; other site 860228000126 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 860228000127 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 860228000128 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 860228000129 TPR motif; other site 860228000130 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 860228000131 TPR repeat; Region: TPR_11; pfam13414 860228000132 TPR motif; other site 860228000133 binding surface 860228000134 TPR repeat; Region: TPR_11; pfam13414 860228000135 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 860228000136 binding surface 860228000137 TPR repeat; Region: TPR_11; pfam13414 860228000138 TPR motif; other site 860228000139 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 860228000140 putative active site [active] 860228000141 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 860228000142 ATP binding site [chemical binding]; other site 860228000143 putative Mg++ binding site [ion binding]; other site 860228000144 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 860228000145 ATP-binding site [chemical binding]; other site 860228000146 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 860228000147 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 860228000148 Sel1-like repeats; Region: SEL1; smart00671 860228000149 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 860228000150 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 860228000151 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 860228000152 dimer interface [polypeptide binding]; other site 860228000153 substrate binding site [chemical binding]; other site 860228000154 metal binding sites [ion binding]; metal-binding site 860228000155 Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]; Region: PurN; COG0299 860228000156 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 860228000157 active site 860228000158 substrate binding site [chemical binding]; other site 860228000159 cosubstrate binding site; other site 860228000160 catalytic site [active] 860228000161 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 860228000162 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 860228000163 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 860228000164 nucleophilic elbow; other site 860228000165 catalytic triad; other site 860228000166 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 860228000167 G1 box; other site 860228000168 GTP/Mg2+ binding site [chemical binding]; other site 860228000169 Switch I region; other site 860228000170 G2 box; other site 860228000171 G3 box; other site 860228000172 Switch II region; other site 860228000173 G4 box; other site 860228000174 G5 box; other site 860228000175 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 860228000176 putative active site [active] 860228000177 Thiol-activated cytolysin; Region: Thiol_cytolysin; pfam01289 860228000178 Thiol-activated cytolysin; Region: Thiol_cytolysin; pfam01289 860228000179 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 860228000180 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 860228000181 DNA-binding interface [nucleotide binding]; DNA binding site 860228000182 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 860228000183 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 860228000184 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 860228000185 active site 860228000186 HIGH motif; other site 860228000187 nucleotide binding site [chemical binding]; other site 860228000188 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 860228000189 active site 860228000190 KMSKS motif; other site 860228000191 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 860228000192 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; smart00782 860228000193 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 860228000194 PhnA protein; Region: PhnA; pfam03831 860228000195 Dihydroneopterin aldolase; Region: FolB; pfam02152 860228000196 active site 860228000197 Protein of unknown function (DUF3308); Region: DUF3308; pfam11751 860228000198 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 860228000199 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 860228000200 Mechanosensitive ion channel; Region: MS_channel; pfam00924 860228000201 Domain of unknown function (DUF386); Region: DUF386; cl01047 860228000202 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; pfam03626 860228000203 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 860228000204 Subunit I/III interface [polypeptide binding]; other site 860228000205 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 860228000206 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 860228000207 Subunit I/III interface [polypeptide binding]; other site 860228000208 Polyprenyltransferase (cytochrome oxidase assembly factor) [Posttranslational modification, protein turnover, chaperones]; Region: CyoE; COG0109 860228000209 UbiA prenyltransferase family; Region: UbiA; pfam01040 860228000210 Transcriptional regulators [Transcription]; Region: PurR; COG1609 860228000211 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 860228000212 DNA binding site [nucleotide binding] 860228000213 domain linker motif; other site 860228000214 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 860228000215 dimerization interface [polypeptide binding]; other site 860228000216 ligand binding site [chemical binding]; other site 860228000217 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK09412 860228000218 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 860228000219 Protein of unknown function (DUF456); Region: DUF456; pfam04306 860228000220 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 860228000221 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 860228000222 PSP1 C-terminal conserved region; Region: PSP1; cl00770 860228000223 GldH lipoprotein; Region: GldH_lipo; pfam14109 860228000224 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 860228000225 Transglycosylase; Region: Transgly; pfam00912 860228000226 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 860228000227 Transposase, Mutator family; Region: Transposase_mut; pfam00872 860228000228 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 860228000229 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; pfam02559 860228000230 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 860228000231 ATP binding site [chemical binding]; other site 860228000232 putative Mg++ binding site [ion binding]; other site 860228000233 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 860228000234 nucleotide binding region [chemical binding]; other site 860228000235 ATP-binding site [chemical binding]; other site 860228000236 TRCF domain; Region: TRCF; pfam03461 860228000237 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 860228000238 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 860228000239 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 860228000240 alpha subunit interaction interface [polypeptide binding]; other site 860228000241 Walker A motif; other site 860228000242 ATP binding site [chemical binding]; other site 860228000243 Walker B motif; other site 860228000244 inhibitor binding site; inhibition site 860228000245 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 860228000246 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 860228000247 gamma subunit interface [polypeptide binding]; other site 860228000248 LBP interface [polypeptide binding]; other site 860228000249 Heavy-metal-associated domain; Region: HMA; pfam00403 860228000250 metal-binding site [ion binding] 860228000251 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228000252 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 860228000253 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228000254 2TM domain; Region: 2TM; pfam13239 860228000255 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 860228000256 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 860228000257 folate binding site [chemical binding]; other site 860228000258 NADP+ binding site [chemical binding]; other site 860228000259 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 860228000260 DNA repair protein RadA; Provisional; Region: PRK11823 860228000261 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 860228000262 Walker A motif/ATP binding site; other site 860228000263 ATP binding site [chemical binding]; other site 860228000264 Walker B motif; other site 860228000265 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 860228000266 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 860228000267 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 860228000268 putative ATP binding site [chemical binding]; other site 860228000269 putative substrate interface [chemical binding]; other site 860228000270 phosphodiesterase; Provisional; Region: PRK12704 860228000271 gliding motility-associated lipoprotein GldD; Region: GldD_lipo; TIGR03512 860228000272 gliding motility-associated protein GldE; Region: GldE; TIGR03520 860228000273 Domain of unknown function DUF21; Region: DUF21; pfam01595 860228000274 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 860228000275 Transporter associated domain; Region: CorC_HlyC; smart01091 860228000276 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 860228000277 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 860228000278 dimer interface [polypeptide binding]; other site 860228000279 ssDNA binding site [nucleotide binding]; other site 860228000280 tetramer (dimer of dimers) interface [polypeptide binding]; other site 860228000281 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 860228000282 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 860228000283 minor groove reading motif; other site 860228000284 helix-hairpin-helix signature motif; other site 860228000285 substrate binding pocket [chemical binding]; other site 860228000286 active site 860228000287 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 860228000288 DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important...; Region: DNA_Glycosylase_C; cd03431 860228000289 DNA binding and oxoG recognition site [nucleotide binding] 860228000290 twin arginine-targeting protein translocase, TatA/E family; Region: tatAE; TIGR01411 860228000291 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 860228000292 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 860228000293 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 860228000294 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 860228000295 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 860228000296 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 860228000297 Mechanosensitive ion channel; Region: MS_channel; pfam00924 860228000298 Protein of unknown function (DUF2911); Region: DUF2911; pfam11138 860228000299 Tetratricopeptide repeat; Region: TPR_12; pfam13424 860228000300 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 860228000301 binding surface 860228000302 TPR motif; other site 860228000303 Transposase domain (DUF772); Region: DUF772; pfam05598 860228000304 Lipopolysaccharide-assembly; Region: LptE; cl01125 860228000305 Preprotein translocase SecG subunit; Region: SecG; pfam03840 860228000306 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 860228000307 oligomerisation interface [polypeptide binding]; other site 860228000308 mobile loop; other site 860228000309 roof hairpin; other site 860228000310 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 860228000311 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 860228000312 ring oligomerisation interface [polypeptide binding]; other site 860228000313 ATP/Mg binding site [chemical binding]; other site 860228000314 stacking interactions; other site 860228000315 hinge regions; other site 860228000316 DNA protecting protein DprA; Region: dprA; TIGR00732 860228000317 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 860228000318 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 860228000319 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 860228000320 NAD binding site [chemical binding]; other site 860228000321 homodimer interface [polypeptide binding]; other site 860228000322 active site 860228000323 substrate binding site [chemical binding]; other site 860228000324 Conserved TM helix; Region: TM_helix; pfam05552 860228000325 Mechanosensitive ion channel; Region: MS_channel; pfam00924 860228000326 translocation protein TolB; Provisional; Region: tolB; PRK02889 860228000327 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 860228000328 Peptidase S8 family domain in Subtilisin_Novo-like proteins; Region: Peptidases_S8_Subtilisin_Novo-like; cd07483 860228000329 active site 860228000330 catalytic triad [active] 860228000331 Transposase domain (DUF772); Region: DUF772; pfam05598 860228000332 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 860228000333 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 860228000334 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 860228000335 Bacterial Ig-like domain (group 1); Region: BID_1; smart00634 860228000336 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 860228000337 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 860228000338 active site 860228000339 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 860228000340 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 860228000341 ligand binding site [chemical binding]; other site 860228000342 Glutamine phosphoribosylpyrophosphate amidotransferase [Nucleotide transport and metabolism]; Region: PurF; COG0034 860228000343 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 860228000344 active site 860228000345 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 860228000346 active site 860228000347 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 860228000348 Uncharacterized conserved protein [Function unknown]; Region: COG1262 860228000349 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 860228000350 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB...; Region: EcAsnRS_like_N; cd04318 860228000351 putative dimer interface [polypeptide binding]; other site 860228000352 putative anticodon binding site; other site 860228000353 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 860228000354 homodimer interface [polypeptide binding]; other site 860228000355 motif 1; other site 860228000356 motif 2; other site 860228000357 active site 860228000358 motif 3; other site 860228000359 gliding motility-associated lipoprotein GldK; Region: GldK; TIGR03525 860228000360 gliding motility-associated lipoprotein GldJ; Region: GldJ; TIGR03524 860228000361 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 860228000362 gliding motility-associated protein GldL; Region: GldL_gliding; TIGR03513 860228000363 gliding motility-associated protein GldM; Region: GldM_gliding; TIGR03517 860228000364 GldM N-terminal domain; Region: GldM_N; pfam12081 860228000365 GldM C-terminal domain; Region: GldM_C; pfam12080 860228000366 gliding motility associated protien GldN; Region: GldN; TIGR03523 860228000367 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 860228000368 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 860228000369 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; Region: EEP-2; cd09084 860228000370 putative catalytic site [active] 860228000371 putative metal binding site [ion binding]; other site 860228000372 putative phosphate binding site [ion binding]; other site 860228000373 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 860228000374 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 860228000375 catalytic loop [active] 860228000376 iron binding site [ion binding]; other site 860228000377 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 860228000378 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 860228000379 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 860228000380 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 860228000381 NifU-like domain; Region: NifU; cl00484 860228000382 Domain of unknown function DUF59; Region: DUF59; pfam01883 860228000383 cell division ATPase MinD, archaeal; Region: minD_arch; TIGR01969 860228000384 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 860228000385 Walker A motif; other site 860228000386 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 860228000387 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 860228000388 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 860228000389 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 860228000390 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 860228000391 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 860228000392 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 860228000393 S-adenosylmethionine binding site [chemical binding]; other site 860228000394 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 860228000395 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 860228000396 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 860228000397 ATP synthase A chain; Region: ATP-synt_A; cl00413 860228000398 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 860228000399 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 860228000400 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 860228000401 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 860228000402 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 860228000403 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 860228000404 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 860228000405 beta subunit interaction interface [polypeptide binding]; other site 860228000406 Walker A motif; other site 860228000407 ATP binding site [chemical binding]; other site 860228000408 Walker B motif; other site 860228000409 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 860228000410 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 860228000411 core domain interface [polypeptide binding]; other site 860228000412 delta subunit interface [polypeptide binding]; other site 860228000413 epsilon subunit interface [polypeptide binding]; other site 860228000414 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 860228000415 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 860228000416 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 860228000417 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 860228000418 catalytic residues [active] 860228000419 Phosphoglycerate kinase; Region: PGK; pfam00162 860228000420 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 860228000421 substrate binding site [chemical binding]; other site 860228000422 hinge regions; other site 860228000423 ADP binding site [chemical binding]; other site 860228000424 catalytic site [active] 860228000425 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 860228000426 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 860228000427 E3 interaction surface; other site 860228000428 lipoyl attachment site [posttranslational modification]; other site 860228000429 e3 binding domain; Region: E3_binding; pfam02817 860228000430 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 860228000431 Ferredoxin [Energy production and conversion]; Region: COG1146 860228000432 4Fe-4S binding domain; Region: Fer4; pfam00037 860228000433 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 860228000434 NAD(P) binding site [chemical binding]; other site 860228000435 catalytic residues [active] 860228000436 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 860228000437 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 860228000438 catalytic residue [active] 860228000439 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 860228000440 Phosphoglycerate dehydrogenase (PGDH) NAD-binding and catalytic domains; Region: PGDH_2; cd05303 860228000441 putative ligand binding site [chemical binding]; other site 860228000442 NAD binding site [chemical binding]; other site 860228000443 dimerization interface [polypeptide binding]; other site 860228000444 catalytic site [active] 860228000445 Family description; Region: ACT_7; pfam13840 860228000446 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 860228000447 VanZ like family; Region: VanZ; cl01971 860228000448 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 860228000449 lipoyl attachment site [posttranslational modification]; other site 860228000450 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 860228000451 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 860228000452 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 860228000453 active site 860228000454 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 860228000455 Lumazine binding domain; Region: Lum_binding; pfam00677 860228000456 Lumazine binding domain; Region: Lum_binding; pfam00677 860228000457 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 860228000458 Winged helix DNA-binding domain; Region: HTH_34; pfam13601 860228000459 Dienelactone hydrolase family; Region: DLH; pfam01738 860228000460 Domain of unknown function (DUF4263); Region: DUF4263; pfam14082 860228000461 Methyltransferase domain; Region: Methyltransf_26; pfam13659 860228000462 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228000463 2TM domain; Region: 2TM; pfam13239 860228000464 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 860228000465 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 860228000466 dimer interface [polypeptide binding]; other site 860228000467 active site 860228000468 CoA binding pocket [chemical binding]; other site 860228000469 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 860228000470 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 860228000471 carboxyltransferase (CT) interaction site; other site 860228000472 biotinylation site [posttranslational modification]; other site 860228000473 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 860228000474 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 860228000475 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 860228000476 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 860228000477 GTPase RsgA; Reviewed; Region: PRK00098 860228000478 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 860228000479 RNA binding site [nucleotide binding]; other site 860228000480 homodimer interface [polypeptide binding]; other site 860228000481 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 860228000482 GTPase/Zn-binding domain interface [polypeptide binding]; other site 860228000483 GTP/Mg2+ binding site [chemical binding]; other site 860228000484 G4 box; other site 860228000485 G5 box; other site 860228000486 G1 box; other site 860228000487 Switch I region; other site 860228000488 G2 box; other site 860228000489 G3 box; other site 860228000490 Switch II region; other site 860228000491 thymidylate synthase; Reviewed; Region: thyA; PRK01827 860228000492 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 860228000493 dimerization interface [polypeptide binding]; other site 860228000494 active site 860228000495 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 860228000496 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 860228000497 Nucleoside recognition; Region: Gate; pfam07670 860228000498 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 860228000499 Bifunctional nuclease; Region: DNase-RNase; pfam02577 860228000500 UvrB/uvrC motif; Region: UVR; pfam02151 860228000501 SurA N-terminal domain; Region: SurA_N_3; cl07813 860228000502 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 860228000503 PPIC-type PPIASE domain; Region: Rotamase_3; pfam13616 860228000504 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 860228000505 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 860228000506 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 860228000507 substrate binding site [chemical binding]; other site 860228000508 ATP binding site [chemical binding]; other site 860228000509 Protein of unknown function (DUF3251); Region: DUF3251; cl08186 860228000510 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 860228000511 metal-binding site [ion binding] 860228000512 Metallo-peptidase family M12B Reprolysin-like; Region: Reprolysin_2; pfam13574 860228000513 active site 860228000514 C-terminal domain of CHU protein family; Region: CHU_C; pfam13585 860228000515 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 860228000516 active site 860228000517 C-terminal domain of CHU protein family; Region: CHU_C; pfam13585 860228000518 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 860228000519 active site 860228000520 C-terminal domain of CHU protein family; Region: CHU_C; pfam13585 860228000521 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 860228000522 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 860228000523 NAD binding site [chemical binding]; other site 860228000524 putative substrate binding site 2 [chemical binding]; other site 860228000525 putative substrate binding site 1 [chemical binding]; other site 860228000526 active site 860228000527 Phosphate transporter family; Region: PHO4; pfam01384 860228000528 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GpsA; COG0240 860228000529 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 860228000530 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 860228000531 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 860228000532 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 860228000533 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 860228000534 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 860228000535 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 860228000536 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 860228000537 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 860228000538 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 860228000539 HlyD family secretion protein; Region: HlyD_3; pfam13437 860228000540 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 860228000541 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 860228000542 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 860228000543 ligand binding site [chemical binding]; other site 860228000544 flexible hinge region; other site 860228000545 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 860228000546 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 860228000547 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 860228000548 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 860228000549 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 860228000550 HIGH motif; other site 860228000551 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 860228000552 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 860228000553 active site 860228000554 KMSKS motif; other site 860228000555 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 860228000556 tRNA binding surface [nucleotide binding]; other site 860228000557 anticodon binding site; other site 860228000558 Bax inhibitor 1 like; Region: BaxI_1; cl17691 860228000559 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 860228000560 active site 860228000561 DNA polymerase IV; Validated; Region: PRK02406 860228000562 DNA binding site [nucleotide binding] 860228000563 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 860228000564 PAS domain; Region: PAS_9; pfam13426 860228000565 putative active site [active] 860228000566 heme pocket [chemical binding]; other site 860228000567 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 860228000568 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 860228000569 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 860228000570 Cl- selectivity filter; other site 860228000571 Cl- binding residues [ion binding]; other site 860228000572 pore gating glutamate residue; other site 860228000573 dimer interface [polypeptide binding]; other site 860228000574 FOG: CBS domain [General function prediction only]; Region: COG0517 860228000575 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC; Region: CBS_pair_SpoIVFB_EriC_assoc2; cd04613 860228000576 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated; Region: PRK07570 860228000577 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 860228000578 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 860228000579 four helix bundle protein; Region: TIGR02436 860228000580 S23 ribosomal protein; Region: Ribosomal_S23p; pfam05635 860228000581 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07573 860228000582 L-aspartate oxidase; Provisional; Region: PRK06175 860228000583 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 860228000584 succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family; Region: sdhC_b558_fam; TIGR02046 860228000585 Succinate:quinone oxidoreductase (SQR)-like Type B subfamily 2, transmembrane subunit; composed of proteins with similarity to the SQRs of Geobacter metallireducens and Corynebacterium glutamicum. SQR catalyzes the oxidation of succinate to fumarate...; Region: SQR_TypeB_2_TM; cd03498 860228000586 putative Iron-sulfur protein interface [polypeptide binding]; other site 860228000587 proximal heme binding site [chemical binding]; other site 860228000588 distal heme binding site [chemical binding]; other site 860228000589 putative dimer interface [polypeptide binding]; other site 860228000590 pantothenate kinase; Reviewed; Region: PRK13320 860228000591 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 860228000592 binding surface 860228000593 TPR motif; other site 860228000594 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 860228000595 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 860228000596 Domain of unknown function DUF21; Region: DUF21; pfam01595 860228000597 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 860228000598 Transporter associated domain; Region: CorC_HlyC; smart01091 860228000599 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 860228000600 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 860228000601 YceI-like domain; Region: YceI; pfam04264 860228000602 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 860228000603 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 860228000604 homodimer interface [polypeptide binding]; other site 860228000605 oligonucleotide binding site [chemical binding]; other site 860228000606 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 860228000607 IHF - DNA interface [nucleotide binding]; other site 860228000608 IHF dimer interface [polypeptide binding]; other site 860228000609 5-enolpyruvylshikimate-3-phosphate synthase [Amino acid transport and metabolism]; Region: AroA; COG0128 860228000610 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 860228000611 hinge; other site 860228000612 active site 860228000613 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain putative pyrophosphatase YpjD from Bacillus subtilis and its bacterial homologs; Region: NTP-PPase_BsYpjD; cd11531 860228000614 homodimer interface [polypeptide binding]; other site 860228000615 metal binding site [ion binding]; metal-binding site 860228000616 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 860228000617 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 860228000618 Cu(I) binding site [ion binding]; other site 860228000619 FeoA domain; Region: FeoA; pfam04023 860228000620 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 860228000621 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 860228000622 G1 box; other site 860228000623 GTP/Mg2+ binding site [chemical binding]; other site 860228000624 Switch I region; other site 860228000625 G2 box; other site 860228000626 G3 box; other site 860228000627 Switch II region; other site 860228000628 G4 box; other site 860228000629 G5 box; other site 860228000630 Nucleoside recognition; Region: Gate; pfam07670 860228000631 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 860228000632 Nucleoside recognition; Region: Gate; pfam07670 860228000633 Pyruvate kinase [Carbohydrate transport and metabolism]; Region: PykF; COG0469 860228000634 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 860228000635 domain interfaces; other site 860228000636 active site 860228000637 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 860228000638 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 860228000639 dimerization interface [polypeptide binding]; other site 860228000640 active site 860228000641 metal binding site [ion binding]; metal-binding site 860228000642 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 860228000643 dsRNA binding site [nucleotide binding]; other site 860228000644 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 860228000645 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 860228000646 dimer interface [polypeptide binding]; other site 860228000647 active site 860228000648 acyl carrier protein; Provisional; Region: acpP; PRK00982 860228000649 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 860228000650 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 860228000651 potential frameshift: common BLAST hit: gi|256819595|ref|YP_003140874.1| protein involved in gliding motility GldJ 860228000652 gliding motility-associated lipoprotein GldJ; Region: GldJ; TIGR03524 860228000653 gliding motility-associated lipoprotein GldJ; Region: GldJ; TIGR03524 860228000654 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 860228000655 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 860228000656 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 860228000657 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 860228000658 fructose-1,6-bisphosphatase family protein; Region: PLN02628 860228000659 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 860228000660 AMP binding site [chemical binding]; other site 860228000661 metal binding site [ion binding]; metal-binding site 860228000662 active site 860228000663 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 860228000664 catalytic residues [active] 860228000665 FeS assembly protein SufD; Region: sufD; TIGR01981 860228000666 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 860228000667 Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair]; Region: COG1525 860228000668 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 860228000669 Catalytic site; other site 860228000670 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 860228000671 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 860228000672 TPP-binding site [chemical binding]; other site 860228000673 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 860228000674 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 860228000675 ATPase involved in DNA replication [DNA replication, recombination, and repair]; Region: HolB; COG0470 860228000676 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 860228000677 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 860228000678 substrate-cofactor binding pocket; other site 860228000679 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228000680 catalytic residue [active] 860228000681 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 860228000682 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 860228000683 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 860228000684 ligand binding site [chemical binding]; other site 860228000685 Anaphase-promoting complex, cyclosome, subunit 3; Region: Apc3; pfam12895 860228000686 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 860228000687 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 860228000688 TPR motif; other site 860228000689 binding surface 860228000690 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 860228000691 binding surface 860228000692 TPR motif; other site 860228000693 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 860228000694 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 860228000695 Domain of unknown function DUF302; Region: DUF302; cl01364 860228000696 Haemolytic domain; Region: Haemolytic; pfam01809 860228000697 Repair protein; Region: Repair_PSII; pfam04536 860228000698 Repair protein; Region: Repair_PSII; pfam04536 860228000699 LemA family; Region: LemA; cl00742 860228000700 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 860228000701 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 860228000702 DNA binding residues [nucleotide binding] 860228000703 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 860228000704 Peptidase family M23; Region: Peptidase_M23; pfam01551 860228000705 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 860228000706 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 860228000707 motif 1; other site 860228000708 active site 860228000709 motif 2; other site 860228000710 motif 3; other site 860228000711 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 860228000712 DHHA1 domain; Region: DHHA1; pfam02272 860228000713 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 860228000714 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 860228000715 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 860228000716 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 860228000717 active site 860228000718 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 860228000719 S-adenosylmethionine binding site [chemical binding]; other site 860228000720 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 860228000721 NAD(P) binding site [chemical binding]; other site 860228000722 active site 860228000723 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 860228000724 DPM1_like represents putative enzymes similar to eukaryotic DPM1; Region: DPM1_like; cd06442 860228000725 Ligand binding site; other site 860228000726 Putative Catalytic site; other site 860228000727 DXD motif; other site 860228000728 dihydroorotase; Reviewed; Region: PRK09236 860228000729 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 860228000730 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 860228000731 active site 860228000732 Domain of unknown function (DUF4296); Region: DUF4296; pfam14129 860228000733 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 860228000734 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 860228000735 active site 860228000736 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 860228000737 Clp amino terminal domain; Region: Clp_N; pfam02861 860228000738 Clp amino terminal domain; Region: Clp_N; pfam02861 860228000739 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 860228000740 Walker A motif; other site 860228000741 ATP binding site [chemical binding]; other site 860228000742 Walker B motif; other site 860228000743 arginine finger; other site 860228000744 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 860228000745 Walker A motif; other site 860228000746 ATP binding site [chemical binding]; other site 860228000747 Walker B motif; other site 860228000748 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 860228000749 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 860228000750 classical (c) SDRs; Region: SDR_c; cd05233 860228000751 NAD(P) binding site [chemical binding]; other site 860228000752 active site 860228000753 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; Region: EEP-1; cd09083 860228000754 putative catalytic site [active] 860228000755 putative metal binding site [ion binding]; other site 860228000756 putative phosphate binding site [ion binding]; other site 860228000757 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 860228000758 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 860228000759 S-adenosylmethionine binding site [chemical binding]; other site 860228000760 Protein of unknown function (DUF3822); Region: DUF3822; pfam12864 860228000761 Type IV pilin PilA; Region: Pilin_PilA; pfam14245 860228000762 AAA domain; Region: AAA_30; pfam13604 860228000763 Family description; Region: UvrD_C_2; pfam13538 860228000764 luciferase-type oxidoreductase, BA3436 family; Region: lucif_BA3436; TIGR03571 860228000765 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 860228000766 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 860228000767 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 860228000768 Ligand binding site; other site 860228000769 oligomer interface; other site 860228000770 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 860228000771 CoA binding domain; Region: CoA_binding; smart00881 860228000772 CoA-ligase; Region: Ligase_CoA; pfam00549 860228000773 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 860228000774 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 860228000775 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 860228000776 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 860228000777 translation initiation factor IF-2; Region: IF-2; TIGR00487 860228000778 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 860228000779 G1 box; other site 860228000780 putative GEF interaction site [polypeptide binding]; other site 860228000781 GTP/Mg2+ binding site [chemical binding]; other site 860228000782 Switch I region; other site 860228000783 G2 box; other site 860228000784 G3 box; other site 860228000785 Switch II region; other site 860228000786 G4 box; other site 860228000787 G5 box; other site 860228000788 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 860228000789 Translation-initiation factor 2; Region: IF-2; pfam11987 860228000790 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 860228000791 transcription termination factor NusA; Region: NusA; TIGR01953 860228000792 NusA N-terminal domain; Region: NusA_N; pfam08529 860228000793 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 860228000794 RNA binding site [nucleotide binding]; other site 860228000795 homodimer interface [polypeptide binding]; other site 860228000796 NusA-like KH domain; Region: KH_5; pfam13184 860228000797 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 860228000798 G-X-X-G motif; other site 860228000799 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 860228000800 putative oligomer interface [polypeptide binding]; other site 860228000801 putative RNA binding site [nucleotide binding]; other site 860228000802 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 860228000803 Ligand Binding Site [chemical binding]; other site 860228000804 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 860228000805 Ligand Binding Site [chemical binding]; other site 860228000806 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 860228000807 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 860228000808 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cl17708 860228000809 domain interfaces; other site 860228000810 active site 860228000811 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 860228000812 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 860228000813 tRNA; other site 860228000814 putative tRNA binding site [nucleotide binding]; other site 860228000815 putative NADP binding site [chemical binding]; other site 860228000816 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 860228000817 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 860228000818 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 860228000819 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 860228000820 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 860228000821 MG2 domain; Region: A2M_N; pfam01835 860228000822 Alpha-2-macroglobulin family; Region: A2M; pfam00207 860228000823 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 860228000824 surface patch; other site 860228000825 thioester region; other site 860228000826 specificity defining residues; other site 860228000827 C-terminal domain of CHU protein family; Region: CHU_C; pfam13585 860228000828 Protein of unknown function (DUF3308); Region: DUF3308; pfam11751 860228000829 TPR repeat; Region: TPR_11; pfam13414 860228000830 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 860228000831 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 860228000832 ligand binding site [chemical binding]; other site 860228000833 Transposase, Mutator family; Region: Transposase_mut; pfam00872 860228000834 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228000835 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 860228000836 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228000837 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 860228000838 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 860228000839 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 860228000840 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 860228000841 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 860228000842 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 860228000843 DNA binding residues [nucleotide binding] 860228000844 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228000845 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 860228000846 Walker A/P-loop; other site 860228000847 ATP binding site [chemical binding]; other site 860228000848 Q-loop/lid; other site 860228000849 ABC transporter signature motif; other site 860228000850 Walker B; other site 860228000851 D-loop; other site 860228000852 H-loop/switch region; other site 860228000853 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 860228000854 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 860228000855 ligand binding site [chemical binding]; other site 860228000856 flexible hinge region; other site 860228000857 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 860228000858 non-specific DNA interactions [nucleotide binding]; other site 860228000859 DNA binding site [nucleotide binding] 860228000860 sequence specific DNA binding site [nucleotide binding]; other site 860228000861 putative cAMP binding site [chemical binding]; other site 860228000862 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 860228000863 Aspartase; Region: Aspartase; cd01357 860228000864 active sites [active] 860228000865 tetramer interface [polypeptide binding]; other site 860228000866 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 860228000867 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 860228000868 Bacterial Ig-like domain; Region: Big_5; pfam13205 860228000869 GTPase Era; Reviewed; Region: era; PRK00089 860228000870 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 860228000871 G1 box; other site 860228000872 GTP/Mg2+ binding site [chemical binding]; other site 860228000873 Switch I region; other site 860228000874 G2 box; other site 860228000875 Switch II region; other site 860228000876 G3 box; other site 860228000877 G4 box; other site 860228000878 G5 box; other site 860228000879 KH domain; Region: KH_2; pfam07650 860228000880 Domain of unknown function (DUF1287); Region: DUF1287; pfam06940 860228000881 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 860228000882 Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoproteins. This enzyme is an amidase located inside lysosomes. Mutation of this gene in humans causes a genetic disorder known as aspartylglycosaminuria (AGU)...; Region: Glycosylasparaginase; cd04513 860228000883 active site 860228000884 dimer interface [polypeptide binding]; other site 860228000885 catalytic nucleophile [active] 860228000886 FOG: WD40 repeat [General function prediction only]; Region: COG2319 860228000887 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 860228000888 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 860228000889 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228000890 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 860228000891 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228000892 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 860228000893 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228000894 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 860228000895 S-adenosylmethionine binding site [chemical binding]; other site 860228000896 probable oxidoreductase, LLM family; Region: LLM_2I7G; TIGR03858 860228000897 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 860228000898 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 860228000899 starch binding outer membrane protein SusD; Region: SusD; cl17845 860228000900 starch binding outer membrane protein SusD; Region: SusD; cl17845 860228000901 Domain of unknown function (DUF4302); Region: DUF4302; pfam14135 860228000902 Carbohydrate binding domain; Region: CBM_4_9; pfam02018 860228000903 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 860228000904 Interdomain contacts; other site 860228000905 Cytokine receptor motif; other site 860228000906 probable DNA metabolism protein; Region: SAM_7_link_chp; TIGR03915 860228000907 putative DNA modification/repair radical SAM protein; Region: rSAM_link_UDG; TIGR03916 860228000908 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 860228000909 FeS/SAM binding site; other site 860228000910 Sulfatase; Region: Sulfatase; cl17466 860228000911 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 860228000912 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 860228000913 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 860228000914 active site 860228000915 HIGH motif; other site 860228000916 nucleotide binding site [chemical binding]; other site 860228000917 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 860228000918 KMSKS motif; other site 860228000919 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 860228000920 tRNA binding surface [nucleotide binding]; other site 860228000921 anticodon binding site; other site 860228000922 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 860228000923 GTP cyclohydrolase I; Provisional; Region: PLN03044 860228000924 active site 860228000925 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 860228000926 dimer interface [polypeptide binding]; other site 860228000927 allosteric magnesium binding site [ion binding]; other site 860228000928 active site 860228000929 aspartate-rich active site metal binding site; other site 860228000930 Schiff base residues; other site 860228000931 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i)...; Region: GH20_chitobiase-like; cd06563 860228000932 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 860228000933 active site 860228000934 Fn3 associated; Region: Fn3_assoc; pfam13287 860228000935 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 860228000936 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 860228000937 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 860228000938 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 860228000939 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 860228000940 dimer interface [polypeptide binding]; other site 860228000941 putative anticodon binding site; other site 860228000942 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 860228000943 motif 1; other site 860228000944 active site 860228000945 motif 2; other site 860228000946 motif 3; other site 860228000947 Protein of unknown function (DUF3308); Region: DUF3308; cl14675 860228000948 Sporulation related domain; Region: SPOR; pfam05036 860228000949 C-terminal domain of CHU protein family; Region: CHU_C; cl17875 860228000950 Transglycosylase-like domain; Region: Transglycosylas; pfam06737 860228000951 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 860228000952 active site 860228000953 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 860228000954 putative active site [active] 860228000955 putative metal binding site [ion binding]; other site 860228000956 Domain of unknown function (DUF4402); Region: DUF4402; pfam14352 860228000957 C-terminal domain of CHU protein family; Region: CHU_C; pfam13585 860228000958 Protein of unknown function (DUF3308); Region: DUF3308; pfam11751 860228000959 TPR repeat; Region: TPR_11; pfam13414 860228000960 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 860228000961 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 860228000962 ligand binding site [chemical binding]; other site 860228000963 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 860228000964 putative active site [active] 860228000965 putative metal binding site [ion binding]; other site 860228000966 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 860228000967 RNA/DNA hybrid binding site [nucleotide binding]; other site 860228000968 active site 860228000969 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 860228000970 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i)...; Region: GH20_chitobiase-like; cd06563 860228000971 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 860228000972 active site 860228000973 Fn3 associated; Region: Fn3_assoc; pfam13287 860228000974 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 860228000975 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 860228000976 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 860228000977 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 860228000978 Glycogen synthase; Region: Glycogen_syn; pfam05693 860228000979 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 860228000980 alpha-glucan phosphorylases; Region: more_P_ylases; TIGR02094 860228000981 N-terminal catalytic domain of a thermoactive alpha-amylase from Methanococcus jannaschii and similar proteins; glycoside hydrolase family 57 (GH57); Region: GH57N_MJA1_like; cd10795 860228000982 Glycosyl hydrolase family 57; Region: Glyco_hydro_57; pfam03065 860228000983 putative active site [active] 860228000984 catalytic site [active] 860228000985 Starch synthase catalytic domain; Region: Glyco_transf_5; pfam08323 860228000986 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 860228000987 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 860228000988 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 860228000989 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 860228000990 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 860228000991 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 860228000992 Glycogen debranching enzyme N terminal; Region: GDE_N; pfam12439 860228000993 glycogen debranching enzyme, archaeal type, putative; Region: gde_arch; TIGR01561 860228000994 Amylo-alpha-1,6-glucosidase; Region: GDE_C; pfam06202 860228000995 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 860228000996 Fic/DOC family; Region: Fic; pfam02661 860228000997 Fic/DOC family; Region: Fic; cl00960 860228000998 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]; Region: GlgB; COG0296 860228000999 N-terminal Early set domain associated with the catalytic domain of eukaryotic glycogen branching enzyme (also called 1,4 alpha glucan branching enzyme); Region: E_set_GBE_euk_N; cd02854 860228001000 Alpha amylase catalytic domain found in bacterial and eukaryotic branching enzymes; Region: AmyAc_bac_euk_BE; cd11321 860228001001 active site 860228001002 catalytic site [active] 860228001003 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 860228001004 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 860228001005 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 860228001006 Uncharacterized conserved protein [Function unknown]; Region: COG3743 860228001007 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 860228001008 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 860228001009 active site 860228001010 multimer interface [polypeptide binding]; other site 860228001011 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 860228001012 active site 860228001013 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 860228001014 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 860228001015 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 860228001016 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 860228001017 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 860228001018 transmembrane helices; other site 860228001019 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 860228001020 TrkA-C domain; Region: TrkA_C; pfam02080 860228001021 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 860228001022 TrkA-C domain; Region: TrkA_C; pfam02080 860228001023 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 860228001024 CAAX protease self-immunity; Region: Abi; pfam02517 860228001025 heat shock protein 90; Provisional; Region: PRK05218 860228001026 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 860228001027 ATP binding site [chemical binding]; other site 860228001028 Mg2+ binding site [ion binding]; other site 860228001029 G-X-G motif; other site 860228001030 The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases; Region: URO-D_CIMS_like; cl00464 860228001031 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 860228001032 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 860228001033 active site 860228001034 (T/H)XGH motif; other site 860228001035 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 860228001036 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 860228001037 catalytic site [active] 860228001038 G-X2-G-X-G-K; other site 860228001039 hypothetical protein; Provisional; Region: PRK11820 860228001040 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 860228001041 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 860228001042 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 860228001043 S17 interaction site [polypeptide binding]; other site 860228001044 S8 interaction site; other site 860228001045 16S rRNA interaction site [nucleotide binding]; other site 860228001046 streptomycin interaction site [chemical binding]; other site 860228001047 23S rRNA interaction site [nucleotide binding]; other site 860228001048 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 860228001049 30S ribosomal protein S7; Validated; Region: PRK05302 860228001050 elongation factor G; Reviewed; Region: PRK12739 860228001051 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 860228001052 G1 box; other site 860228001053 putative GEF interaction site [polypeptide binding]; other site 860228001054 GTP/Mg2+ binding site [chemical binding]; other site 860228001055 Switch I region; other site 860228001056 G2 box; other site 860228001057 G3 box; other site 860228001058 Switch II region; other site 860228001059 G4 box; other site 860228001060 G5 box; other site 860228001061 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 860228001062 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 860228001063 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 860228001064 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 860228001065 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 860228001066 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 860228001067 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 860228001068 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 860228001069 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 860228001070 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 860228001071 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 860228001072 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 860228001073 putative translocon binding site; other site 860228001074 protein-rRNA interface [nucleotide binding]; other site 860228001075 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 860228001076 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 860228001077 G-X-X-G motif; other site 860228001078 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 860228001079 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 860228001080 23S rRNA interface [nucleotide binding]; other site 860228001081 5S rRNA interface [nucleotide binding]; other site 860228001082 putative antibiotic binding site [chemical binding]; other site 860228001083 L25 interface [polypeptide binding]; other site 860228001084 L27 interface [polypeptide binding]; other site 860228001085 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 860228001086 23S rRNA interface [nucleotide binding]; other site 860228001087 putative translocon interaction site; other site 860228001088 signal recognition particle (SRP54) interaction site; other site 860228001089 L23 interface [polypeptide binding]; other site 860228001090 trigger factor interaction site; other site 860228001091 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 860228001092 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 860228001093 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 860228001094 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 860228001095 RNA binding site [nucleotide binding]; other site 860228001096 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 860228001097 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 860228001098 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 860228001099 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 860228001100 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 860228001101 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 860228001102 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 860228001103 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 860228001104 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 860228001105 5S rRNA interface [nucleotide binding]; other site 860228001106 L27 interface [polypeptide binding]; other site 860228001107 23S rRNA interface [nucleotide binding]; other site 860228001108 L5 interface [polypeptide binding]; other site 860228001109 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 860228001110 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 860228001111 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 860228001112 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 860228001113 23S rRNA binding site [nucleotide binding]; other site 860228001114 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 860228001115 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 860228001116 SecY translocase; Region: SecY; pfam00344 860228001117 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 860228001118 rRNA binding site [nucleotide binding]; other site 860228001119 predicted 30S ribosome binding site; other site 860228001120 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 860228001121 30S ribosomal protein S13; Region: bact_S13; TIGR03631 860228001122 30S ribosomal protein S11; Validated; Region: PRK05309 860228001123 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 860228001124 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 860228001125 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 860228001126 RNA binding surface [nucleotide binding]; other site 860228001127 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 860228001128 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 860228001129 alphaNTD homodimer interface [polypeptide binding]; other site 860228001130 alphaNTD - beta interaction site [polypeptide binding]; other site 860228001131 alphaNTD - beta' interaction site [polypeptide binding]; other site 860228001132 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 860228001133 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 860228001134 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 860228001135 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 860228001136 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 860228001137 catalytic site [active] 860228001138 subunit interface [polypeptide binding]; other site 860228001139 Methyltransferase domain; Region: Methyltransf_23; pfam13489 860228001140 enolase; Provisional; Region: eno; PRK00077 860228001141 Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions; Region: enolase; cd03313 860228001142 dimer interface [polypeptide binding]; other site 860228001143 metal binding site [ion binding]; metal-binding site 860228001144 substrate binding pocket [chemical binding]; other site 860228001145 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 860228001146 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 860228001147 Large-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscL; COG1970 860228001148 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 860228001149 signal peptide peptidase SppA, 67K type; Region: SppA_67K; TIGR00705 860228001150 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 860228001151 tandem repeat interface [polypeptide binding]; other site 860228001152 oligomer interface [polypeptide binding]; other site 860228001153 active site residues [active] 860228001154 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 860228001155 tandem repeat interface [polypeptide binding]; other site 860228001156 oligomer interface [polypeptide binding]; other site 860228001157 active site residues [active] 860228001158 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 860228001159 catalytic center binding site [active] 860228001160 ATP binding site [chemical binding]; other site 860228001161 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 860228001162 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1; Region: dNK; cd01673 860228001163 Substrate-binding site [chemical binding]; other site 860228001164 Substrate specificity [chemical binding]; other site 860228001165 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 860228001166 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 860228001167 active site 860228001168 Transcriptional regulators [Transcription]; Region: FadR; COG2186 860228001169 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 860228001170 DNA-binding site [nucleotide binding]; DNA binding site 860228001171 FCD domain; Region: FCD; pfam07729 860228001172 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cd00249 860228001173 dimerization interface [polypeptide binding]; other site 860228001174 putative active cleft [active] 860228001175 Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates as well as playing roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold...; Region: Sialidase; cd00260 860228001176 catalytic site [active] 860228001177 BNR repeat-like domain; Region: BNR_2; pfam13088 860228001178 Asp-box motif; other site 860228001179 PA14 domain; Region: PA14; cl08459 860228001180 C-terminal domain of CHU protein family; Region: CHU_C; pfam13585 860228001181 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 860228001182 DoxX; Region: DoxX; pfam07681 860228001183 Pirin; Region: Pirin; pfam02678 860228001184 Pirin-related protein [General function prediction only]; Region: COG1741 860228001185 OsmC-like protein; Region: OsmC; cl00767 860228001186 GxxExxY protein; Region: GxxExxY; TIGR04256 860228001187 Predicted flavoprotein [General function prediction only]; Region: COG0431 860228001188 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 860228001189 Pirin-related protein [General function prediction only]; Region: COG1741 860228001190 Pirin; Region: Pirin; pfam02678 860228001191 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 860228001192 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 860228001193 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 860228001194 ligand binding site [chemical binding]; other site 860228001195 flexible hinge region; other site 860228001196 Domain of unknown function (DUF1910); Region: DUF1910; pfam08928 860228001197 Domain of unknown function (DUF1911); Region: DUF1911; pfam08929 860228001198 Domain of unknown function (DUF1910); Region: DUF1910; pfam08928 860228001199 Domain of unknown function (DUF1911); Region: DUF1911; pfam08929 860228001200 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 860228001201 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 860228001202 methionine sulfoxide reductase A; Provisional; Region: PRK14054 860228001203 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 860228001204 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 860228001205 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 860228001206 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228001207 Walker A/P-loop; other site 860228001208 ATP binding site [chemical binding]; other site 860228001209 Q-loop/lid; other site 860228001210 ABC transporter signature motif; other site 860228001211 Walker B; other site 860228001212 D-loop; other site 860228001213 H-loop/switch region; other site 860228001214 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 860228001215 Bacterial membrane protein YfhO; Region: YfhO; pfam09586 860228001216 Bacterial membrane protein YfhO; Region: YfhO; pfam09586 860228001217 Lipocalin-like domain; Region: Lipocalin_4; pfam13648 860228001218 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; pfam01219 860228001219 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 860228001220 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 860228001221 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 860228001222 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 860228001223 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 860228001224 amino acid/peptide transporter (Peptide:H+ symporter), bacterial; Region: yjdL_sub1_fam; TIGR00924 860228001225 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 860228001226 putative substrate translocation pore; other site 860228001227 POT family; Region: PTR2; cl17359 860228001228 CRISPR/Cas system-associated protein Cas8a1; Region: Cas8a1_I-A; cd09744 860228001229 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 860228001230 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 860228001231 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228001232 Walker A/P-loop; other site 860228001233 ATP binding site [chemical binding]; other site 860228001234 Q-loop/lid; other site 860228001235 ABC transporter signature motif; other site 860228001236 Walker B; other site 860228001237 D-loop; other site 860228001238 H-loop/switch region; other site 860228001239 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 860228001240 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 860228001241 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 860228001242 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 860228001243 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 860228001244 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 860228001245 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 860228001246 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 860228001247 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 860228001248 ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]; Region: SpoVK; COG0464 860228001249 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 860228001250 Walker A motif; other site 860228001251 ATP binding site [chemical binding]; other site 860228001252 Walker B motif; other site 860228001253 arginine finger; other site 860228001254 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 860228001255 tetramer interface [polypeptide binding]; other site 860228001256 TPP-binding site [chemical binding]; other site 860228001257 heterodimer interface [polypeptide binding]; other site 860228001258 phosphorylation loop region [posttranslational modification] 860228001259 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 860228001260 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 860228001261 PYR/PP interface [polypeptide binding]; other site 860228001262 dimer interface [polypeptide binding]; other site 860228001263 TPP binding site [chemical binding]; other site 860228001264 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 860228001265 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 860228001266 starch binding outer membrane protein SusD; Region: SusD; cd08977 860228001267 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 860228001268 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228001269 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 860228001270 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 860228001271 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 860228001272 active site 860228001273 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 860228001274 Isochorismatase family; Region: Isochorismatase; pfam00857 860228001275 catalytic triad [active] 860228001276 metal binding site [ion binding]; metal-binding site 860228001277 conserved cis-peptide bond; other site 860228001278 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 860228001279 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 860228001280 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 860228001281 protein binding site [polypeptide binding]; other site 860228001282 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 860228001283 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 860228001284 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 860228001285 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 860228001286 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 860228001287 E-class dimer interface [polypeptide binding]; other site 860228001288 P-class dimer interface [polypeptide binding]; other site 860228001289 active site 860228001290 Cu2+ binding site [ion binding]; other site 860228001291 Zn2+ binding site [ion binding]; other site 860228001292 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 860228001293 Prephenate dehydratase; Region: PDT; pfam00800 860228001294 C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme; Region: ACT_CM-PDT; cd04905 860228001295 putative L-Phe binding site [chemical binding]; other site 860228001296 prephenate dehydrogenase; Validated; Region: PRK08507 860228001297 Prephenate dehydrogenase; Region: PDH; pfam02153 860228001298 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 860228001299 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 860228001300 Chorismate mutase type II; Region: CM_2; smart00830 860228001301 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 860228001302 23S rRNA binding site [nucleotide binding]; other site 860228001303 L21 binding site [polypeptide binding]; other site 860228001304 L13 binding site [polypeptide binding]; other site 860228001305 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 860228001306 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 860228001307 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 860228001308 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 860228001309 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 860228001310 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 860228001311 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 860228001312 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 860228001313 active site 860228001314 dimer interface [polypeptide binding]; other site 860228001315 motif 1; other site 860228001316 motif 2; other site 860228001317 motif 3; other site 860228001318 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 860228001319 anticodon binding site; other site 860228001320 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 860228001321 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 860228001322 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 860228001323 FeS/SAM binding site; other site 860228001324 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 860228001325 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 860228001326 dimer interface [polypeptide binding]; other site 860228001327 active site 860228001328 CoA binding pocket [chemical binding]; other site 860228001329 Yqey-like protein; Region: YqeY; pfam09424 860228001330 ribosome recycling factor; Reviewed; Region: frr; PRK00083 860228001331 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 860228001332 hinge region; other site 860228001333 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 860228001334 putative nucleotide binding site [chemical binding]; other site 860228001335 uridine monophosphate binding site [chemical binding]; other site 860228001336 homohexameric interface [polypeptide binding]; other site 860228001337 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 860228001338 active site 860228001339 putative DNA-binding cleft [nucleotide binding]; other site 860228001340 dimer interface [polypeptide binding]; other site 860228001341 coproporphyrinogen III oxidase; Provisional; Region: PRK08599 860228001342 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 860228001343 FeS/SAM binding site; other site 860228001344 HemN C-terminal domain; Region: HemN_C; pfam06969 860228001345 Protein of unknown function (DUF2400); Region: DUF2400; pfam09674 860228001346 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 860228001347 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 860228001348 Walker A/P-loop; other site 860228001349 ATP binding site [chemical binding]; other site 860228001350 Q-loop/lid; other site 860228001351 ABC transporter signature motif; other site 860228001352 Walker B; other site 860228001353 D-loop; other site 860228001354 H-loop/switch region; other site 860228001355 cytidylate kinase; Provisional; Region: cmk; PRK00023 860228001356 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 860228001357 active site 860228001358 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 860228001359 CMP-binding site; other site 860228001360 The sites determining sugar specificity; other site 860228001361 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 860228001362 active site 860228001363 catalytic residues [active] 860228001364 galactokinase; Provisional; Region: PRK05322 860228001365 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 860228001366 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 860228001367 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 860228001368 Domain of unknown function (DUF1200); Region: DUF1200; pfam06713 860228001369 Domain of unknown function (DUF1200); Region: DUF1200; pfam06713 860228001370 exopolyphosphatase; Region: exo_poly_only; TIGR03706 860228001371 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 860228001372 polyphosphate kinase; Provisional; Region: PRK05443 860228001373 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 860228001374 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 860228001375 Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C1_like; cd09164 860228001376 domain interface [polypeptide binding]; other site 860228001377 active site 860228001378 catalytic site [active] 860228001379 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 860228001380 domain interface [polypeptide binding]; other site 860228001381 active site 860228001382 catalytic site [active] 860228001383 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 860228001384 catalytic core [active] 860228001385 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 860228001386 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 860228001387 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated; Region: PRK06080 860228001388 UbiA prenyltransferase family; Region: UbiA; pfam01040 860228001389 Predicted nuclease (RecB family) [General function prediction only]; Region: COG2251 860228001390 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 860228001391 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 860228001392 substrate binding site [chemical binding]; other site 860228001393 oxyanion hole (OAH) forming residues; other site 860228001394 trimer interface [polypeptide binding]; other site 860228001395 short chain dehydrogenase; Provisional; Region: PRK06179 860228001396 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 860228001397 NADP binding site [chemical binding]; other site 860228001398 active site 860228001399 steroid binding site; other site 860228001400 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 860228001401 active site 860228001402 intersubunit interactions; other site 860228001403 catalytic residue [active] 860228001404 Domain of unknown function (DUF4252); Region: DUF4252; pfam14060 860228001405 chaperone protein DnaJ; Provisional; Region: PRK14284 860228001406 Bacterial SH3 domain; Region: SH3_3; cl17532 860228001407 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 860228001408 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 860228001409 C-terminal processing peptidase-like; serine protease family S41; Region: Peptidase_S41_CPP_like; cd07561 860228001410 Catalytic dyad [active] 860228001411 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 860228001412 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 860228001413 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 860228001414 DNA binding residues [nucleotide binding] 860228001415 Domain of unknown function (DUF4252); Region: DUF4252; pfam14060 860228001416 Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1- carboxylate synthase (MenD) and related proteins; Region: TPP_PYR_MenD; cd07037 860228001417 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 860228001418 dimer interface [polypeptide binding]; other site 860228001419 tetramer interface [polypeptide binding]; other site 860228001420 PYR/PP interface [polypeptide binding]; other site 860228001421 TPP binding site [chemical binding]; other site 860228001422 Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key...; Region: TPP_SHCHC_synthase; cd02009 860228001423 TPP-binding site; other site 860228001424 Protein of unknown function (DUF2853); Region: DUF2853; pfam11015 860228001425 Penicillinase repressor; Region: Pencillinase_R; pfam03965 860228001426 Antirepressor regulating drug resistance, predicted signal transduction N-terminal membrane component [Transcription / Signal transduction mechanisms]; Region: MecR1; COG4219 860228001427 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 860228001428 threonine dehydratase; Validated; Region: PRK08639 860228001429 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 860228001430 tetramer interface [polypeptide binding]; other site 860228001431 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228001432 catalytic residue [active] 860228001433 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 860228001434 putative Ile/Val binding site [chemical binding]; other site 860228001435 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 860228001436 ketol-acid reductoisomerase; Validated; Region: PRK05225 860228001437 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 860228001438 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 860228001439 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 860228001440 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 860228001441 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 860228001442 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 860228001443 acetolactate synthase, large subunit, biosynthetic type; Region: acolac_lg; TIGR00118 860228001444 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 860228001445 PYR/PP interface [polypeptide binding]; other site 860228001446 dimer interface [polypeptide binding]; other site 860228001447 TPP binding site [chemical binding]; other site 860228001448 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 860228001449 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 860228001450 TPP-binding site [chemical binding]; other site 860228001451 dimer interface [polypeptide binding]; other site 860228001452 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 860228001453 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 860228001454 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 860228001455 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 860228001456 active site 860228001457 HIGH motif; other site 860228001458 nucleotide binding site [chemical binding]; other site 860228001459 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 860228001460 KMSK motif region; other site 860228001461 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 860228001462 tRNA binding surface [nucleotide binding]; other site 860228001463 anticodon binding site; other site 860228001464 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 860228001465 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 860228001466 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 860228001467 active site 860228001468 TRAM domain; Region: TRAM; cl01282 860228001469 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 860228001470 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 860228001471 S-adenosylmethionine binding site [chemical binding]; other site 860228001472 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 860228001473 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 860228001474 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 860228001475 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 860228001476 Ligand binding site [chemical binding]; other site 860228001477 Electron transfer flavoprotein domain; Region: ETF; pfam01012 860228001478 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 860228001479 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 860228001480 alpha subunit interface [polypeptide binding]; other site 860228001481 TPP binding site [chemical binding]; other site 860228001482 heterodimer interface [polypeptide binding]; other site 860228001483 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 860228001484 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228001485 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 860228001486 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 860228001487 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 860228001488 dimerization interface [polypeptide binding]; other site 860228001489 active site 860228001490 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 860228001491 Shikimate kinase; Region: SKI; pfam01202 860228001492 ADP binding site [chemical binding]; other site 860228001493 magnesium binding site [ion binding]; other site 860228001494 putative shikimate binding site; other site 860228001495 Uncharacterized protein conserved in bacteria (DUF2317); Region: DUF2317; pfam10079 860228001496 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4365 860228001497 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 860228001498 Integrase core domain; Region: rve; pfam00665 860228001499 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 860228001500 cofactor binding site; other site 860228001501 DNA binding site [nucleotide binding] 860228001502 substrate interaction site [chemical binding]; other site 860228001503 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 860228001504 dimer interface [polypeptide binding]; other site 860228001505 Predicted membrane protein [Function unknown]; Region: COG4270 860228001506 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 860228001507 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 860228001508 ligand binding site [chemical binding]; other site 860228001509 flexible hinge region; other site 860228001510 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 860228001511 Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarB; COG0458 860228001512 ATP-grasp domain; Region: ATP-grasp_4; cl17255 860228001513 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 860228001514 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; smart01096 860228001515 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 860228001516 Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarB; COG0458 860228001517 ATP-grasp domain; Region: ATP-grasp_4; cl17255 860228001518 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 860228001519 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 860228001520 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 860228001521 DNA-binding interface [nucleotide binding]; DNA binding site 860228001522 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 860228001523 Helix-turn-helix domain; Region: HTH_38; pfam13936 860228001524 Integrase core domain; Region: rve; pfam00665 860228001525 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 860228001526 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 860228001527 RNA binding site [nucleotide binding]; other site 860228001528 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 860228001529 RNA binding site [nucleotide binding]; other site 860228001530 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 860228001531 RNA binding site [nucleotide binding]; other site 860228001532 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 860228001533 RNA binding site [nucleotide binding]; other site 860228001534 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 860228001535 RNA binding site [nucleotide binding]; other site 860228001536 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 860228001537 oligomerization interface [polypeptide binding]; other site 860228001538 active site 860228001539 metal binding site [ion binding]; metal-binding site 860228001540 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 860228001541 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 860228001542 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 860228001543 active site 860228001544 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 860228001545 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 860228001546 active site 860228001547 DNA binding site [nucleotide binding] 860228001548 Int/Topo IB signature motif; other site 860228001549 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 860228001550 30S subunit binding site; other site 860228001551 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 860228001552 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 860228001553 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 860228001554 ligand binding site [chemical binding]; other site 860228001555 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 860228001556 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 860228001557 ligand binding site [chemical binding]; other site 860228001558 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 860228001559 Part of AAA domain; Region: AAA_19; pfam13245 860228001560 Family description; Region: UvrD_C_2; pfam13538 860228001561 Domain of unknown function (DUF3127); Region: DUF3127; pfam11325 860228001562 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 860228001563 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 860228001564 Protein of unknown function (DUF3109); Region: DUF3109; pfam11307 860228001565 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 860228001566 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 860228001567 dimer interface [polypeptide binding]; other site 860228001568 catalytic triad [active] 860228001569 phosphoglucosamine mutase; Region: Arch_GlmM; TIGR03990 860228001570 The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine...; Region: phosphohexomutase; cl03757 860228001571 active site 860228001572 substrate binding site [chemical binding]; other site 860228001573 metal binding site [ion binding]; metal-binding site 860228001574 S-adenosyl-l-methionine hydroxide adenosyltransferase; Region: SAM_adeno_trans; pfam01887 860228001575 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 860228001576 transcription termination factor Rho; Provisional; Region: PRK12608 860228001577 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 860228001578 RNA binding site [nucleotide binding]; other site 860228001579 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 860228001580 multimer interface [polypeptide binding]; other site 860228001581 Walker A motif; other site 860228001582 ATP binding site [chemical binding]; other site 860228001583 Walker B motif; other site 860228001584 Uncharacterized protein related to glutamine synthetase [General function prediction only]; Region: COG3968 860228001585 Glutamine synthetase type III N terminal; Region: GSIII_N; pfam12437 860228001586 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 860228001587 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 860228001588 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 860228001589 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 860228001590 NAD(P) binding site [chemical binding]; other site 860228001591 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 860228001592 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 860228001593 tetramerization interface [polypeptide binding]; other site 860228001594 active site 860228001595 pantoate--beta-alanine ligase; Region: panC; TIGR00018 860228001596 Pantoate-beta-alanine ligase; Region: PanC; cd00560 860228001597 active site 860228001598 ATP-binding site [chemical binding]; other site 860228001599 pantoate-binding site; other site 860228001600 HXXH motif; other site 860228001601 Starch synthase catalytic domain; Region: Glyco_transf_5; pfam08323 860228001602 Domain of unknown function (DUF4270); Region: DUF4270; pfam14092 860228001603 NigD-like protein; Region: NigD; pfam12667 860228001604 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 860228001605 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 860228001606 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 860228001607 DNA binding residues [nucleotide binding] 860228001608 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 860228001609 Thiol-activated cytolysin; Region: Thiol_cytolysin; pfam01289 860228001610 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 860228001611 Uncharacterized conserved protein [Function unknown]; Region: COG2353 860228001612 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 860228001613 DinB superfamily; Region: DinB_2; pfam12867 860228001614 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 860228001615 Cyclic nucleotide-binding domain; Region: cNMP_binding; pfam00027 860228001616 ligand binding site [chemical binding]; other site 860228001617 flexible hinge region; other site 860228001618 Peptidase M1 family Aminopeptidase N; Region: M1_APN_4; cd09603 860228001619 Peptidase family M1; Region: Peptidase_M1; pfam01433 860228001620 Zn binding site [ion binding]; other site 860228001621 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 860228001622 HEAT repeats; Region: HEAT_2; pfam13646 860228001623 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 860228001624 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 860228001625 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 860228001626 putative acyl-acceptor binding pocket; other site 860228001627 Rhomboid family; Region: Rhomboid; pfam01694 860228001628 Parallel beta-helix repeat of pectate lyase; Region: PbH1; pfam13573 860228001629 Parallel beta-helix repeat of pectate lyase; Region: PbH1; pfam13573 860228001630 Parallel beta-helix repeat of pectate lyase; Region: PbH1; pfam13573 860228001631 Parallel beta-helix repeat of pectate lyase; Region: PbH1; pfam13573 860228001632 Parallel beta-helix repeat of pectate lyase; Region: PbH1; pfam13573 860228001633 Parallel beta-helix repeat of pectate lyase; Region: PbH1; pfam13573 860228001634 gliding motility-associated C-terminal domain; Region: Bac_Flav_CTERM; TIGR04131 860228001635 GMP synthase; Reviewed; Region: guaA; PRK00074 860228001636 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 860228001637 AMP/PPi binding site [chemical binding]; other site 860228001638 candidate oxyanion hole; other site 860228001639 catalytic triad [active] 860228001640 potential glutamine specificity residues [chemical binding]; other site 860228001641 The C-terminal domain of GMP synthetase. It contains two subdomains; the ATP pyrophosphatase domain which closes to the N-termial and the dimerization domain at C-terminal end. The ATP-PPase is a twisted, five-stranded parallel beta-sheet sandwiched...; Region: GMP_synthase_C; cd01997 860228001642 ATP Binding subdomain [chemical binding]; other site 860228001643 Ligand Binding sites [chemical binding]; other site 860228001644 Dimerization subdomain; other site 860228001645 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 860228001646 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 860228001647 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 860228001648 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 860228001649 putative substrate translocation pore; other site 860228001650 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 860228001651 POT family; Region: PTR2; cl17359 860228001652 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 860228001653 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 860228001654 CoenzymeA binding site [chemical binding]; other site 860228001655 subunit interaction site [polypeptide binding]; other site 860228001656 PHB binding site; other site 860228001657 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 860228001658 OstA-like protein; Region: OstA_2; pfam13100 860228001659 Domain of Unknown Function (DUF1599); Region: DUF1599; pfam07659 860228001660 Domain of Unknown Function (DUF1599); Region: DUF1599; pfam07659 860228001661 Predicted membrane protein [Function unknown]; Region: COG2259 860228001662 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 860228001663 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 860228001664 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 860228001665 Walker A/P-loop; other site 860228001666 ATP binding site [chemical binding]; other site 860228001667 Q-loop/lid; other site 860228001668 ABC transporter signature motif; other site 860228001669 Walker B; other site 860228001670 D-loop; other site 860228001671 H-loop/switch region; other site 860228001672 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 860228001673 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 860228001674 S-adenosylmethionine binding site [chemical binding]; other site 860228001675 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; pfam02617 860228001676 Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to...; Region: MGS; cd01422 860228001677 active site 860228001678 dimer interfaces [polypeptide binding]; other site 860228001679 catalytic residues [active] 860228001680 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 860228001681 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 860228001682 quinone interaction residues [chemical binding]; other site 860228001683 active site 860228001684 catalytic residues [active] 860228001685 FMN binding site [chemical binding]; other site 860228001686 substrate binding site [chemical binding]; other site 860228001687 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 860228001688 Sulfatase; Region: Sulfatase; cl17466 860228001689 Sulfatase; Region: Sulfatase; cl17466 860228001690 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 860228001691 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 860228001692 ABC transporter; Region: ABC_tran_2; pfam12848 860228001693 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 860228001694 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 860228001695 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat1; cd02203 860228001696 dimerization interface [polypeptide binding]; other site 860228001697 ATP binding site [chemical binding]; other site 860228001698 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), second repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat2; cd02204 860228001699 dimerization interface [polypeptide binding]; other site 860228001700 ATP binding site [chemical binding]; other site 860228001701 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 860228001702 putative active site [active] 860228001703 catalytic triad [active] 860228001704 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 860228001705 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 860228001706 E3 interaction surface; other site 860228001707 lipoyl attachment site [posttranslational modification]; other site 860228001708 e3 binding domain; Region: E3_binding; pfam02817 860228001709 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 860228001710 recombination protein RecR; Reviewed; Region: recR; PRK00076 860228001711 RecR protein; Region: RecR; pfam02132 860228001712 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 860228001713 putative active site [active] 860228001714 putative metal-binding site [ion binding]; other site 860228001715 tetramer interface [polypeptide binding]; other site 860228001716 diaminopimelate decarboxylase; Region: lysA; TIGR01048 860228001717 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 860228001718 active site 860228001719 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 860228001720 substrate binding site [chemical binding]; other site 860228001721 catalytic residues [active] 860228001722 dimer interface [polypeptide binding]; other site 860228001723 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 860228001724 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 860228001725 NodB motif; other site 860228001726 active site 860228001727 catalytic site [active] 860228001728 metal binding site [ion binding]; metal-binding site 860228001729 UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]; Region: MurC; COG0773 860228001730 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 860228001731 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 860228001732 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 860228001733 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 860228001734 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 860228001735 Gram-negative bacterial tonB protein; Region: TonB; cl10048 860228001736 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 860228001737 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 860228001738 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 860228001739 helicase, putative, RecD/TraA family; Region: recD_rel; TIGR01448 860228001740 Delta(1)-pyrroline-5-carboxylate dehydrogenase, ALDH families 4 and 17; Region: ALDH_F4-17_P5CDH; cd07123 860228001741 delta-1-pyrroline-5-carboxylate dehydrogenase, group 1; Region: D1pyr5carbox1; TIGR01236 860228001742 Glutamate binding site [chemical binding]; other site 860228001743 NAD binding site [chemical binding]; other site 860228001744 catalytic residues [active] 860228001745 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 860228001746 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 860228001747 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 860228001748 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 860228001749 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 860228001750 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 860228001751 FtsH Extracellular; Region: FtsH_ext; pfam06480 860228001752 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 860228001753 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 860228001754 Walker A motif; other site 860228001755 ATP binding site [chemical binding]; other site 860228001756 Walker B motif; other site 860228001757 arginine finger; other site 860228001758 Peptidase family M41; Region: Peptidase_M41; pfam01434 860228001759 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 860228001760 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 860228001761 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 860228001762 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 860228001763 hypothetical protein; Provisional; Region: PRK12378 860228001764 Uncharacterized conserved protein [Function unknown]; Region: COG4121 860228001765 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 860228001766 active site clefts [active] 860228001767 zinc binding site [ion binding]; other site 860228001768 dimer interface [polypeptide binding]; other site 860228001769 Mechanosensitive ion channel; Region: MS_channel; pfam00924 860228001770 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 860228001771 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 860228001772 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 860228001773 active site 860228001774 HIGH motif; other site 860228001775 nucleotide binding site [chemical binding]; other site 860228001776 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 860228001777 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 860228001778 active site 860228001779 KMSKS motif; other site 860228001780 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 860228001781 tRNA binding surface [nucleotide binding]; other site 860228001782 anticodon binding site; other site 860228001783 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 860228001784 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 860228001785 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 860228001786 potential protein location (Hypothetical protein Ccan_07420 [Capnocytophaga canimorsus Cc5]) that overlaps RNA (5S ribosomal RNA (5S rRNA)) 860228001787 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 860228001788 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 860228001789 Active Sites [active] 860228001790 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 860228001791 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 860228001792 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 860228001793 DNA binding residues [nucleotide binding] 860228001794 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 860228001795 trigger factor; Provisional; Region: tig; PRK01490 860228001796 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 860228001797 Clp protease; Region: CLP_protease; pfam00574 860228001798 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 860228001799 oligomer interface [polypeptide binding]; other site 860228001800 active site residues [active] 860228001801 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 860228001802 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 860228001803 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 860228001804 Walker A motif; other site 860228001805 ATP binding site [chemical binding]; other site 860228001806 Walker B motif; other site 860228001807 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 860228001808 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 860228001809 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 860228001810 Active Sites [active] 860228001811 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 860228001812 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 860228001813 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 860228001814 Domain of unknown function (DUF4349); Region: DUF4349; pfam14257 860228001815 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 860228001816 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 860228001817 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 860228001818 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 860228001819 RNA binding site [nucleotide binding]; other site 860228001820 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4152 860228001821 ATP-binding cassette domain of an uncharacterized transporter; Region: ABC_putative_ATPase; cd03269 860228001822 Walker A/P-loop; other site 860228001823 ATP binding site [chemical binding]; other site 860228001824 Q-loop/lid; other site 860228001825 ABC transporter signature motif; other site 860228001826 Walker B; other site 860228001827 D-loop; other site 860228001828 H-loop/switch region; other site 860228001829 Domain of unknown function (DUF4162); Region: DUF4162; pfam13732 860228001830 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 860228001831 DNA polymerase III subunit beta; Validated; Region: PRK05643 860228001832 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 860228001833 putative DNA binding surface [nucleotide binding]; other site 860228001834 dimer interface [polypeptide binding]; other site 860228001835 beta-clamp/clamp loader binding surface; other site 860228001836 beta-clamp/translesion DNA polymerase binding surface; other site 860228001837 gliding-associated putative ABC transporter substrate-binding component GldG; Region: GldG; TIGR03521 860228001838 gliding motility-associated ABC transporter permease protein GldF; Region: ABC_perm_GldF; TIGR03518 860228001839 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; cd06259 860228001840 putative active site [active] 860228001841 Response regulator receiver domain; Region: Response_reg; pfam00072 860228001842 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 860228001843 active site 860228001844 phosphorylation site [posttranslational modification] 860228001845 intermolecular recognition site; other site 860228001846 dimerization interface [polypeptide binding]; other site 860228001847 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 860228001848 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 860228001849 Walker A motif; other site 860228001850 ATP binding site [chemical binding]; other site 860228001851 Walker B motif; other site 860228001852 arginine finger; other site 860228001853 Protein of unknown function (DUF819); Region: DUF819; cl02317 860228001854 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 860228001855 Na+/H+ antiporter NhaC; Region: antiport_nhaC; TIGR00931 860228001856 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 860228001857 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 860228001858 ATP binding site [chemical binding]; other site 860228001859 Mg2+ binding site [ion binding]; other site 860228001860 G-X-G motif; other site 860228001861 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second...; Region: TopoII_MutL_Trans; cl02783 860228001862 ATP binding site [chemical binding]; other site 860228001863 TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands...; Region: TOPRIM_TopoIIA_like; cd01030 860228001864 active site 860228001865 putative metal-binding site [ion binding]; other site 860228001866 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 860228001867 Helix-turn-helix domain; Region: HTH_38; pfam13936 860228001868 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 860228001869 NAD(P) binding site [chemical binding]; other site 860228001870 active site 860228001871 cell division ATP-binding protein FtsE; Region: FtsE; TIGR02673 860228001872 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228001873 Walker A/P-loop; other site 860228001874 ATP binding site [chemical binding]; other site 860228001875 Q-loop/lid; other site 860228001876 ABC transporter signature motif; other site 860228001877 Walker B; other site 860228001878 D-loop; other site 860228001879 H-loop/switch region; other site 860228001880 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 860228001881 Peptidase family M23; Region: Peptidase_M23; pfam01551 860228001882 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 860228001883 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 860228001884 CoA-ligase; Region: Ligase_CoA; pfam00549 860228001885 Protein of unknown function (DUF3308); Region: DUF3308; pfam11751 860228001886 Metallo-peptidase family M12B Reprolysin-like; Region: Reprolysin_2; pfam13574 860228001887 active site 860228001888 Thrombospondin type 3 repeat; Region: TSP_3; pfam02412 860228001889 Thrombospondin type 3 repeat; Region: TSP_3; pfam02412 860228001890 Thrombospondin type 3 repeat; Region: TSP_3; pfam02412 860228001891 C-terminal domain of CHU protein family; Region: CHU_C; pfam13585 860228001892 transcription antitermination factor NusB; Region: nusB; TIGR01951 860228001893 Preprotein translocase subunit; Region: YajC; pfam02699 860228001894 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 860228001895 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and...; Region: PGM2; cd05799 860228001896 active site 860228001897 substrate binding site [chemical binding]; other site 860228001898 metal binding site [ion binding]; metal-binding site 860228001899 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 860228001900 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 860228001901 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 860228001902 Walker A/P-loop; other site 860228001903 ATP binding site [chemical binding]; other site 860228001904 Q-loop/lid; other site 860228001905 ABC transporter signature motif; other site 860228001906 Walker B; other site 860228001907 D-loop; other site 860228001908 H-loop/switch region; other site 860228001909 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 860228001910 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 860228001911 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 860228001912 DNA binding residues [nucleotide binding] 860228001913 TRL-like protein family; Region: TRL; pfam13146 860228001914 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK02484 860228001915 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 860228001916 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 860228001917 N-terminal plug; other site 860228001918 ligand-binding site [chemical binding]; other site 860228001919 Bacterial proteins similar to Porphyromonas gingivalis HmuY; Region: HmuY; cd12105 860228001920 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 860228001921 G1 box; other site 860228001922 GTP/Mg2+ binding site [chemical binding]; other site 860228001923 G2 box; other site 860228001924 G3 box; other site 860228001925 Switch II region; other site 860228001926 50S ribosome-binding GTPase; Region: MMR_HSR1; pfam01926 860228001927 G1 box; other site 860228001928 GTP/Mg2+ binding site [chemical binding]; other site 860228001929 G2 box; other site 860228001930 Switch I region; other site 860228001931 G3 box; other site 860228001932 Switch II region; other site 860228001933 G4 box; other site 860228001934 G5 box; other site 860228001935 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 860228001936 active site 860228001937 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 860228001938 elongation factor G; Reviewed; Region: PRK12740 860228001939 G1 box; other site 860228001940 putative GEF interaction site [polypeptide binding]; other site 860228001941 GTP/Mg2+ binding site [chemical binding]; other site 860228001942 Switch I region; other site 860228001943 G2 box; other site 860228001944 G3 box; other site 860228001945 Switch II region; other site 860228001946 G4 box; other site 860228001947 G5 box; other site 860228001948 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 860228001949 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 860228001950 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 860228001951 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 860228001952 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 860228001953 Isopentenyldiphosphate isomerase [Lipid metabolism]; Region: Idi; COG1443 860228001954 Isopentenyl diphosphate (IPP) isomerase, a member of the Nudix hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated...; Region: IPP_Isomerase; cd02885 860228001955 active site 860228001956 metal binding site [ion binding]; metal-binding site 860228001957 nudix motif; other site 860228001958 N-acetylmuramic acid-6-phosphate etherase; Reviewed; Region: murQ; PRK05441 860228001959 N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid...; Region: SIS_Etherase; cd05007 860228001960 putative active site [active] 860228001961 Peptidase M60-like family; Region: M60-like; pfam13402 860228001962 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 860228001963 Homeodomain-like domain; Region: HTH_23; pfam13384 860228001964 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 860228001965 GTP-binding protein Der; Reviewed; Region: PRK00093 860228001966 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 860228001967 G1 box; other site 860228001968 GTP/Mg2+ binding site [chemical binding]; other site 860228001969 Switch I region; other site 860228001970 G2 box; other site 860228001971 Switch II region; other site 860228001972 G3 box; other site 860228001973 G4 box; other site 860228001974 G5 box; other site 860228001975 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 860228001976 G1 box; other site 860228001977 GTP/Mg2+ binding site [chemical binding]; other site 860228001978 Switch I region; other site 860228001979 G2 box; other site 860228001980 G3 box; other site 860228001981 Switch II region; other site 860228001982 G4 box; other site 860228001983 G5 box; other site 860228001984 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 860228001985 binding surface 860228001986 TPR motif; other site 860228001987 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 860228001988 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 860228001989 potential frameshift: common BLAST hit: gi|162456493|ref|YP_001618860.1| DNA helicase 860228001990 AAA domain; Region: AAA_12; pfam13087 860228001991 AAA domain; Region: AAA_11; pfam13086 860228001992 Part of AAA domain; Region: AAA_19; pfam13245 860228001993 Transposase and inactivated derivatives, IS1 family [DNA replication, recombination, and repair]; Region: InsB; COG1662 860228001994 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 860228001995 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 860228001996 replicative DNA helicase; Region: DnaB; TIGR00665 860228001997 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 860228001998 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 860228001999 Walker A motif; other site 860228002000 ATP binding site [chemical binding]; other site 860228002001 Walker B motif; other site 860228002002 DNA binding loops [nucleotide binding] 860228002003 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 860228002004 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 860228002005 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228002006 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 860228002007 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228002008 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 860228002009 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 860228002010 ATP binding site [chemical binding]; other site 860228002011 Mg2+ binding site [ion binding]; other site 860228002012 G-X-G motif; other site 860228002013 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 860228002014 ATP binding site [chemical binding]; other site 860228002015 MutL C terminal dimerisation domain; Region: MutL_C; smart00853 860228002016 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 860228002017 Rhomboid family; Region: Rhomboid; pfam01694 860228002018 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 860228002019 active site 860228002020 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 860228002021 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 860228002022 Walker A motif; other site 860228002023 ATP binding site [chemical binding]; other site 860228002024 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 860228002025 Walker B motif; other site 860228002026 arginine finger; other site 860228002027 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 860228002028 DnaA box-binding interface [nucleotide binding]; other site 860228002029 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 860228002030 Low molecular weight phosphatase family; Region: LMWPc; cd00115 860228002031 active site 860228002032 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 860228002033 putative SAM binding site [chemical binding]; other site 860228002034 homodimer interface [polypeptide binding]; other site 860228002035 Na(+)/iodide (NIS) and Na(+)/multivitamin (SMVT) cotransporters, and related proteins; solute binding domain; Region: SLC5sbd_NIS-like; cd10326 860228002036 Na binding site [ion binding]; other site 860228002037 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 860228002038 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 860228002039 active site 860228002040 dimer interface [polypeptide binding]; other site 860228002041 Phosphomannose isomerase [Carbohydrate transport and metabolism]; Region: ManA; COG1482 860228002042 Alpha-Mannosidase Binding Domain of Atg19/34; Region: ABD; cl15429 860228002043 ligand binding site [chemical binding]; other site 860228002044 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 860228002045 Bacterial Ig-like domain (group 2); Region: Big_2; cl02708 860228002046 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 860228002047 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 860228002048 catalytic residues [active] 860228002049 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 860228002050 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 860228002051 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 860228002052 Protein export membrane protein; Region: SecD_SecF; pfam02355 860228002053 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 860228002054 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 860228002055 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 860228002056 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 860228002057 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 860228002058 Peptidase S46; Region: Peptidase_S46; pfam10459 860228002059 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 860228002060 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4856 860228002061 YbbR-like protein; Region: YbbR; pfam07949 860228002062 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 860228002063 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 860228002064 CoA-binding site [chemical binding]; other site 860228002065 ATP-binding [chemical binding]; other site 860228002066 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 860228002067 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 860228002068 dimer interface [polypeptide binding]; other site 860228002069 phosphorylation site [posttranslational modification] 860228002070 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 860228002071 ATP binding site [chemical binding]; other site 860228002072 Mg2+ binding site [ion binding]; other site 860228002073 G-X-G motif; other site 860228002074 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 860228002075 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 860228002076 active site 860228002077 phosphorylation site [posttranslational modification] 860228002078 intermolecular recognition site; other site 860228002079 dimerization interface [polypeptide binding]; other site 860228002080 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 860228002081 DNA binding site [nucleotide binding] 860228002082 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 860228002083 Glutamine amidotransferase class-I; Region: GATase; pfam00117 860228002084 glutamine binding [chemical binding]; other site 860228002085 catalytic triad [active] 860228002086 indole-3-glycerol-phosphate synthase; Reviewed; Region: trpC; PRK00278 860228002087 phosphate binding site [ion binding]; other site 860228002088 excinuclease ABC subunit B; Provisional; Region: PRK05298 860228002089 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 860228002090 ATP binding site [chemical binding]; other site 860228002091 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 860228002092 nucleotide binding region [chemical binding]; other site 860228002093 ATP-binding site [chemical binding]; other site 860228002094 Ultra-violet resistance protein B; Region: UvrB; pfam12344 860228002095 UvrB/uvrC motif; Region: UVR; pfam02151 860228002096 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 860228002097 Shikimate 5-dehydrogenase [Amino acid transport and metabolism]; Region: AroE; COG0169 860228002098 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 860228002099 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 860228002100 shikimate binding site; other site 860228002101 NAD(P) binding site [chemical binding]; other site 860228002102 Domain of unknown function (DUF368); Region: DUF368; pfam04018 860228002103 Domain of unknown function (DUF368); Region: DUF368; pfam04018 860228002104 Proline dehydrogenase; Region: Pro_dh; cl03282 860228002105 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 860228002106 active site 860228002107 dimer interface [polypeptide binding]; other site 860228002108 metal binding site [ion binding]; metal-binding site 860228002109 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 860228002110 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228002111 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228002112 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 860228002113 starch binding outer membrane protein SusD; Region: SusD; cd08977 860228002114 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 860228002115 active site 860228002116 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 860228002117 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 860228002118 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 860228002119 Transposase; Region: HTH_Tnp_1; pfam01527 860228002120 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 860228002121 Integrase core domain; Region: rve; pfam00665 860228002122 Integrase core domain; Region: rve_3; cl15866 860228002123 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 860228002124 PAS fold; Region: PAS_3; pfam08447 860228002125 putative active site [active] 860228002126 heme pocket [chemical binding]; other site 860228002127 fumarate hydratase; Reviewed; Region: fumC; PRK00485 860228002128 Class II fumarases; Region: Fumarase_classII; cd01362 860228002129 active site 860228002130 tetramer interface [polypeptide binding]; other site 860228002131 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 860228002132 Alpha-L-fucosidase; Region: Alpha_L_fucos; cl12119 860228002133 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 860228002134 Fn3 associated; Region: Fn3_assoc; pfam13287 860228002135 Coagulation factor 5/8 C-terminal domain, discoidin domain; Region: FA58C; smart00231 860228002136 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 860228002137 sugar binding site [chemical binding]; other site 860228002138 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 860228002139 active site 860228002140 Thioesterase-like superfamily; Region: 4HBT_2; pfam13279 860228002141 active site 2 [active] 860228002142 active site 1 [active] 860228002143 putative C-S lyase; Region: C_S_lyase_PatB; TIGR04350 860228002144 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 860228002145 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228002146 homodimer interface [polypeptide binding]; other site 860228002147 catalytic residue [active] 860228002148 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 860228002149 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 860228002150 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 860228002151 FMN-binding domain; Region: FMN_bind; cl01081 860228002152 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 860228002153 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 860228002154 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 860228002155 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 860228002156 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 860228002157 catalytic loop [active] 860228002158 iron binding site [ion binding]; other site 860228002159 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 860228002160 FAD binding pocket [chemical binding]; other site 860228002161 FAD binding motif [chemical binding]; other site 860228002162 phosphate binding motif [ion binding]; other site 860228002163 beta-alpha-beta structure motif; other site 860228002164 NAD binding pocket [chemical binding]; other site 860228002165 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 860228002166 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 860228002167 active site 860228002168 peptide chain release factor 1; Validated; Region: prfA; PRK00591 860228002169 This domain is found in peptide chain release factors; Region: PCRF; smart00937 860228002170 RF-1 domain; Region: RF-1; pfam00472 860228002171 Protein of unknown function (DUF2911); Region: DUF2911; pfam11138 860228002172 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 860228002173 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 860228002174 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 860228002175 S-adenosylmethionine binding site [chemical binding]; other site 860228002176 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 860228002177 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 860228002178 catalytic residue [active] 860228002179 putative FPP diphosphate binding site; other site 860228002180 putative FPP binding hydrophobic cleft; other site 860228002181 dimer interface [polypeptide binding]; other site 860228002182 putative IPP diphosphate binding site; other site 860228002183 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 860228002184 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 860228002185 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 860228002186 Surface antigen; Region: Bac_surface_Ag; pfam01103 860228002187 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 860228002188 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 860228002189 periplasmic chaperone; Provisional; Region: PRK10780 860228002190 glutamate racemase; Provisional; Region: PRK00865 860228002191 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 860228002192 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 860228002193 hypothetical protein; Validated; Region: PRK02101 860228002194 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 860228002195 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 860228002196 CysD dimerization site [polypeptide binding]; other site 860228002197 G1 box; other site 860228002198 putative GEF interaction site [polypeptide binding]; other site 860228002199 GTP/Mg2+ binding site [chemical binding]; other site 860228002200 Switch I region; other site 860228002201 G2 box; other site 860228002202 G3 box; other site 860228002203 Switch II region; other site 860228002204 G4 box; other site 860228002205 G5 box; other site 860228002206 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 860228002207 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 860228002208 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 860228002209 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 860228002210 Walker A/P-loop; other site 860228002211 ATP binding site [chemical binding]; other site 860228002212 Q-loop/lid; other site 860228002213 ABC transporter signature motif; other site 860228002214 Walker B; other site 860228002215 D-loop; other site 860228002216 H-loop/switch region; other site 860228002217 Protein of unknown function (DUF4199); Region: DUF4199; pfam13858 860228002218 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 860228002219 E3 interaction surface; other site 860228002220 lipoyl attachment site [posttranslational modification]; other site 860228002221 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 860228002222 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 860228002223 E3 interaction surface; other site 860228002224 lipoyl attachment site [posttranslational modification]; other site 860228002225 e3 binding domain; Region: E3_binding; pfam02817 860228002226 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 860228002227 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 860228002228 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 860228002229 tetramer interface [polypeptide binding]; other site 860228002230 TPP-binding site [chemical binding]; other site 860228002231 heterodimer interface [polypeptide binding]; other site 860228002232 phosphorylation loop region [posttranslational modification] 860228002233 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 860228002234 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 860228002235 acyl-activating enzyme (AAE) consensus motif; other site 860228002236 AMP binding site [chemical binding]; other site 860228002237 active site 860228002238 CoA binding site [chemical binding]; other site 860228002239 acetyl-CoA synthetase; Provisional; Region: PRK00174 860228002240 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 860228002241 active site 860228002242 CoA binding site [chemical binding]; other site 860228002243 acyl-activating enzyme (AAE) consensus motif; other site 860228002244 AMP binding site [chemical binding]; other site 860228002245 acetate binding site [chemical binding]; other site 860228002246 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 860228002247 active sites [active] 860228002248 tetramer interface [polypeptide binding]; other site 860228002249 This domain is found in peptide chain release factors; Region: PCRF; smart00937 860228002250 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 860228002251 RF-1 domain; Region: RF-1; pfam00472 860228002252 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 860228002253 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 860228002254 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 860228002255 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 860228002256 DNA binding residues [nucleotide binding] 860228002257 Protein of unknown function, DUF417; Region: DUF417; cl01162 860228002258 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 860228002259 methionine sulfoxide reductase B; Provisional; Region: PRK00222 860228002260 SelR domain; Region: SelR; pfam01641 860228002261 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 860228002262 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 860228002263 catalytic residues [active] 860228002264 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 860228002265 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 860228002266 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 860228002267 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 860228002268 HlyD family secretion protein; Region: HlyD_3; pfam13437 860228002269 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 860228002270 putative DNA binding site [nucleotide binding]; other site 860228002271 Predicted transcriptional regulators [Transcription]; Region: COG1510 860228002272 putative Zn2+ binding site [ion binding]; other site 860228002273 membrane protein insertase; Provisional; Region: PRK01318 860228002274 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 860228002275 Recombination protein O C terminal; Region: RecO_C; pfam02565 860228002276 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 860228002277 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 860228002278 Flavoprotein; Region: Flavoprotein; pfam02441 860228002279 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 860228002280 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; pfam01192 860228002281 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 860228002282 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228002283 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 860228002284 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228002285 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 860228002286 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 860228002287 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 860228002288 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 860228002289 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 860228002290 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 860228002291 dimerization interface [polypeptide binding]; other site 860228002292 ATP binding site [chemical binding]; other site 860228002293 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 860228002294 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 860228002295 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 860228002296 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 860228002297 Uncharacterized conserved protein [Function unknown]; Region: COG0327 860228002298 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 860228002299 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3323 860228002300 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 860228002301 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 860228002302 Putative zinc ribbon domain; Region: DUF164; pfam02591 860228002303 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 860228002304 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 860228002305 homodimer interface [polypeptide binding]; other site 860228002306 metal binding site [ion binding]; metal-binding site 860228002307 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 860228002308 homodimer interface [polypeptide binding]; other site 860228002309 active site 860228002310 putative chemical substrate binding site [chemical binding]; other site 860228002311 metal binding site [ion binding]; metal-binding site 860228002312 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 860228002313 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 860228002314 FtsX-like permease family; Region: FtsX; pfam02687 860228002315 Protein of unknown function, DUF393; Region: DUF393; pfam04134 860228002316 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 860228002317 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 860228002318 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 860228002319 Cupredoxin-like domain; Region: Cupredoxin_1; cl17234 860228002320 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 860228002321 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 860228002322 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway; Region: UMPK; cd02023 860228002323 dephospho-CoA kinase; Region: TIGR00152 860228002324 ATP-binding site [chemical binding]; other site 860228002325 Sugar specificity; other site 860228002326 Pyrimidine base specificity; other site 860228002327 Vacuole effluxer Atg22 like; Region: ATG22; pfam11700 860228002328 Peptidase family M48; Region: Peptidase_M48; pfam01435 860228002329 Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Region: PyrR; COG2065 860228002330 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 860228002331 active site 860228002332 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 860228002333 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 860228002334 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 860228002335 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 860228002336 gliding motility-associated C-terminal domain; Region: Bac_Flav_CTERM; TIGR04131 860228002337 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 860228002338 Predicted transcriptional regulators [Transcription]; Region: COG1733 860228002339 Pirin-related protein [General function prediction only]; Region: COG1741 860228002340 Pirin; Region: Pirin; pfam02678 860228002341 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 860228002342 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 860228002343 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 860228002344 Sec1 family; Region: Sec1; cl15415 860228002345 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 860228002346 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 860228002347 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 860228002348 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cd06260 860228002349 putative active site [active] 860228002350 This entry represents the putative helicase A859L; Region: T5orf172; smart00974 860228002351 Domain of unknown function (DUF4377); Region: DUF4377; pfam14302 860228002352 META domain; Region: META; pfam03724 860228002353 META domain; Region: META; pfam03724 860228002354 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 860228002355 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 860228002356 inhibitor-cofactor binding pocket; inhibition site 860228002357 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228002358 catalytic residue [active] 860228002359 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 860228002360 putative rRNA binding site [nucleotide binding]; other site 860228002361 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 860228002362 phosphodiesterase YaeI; Provisional; Region: PRK11340 860228002363 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 860228002364 putative active site [active] 860228002365 putative metal binding site [ion binding]; other site 860228002366 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 860228002367 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 860228002368 G1 box; other site 860228002369 putative GEF interaction site [polypeptide binding]; other site 860228002370 GTP/Mg2+ binding site [chemical binding]; other site 860228002371 Switch I region; other site 860228002372 G2 box; other site 860228002373 G3 box; other site 860228002374 Switch II region; other site 860228002375 G4 box; other site 860228002376 G5 box; other site 860228002377 RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the...; Region: RF3_II; cd03689 860228002378 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 860228002379 homopentamer interface [polypeptide binding]; other site 860228002380 active site 860228002381 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 860228002382 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 860228002383 binding surface 860228002384 TPR motif; other site 860228002385 recombination protein F; Reviewed; Region: recF; PRK00064 860228002386 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228002387 Walker A/P-loop; other site 860228002388 ATP binding site [chemical binding]; other site 860228002389 Q-loop/lid; other site 860228002390 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228002391 ABC transporter signature motif; other site 860228002392 Walker B; other site 860228002393 D-loop; other site 860228002394 H-loop/switch region; other site 860228002395 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 860228002396 Two component regulator propeller; Region: Reg_prop; pfam07494 860228002397 Histidine kinase; Region: His_kinase; pfam06580 860228002398 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 860228002399 Mg2+ binding site [ion binding]; other site 860228002400 G-X-G motif; other site 860228002401 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 860228002402 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 860228002403 active site 860228002404 phosphorylation site [posttranslational modification] 860228002405 intermolecular recognition site; other site 860228002406 dimerization interface [polypeptide binding]; other site 860228002407 LytTr DNA-binding domain; Region: LytTR; pfam04397 860228002408 Protein of unknown function (DUF1810); Region: DUF1810; cl02370 860228002409 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 860228002410 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine; Region: CBS_like; cd01561 860228002411 dimer interface [polypeptide binding]; other site 860228002412 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228002413 catalytic residue [active] 860228002414 DNA repair and recombination protein RadA; Validated; Region: radA; PRK04301 860228002415 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 860228002416 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 860228002417 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 860228002418 catalytic residue [active] 860228002419 Domain of unknown function (DUF4300); Region: DUF4300; pfam14133 860228002420 Uncharacterized protein conserved in Bacteroidetes; Region: Bacuni_01323_like; cd12871 860228002421 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 860228002422 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228002423 Walker A/P-loop; other site 860228002424 ATP binding site [chemical binding]; other site 860228002425 Q-loop/lid; other site 860228002426 ABC transporter signature motif; other site 860228002427 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 860228002428 Walker B; other site 860228002429 D-loop; other site 860228002430 H-loop/switch region; other site 860228002431 ABC transporter; Region: ABC_tran_2; pfam12848 860228002432 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 860228002433 Thermotoga maritima CorA_like subfamily; Region: TmCorA-like_1; cd12828 860228002434 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 860228002435 oligomer interface [polypeptide binding]; other site 860228002436 metal binding site [ion binding]; metal-binding site 860228002437 metal binding site [ion binding]; metal-binding site 860228002438 Cl binding site [ion binding]; other site 860228002439 aspartate ring; other site 860228002440 basic sphincter; other site 860228002441 putative hydrophobic gate; other site 860228002442 periplasmic entrance; other site 860228002443 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_1; cd07818 860228002444 putative hydrophobic ligand binding site [chemical binding]; other site 860228002445 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 860228002446 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 860228002447 active site 860228002448 motif I; other site 860228002449 motif II; other site 860228002450 Domain of unknown function (DUF2520); Region: DUF2520; pfam10728 860228002451 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 860228002452 Zonular occludens toxin (Zot); Region: Zot; cl17485 860228002453 Bacterial SH3 domain; Region: SH3_3; cl17532 860228002454 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 860228002455 NlpC/P60 family; Region: NLPC_P60; pfam00877 860228002456 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 860228002457 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 860228002458 glyceraldehyde-3-phosphate dehydrogenase; Provisional; Region: PTZ00023 860228002459 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 860228002460 DinB family; Region: DinB; cl17821 860228002461 DinB superfamily; Region: DinB_2; pfam12867 860228002462 6-phosphofructokinase; Provisional; Region: PRK03202 860228002463 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 860228002464 active site 860228002465 ADP/pyrophosphate binding site [chemical binding]; other site 860228002466 dimerization interface [polypeptide binding]; other site 860228002467 allosteric effector site; other site 860228002468 fructose-1,6-bisphosphate binding site; other site 860228002469 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 860228002470 putative substrate translocation pore; other site 860228002471 glucose/galactose transporter; Region: gluP; TIGR01272 860228002472 Restriction endonuclease [Defense mechanisms]; Region: COG3587 860228002473 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 860228002474 non-specific DNA binding site [nucleotide binding]; other site 860228002475 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 860228002476 salt bridge; other site 860228002477 sequence-specific DNA binding site [nucleotide binding]; other site 860228002478 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase_like_7; cd04502 860228002479 active site 860228002480 catalytic triad [active] 860228002481 oxyanion hole [active] 860228002482 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 860228002483 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 860228002484 Ion transport protein; Region: Ion_trans; pfam00520 860228002485 Ion channel; Region: Ion_trans_2; pfam07885 860228002486 putative hydrolase; Provisional; Region: PRK11460 860228002487 Predicted esterase [General function prediction only]; Region: COG0400 860228002488 dihydroorotase; Validated; Region: pyrC; PRK09357 860228002489 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 860228002490 active site 860228002491 Uncharacterized ACR, COG1678; Region: DUF179; pfam02622 860228002492 Predicted transcriptional regulators [Transcription]; Region: COG1695 860228002493 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 860228002494 PspC domain; Region: PspC; pfam04024 860228002495 PspC domain; Region: PspC; pfam04024 860228002496 o-succinylbenzoate synthase; Region: menC_gamma/gm+; TIGR01927 860228002497 o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway; Region: OSBS; cd03320 860228002498 active site 860228002499 DNA polymerase III subunit epsilon; Validated; Region: PRK06310 860228002500 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 860228002501 active site 860228002502 catalytic site [active] 860228002503 substrate binding site [chemical binding]; other site 860228002504 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 860228002505 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 860228002506 active site 860228002507 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 860228002508 generic binding surface I; other site 860228002509 generic binding surface II; other site 860228002510 WYL domain; Region: WYL; pfam13280 860228002511 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 860228002512 potential frameshift: common BLAST hit: gi|60683316|ref|YP_213460.1| putative transposase 860228002513 Integrase core domain; Region: rve; pfam00665 860228002514 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 860228002515 Helix-turn-helix domain; Region: HTH_38; pfam13936 860228002516 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 860228002517 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 860228002518 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 860228002519 Active Sites [active] 860228002520 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c_3; pfam13589 860228002521 ATP binding site [chemical binding]; other site 860228002522 Mg2+ binding site [ion binding]; other site 860228002523 G-X-G motif; other site 860228002524 Predicted restriction endonuclease [Defense mechanisms]; Region: COG3440 860228002525 HNH endonuclease; Region: HNH_2; pfam13391 860228002526 Domain of unknown function (DUF1832); Region: DUF1832; cl07463 860228002527 AAA-like domain; Region: AAA_10; pfam12846 860228002528 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c_3; pfam13589 860228002529 ATP binding site [chemical binding]; other site 860228002530 Mg2+ binding site [ion binding]; other site 860228002531 G-X-G motif; other site 860228002532 Helix-turn-helix domain; Region: HTH_17; pfam12728 860228002533 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 860228002534 integrase; Provisional; Region: int; PHA02601 860228002535 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 860228002536 active site 860228002537 DNA binding site [nucleotide binding] 860228002538 Int/Topo IB signature motif; other site 860228002539 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 860228002540 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 860228002541 trmE is a tRNA modification GTPase; Region: trmE; cd04164 860228002542 G1 box; other site 860228002543 GTP/Mg2+ binding site [chemical binding]; other site 860228002544 Switch I region; other site 860228002545 G2 box; other site 860228002546 Switch II region; other site 860228002547 G3 box; other site 860228002548 G4 box; other site 860228002549 G5 box; other site 860228002550 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 860228002551 peptidase T; Region: peptidase-T; TIGR01882 860228002552 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 860228002553 metal binding site [ion binding]; metal-binding site 860228002554 dimer interface [polypeptide binding]; other site 860228002555 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 860228002556 Transcriptional regulator [Transcription]; Region: LysR; COG0583 860228002557 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 860228002558 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 860228002559 dimerization interface [polypeptide binding]; other site 860228002560 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 860228002561 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 860228002562 dimerization interface [polypeptide binding]; other site 860228002563 DPS ferroxidase diiron center [ion binding]; other site 860228002564 ion pore; other site 860228002565 UPF0126 domain; Region: UPF0126; pfam03458 860228002566 Predicted membrane protein [Function unknown]; Region: COG2860 860228002567 UPF0126 domain; Region: UPF0126; pfam03458 860228002568 Peptidase M1 family containing bacterial Aminopeptidase N; Region: M1_APN_5; cd09604 860228002569 Zn binding site [ion binding]; other site 860228002570 Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E; Region: GAT1_Peptidase_E; cd03146 860228002571 active site pocket [active] 860228002572 oxyanion hole [active] 860228002573 catalytic triad [active] 860228002574 active site nucleophile [active] 860228002575 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 860228002576 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 860228002577 Potassium binding sites [ion binding]; other site 860228002578 Cesium cation binding sites [ion binding]; other site 860228002579 potential frameshift: common BLAST hit: gi|256820706|ref|YP_003141985.1| DNA polymerase III, subunits gamma and tau 860228002580 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14970 860228002581 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 860228002582 Walker A motif; other site 860228002583 ATP binding site [chemical binding]; other site 860228002584 Walker B motif; other site 860228002585 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 860228002586 arginine finger; other site 860228002587 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 860228002588 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14971 860228002589 Repair protein; Region: Repair_PSII; pfam04536 860228002590 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 860228002591 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 860228002592 S-adenosylmethionine binding site [chemical binding]; other site 860228002593 Escherichia coli UshA-like family, N-terminal metallophosphatase domain; Region: MPP_UshA_N_like; cd00845 860228002594 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 860228002595 active site 860228002596 metal binding site [ion binding]; metal-binding site 860228002597 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 860228002598 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 860228002599 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 860228002600 dimer interface [polypeptide binding]; other site 860228002601 active site 860228002602 catalytic residue [active] 860228002603 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 860228002604 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 860228002605 hexamer interface [polypeptide binding]; other site 860228002606 ligand binding site [chemical binding]; other site 860228002607 putative active site [active] 860228002608 NAD(P) binding site [chemical binding]; other site 860228002609 Domain of unknown function (DUF4258); Region: DUF4258; pfam14076 860228002610 DEAD-like helicases superfamily; Region: DEXDc; smart00487 860228002611 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 860228002612 ATP binding site [chemical binding]; other site 860228002613 putative Mg++ binding site [ion binding]; other site 860228002614 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 860228002615 nucleotide binding region [chemical binding]; other site 860228002616 ATP-binding site [chemical binding]; other site 860228002617 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 860228002618 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 860228002619 putative active site [active] 860228002620 substrate binding site [chemical binding]; other site 860228002621 putative cosubstrate binding site; other site 860228002622 catalytic site [active] 860228002623 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 860228002624 substrate binding site [chemical binding]; other site 860228002625 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 860228002626 IHF dimer interface [polypeptide binding]; other site 860228002627 IHF - DNA interface [nucleotide binding]; other site 860228002628 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of...; Region: MM_CoA_mutase; cl00817 860228002629 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of...; Region: MM_CoA_mutase; cl00817 860228002630 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 860228002631 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 860228002632 PA_M28_2: Protease-associated (PA) domain, peptidase family M28, subfamily-2. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions; Region: PA_M28_2; cd04815 860228002633 PA/protease or protease-like domain interface [polypeptide binding]; other site 860228002634 M28 Zn-Peptidase Plasma glutamate carboxypeptidase; Region: M28_Pgcp_like; cd03883 860228002635 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 860228002636 metal binding site [ion binding]; metal-binding site 860228002637 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 860228002638 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 860228002639 dimerization interface 3.5A [polypeptide binding]; other site 860228002640 active site 860228002641 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 860228002642 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 860228002643 dimer interface [polypeptide binding]; other site 860228002644 active site 860228002645 CoA binding pocket [chemical binding]; other site 860228002646 seryl-tRNA synthetase; Provisional; Region: PRK05431 860228002647 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 860228002648 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 860228002649 dimer interface [polypeptide binding]; other site 860228002650 active site 860228002651 motif 1; other site 860228002652 motif 2; other site 860228002653 motif 3; other site 860228002654 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 860228002655 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 860228002656 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl17418 860228002657 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 860228002658 putative DNA binding site [nucleotide binding]; other site 860228002659 putative Zn2+ binding site [ion binding]; other site 860228002660 AsnC family; Region: AsnC_trans_reg; pfam01037 860228002661 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_2; cd06239 860228002662 putative active site [active] 860228002663 Zn binding site [ion binding]; other site 860228002664 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 860228002665 non-specific DNA binding site [nucleotide binding]; other site 860228002666 salt bridge; other site 860228002667 sequence-specific DNA binding site [nucleotide binding]; other site 860228002668 potential frameshift: common BLAST hit: gi|256820770|ref|YP_003142049.1| glycosyl transferase group 1 860228002669 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 860228002670 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 860228002671 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 860228002672 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 860228002673 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 860228002674 dimer interface [polypeptide binding]; other site 860228002675 active site 860228002676 glycine-pyridoxal phosphate binding site [chemical binding]; other site 860228002677 folate binding site [chemical binding]; other site 860228002678 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 860228002679 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 860228002680 dimerization interface [polypeptide binding]; other site 860228002681 putative DNA binding site [nucleotide binding]; other site 860228002682 putative Zn2+ binding site [ion binding]; other site 860228002683 AsnC family; Region: AsnC_trans_reg; pfam01037 860228002684 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 860228002685 NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like...; Region: PA_degradation_oxidoreductase_like; cd06214 860228002686 FAD binding pocket [chemical binding]; other site 860228002687 FAD binding motif [chemical binding]; other site 860228002688 phosphate binding motif [ion binding]; other site 860228002689 beta-alpha-beta structure motif; other site 860228002690 NAD(p) ribose binding residues [chemical binding]; other site 860228002691 NAD binding pocket [chemical binding]; other site 860228002692 NAD(P)-pyrophosphate-nicotinamide binding residues [chemical binding]; other site 860228002693 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 860228002694 catalytic loop [active] 860228002695 iron binding site [ion binding]; other site 860228002696 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 860228002697 DHH family; Region: DHH; pfam01368 860228002698 DHHA1 domain; Region: DHHA1; pfam02272 860228002699 peptidyl-prolyl isomerase, gliding motility-associated; Region: ppisom_GldI; TIGR03516 860228002700 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 860228002701 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 860228002702 active site 860228002703 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 860228002704 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 860228002705 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 860228002706 substrate binding site [chemical binding]; other site 860228002707 oxyanion hole (OAH) forming residues; other site 860228002708 trimer interface [polypeptide binding]; other site 860228002709 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 860228002710 intersubunit interface [polypeptide binding]; other site 860228002711 active site 860228002712 catalytic residue [active] 860228002713 glucosamine-6-phosphate deaminase-like protein; Validated; Region: PRK02122 860228002714 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or...; Region: GlcN6P_deaminase; cd01399 860228002715 active site 860228002716 trimer interface [polypeptide binding]; other site 860228002717 allosteric site; other site 860228002718 active site lid [active] 860228002719 hexamer (dimer of trimers) interface [polypeptide binding]; other site 860228002720 GlcNAc-PI de-N-acetylase; Region: PIG-L; pfam02585 860228002721 RHS protein; Region: RHS; pfam03527 860228002722 RHS protein; Region: RHS; pfam03527 860228002723 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 860228002724 RHS Repeat; Region: RHS_repeat; pfam05593 860228002725 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 860228002726 RHS protein; Region: RHS; pfam03527 860228002727 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 860228002728 A nuclease family of the HNH/ENDO VII superfamily with conserved AHH; Region: AHH; pfam14412 860228002729 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 860228002730 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 860228002731 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 860228002732 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 860228002733 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 860228002734 DNA binding residues [nucleotide binding] 860228002735 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 860228002736 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228002737 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 860228002738 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 860228002739 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 860228002740 starch binding outer membrane protein SusD; Region: SusD; cd08977 860228002741 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 860228002742 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 860228002743 catalytic residues [active] 860228002744 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 860228002745 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 860228002746 substrate binding site [chemical binding]; other site 860228002747 hexamer interface [polypeptide binding]; other site 860228002748 metal binding site [ion binding]; metal-binding site 860228002749 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 860228002750 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 860228002751 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 860228002752 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228002753 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228002754 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 860228002755 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 860228002756 Tetramer interface [polypeptide binding]; other site 860228002757 active site 860228002758 FMN-binding site [chemical binding]; other site 860228002759 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 860228002760 putative efflux protein, MATE family; Region: matE; TIGR00797 860228002761 cation binding site [ion binding]; other site 860228002762 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 860228002763 Clp amino terminal domain; Region: Clp_N; pfam02861 860228002764 Clp amino terminal domain; Region: Clp_N; pfam02861 860228002765 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 860228002766 Walker A motif; other site 860228002767 ATP binding site [chemical binding]; other site 860228002768 Walker B motif; other site 860228002769 arginine finger; other site 860228002770 UvrB/uvrC motif; Region: UVR; pfam02151 860228002771 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 860228002772 Walker A motif; other site 860228002773 ATP binding site [chemical binding]; other site 860228002774 Walker B motif; other site 860228002775 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 860228002776 NlpC/P60 family; Region: NLPC_P60; pfam00877 860228002777 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 860228002778 Competence protein; Region: Competence; pfam03772 860228002779 potential frameshift: common BLAST hit: gi|336173508|ref|YP_004580646.1| Peroxiredoxin 860228002780 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 860228002781 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 860228002782 catalytic triad [active] 860228002783 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 860228002784 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 860228002785 minor groove reading motif; other site 860228002786 helix-hairpin-helix signature motif; other site 860228002787 substrate binding pocket [chemical binding]; other site 860228002788 active site 860228002789 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 860228002790 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 860228002791 dimer interface [polypeptide binding]; other site 860228002792 conserved gate region; other site 860228002793 putative PBP binding loops; other site 860228002794 ABC-ATPase subunit interface; other site 860228002795 Ornithine/acetylornithine aminotransferase [Amino acid transport and metabolism]; Region: ArgD; COG4992 860228002796 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 860228002797 inhibitor-cofactor binding pocket; inhibition site 860228002798 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228002799 catalytic residue [active] 860228002800 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 860228002801 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 860228002802 Ligand binding site; other site 860228002803 Putative Catalytic site; other site 860228002804 DXD motif; other site 860228002805 IS1 transposase; Region: DDE_Tnp_IS1; cl00721 860228002806 IS1 transposase; Region: DDE_Tnp_IS1; cl00721 860228002807 potential frameshift: common BLAST hit: gi|148653735|ref|YP_001280828.1| IS1 transposase 860228002808 IS1 transposase; Region: DDE_Tnp_IS1; cl00721 860228002809 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 860228002810 CTP synthetase; Validated; Region: pyrG; PRK05380 860228002811 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 860228002812 Catalytic site [active] 860228002813 active site 860228002814 UTP binding site [chemical binding]; other site 860228002815 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 860228002816 active site 860228002817 putative oxyanion hole; other site 860228002818 catalytic triad [active] 860228002819 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 860228002820 Class I ribonucleotide reductase; Region: RNR_I; cd01679 860228002821 active site 860228002822 dimer interface [polypeptide binding]; other site 860228002823 catalytic residues [active] 860228002824 effector binding site; other site 860228002825 R2 peptide binding site; other site 860228002826 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 860228002827 dimer interface [polypeptide binding]; other site 860228002828 putative radical transfer pathway; other site 860228002829 diiron center [ion binding]; other site 860228002830 tyrosyl radical; other site 860228002831 LrgB-like family; Region: LrgB; pfam04172 860228002832 LrgA family; Region: LrgA; pfam03788 860228002833 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 860228002834 Peptidase S46; Region: Peptidase_S46; pfam10459 860228002835 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 860228002836 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 860228002837 Transposase [DNA replication, recombination, and repair]; Region: COG5433 860228002838 WYL domain; Region: WYL; pfam13280 860228002839 adenylosuccinate lyase; Provisional; Region: PRK09285 860228002840 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 860228002841 tetramer interface [polypeptide binding]; other site 860228002842 active site 860228002843 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 860228002844 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 860228002845 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 860228002846 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 860228002847 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 860228002848 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 860228002849 SmpB-tmRNA interface; other site 860228002850 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 860228002851 catalytic residues [active] 860228002852 catalytic nucleophile [active] 860228002853 Presynaptic Site I dimer interface [polypeptide binding]; other site 860228002854 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 860228002855 Synaptic Flat tetramer interface [polypeptide binding]; other site 860228002856 Synaptic Site I dimer interface [polypeptide binding]; other site 860228002857 DNA binding site [nucleotide binding] 860228002858 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]; Region: COG3341 860228002859 Caulimovirus viroplasmin; Region: Cauli_VI; pfam01693 860228002860 RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Region: RNase_H; cl14782 860228002861 RNA/DNA hybrid binding site [nucleotide binding]; other site 860228002862 active site 860228002863 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 860228002864 HD domain; Region: HD_4; pfam13328 860228002865 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 860228002866 synthetase active site [active] 860228002867 NTP binding site [chemical binding]; other site 860228002868 metal binding site [ion binding]; metal-binding site 860228002869 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 860228002870 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 860228002871 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 860228002872 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228002873 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 860228002874 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228002875 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 860228002876 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 860228002877 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 860228002878 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 860228002879 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 860228002880 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 860228002881 Predicted permeases [General function prediction only]; Region: COG0795 860228002882 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 860228002883 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 860228002884 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 860228002885 ATP binding site [chemical binding]; other site 860228002886 Mg2+ binding site [ion binding]; other site 860228002887 G-X-G motif; other site 860228002888 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 860228002889 anchoring element; other site 860228002890 dimer interface [polypeptide binding]; other site 860228002891 ATP binding site [chemical binding]; other site 860228002892 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 860228002893 active site 860228002894 putative metal-binding site [ion binding]; other site 860228002895 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 860228002896 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 860228002897 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 860228002898 putative catalytic residue [active] 860228002899 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 860228002900 EamA-like transporter family; Region: EamA; pfam00892 860228002901 TPR repeat; Region: TPR_11; pfam13414 860228002902 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 860228002903 binding surface 860228002904 TPR motif; other site 860228002905 Bacterial SH3 domain; Region: SH3_3; pfam08239 860228002906 Oxygen tolerance; Region: BatD; pfam13584 860228002907 TPR repeat; Region: TPR_11; pfam13414 860228002908 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 860228002909 binding surface 860228002910 TPR motif; other site 860228002911 Tetratricopeptide repeat; Region: TPR_12; pfam13424 860228002912 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 860228002913 metal ion-dependent adhesion site (MIDAS); other site 860228002914 Conserved hypothetical protein (DUF2461); Region: DUF2461; pfam09365 860228002915 Aerotolerance regulator N-terminal; Region: BatA; pfam07584 860228002916 VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b...; Region: vWA_BatA_type; cd01467 860228002917 metal ion-dependent adhesion site (MIDAS); other site 860228002918 Oxygen tolerance; Region: BatD; pfam13584 860228002919 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 860228002920 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 860228002921 metal ion-dependent adhesion site (MIDAS); other site 860228002922 MoxR-like ATPases [General function prediction only]; Region: COG0714 860228002923 ATPase family associated with various cellular activities (AAA); Region: AAA_3; pfam07726 860228002924 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 860228002925 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 860228002926 substrate binding pocket [chemical binding]; other site 860228002927 chain length determination region; other site 860228002928 substrate-Mg2+ binding site; other site 860228002929 catalytic residues [active] 860228002930 aspartate-rich region 1; other site 860228002931 active site lid residues [active] 860228002932 aspartate-rich region 2; other site 860228002933 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 860228002934 binding surface 860228002935 TPR motif; other site 860228002936 TPR repeat; Region: TPR_11; pfam13414 860228002937 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 860228002938 binding surface 860228002939 TPR motif; other site 860228002940 TPR repeat; Region: TPR_11; pfam13414 860228002941 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 860228002942 binding surface 860228002943 TPR repeat; Region: TPR_11; pfam13414 860228002944 TPR motif; other site 860228002945 Tetratricopeptide repeat; Region: TPR_12; pfam13424 860228002946 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 860228002947 binding surface 860228002948 TPR motif; other site 860228002949 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 860228002950 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 860228002951 transmembrane helices; other site 860228002952 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 860228002953 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 860228002954 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 860228002955 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 860228002956 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 860228002957 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228002958 Walker A/P-loop; other site 860228002959 ATP binding site [chemical binding]; other site 860228002960 Q-loop/lid; other site 860228002961 ABC transporter signature motif; other site 860228002962 Walker B; other site 860228002963 D-loop; other site 860228002964 H-loop/switch region; other site 860228002965 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 860228002966 alanine racemase; Reviewed; Region: alr; PRK00053 860228002967 active site 860228002968 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 860228002969 dimer interface [polypeptide binding]; other site 860228002970 substrate binding site [chemical binding]; other site 860228002971 catalytic residues [active] 860228002972 Alpha-L-fucosidase; Region: Alpha_L_fucos; pfam01120 860228002973 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 860228002974 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 860228002975 active site residue [active] 860228002976 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 860228002977 active site 860228002978 dimerization interface [polypeptide binding]; other site 860228002979 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 860228002980 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 860228002981 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 860228002982 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 860228002983 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 860228002984 Superfamily II DNA helicase [DNA replication, recombination, and repair]; Region: RecQ; COG0514 860228002985 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 860228002986 ATP binding site [chemical binding]; other site 860228002987 putative Mg++ binding site [ion binding]; other site 860228002988 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 860228002989 nucleotide binding region [chemical binding]; other site 860228002990 ATP-binding site [chemical binding]; other site 860228002991 RQC domain; Region: RQC; pfam09382 860228002992 HRDC domain; Region: HRDC; pfam00570 860228002993 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 860228002994 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 860228002995 putative active site [active] 860228002996 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 860228002997 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 860228002998 active site 860228002999 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 860228003000 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 860228003001 elongation factor Ts; Provisional; Region: tsf; PRK09377 860228003002 UBA/TS-N domain; Region: UBA; pfam00627 860228003003 Elongation factor TS; Region: EF_TS; pfam00889 860228003004 Elongation factor TS; Region: EF_TS; pfam00889 860228003005 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 860228003006 rRNA interaction site [nucleotide binding]; other site 860228003007 S8 interaction site; other site 860228003008 putative laminin-1 binding site; other site 860228003009 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 860228003010 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 860228003011 23S rRNA interface [nucleotide binding]; other site 860228003012 L3 interface [polypeptide binding]; other site 860228003013 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228003014 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 860228003015 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 860228003016 N-terminal plug; other site 860228003017 ligand-binding site [chemical binding]; other site 860228003018 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 860228003019 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 860228003020 RteC protein; Region: RteC; pfam09357 860228003021 Bacterial Ig-like domain; Region: Big_5; pfam13205 860228003022 Transposase and inactivated derivatives, IS1 family [DNA replication, recombination, and repair]; Region: InsB; COG1662 860228003023 TANFOR domain; Region: T_forsyth_147; TIGR02542 860228003024 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 860228003025 A nuclease family of the HNH/ENDO VII superfamily with conserved AHH; Region: AHH; pfam14412 860228003026 Parallel beta-helix repeat of pectate lyase; Region: PbH1; pfam13573 860228003027 Parallel beta-helix repeat of pectate lyase; Region: PbH1; pfam13573 860228003028 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 860228003029 Lipocalin-like domain; Region: Lipocalin_4; pfam13648 860228003030 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 860228003031 Interdomain contacts; other site 860228003032 Cytokine receptor motif; other site 860228003033 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 860228003034 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 860228003035 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 860228003036 active site 860228003037 DNA binding site [nucleotide binding] 860228003038 Int/Topo IB signature motif; other site 860228003039 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 860228003040 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 860228003041 Proteins of 100 residues with WXG; Region: WXG100; cl02005 860228003042 Axonemal dynein light chain; Region: Ax_dynein_light; pfam10211 860228003043 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 860228003044 metal ion-dependent adhesion site (MIDAS); other site 860228003045 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 860228003046 active site 860228003047 ATP binding site [chemical binding]; other site 860228003048 substrate binding site [chemical binding]; other site 860228003049 activation loop (A-loop); other site 860228003050 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 860228003051 active site 860228003052 ATP binding site [chemical binding]; other site 860228003053 substrate binding site [chemical binding]; other site 860228003054 activation loop (A-loop); other site 860228003055 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 860228003056 Sel1-like repeats; Region: SEL1; smart00671 860228003057 Sel1-like repeats; Region: SEL1; smart00671 860228003058 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 860228003059 binding surface 860228003060 TPR motif; other site 860228003061 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 860228003062 binding surface 860228003063 TPR motif; other site 860228003064 TPR repeat; Region: TPR_11; pfam13414 860228003065 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 860228003066 TPR motif; other site 860228003067 binding surface 860228003068 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 860228003069 Transposase and inactivated derivatives, IS1 family [DNA replication, recombination, and repair]; Region: InsB; COG1662 860228003070 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 860228003071 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 860228003072 AAA domain; Region: AAA_21; pfam13304 860228003073 Domain of unknown function (DUF4134); Region: DUF4134; pfam13572 860228003074 Domain of unknown function (DUF4133); Region: DUF4133; pfam13571 860228003075 Domain of unknown function, B. Theta Gene description (DUF3875); Region: DUF3875; pfam12991 860228003076 Transposase and inactivated derivatives, IS1 family [DNA replication, recombination, and repair]; Region: InsB; COG1662 860228003077 Bacteroides conjugative transposon TraK protein; Region: Bac_Flav_CT_K; TIGR03781 860228003078 Bacteroides conjugative transposon TraM protein; Region: Bac_Flav_CT_M; TIGR03779 860228003079 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 860228003080 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 860228003081 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 860228003082 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; cl17512 860228003083 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 860228003084 oligomeric interface; other site 860228003085 putative active site [active] 860228003086 homodimer interface [polypeptide binding]; other site 860228003087 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 860228003088 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 860228003089 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_5; cd04962 860228003090 N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA; Region: thiol_BshA; TIGR03999 860228003091 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 860228003092 ligand binding site [chemical binding]; other site 860228003093 active site 860228003094 UGI interface [polypeptide binding]; other site 860228003095 catalytic site [active] 860228003096 gliding motility-associated ABC transporter ATP-binding subunit GldA; Region: GldA_ABC_ATP; TIGR03522 860228003097 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 860228003098 Walker A/P-loop; other site 860228003099 ATP binding site [chemical binding]; other site 860228003100 Q-loop/lid; other site 860228003101 ABC transporter signature motif; other site 860228003102 Walker B; other site 860228003103 D-loop; other site 860228003104 H-loop/switch region; other site 860228003105 UGMP family protein; Validated; Region: PRK09604 860228003106 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 860228003107 Family of unknown function (DUF490); Region: DUF490; pfam04357 860228003108 M28 Zn-Peptidases containing a PA domain insert and associated with a PDZ domain; Region: M28_like_PA_PDZ_associated; cd05663 860228003109 Peptidase family M28; Region: Peptidase_M28; pfam04389 860228003110 metal binding site [ion binding]; metal-binding site 860228003111 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 860228003112 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 860228003113 Walker A/P-loop; other site 860228003114 ATP binding site [chemical binding]; other site 860228003115 Q-loop/lid; other site 860228003116 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 860228003117 ABC transporter signature motif; other site 860228003118 Walker B; other site 860228003119 D-loop; other site 860228003120 H-loop/switch region; other site 860228003121 7TM receptor with intracellular HD hydrolase; Region: 7TM-7TMR_HD; pfam07698 860228003122 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 860228003123 Zn2+ binding site [ion binding]; other site 860228003124 Mg2+ binding site [ion binding]; other site 860228003125 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 860228003126 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 860228003127 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 860228003128 ABC transporter; Region: ABC_tran_2; pfam12848 860228003129 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 860228003130 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 860228003131 active site 860228003132 oxyanion hole [active] 860228003133 catalytic triad [active] 860228003134 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 860228003135 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 860228003136 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 860228003137 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 860228003138 catalytic residue [active] 860228003139 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 860228003140 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 860228003141 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 860228003142 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 860228003143 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 860228003144 N-acetyl-D-glucosamine binding site [chemical binding]; other site 860228003145 catalytic residue [active] 860228003146 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 860228003147 Predicted acetyltransferase [General function prediction only]; Region: COG2388 860228003148 HYR domain; Region: HYR; pfam02494 860228003149 gliding motility-associated C-terminal domain; Region: Bac_Flav_CTERM; TIGR04131 860228003150 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 860228003151 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 860228003152 tetramer interface [polypeptide binding]; other site 860228003153 heme binding pocket [chemical binding]; other site 860228003154 NADPH binding site [chemical binding]; other site 860228003155 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 860228003156 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 860228003157 active site 860228003158 phosphorylation site [posttranslational modification] 860228003159 intermolecular recognition site; other site 860228003160 dimerization interface [polypeptide binding]; other site 860228003161 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 860228003162 DNA binding site [nucleotide binding] 860228003163 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 860228003164 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 860228003165 dimer interface [polypeptide binding]; other site 860228003166 phosphorylation site [posttranslational modification] 860228003167 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 860228003168 ATP binding site [chemical binding]; other site 860228003169 Mg2+ binding site [ion binding]; other site 860228003170 G-X-G motif; other site 860228003171 Protein of unknown function (DUF493); Region: DUF493; pfam04359 860228003172 Domain of unknown function (DUF4290); Region: DUF4290; pfam14123 860228003173 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 860228003174 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 860228003175 hinge; other site 860228003176 active site 860228003177 CAAX protease self-immunity; Region: Abi; pfam02517 860228003178 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 860228003179 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 860228003180 AMP binding site [chemical binding]; other site 860228003181 active site 860228003182 acyl-activating enzyme (AAE) consensus motif; other site 860228003183 CoA binding site [chemical binding]; other site 860228003184 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA; cd03877 860228003185 Peptidase family M28; Region: Peptidase_M28; pfam04389 860228003186 metal binding site [ion binding]; metal-binding site 860228003187 transketolase; Reviewed; Region: PRK05899 860228003188 Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the...; Region: TPP_TK; cd02012 860228003189 TPP-binding site [chemical binding]; other site 860228003190 dimer interface [polypeptide binding]; other site 860228003191 aspartate aminotransferase; Provisional; Region: PRK05764 860228003192 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 860228003193 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228003194 homodimer interface [polypeptide binding]; other site 860228003195 catalytic residue [active] 860228003196 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 860228003197 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 860228003198 active site 860228003199 NTP binding site [chemical binding]; other site 860228003200 metal binding triad [ion binding]; metal-binding site 860228003201 antibiotic binding site [chemical binding]; other site 860228003202 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]; Region: COG3958 860228003203 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 860228003204 PYR/PP interface [polypeptide binding]; other site 860228003205 dimer interface [polypeptide binding]; other site 860228003206 TPP binding site [chemical binding]; other site 860228003207 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 860228003208 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 860228003209 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 860228003210 active site 860228003211 Int/Topo IB signature motif; other site 860228003212 Flagellin N-methylase; Region: FliB; pfam03692 860228003213 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 860228003214 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 860228003215 Walker A/P-loop; other site 860228003216 ATP binding site [chemical binding]; other site 860228003217 Q-loop/lid; other site 860228003218 ABC transporter signature motif; other site 860228003219 Walker B; other site 860228003220 D-loop; other site 860228003221 H-loop/switch region; other site 860228003222 ABC transporter; Region: ABC_tran_2; pfam12848 860228003223 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 860228003224 Protein of unknown function (DUF3276); Region: DUF3276; pfam11680 860228003225 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 860228003226 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 860228003227 FeS/SAM binding site; other site 860228003228 HemN C-terminal domain; Region: HemN_C; pfam06969 860228003229 Uncharacterized protein conserved in bacteria containing a pentein-type domain [Function unknown]; Region: COG4874 860228003230 Amidinotransferase; Region: Amidinotransf; pfam02274 860228003231 Amidinotransferase; Region: Amidinotransf; cl12043 860228003232 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 860228003233 dimer interface [polypeptide binding]; other site 860228003234 Citrate synthase; Region: Citrate_synt; pfam00285 860228003235 active site 860228003236 citrylCoA binding site [chemical binding]; other site 860228003237 NADH binding [chemical binding]; other site 860228003238 cationic pore residues; other site 860228003239 oxalacetate/citrate binding site [chemical binding]; other site 860228003240 coenzyme A binding site [chemical binding]; other site 860228003241 catalytic triad [active] 860228003242 integral membrane protein, YccS/YhfK family; Region: YCCS_YHJK; TIGR01667 860228003243 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 860228003244 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 860228003245 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 860228003246 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 860228003247 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228003248 catalytic residue [active] 860228003249 X-Pro dipeptidyl-peptidase (S15 family); Region: Peptidase_S15; pfam02129 860228003250 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 860228003251 YceG-like family; Region: YceG; pfam02618 860228003252 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 860228003253 dimerization interface [polypeptide binding]; other site 860228003254 Aspartokinases [Amino acid transport and metabolism]; Region: LysC; COG0527 860228003255 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 860228003256 nucleotide binding site [chemical binding]; other site 860228003257 substrate binding site [chemical binding]; other site 860228003258 IgA Peptidase M64; Region: Peptidase_M64; pfam09471 860228003259 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 860228003260 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 860228003261 putative active site [active] 860228003262 Dehydroquinase class II; Region: DHquinase_II; pfam01220 860228003263 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 860228003264 trimer interface [polypeptide binding]; other site 860228003265 active site 860228003266 dimer interface [polypeptide binding]; other site 860228003267 MutS domain III; Region: MutS_III; pfam05192 860228003268 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228003269 Walker A/P-loop; other site 860228003270 ATP binding site [chemical binding]; other site 860228003271 Q-loop/lid; other site 860228003272 ABC transporter signature motif; other site 860228003273 Walker B; other site 860228003274 D-loop; other site 860228003275 H-loop/switch region; other site 860228003276 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 860228003277 DEAD-like helicases superfamily; Region: DEXDc; smart00487 860228003278 ATP binding site [chemical binding]; other site 860228003279 Mg++ binding site [ion binding]; other site 860228003280 motif III; other site 860228003281 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 860228003282 nucleotide binding region [chemical binding]; other site 860228003283 ATP-binding site [chemical binding]; other site 860228003284 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 860228003285 RNA binding site [nucleotide binding]; other site 860228003286 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228003287 Predicted transcriptional regulators [Transcription]; Region: COG1695 860228003288 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 860228003289 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 860228003290 Transposase and inactivated derivatives, IS1 family [DNA replication, recombination, and repair]; Region: InsB; COG1662 860228003291 DNA gyrase subunit A; Validated; Region: PRK05560 860228003292 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 860228003293 CAP-like domain; other site 860228003294 active site 860228003295 primary dimer interface [polypeptide binding]; other site 860228003296 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 860228003297 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 860228003298 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 860228003299 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 860228003300 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 860228003301 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 860228003302 TPR repeat; Region: TPR_11; pfam13414 860228003303 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 860228003304 binding surface 860228003305 TPR motif; other site 860228003306 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 860228003307 binding surface 860228003308 TPR motif; other site 860228003309 TPR repeat; Region: TPR_11; pfam13414 860228003310 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 860228003311 binding surface 860228003312 TPR motif; other site 860228003313 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 860228003314 primosomal protein N' Region: priA; TIGR00595 860228003315 ATP binding site [chemical binding]; other site 860228003316 putative Mg++ binding site [ion binding]; other site 860228003317 helicase superfamily c-terminal domain; Region: HELICc; smart00490 860228003318 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 860228003319 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 860228003320 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 860228003321 Ligand Binding Site [chemical binding]; other site 860228003322 TilS substrate C-terminal domain; Region: TilS_C; smart00977 860228003323 aminodeoxychorismate synthase, component I, clade 2; Region: PabB-clade2; TIGR01824 860228003324 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 860228003325 HD superfamily phosphohydrolases [General function prediction only]; Region: COG1078 860228003326 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 860228003327 Zn2+ binding site [ion binding]; other site 860228003328 Mg2+ binding site [ion binding]; other site 860228003329 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 860228003330 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 860228003331 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 860228003332 trimer interface [polypeptide binding]; other site 860228003333 active site 860228003334 UDP-GlcNAc binding site [chemical binding]; other site 860228003335 lipid binding site [chemical binding]; lipid-binding site 860228003336 bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed; Region: PRK13188 860228003337 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 860228003338 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 860228003339 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 860228003340 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 860228003341 active site 860228003342 elongation factor P; Validated; Region: PRK00529 860228003343 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 860228003344 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 860228003345 RNA binding site [nucleotide binding]; other site 860228003346 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 860228003347 RNA binding site [nucleotide binding]; other site 860228003348 Asparagine synthetase (aspartate-ammonia ligase) (AsnA) catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. AsnA is a homodimeric enzyme which is structurally similiar to the catalytic core domain of class II...; Region: AsnA; cd00645 860228003349 dimer interface [polypeptide binding]; other site 860228003350 active site 860228003351 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 860228003352 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 860228003353 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 860228003354 trimer interface [polypeptide binding]; other site 860228003355 active site 860228003356 UDP-GlcNAc binding site [chemical binding]; other site 860228003357 lipid binding site [chemical binding]; lipid-binding site 860228003358 lipoyl synthase; Provisional; Region: PRK05481 860228003359 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 860228003360 FeS/SAM binding site; other site 860228003361 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 860228003362 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 860228003363 active site 860228003364 (T/H)XGH motif; other site 860228003365 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 860228003366 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 860228003367 ATP-grasp domain; Region: ATP-grasp_4; cl17255 860228003368 Protein of unknown function (DUF2459); Region: DUF2459; pfam09601 860228003369 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 860228003370 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 860228003371 dimer interface [polypeptide binding]; other site 860228003372 conserved gate region; other site 860228003373 putative PBP binding loops; other site 860228003374 ABC-ATPase subunit interface; other site 860228003375 C-terminal peptidase (prc); Region: prc; TIGR00225 860228003376 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 860228003377 protein binding site [polypeptide binding]; other site 860228003378 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 860228003379 Catalytic dyad [active] 860228003380 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 860228003381 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 860228003382 Cytochrome c; Region: Cytochrom_C; pfam00034 860228003383 Outer membrane protein Omp28; Region: Omp28; pfam11551 860228003384 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 860228003385 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 860228003386 catalytic residues [active] 860228003387 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 860228003388 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 860228003389 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 860228003390 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 860228003391 catalytic residue [active] 860228003392 malate dehydrogenase; Reviewed; Region: PRK06223 860228003393 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 860228003394 dimer interface [polypeptide binding]; other site 860228003395 NAD(P) binding site [chemical binding]; other site 860228003396 tetramer (dimer of dimers) interface [polypeptide binding]; other site 860228003397 substrate binding site [chemical binding]; other site 860228003398 Protein of unknown function (DUF721); Region: DUF721; pfam05258 860228003399 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Deinococcus radiodurans DR2231 protein and its bacterial homologs; Region: NTP-PPase_DR2231_like; cd11530 860228003400 metal binding site [ion binding]; metal-binding site 860228003401 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 860228003402 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 860228003403 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 860228003404 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228003405 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 860228003406 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 860228003407 starch binding outer membrane protein SusD; Region: SusD; cd08977 860228003408 O-Glycosyl hydrolase family 30; Region: Glyco_hydro_30; pfam02055 860228003409 O-Glycosyl hydrolase [Cell envelope biogenesis, outer membrane]; Region: COG5520 860228003410 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 860228003411 active site 860228003412 catalytic triad [active] 860228003413 oxyanion hole [active] 860228003414 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 860228003415 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 860228003416 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 860228003417 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 860228003418 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 860228003419 putative active site [active] 860228003420 putative metal binding site [ion binding]; other site 860228003421 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 860228003422 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 860228003423 active site 860228003424 Riboflavin kinase; Region: Flavokinase; pfam01687 860228003425 Domain of unknown function (DUF389); Region: DUF389; pfam04087 860228003426 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 860228003427 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 860228003428 motif II; other site 860228003429 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 860228003430 active site 860228003431 catalytic residues [active] 860228003432 metal binding site [ion binding]; metal-binding site 860228003433 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 860228003434 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 860228003435 S-adenosylmethionine binding site [chemical binding]; other site 860228003436 Colicin V production protein; Region: Colicin_V; pfam02674 860228003437 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 860228003438 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 860228003439 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 860228003440 active site residue [active] 860228003441 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 860228003442 active site residue [active] 860228003443 Protein of unknown function (DUF805); Region: DUF805; pfam05656 860228003444 Predicted transporter component [General function prediction only]; Region: COG2391 860228003445 Sulphur transport; Region: Sulf_transp; pfam04143 860228003446 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 860228003447 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 860228003448 ligand binding site [chemical binding]; other site 860228003449 flexible hinge region; other site 860228003450 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 860228003451 putative switch regulator; other site 860228003452 non-specific DNA interactions [nucleotide binding]; other site 860228003453 DNA binding site [nucleotide binding] 860228003454 sequence specific DNA binding site [nucleotide binding]; other site 860228003455 putative cAMP binding site [chemical binding]; other site 860228003456 Protein of unknown function (DUF1624); Region: DUF1624; cl01394 860228003457 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 860228003458 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 860228003459 G1 box; other site 860228003460 putative GEF interaction site [polypeptide binding]; other site 860228003461 GTP/Mg2+ binding site [chemical binding]; other site 860228003462 Switch I region; other site 860228003463 G2 box; other site 860228003464 G3 box; other site 860228003465 Switch II region; other site 860228003466 G4 box; other site 860228003467 G5 box; other site 860228003468 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 860228003469 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 860228003470 HYR domain; Region: HYR; pfam02494 860228003471 Transposase, Mutator family; Region: Transposase_mut; pfam00872 860228003472 gliding motility-associated C-terminal domain; Region: Bac_Flav_CTERM; TIGR04131 860228003473 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cd00995 860228003474 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 860228003475 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 860228003476 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 860228003477 GTP-binding protein YchF; Reviewed; Region: PRK09601 860228003478 YchF GTPase; Region: YchF; cd01900 860228003479 G1 box; other site 860228003480 GTP/Mg2+ binding site [chemical binding]; other site 860228003481 Switch I region; other site 860228003482 G2 box; other site 860228003483 Switch II region; other site 860228003484 G3 box; other site 860228003485 G4 box; other site 860228003486 G5 box; other site 860228003487 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 860228003488 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 860228003489 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 860228003490 generic binding surface II; other site 860228003491 ssDNA binding site; other site 860228003492 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 860228003493 ATP binding site [chemical binding]; other site 860228003494 putative Mg++ binding site [ion binding]; other site 860228003495 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 860228003496 nucleotide binding region [chemical binding]; other site 860228003497 ATP-binding site [chemical binding]; other site 860228003498 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 860228003499 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 860228003500 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 860228003501 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 860228003502 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 860228003503 catalytic residue [active] 860228003504 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 860228003505 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 860228003506 Cell division protein ZapA; Region: ZapA; pfam05164 860228003507 phosphodiesterase; Provisional; Region: PRK12704 860228003508 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 860228003509 Zn2+ binding site [ion binding]; other site 860228003510 Mg2+ binding site [ion binding]; other site 860228003511 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 860228003512 ligand binding site [chemical binding]; other site 860228003513 Glutamine cyclotransferase [Posttranslational modification, protein turnover, chaperones]; Region: COG3823 860228003514 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 860228003515 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 860228003516 Probable Catalytic site; other site 860228003517 metal-binding site 860228003518 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N_2; pfam13588 860228003519 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 860228003520 DNA polymerase III, delta subunit; Region: holA; TIGR01128 860228003521 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 860228003522 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 860228003523 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 860228003524 active site 860228003525 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 860228003526 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 860228003527 propionate/acetate kinase; Provisional; Region: PRK12379 860228003528 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 860228003529 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 860228003530 phosphate acetyltransferase; Reviewed; Region: PRK05632 860228003531 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 860228003532 DRTGG domain; Region: DRTGG; pfam07085 860228003533 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 860228003534 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09638 860228003535 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 860228003536 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cl00083 860228003537 CRISPR-associated protein Cas9/Csn1, subtype II/NMEMI; Region: cas_Csn1; TIGR01865 860228003538 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cl00083 860228003539 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 860228003540 Interdomain contacts; other site 860228003541 Endonuclease I; Region: Endonuclease_1; cl01003 860228003542 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 860228003543 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 860228003544 FtsX-like permease family; Region: FtsX; pfam02687 860228003545 Protein of unknown function (DUF1343); Region: DUF1343; pfam07075 860228003546 Maf-like protein; Region: Maf; pfam02545 860228003547 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 860228003548 active site 860228003549 dimer interface [polypeptide binding]; other site 860228003550 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 860228003551 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 860228003552 NAD(P) binding site [chemical binding]; other site 860228003553 homotetramer interface [polypeptide binding]; other site 860228003554 homodimer interface [polypeptide binding]; other site 860228003555 active site 860228003556 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 860228003557 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 860228003558 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 860228003559 PspC domain; Region: PspC; cl00864 860228003560 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 860228003561 hydrophobic ligand binding site; other site 860228003562 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 860228003563 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cd00449 860228003564 homodimer interface [polypeptide binding]; other site 860228003565 substrate-cofactor binding pocket; other site 860228003566 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228003567 catalytic residue [active] 860228003568 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 860228003569 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 860228003570 putative active site [active] 860228003571 catalytic triad [active] 860228003572 putative dimer interface [polypeptide binding]; other site 860228003573 cyclically-permuted mutarotase family protein; Region: mutarot_permut; TIGR03548 860228003574 uncharacterized subgroup of the Na(+)/iodide (NIS) cotransporter subfamily; putative solute-binding domain; Region: SLC5sbd_NIS-like_u3; cd11495 860228003575 putative transporter; Provisional; Region: PRK10484 860228003576 Na binding site [ion binding]; other site 860228003577 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 860228003578 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 860228003579 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 860228003580 FeS/SAM binding site; other site 860228003581 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]; Region: FolD; COG0190 860228003582 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 860228003583 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 860228003584 homodimer interface [polypeptide binding]; other site 860228003585 NADP binding site [chemical binding]; other site 860228003586 substrate binding site [chemical binding]; other site 860228003587 signal recognition particle protein; Provisional; Region: PRK10867 860228003588 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 860228003589 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 860228003590 P loop; other site 860228003591 GTP binding site [chemical binding]; other site 860228003592 Signal peptide binding domain; Region: SRP_SPB; pfam02978 860228003593 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 860228003594 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 860228003595 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 860228003596 ribonuclease Z; Reviewed; Region: PRK00055 860228003597 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 860228003598 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 860228003599 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 860228003600 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 860228003601 Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Region: PyrR; COG2065 860228003602 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 860228003603 active site 860228003604 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 860228003605 NADH dehydrogenase subunit 6; Provisional; Region: ND6; cl17624 860228003606 O-Antigen ligase; Region: Wzy_C; pfam04932 860228003607 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 860228003608 TPR motif; other site 860228003609 binding surface 860228003610 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 860228003611 TPR repeat; Region: TPR_11; pfam13414 860228003612 TPR motif; other site 860228003613 binding surface 860228003614 fumarylacetoacetase; Region: PLN02856 860228003615 Domain of unknown function (DUF1969); Region: DUF1969; pfam09298 860228003616 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 860228003617 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 860228003618 catalytic core [active] 860228003619 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 860228003620 37-kD nucleoid-associated bacterial protein; Region: NA37; pfam04245 860228003621 Plasmid pRiA4b ORF-3-like protein; Region: PRiA4_ORF3; pfam07929 860228003622 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 860228003623 hydrophobic ligand binding site; other site 860228003624 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 860228003625 active site 860228003626 Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the Nudix hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most...; Region: Ap6A_hydrolase; cd03673 860228003627 active site 860228003628 Ap6A binding site [chemical binding]; other site 860228003629 nudix motif; other site 860228003630 metal binding site [ion binding]; metal-binding site 860228003631 Deoxyhypusine synthase; Region: DS; cl00826 860228003632 deoxyhypusine synthase; Region: dhys; TIGR00321 860228003633 potential frameshift: common BLAST hit: gi|313207185|ref|YP_004046362.1| agmatinase 860228003634 Agmatinase and related proteins; Region: Agmatinase-like_2; cd11593 860228003635 putative active site [active] 860228003636 Mn binding site [ion binding]; other site 860228003637 Arginase-like and histone-like hydrolases; Region: Arginase_HDAC; cl17011 860228003638 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 860228003639 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 860228003640 dimer interface [polypeptide binding]; other site 860228003641 active site 860228003642 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 860228003643 catalytic residues [active] 860228003644 substrate binding site [chemical binding]; other site 860228003645 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 860228003646 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 860228003647 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 860228003648 ABC transporter; Region: ABC_tran_2; pfam12848 860228003649 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 860228003650 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 860228003651 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 860228003652 HEAT repeats; Region: HEAT_2; pfam13646 860228003653 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 860228003654 binding surface 860228003655 TPR motif; other site 860228003656 Tetratricopeptide repeat; Region: TPR_16; pfam13432 860228003657 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 860228003658 binding surface 860228003659 TPR motif; other site 860228003660 TPR repeat; Region: TPR_11; pfam13414 860228003661 Tetratricopeptide repeat; Region: TPR_12; pfam13424 860228003662 VPS10 domain; Region: VPS10; smart00602 860228003663 Phosphotransferase enzyme family; Region: APH; pfam01636 860228003664 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 860228003665 active site 860228003666 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 860228003667 PhoH-like protein; Region: PhoH; pfam02562 860228003668 Protein of unknown function (DUF3810); Region: DUF3810; pfam12725 860228003669 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 860228003670 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 860228003671 metal binding site [ion binding]; metal-binding site 860228003672 dimer interface [polypeptide binding]; other site 860228003673 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 860228003674 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 860228003675 5S rRNA interface [nucleotide binding]; other site 860228003676 CTC domain interface [polypeptide binding]; other site 860228003677 L16 interface [polypeptide binding]; other site 860228003678 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 860228003679 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 860228003680 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 860228003681 active site 860228003682 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; pfam04307 860228003683 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 860228003684 Protein of unknown function (DUF3098); Region: DUF3098; pfam11297 860228003685 Bacitracin resistance protein BacA; Region: BacA; pfam02673 860228003686 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 860228003687 catalytic motif [active] 860228003688 Catalytic residue [active] 860228003689 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 860228003690 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 860228003691 active site 860228003692 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 860228003693 putative acyl-acceptor binding pocket; other site 860228003694 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 860228003695 active site 860228003696 homodimer interface [polypeptide binding]; other site 860228003697 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 860228003698 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 860228003699 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 860228003700 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 860228003701 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 860228003702 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 860228003703 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 860228003704 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 860228003705 ligand binding site [chemical binding]; other site 860228003706 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 860228003707 Beta-lactamase; Region: Beta-lactamase; pfam00144 860228003708 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 860228003709 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 860228003710 dimer interface [polypeptide binding]; other site 860228003711 phosphorylation site [posttranslational modification] 860228003712 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 860228003713 ATP binding site [chemical binding]; other site 860228003714 Mg2+ binding site [ion binding]; other site 860228003715 G-X-G motif; other site 860228003716 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 860228003717 Response regulator receiver domain; Region: Response_reg; pfam00072 860228003718 active site 860228003719 phosphorylation site [posttranslational modification] 860228003720 intermolecular recognition site; other site 860228003721 dimerization interface [polypeptide binding]; other site 860228003722 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 860228003723 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 860228003724 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 860228003725 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 860228003726 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 860228003727 active site 860228003728 Predicted integral membrane protein [Function unknown]; Region: COG5615 860228003729 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 860228003730 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 860228003731 active site 860228003732 phosphorylation site [posttranslational modification] 860228003733 intermolecular recognition site; other site 860228003734 dimerization interface [polypeptide binding]; other site 860228003735 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 860228003736 Walker A motif; other site 860228003737 ATP binding site [chemical binding]; other site 860228003738 Walker B motif; other site 860228003739 arginine finger; other site 860228003740 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 860228003741 bacillithiol system oxidoreductase, YphP/YqiW family; Region: YphP_YqiW; TIGR04191 860228003742 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 860228003743 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 860228003744 putative acyl-acceptor binding pocket; other site 860228003745 Alkaline phosphatase [Inorganic ion transport and metabolism]; Region: PhoA; COG1785 860228003746 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cl15837 860228003747 active site 860228003748 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 860228003749 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 860228003750 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 860228003751 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 860228003752 putative metal binding site; other site 860228003753 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 860228003754 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 860228003755 Permease; Region: Permease; pfam02405 860228003756 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 860228003757 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 860228003758 Walker A/P-loop; other site 860228003759 ATP binding site [chemical binding]; other site 860228003760 Q-loop/lid; other site 860228003761 ABC transporter signature motif; other site 860228003762 Walker B; other site 860228003763 D-loop; other site 860228003764 H-loop/switch region; other site 860228003765 Protein of unknown function (DUF423); Region: DUF423; pfam04241 860228003766 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 860228003767 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 860228003768 active site 860228003769 substrate-binding site [chemical binding]; other site 860228003770 metal-binding site [ion binding] 860228003771 ATP binding site [chemical binding]; other site 860228003772 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 860228003773 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 860228003774 putative DNA binding site [nucleotide binding]; other site 860228003775 putative Zn2+ binding site [ion binding]; other site 860228003776 AsnC family; Region: AsnC_trans_reg; pfam01037 860228003777 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 860228003778 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1; Region: dNK; cd01673 860228003779 Substrate-binding site [chemical binding]; other site 860228003780 Substrate specificity [chemical binding]; other site 860228003781 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 860228003782 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 860228003783 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 860228003784 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 860228003785 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 860228003786 Chitobiase/beta-hexosaminidase C-terminal domain; Region: CHB_HEX_C; pfam03174 860228003787 Coagulation factor 5/8 C-terminal domain, discoidin domain; Region: FA58C; smart00231 860228003788 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 860228003789 sugar binding site [chemical binding]; other site 860228003790 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 860228003791 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 860228003792 active site 860228003793 motif I; other site 860228003794 motif II; other site 860228003795 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 860228003796 Chain length determinant protein [Cell envelope biogenesis, outer membrane]; Region: WzzB; COG3765 860228003797 Chain length determinant protein; Region: Wzz; pfam02706 860228003798 G-rich domain on putative tyrosine kinase; Region: GNVR; pfam13807 860228003799 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 860228003800 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 860228003801 SLBB domain; Region: SLBB; pfam10531 860228003802 SLBB domain; Region: SLBB; pfam10531 860228003803 SLBB domain; Region: SLBB; pfam10531 860228003804 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 860228003805 SLBB domain; Region: SLBB; pfam10531 860228003806 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 860228003807 SLBB domain; Region: SLBB; pfam10531 860228003808 Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the...; Region: deoxycytidylate_deaminase; cd01286 860228003809 catalytic motif [active] 860228003810 Zn binding site [ion binding]; other site 860228003811 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 860228003812 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228003813 Walker A/P-loop; other site 860228003814 ATP binding site [chemical binding]; other site 860228003815 Q-loop/lid; other site 860228003816 ABC transporter signature motif; other site 860228003817 Walker B; other site 860228003818 D-loop; other site 860228003819 H-loop/switch region; other site 860228003820 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 860228003821 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 860228003822 putative tRNA-binding site [nucleotide binding]; other site 860228003823 B3/4 domain; Region: B3_4; pfam03483 860228003824 tRNA synthetase B5 domain; Region: B5; pfam03484 860228003825 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 860228003826 dimer interface [polypeptide binding]; other site 860228003827 motif 1; other site 860228003828 motif 3; other site 860228003829 motif 2; other site 860228003830 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 860228003831 Protein of unknown function (DUF2795); Region: DUF2795; pfam11387 860228003832 preprotein translocase subunit SecA; Reviewed; Region: secA; PRK12901 860228003833 DEAD/DEAH box helicase; Region: DEAD; pfam00270 860228003834 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 860228003835 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 860228003836 nucleotide binding region [chemical binding]; other site 860228003837 ATP-binding site [chemical binding]; other site 860228003838 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 860228003839 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 860228003840 DXD motif; other site 860228003841 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 860228003842 MgtE intracellular N domain; Region: MgtE_N; smart00924 860228003843 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 860228003844 Divalent cation transporter; Region: MgtE; pfam01769 860228003845 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 860228003846 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 860228003847 S-adenosylmethionine binding site [chemical binding]; other site 860228003848 Domain of unknown function (DUF4286); Region: DUF4286; pfam14114 860228003849 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 860228003850 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 860228003851 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 860228003852 DNA binding residues [nucleotide binding] 860228003853 bacillithiol biosynthesis deacetylase BshB1; Region: thiol_BshB1; TIGR04001 860228003854 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 860228003855 catalytic residues [active] 860228003856 dimer interface [polypeptide binding]; other site 860228003857 Domain of unknown function (DUF4091); Region: DUF4091; pfam13320 860228003858 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 860228003859 Mevalonate pyrophosphate decarboxylase [Lipid metabolism]; Region: MVD1; COG3407 860228003860 diphosphomevalonate decarboxylase; Region: PLN02407 860228003861 diphosphomevalonate decarboxylase; Region: PLN02407 860228003862 mevalonate kinase; Region: mevalon_kin; TIGR00549 860228003863 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 860228003864 UbiA prenyltransferase family; Region: UbiA; pfam01040 860228003865 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]; Region: UbiA; cl00337 860228003866 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 860228003867 N-acetyl-D-glucosamine binding site [chemical binding]; other site 860228003868 catalytic residue [active] 860228003869 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 860228003870 flavoprotein, HI0933 family; Region: TIGR00275 860228003871 conserved hypothetical protein; Region: TIGR02231 860228003872 N-terminal domain of unknown function (DUF4140); Region: DUF4140; pfam13600 860228003873 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 860228003874 Protein of unknown function (DUF4230); Region: DUF4230; pfam14014 860228003875 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 860228003876 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 860228003877 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 860228003878 catalytic residue [active] 860228003879 AAA domain; Region: AAA_26; pfam13500 860228003880 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 860228003881 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 860228003882 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 860228003883 acyl-activating enzyme (AAE) consensus motif; other site 860228003884 putative AMP binding site [chemical binding]; other site 860228003885 putative active site [active] 860228003886 putative CoA binding site [chemical binding]; other site 860228003887 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 860228003888 metal binding site 2 [ion binding]; metal-binding site 860228003889 putative DNA binding helix; other site 860228003890 metal binding site 1 [ion binding]; metal-binding site 860228003891 dimer interface [polypeptide binding]; other site 860228003892 structural Zn2+ binding site [ion binding]; other site 860228003893 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 860228003894 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 860228003895 GDP-binding site [chemical binding]; other site 860228003896 ACT binding site; other site 860228003897 IMP binding site; other site 860228003898 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 860228003899 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 860228003900 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 860228003901 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 860228003902 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 860228003903 ligand binding site [chemical binding]; other site 860228003904 OsmC-like protein; Region: OsmC; pfam02566 860228003905 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 860228003906 Sulfatase; Region: Sulfatase; pfam00884 860228003907 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 860228003908 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 860228003909 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 860228003910 Walker A/P-loop; other site 860228003911 ATP binding site [chemical binding]; other site 860228003912 Q-loop/lid; other site 860228003913 ABC transporter signature motif; other site 860228003914 Walker B; other site 860228003915 D-loop; other site 860228003916 H-loop/switch region; other site 860228003917 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228003918 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 860228003919 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228003920 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228003921 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 860228003922 active site 860228003923 metal binding site [ion binding]; metal-binding site 860228003924 homotetramer interface [polypeptide binding]; other site 860228003925 Predicted membrane protein [Function unknown]; Region: COG3059 860228003926 glycine dehydrogenase; Provisional; Region: PRK05367 860228003927 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 860228003928 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 860228003929 catalytic residue [active] 860228003930 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 860228003931 tetramer interface [polypeptide binding]; other site 860228003932 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228003933 catalytic residue [active] 860228003934 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 860228003935 Uncharacterized conserved protein [Function unknown]; Region: COG1739 860228003936 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 860228003937 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 860228003938 Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the...; Region: Riboflavin_deaminase-reductase; cd01284 860228003939 catalytic motif [active] 860228003940 Zn binding site [ion binding]; other site 860228003941 RibD C-terminal domain; Region: RibD_C; cl17279 860228003942 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 860228003943 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 860228003944 S-adenosylmethionine binding site [chemical binding]; other site 860228003945 Domain of unknown function (DUF4293); Region: DUF4293; pfam14126 860228003946 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 860228003947 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 860228003948 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 860228003949 P loop; other site 860228003950 GTP binding site [chemical binding]; other site 860228003951 Domain of unknown function (DUF4295); Region: DUF4295; pfam14128 860228003952 ribosomal protein L33; Region: rpl33; CHL00104 860228003953 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 860228003954 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 860228003955 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 860228003956 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 860228003957 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 860228003958 active site 860228003959 catalytic site [active] 860228003960 substrate binding site [chemical binding]; other site 860228003961 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 860228003962 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 860228003963 Transposase [DNA replication, recombination, and repair]; Region: COG5433 860228003964 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 860228003965 Transposase and inactivated derivatives, IS1 family [DNA replication, recombination, and repair]; Region: InsB; COG1662 860228003966 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 860228003967 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 860228003968 DNA-binding interface [nucleotide binding]; DNA binding site 860228003969 Smr domain; Region: Smr; cl02619 860228003970 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 860228003971 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 860228003972 catalytic residues [active] 860228003973 Lipocalin-like domain; Region: Lipocalin_4; pfam13648 860228003974 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_4; cd06241 860228003975 putative active site [active] 860228003976 Zn binding site [ion binding]; other site 860228003977 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 860228003978 PAS fold; Region: PAS_3; pfam08447 860228003979 putative active site [active] 860228003980 heme pocket [chemical binding]; other site 860228003981 16S rRNA methyltransferase B; Provisional; Region: PRK14902 860228003982 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 860228003983 S-adenosylmethionine binding site [chemical binding]; other site 860228003984 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 860228003985 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 860228003986 non-specific DNA binding site [nucleotide binding]; other site 860228003987 salt bridge; other site 860228003988 sequence-specific DNA binding site [nucleotide binding]; other site 860228003989 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 860228003990 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 860228003991 Transposase, Mutator family; Region: Transposase_mut; pfam00872 860228003992 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 860228003993 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 860228003994 nucleotide binding pocket [chemical binding]; other site 860228003995 K-X-D-G motif; other site 860228003996 catalytic site [active] 860228003997 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 860228003998 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 860228003999 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 860228004000 Dimer interface [polypeptide binding]; other site 860228004001 BRCT sequence motif; other site 860228004002 exonuclease, DNA polymerase III, epsilon subunit family; Region: dnaq; TIGR00573 860228004003 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 860228004004 active site 860228004005 catalytic site [active] 860228004006 substrate binding site [chemical binding]; other site 860228004007 nucleotide excision repair endonuclease; Provisional; Region: PRK10545 860228004008 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 860228004009 GIY-YIG motif/motif A; other site 860228004010 active site 860228004011 catalytic site [active] 860228004012 putative DNA binding site [nucleotide binding]; other site 860228004013 metal binding site [ion binding]; metal-binding site 860228004014 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 860228004015 Alpha-L-fucosidase; Region: Alpha_L_fucos; cl12119 860228004016 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 860228004017 RF-1 domain; Region: RF-1; cl17422 860228004018 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 860228004019 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 860228004020 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 860228004021 nucleotide binding site [chemical binding]; other site 860228004022 NEF interaction site [polypeptide binding]; other site 860228004023 SBD interface [polypeptide binding]; other site 860228004024 Transposase, Mutator family; Region: Transposase_mut; pfam00872 860228004025 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 860228004026 Bacillus subtilis YydB and related proteins, metallophosphatase domain; Region: MPP_YydB; cd07400 860228004027 putative active site [active] 860228004028 putative metal binding site [ion binding]; other site 860228004029 Predicted NTPase (NACHT family) [Signal transduction mechanisms]; Region: COG5635 860228004030 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 860228004031 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 860228004032 ATP binding site [chemical binding]; other site 860228004033 putative Mg++ binding site [ion binding]; other site 860228004034 Peptide-N-glycosidase F, N terminal; Region: N-glycanase_N; pfam09112 860228004035 Peptide-N-glycosidase F, C terminal; Region: N-glycanase_C; pfam09113 860228004036 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 860228004037 dimer interface [polypeptide binding]; other site 860228004038 catalytic triad [active] 860228004039 peroxidatic and resolving cysteines [active] 860228004040 Acetyl-CoA hydrolase [Energy production and conversion]; Region: ACH1; COG0427 860228004041 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 860228004042 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 860228004043 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 860228004044 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 860228004045 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 860228004046 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 860228004047 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 860228004048 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 860228004049 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 860228004050 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 860228004051 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12647 860228004052 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 860228004053 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 860228004054 Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism]; Region: MnhB; COG2111 860228004055 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12509 860228004056 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK12659 860228004057 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12663 860228004058 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 860228004059 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK12651 860228004060 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12599 860228004061 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 860228004062 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 860228004063 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 860228004064 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 860228004065 Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is...; Region: FBP_aldolase_IIA; cd00946 860228004066 active site 860228004067 intersubunit interface [polypeptide binding]; other site 860228004068 zinc binding site [ion binding]; other site 860228004069 Na+ binding site [ion binding]; other site 860228004070 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 860228004071 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 860228004072 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 860228004073 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 860228004074 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 860228004075 Walker A motif; other site 860228004076 ATP binding site [chemical binding]; other site 860228004077 Walker B motif; other site 860228004078 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 860228004079 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 860228004080 dihydropteroate synthase; Region: DHPS; TIGR01496 860228004081 substrate binding pocket [chemical binding]; other site 860228004082 dimer interface [polypeptide binding]; other site 860228004083 inhibitor binding site; inhibition site 860228004084 Uncharacterized conserved protein [Function unknown]; Region: COG1624 860228004085 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 860228004086 Protein of unknown function (DUF2851); Region: DUF2851; pfam11013 860228004087 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 860228004088 dimer interface [polypeptide binding]; other site 860228004089 FMN binding site [chemical binding]; other site 860228004090 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 860228004091 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 860228004092 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 860228004093 Beta-lactamase; Region: Beta-lactamase; cl17358 860228004094 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 860228004095 Cysteine-rich domain; Region: CCG; pfam02754 860228004096 Cysteine-rich domain; Region: CCG; pfam02754 860228004097 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 860228004098 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 860228004099 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 860228004100 mce related protein; Region: MCE; pfam02470 860228004101 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 860228004102 N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino...; Region: MurNAc-LAA; cd02696 860228004103 active site 860228004104 metal binding site [ion binding]; metal-binding site 860228004105 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 860228004106 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 860228004107 homotrimer interaction site [polypeptide binding]; other site 860228004108 putative active site [active] 860228004109 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; cl15804 860228004110 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08271 860228004111 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 860228004112 HD domain; Region: HD_3; pfam13023 860228004113 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 860228004114 Glycosyl hydrolase family 20 (GH20) catalytic domain of dispersin B (DspB), lacto-N-biosidase (LnbB) and related proteins. Dispersin B is a soluble beta-N-acetylglucosamidase found in bacteria that hydrolyzes the beta-1,6-linkages of PGA (poly-beta-(1,6)...; Region: GH20_DspB_LnbB-like; cd06564 860228004115 active site 860228004116 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 860228004117 Protein of unknown function (DUF3467); Region: DUF3467; pfam11950 860228004118 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 860228004119 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 860228004120 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 860228004121 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 860228004122 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 860228004123 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 860228004124 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 860228004125 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 860228004126 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 860228004127 DNA binding site [nucleotide binding] 860228004128 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 860228004129 Uncharacterized protein conserved in bacteria [Function unknown]; Region: MmcQ; COG2315 860228004130 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 860228004131 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 860228004132 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 860228004133 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 860228004134 RPB11 interaction site [polypeptide binding]; other site 860228004135 RPB12 interaction site [polypeptide binding]; other site 860228004136 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 860228004137 RPB3 interaction site [polypeptide binding]; other site 860228004138 RPB1 interaction site [polypeptide binding]; other site 860228004139 RPB11 interaction site [polypeptide binding]; other site 860228004140 RPB10 interaction site [polypeptide binding]; other site 860228004141 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 860228004142 core dimer interface [polypeptide binding]; other site 860228004143 peripheral dimer interface [polypeptide binding]; other site 860228004144 L10 interface [polypeptide binding]; other site 860228004145 L11 interface [polypeptide binding]; other site 860228004146 putative EF-Tu interaction site [polypeptide binding]; other site 860228004147 putative EF-G interaction site [polypeptide binding]; other site 860228004148 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 860228004149 23S rRNA interface [nucleotide binding]; other site 860228004150 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 860228004151 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 860228004152 mRNA/rRNA interface [nucleotide binding]; other site 860228004153 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 860228004154 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 860228004155 23S rRNA interface [nucleotide binding]; other site 860228004156 L7/L12 interface [polypeptide binding]; other site 860228004157 putative thiostrepton binding site; other site 860228004158 L25 interface [polypeptide binding]; other site 860228004159 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 860228004160 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 860228004161 putative homodimer interface [polypeptide binding]; other site 860228004162 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 860228004163 heterodimer interface [polypeptide binding]; other site 860228004164 homodimer interface [polypeptide binding]; other site 860228004165 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 860228004166 elongation factor Tu; Reviewed; Region: PRK12735 860228004167 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 860228004168 GEF interaction site [polypeptide binding]; other site 860228004169 GTP/Mg2+ binding site [chemical binding]; other site 860228004170 Switch I region; other site 860228004171 G2 box; other site 860228004172 G3 box; other site 860228004173 Switch II region; other site 860228004174 G4 box; other site 860228004175 G5 box; other site 860228004176 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 860228004177 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 860228004178 Antibiotic Binding Site [chemical binding]; other site 860228004179 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 860228004180 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 860228004181 putative acyl-acceptor binding pocket; other site 860228004182 lipid A phosphoethanolamine transferase; Reviewed; Region: PRK09598 860228004183 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 860228004184 Sulfatase; Region: Sulfatase; pfam00884 860228004185 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 860228004186 active site 860228004187 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 860228004188 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 860228004189 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 860228004190 tRNA pseudouridine(55) synthase; Region: TruB; TIGR00431 860228004191 RNA binding site [nucleotide binding]; other site 860228004192 active site 860228004193 Erythromycin esterase; Region: Erythro_esteras; cl17110 860228004194 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 860228004195 trimer interface [polypeptide binding]; other site 860228004196 active site 860228004197 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 860228004198 Domain of unknown function (DUF4292); Region: DUF4292; pfam14125 860228004199 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 860228004200 Peptidase family M23; Region: Peptidase_M23; pfam01551 860228004201 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cd00229 860228004202 catalytic triad [active] 860228004203 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 860228004204 starch binding outer membrane protein SusD; Region: SusD; cl17845 860228004205 SusD family; Region: SusD; pfam07980 860228004206 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 860228004207 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 860228004208 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 860228004209 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 860228004210 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228004211 SurA N-terminal domain; Region: SurA_N; pfam09312 860228004212 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 860228004213 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 860228004214 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 860228004215 RNA methyltransferase, RsmE family; Region: TIGR00046 860228004216 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 860228004217 WbqC-like protein family; Region: WbqC; pfam08889 860228004218 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 860228004219 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 860228004220 Catalytic site [active] 860228004221 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 860228004222 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 860228004223 A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual...; Region: Band_7_4; cd03407 860228004224 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 860228004225 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 860228004226 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 860228004227 DNA polymerase I; Provisional; Region: PRK05755 860228004228 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 860228004229 active site 860228004230 metal binding site 1 [ion binding]; metal-binding site 860228004231 putative 5' ssDNA interaction site; other site 860228004232 metal binding site 3; metal-binding site 860228004233 metal binding site 2 [ion binding]; metal-binding site 860228004234 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 860228004235 putative DNA binding site [nucleotide binding]; other site 860228004236 putative metal binding site [ion binding]; other site 860228004237 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 860228004238 active site 860228004239 catalytic site [active] 860228004240 substrate binding site [chemical binding]; other site 860228004241 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 860228004242 active site 860228004243 DNA binding site [nucleotide binding] 860228004244 catalytic site [active] 860228004245 S-ribosylhomocysteinase; Provisional; Region: PRK02260 860228004246 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 860228004247 DNA methylase; Region: N6_N4_Mtase; pfam01555 860228004248 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 860228004249 S-adenosylmethionine binding site [chemical binding]; other site 860228004250 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14329 860228004251 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 860228004252 TRAM domain; Region: TRAM; pfam01938 860228004253 potential frameshift: common BLAST hit: gi|295132378|ref|YP_003583054.1| two-component system sensor histidine kinase 860228004254 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 860228004255 ATP binding site [chemical binding]; other site 860228004256 Mg2+ binding site [ion binding]; other site 860228004257 G-X-G motif; other site 860228004258 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 860228004259 dimer interface [polypeptide binding]; other site 860228004260 phosphorylation site [posttranslational modification] 860228004261 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 860228004262 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 860228004263 active site 860228004264 phosphorylation site [posttranslational modification] 860228004265 intermolecular recognition site; other site 860228004266 dimerization interface [polypeptide binding]; other site 860228004267 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 860228004268 DNA binding site [nucleotide binding] 860228004269 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 860228004270 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 860228004271 FMN binding site [chemical binding]; other site 860228004272 active site 860228004273 catalytic residues [active] 860228004274 substrate binding site [chemical binding]; other site 860228004275 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 860228004276 TIGR01777 family protein; Region: yfcH 860228004277 NAD(P) binding site [chemical binding]; other site 860228004278 active site 860228004279 dihydrodipicolinate reductase; Provisional; Region: PRK00048 860228004280 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 860228004281 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 860228004282 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 860228004283 ParB-like nuclease domain; Region: ParBc; pfam02195 860228004284 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 860228004285 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 860228004286 P-loop; other site 860228004287 Magnesium ion binding site [ion binding]; other site 860228004288 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 860228004289 Magnesium ion binding site [ion binding]; other site 860228004290 Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR; Region: TER_DECR_SDR_a; cd05369 860228004291 short chain dehydrogenase; Provisional; Region: PRK07677 860228004292 NAD(P) binding site [chemical binding]; other site 860228004293 substrate binding site [chemical binding]; other site 860228004294 homotetramer interface [polypeptide binding]; other site 860228004295 active site 860228004296 homodimer interface [polypeptide binding]; other site 860228004297 hypothetical protein; Provisional; Region: PRK14623 860228004298 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 860228004299 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 860228004300 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 860228004301 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 860228004302 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 860228004303 RecX family; Region: RecX; pfam02631 860228004304 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 860228004305 putative active site [active] 860228004306 putative catalytic site [active] 860228004307 putative DNA binding site [nucleotide binding]; other site 860228004308 putative phosphate binding site [ion binding]; other site 860228004309 metal binding site A [ion binding]; metal-binding site 860228004310 putative AP binding site [nucleotide binding]; other site 860228004311 putative metal binding site B [ion binding]; other site 860228004312 dipeptidyl carboxypeptidase II; Provisional; Region: PRK10280 860228004313 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 860228004314 active site 860228004315 Zn binding site [ion binding]; other site 860228004316 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 860228004317 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 860228004318 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 860228004319 Peptidase M60-like family; Region: M60-like; pfam13402 860228004320 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 860228004321 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 860228004322 potential frameshift: common BLAST hit: gi|319900234|ref|YP_004159962.1| RagB/SusD domain protein 860228004323 starch binding outer membrane protein SusD; Region: SusD; cl17845 860228004324 SusD family; Region: SusD; pfam07980 860228004325 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 860228004326 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228004327 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 860228004328 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 860228004329 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 860228004330 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 860228004331 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 860228004332 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 860228004333 Sulfatase; Region: Sulfatase; cl17466 860228004334 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 860228004335 Mn-dependent transcriptional regulator [Transcription]; Region: TroR; COG1321 860228004336 Iron dependent repressor, metal binding and dimerisation domain; Region: Fe_dep_repr_C; pfam02742 860228004337 This entry represents the core domain of the ferrous iron (Fe2+) transport protein FeoA found in bacteria; Region: FeoA; smart00899 860228004338 FeoA domain; Region: FeoA; pfam04023 860228004339 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 860228004340 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 860228004341 G1 box; other site 860228004342 GTP/Mg2+ binding site [chemical binding]; other site 860228004343 Switch I region; other site 860228004344 G2 box; other site 860228004345 G3 box; other site 860228004346 Switch II region; other site 860228004347 G4 box; other site 860228004348 G5 box; other site 860228004349 Nucleoside recognition; Region: Gate; pfam07670 860228004350 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 860228004351 Nucleoside recognition; Region: Gate; pfam07670 860228004352 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 860228004353 putative peptidase; Provisional; Region: PRK11649 860228004354 Peptidase family M23; Region: Peptidase_M23; pfam01551 860228004355 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 860228004356 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_1; cd05015 860228004357 active site 860228004358 dimer interface [polypeptide binding]; other site 860228004359 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_2; cd05016 860228004360 dimer interface [polypeptide binding]; other site 860228004361 active site 860228004362 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 860228004363 A new structural DNA glycosylase containing HEAT-like repeats; Region: AlkD_like_1; cd07064 860228004364 active site 860228004365 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 860228004366 active site 860228004367 Cellulose synthase catalytic subunit A2 (CESA2) is a catalytic subunit or a catalytic subunit substitute of the cellulose synthase complex; Region: CESA_CaSu_A2; cd06437 860228004368 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 860228004369 DXD motif; other site 860228004370 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 860228004371 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 860228004372 Walker A motif; other site 860228004373 ATP binding site [chemical binding]; other site 860228004374 Walker B motif; other site 860228004375 arginine finger; other site 860228004376 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 860228004377 Domain of unknown function (DUF4289); Region: DUF4289; pfam14121 860228004378 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228004379 Walker A/P-loop; other site 860228004380 ATP binding site [chemical binding]; other site 860228004381 Q-loop/lid; other site 860228004382 ABC transporter signature motif; other site 860228004383 Walker B; other site 860228004384 D-loop; other site 860228004385 H-loop/switch region; other site 860228004386 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 860228004387 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 860228004388 RNA binding surface [nucleotide binding]; other site 860228004389 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 860228004390 active site 860228004391 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 860228004392 active site 860228004393 catalytic motif [active] 860228004394 Zn binding site [ion binding]; other site 860228004395 Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism]; Region: CutC; COG3142 860228004396 phosphodiesterase YaeI; Provisional; Region: PRK11340 860228004397 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 860228004398 putative active site [active] 860228004399 putative metal binding site [ion binding]; other site 860228004400 gliding motility-associated protein GldC; Region: GldC; TIGR03515 860228004401 gliding motility-associated lipoprotein GldB; Region: GldB_lipo; TIGR03514 860228004402 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 860228004403 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 860228004404 dimer interface [polypeptide binding]; other site 860228004405 decamer (pentamer of dimers) interface [polypeptide binding]; other site 860228004406 catalytic triad [active] 860228004407 peroxidatic and resolving cysteines [active] 860228004408 chaperone protein DnaJ; Provisional; Region: PRK14289 860228004409 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 860228004410 HSP70 interaction site [polypeptide binding]; other site 860228004411 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 860228004412 substrate binding site [polypeptide binding]; other site 860228004413 dimer interface [polypeptide binding]; other site 860228004414 GrpE; Region: GrpE; pfam01025 860228004415 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 860228004416 dimer interface [polypeptide binding]; other site 860228004417 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 860228004418 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 860228004419 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 860228004420 active site 860228004421 motif I; other site 860228004422 motif II; other site 860228004423 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 860228004424 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 860228004425 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 860228004426 Transposase [DNA replication, recombination, and repair]; Region: COG5433 860228004427 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 860228004428 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 860228004429 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 860228004430 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 860228004431 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 860228004432 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 860228004433 Protein of unknown function (DUF1648); Region: DUF1648; pfam07853 860228004434 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 860228004435 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 860228004436 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 860228004437 Surface antigen; Region: Bac_surface_Ag; pfam01103 860228004438 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 860228004439 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 860228004440 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 860228004441 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 860228004442 active site 860228004443 HIGH motif; other site 860228004444 KMSKS motif; other site 860228004445 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 860228004446 tRNA binding surface [nucleotide binding]; other site 860228004447 anticodon binding site; other site 860228004448 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 860228004449 dimer interface [polypeptide binding]; other site 860228004450 putative tRNA-binding site [nucleotide binding]; other site 860228004451 Inner membrane protein import complex subunit Tim54; Region: Tim54; pfam11711 860228004452 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1649 860228004453 Putative glycosyl hydrolase domain; Region: DUF4015; cl17870 860228004454 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 860228004455 beta-N-acetylglucosaminidase; Region: NAGidase; pfam07555 860228004456 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 860228004457 AIR carboxylase; Region: AIRC; pfam00731 860228004458 Phospholipase A1; Region: PLA1; pfam02253 860228004459 substrate binding site [chemical binding]; other site 860228004460 dimerization interface [polypeptide binding]; other site 860228004461 active site 860228004462 calcium binding site [ion binding]; other site 860228004463 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 860228004464 NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase and ALDH family 11; Region: ALDH_F11_NP-GAPDH; cd07082 860228004465 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 860228004466 tetrameric interface [polypeptide binding]; other site 860228004467 activator binding site; other site 860228004468 NADP binding site [chemical binding]; other site 860228004469 substrate binding site [chemical binding]; other site 860228004470 catalytic residues [active] 860228004471 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 860228004472 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 860228004473 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 860228004474 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 860228004475 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK01911 860228004476 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03708 860228004477 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 860228004478 Domain of unknown function (DUF4294); Region: DUF4294; pfam14127 860228004479 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 860228004480 Transglycosylase; Region: Transgly; pfam00912 860228004481 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 860228004482 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 860228004483 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 860228004484 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 860228004485 NAD(P) binding site [chemical binding]; other site 860228004486 active site 860228004487 Protein of unknown function (DUF2797); Region: DUF2797; pfam10977 860228004488 GH3 auxin-responsive promoter; Region: GH3; pfam03321 860228004489 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 860228004490 Sulfatase; Region: Sulfatase; pfam00884 860228004491 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 860228004492 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 860228004493 Trans-2-enoyl-CoA reductase catalytic region; Region: Enoyl_reductase; pfam12241 860228004494 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 860228004495 Family description; Region: DsbD_2; pfam13386 860228004496 FixH; Region: FixH; pfam05751 860228004497 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 860228004498 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 860228004499 active site 860228004500 catalytic residues [active] 860228004501 metal binding site [ion binding]; metal-binding site 860228004502 multifunctional aminopeptidase A; Provisional; Region: PRK00913 860228004503 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 860228004504 interface (dimer of trimers) [polypeptide binding]; other site 860228004505 Substrate-binding/catalytic site; other site 860228004506 Zn-binding sites [ion binding]; other site 860228004507 Transposase, Mutator family; Region: Transposase_mut; pfam00872 860228004508 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 860228004509 Transposase; Region: DDE_Tnp_ISL3; pfam01610 860228004510 PIF1-like helicase; Region: PIF1; pfam05970 860228004511 Family description; Region: UvrD_C_2; pfam13538 860228004512 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 860228004513 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 860228004514 active site 860228004515 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 860228004516 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 860228004517 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 860228004518 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 860228004519 catalytic site [active] 860228004520 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 860228004521 active site 860228004522 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 860228004523 prolyl-tRNA synthetase; Provisional; Region: PRK08661 860228004524 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_arch_euk; cd00778 860228004525 dimer interface [polypeptide binding]; other site 860228004526 motif 1; other site 860228004527 active site 860228004528 motif 2; other site 860228004529 motif 3; other site 860228004530 ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in...; Region: ProRS_anticodon_zinc; cd00862 860228004531 anticodon binding site; other site 860228004532 zinc-binding site [ion binding]; other site 860228004533 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 860228004534 putative hydrolase; Provisional; Region: PRK02113 860228004535 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 860228004536 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 860228004537 RimM N-terminal domain; Region: RimM; pfam01782 860228004538 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 860228004539 Protein of unknown function (DUF3373); Region: DUF3373; pfam11853 860228004540 comF family protein; Region: comF; TIGR00201 860228004541 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 860228004542 active site 860228004543 glycyl-tRNA synthetase; Provisional; Region: PRK04173 860228004544 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 860228004545 motif 1; other site 860228004546 Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3...; Region: GlyRS-like_core; cd00774 860228004547 active site 860228004548 motif 2; other site 860228004549 motif 3; other site 860228004550 GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: GlyRS_anticodon; cd00858 860228004551 anticodon binding site; other site 860228004552 PAS domain; Region: PAS_9; pfam13426 860228004553 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 860228004554 putative active site [active] 860228004555 heme pocket [chemical binding]; other site 860228004556 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 860228004557 metal-binding site [ion binding] 860228004558 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 860228004559 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 860228004560 metal-binding site [ion binding] 860228004561 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 860228004562 Soluble P-type ATPase [General function prediction only]; Region: COG4087 860228004563 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 860228004564 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 860228004565 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 860228004566 aspartate aminotransferase; Provisional; Region: PRK05764 860228004567 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 860228004568 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228004569 homodimer interface [polypeptide binding]; other site 860228004570 catalytic residue [active] 860228004571 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 860228004572 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 860228004573 trimer interface [polypeptide binding]; other site 860228004574 putative metal binding site [ion binding]; other site 860228004575 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 860228004576 Short C-terminal domain; Region: SHOCT; pfam09851 860228004577 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 860228004578 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 860228004579 inhibitor-cofactor binding pocket; inhibition site 860228004580 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228004581 catalytic residue [active] 860228004582 Predicted membrane protein, putative toxin regulator [General function prediction only]; Region: PfoR; COG3641 860228004583 Phosphotransferase system, EIIC; Region: PTS_EIIC_2; pfam13303 860228004584 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 860228004585 Predicted metalloprotease [General function prediction only]; Region: COG2321 860228004586 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 860228004587 ribonuclease P; Reviewed; Region: rnpA; PRK01903 860228004588 Peptidase M1 family containing bacterial Aminopeptidase N; Region: M1_APN_5; cd09604 860228004589 Zn binding site [ion binding]; other site 860228004590 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 860228004591 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 860228004592 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; PRK11125 860228004593 cytochrome c nitrate reductase, small subunit; Region: cytochr_NrfH; TIGR03153 860228004594 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 860228004595 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 860228004596 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 860228004597 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 860228004598 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 860228004599 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 860228004600 TPP-binding site; other site 860228004601 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 860228004602 PYR/PP interface [polypeptide binding]; other site 860228004603 dimer interface [polypeptide binding]; other site 860228004604 TPP binding site [chemical binding]; other site 860228004605 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 860228004606 Protein of unknown function (DUF3078); Region: DUF3078; pfam11276 860228004607 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 860228004608 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 860228004609 inhibitor-cofactor binding pocket; inhibition site 860228004610 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228004611 catalytic residue [active] 860228004612 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 860228004613 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 860228004614 FtsX-like permease family; Region: FtsX; pfam02687 860228004615 Ribosome-binding factor A; Region: RBFA; pfam02033 860228004616 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 860228004617 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 860228004618 TrkA-C domain; Region: TrkA_C; pfam02080 860228004619 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 860228004620 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228004621 Walker A/P-loop; other site 860228004622 ATP binding site [chemical binding]; other site 860228004623 Q-loop/lid; other site 860228004624 ABC transporter signature motif; other site 860228004625 Walker B; other site 860228004626 D-loop; other site 860228004627 H-loop/switch region; other site 860228004628 RloB-like protein; Region: RloB; pfam13707 860228004629 AAA domain; Region: AAA_21; pfam13304 860228004630 potential frameshift: common BLAST hit: gi|146298328|ref|YP_001192919.1| leucyl-tRNA synthetase 860228004631 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 860228004632 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 860228004633 active site 860228004634 KMSKS motif; other site 860228004635 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 860228004636 tRNA binding surface [nucleotide binding]; other site 860228004637 Anticodon-binding domain of tRNA; Region: Anticodon_1; pfam08264 860228004638 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 860228004639 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 860228004640 active site 860228004641 HIGH motif; other site 860228004642 nucleotide binding site [chemical binding]; other site 860228004643 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 860228004644 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 860228004645 putative metal binding site [ion binding]; other site 860228004646 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 860228004647 HSP70 interaction site [polypeptide binding]; other site 860228004648 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 860228004649 DHH family; Region: DHH; pfam01368 860228004650 DHHA1 domain; Region: DHHA1; pfam02272 860228004651 Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]; Region: COG1765 860228004652 cytochrome c oxidase, subunit I; Region: CtaD_CoxA; TIGR02891 860228004653 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 860228004654 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 860228004655 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 860228004656 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 860228004657 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 860228004658 Protein of unknown function (DUF3341); Region: DUF3341; pfam11821 860228004659 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 860228004660 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 860228004661 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 860228004662 molybdopterin cofactor binding site; other site 860228004663 The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region...; Region: MopB_CT_PHLH; cd02784 860228004664 4Fe-4S binding domain; Region: Fer4_2; pfam12797 860228004665 4Fe-4S dicluster domain; Region: Fer4_11; pfam13247 860228004666 putative heme-binding domain, Pirellula/Verrucomicrobium type; Region: CxxCH_TIGR02603 860228004667 Cytochrome c; Region: Cytochrom_C; pfam00034 860228004668 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 860228004669 heme-binding residues [chemical binding]; other site 860228004670 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 860228004671 Malic enzyme, N-terminal domain; Region: malic; pfam00390 860228004672 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 860228004673 putative NAD(P) binding site [chemical binding]; other site 860228004674 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 860228004675 The BURPS668_1122 family of deaminases; Region: Toxin-deaminase; pfam14424 860228004676 The BURPS668_1122 family of deaminases; Region: Toxin-deaminase; pfam14424 860228004677 The BURPS668_1122 family of deaminases; Region: Toxin-deaminase; pfam14424 860228004678 The BURPS668_1122 family of deaminases; Region: Toxin-deaminase; pfam14424 860228004679 The BURPS668_1122 family of deaminases; Region: Toxin-deaminase; pfam14424 860228004680 The BURPS668_1122 family of deaminases; Region: Toxin-deaminase; pfam14424 860228004681 The BURPS668_1122 family of deaminases; Region: Toxin-deaminase; pfam14424 860228004682 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 860228004683 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 860228004684 aconitate hydratase; Validated; Region: PRK07229 860228004685 Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: AcnA_Mitochondrial; cd01584 860228004686 substrate binding site [chemical binding]; other site 860228004687 ligand binding site [chemical binding]; other site 860228004688 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 860228004689 substrate binding site [chemical binding]; other site 860228004690 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 860228004691 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 860228004692 putative substrate translocation pore; other site 860228004693 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 860228004694 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 860228004695 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 860228004696 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 860228004697 RNA binding surface [nucleotide binding]; other site 860228004698 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 860228004699 active site 860228004700 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 860228004701 PASTA domain. This domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and...; Region: PASTA; cl02768 860228004702 Membrane protein of unknown function; Region: DUF360; pfam04020 860228004703 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 860228004704 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 860228004705 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 860228004706 active site 860228004707 hydrophilic channel; other site 860228004708 dimerization interface [polypeptide binding]; other site 860228004709 catalytic residues [active] 860228004710 active site lid [active] 860228004711 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 860228004712 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 860228004713 catalytic residues [active] 860228004714 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 860228004715 FAD binding domain; Region: FAD_binding_4; pfam01565 860228004716 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 860228004717 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 860228004718 MutS domain I; Region: MutS_I; pfam01624 860228004719 MutS domain II; Region: MutS_II; pfam05188 860228004720 MutS domain III; Region: MutS_III; pfam05192 860228004721 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 860228004722 Walker A/P-loop; other site 860228004723 ATP binding site [chemical binding]; other site 860228004724 Q-loop/lid; other site 860228004725 ABC transporter signature motif; other site 860228004726 Walker B; other site 860228004727 D-loop; other site 860228004728 H-loop/switch region; other site 860228004729 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 860228004730 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 860228004731 active site 860228004732 HIGH motif; other site 860228004733 dimer interface [polypeptide binding]; other site 860228004734 KMSKS motif; other site 860228004735 FeS assembly ATPase SufC; Region: sufC; TIGR01978 860228004736 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 860228004737 Walker A/P-loop; other site 860228004738 ATP binding site [chemical binding]; other site 860228004739 Q-loop/lid; other site 860228004740 ABC transporter signature motif; other site 860228004741 Walker B; other site 860228004742 D-loop; other site 860228004743 H-loop/switch region; other site 860228004744 Predicted peptidase [General function prediction only]; Region: COG4099 860228004745 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 860228004746 conserved hypothetical protein; Region: MJ1255; TIGR00661 860228004747 Glycosyltransferase family 28 C-terminal domain; Region: Glyco_tran_28_C; cl17369 860228004748 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 860228004749 putative ABC transporter; Region: ycf24; CHL00085 860228004750 S23 ribosomal protein; Region: Ribosomal_S23p; pfam05635 860228004751 four helix bundle protein; Region: TIGR02436 860228004752 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 860228004753 ornithine aminotransferase; Region: Orn_aminotrans; TIGR01885 860228004754 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 860228004755 inhibitor-cofactor binding pocket; inhibition site 860228004756 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228004757 catalytic residue [active] 860228004758 starch binding outer membrane protein SusD; Region: SusD; cl17845 860228004759 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 860228004760 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228004761 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 860228004762 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228004763 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 860228004764 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 860228004765 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 860228004766 ZIP Zinc transporter; Region: Zip; pfam02535 860228004767 Domain of unknown function (DUF4268); Region: DUF4268; pfam14088 860228004768 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 860228004769 AAK_AK-HSDH-like: Amino Acid Kinase Superfamily (AAK), AK-HSDH-like; this family includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK- homoserine dehydrogenase (HSDH). These aspartokinases are found in such...; Region: AAK_AK-HSDH-like; cd04243 860228004770 putative catalytic residues [active] 860228004771 nucleotide binding site [chemical binding]; other site 860228004772 aspartate binding site [chemical binding]; other site 860228004773 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 860228004774 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 860228004775 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 860228004776 potential frameshift: common BLAST hit: gi|256819254|ref|YP_003140533.1| alpha/beta hydrolase fold protein 860228004777 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 860228004778 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 860228004779 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 860228004780 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 860228004781 homodimer interface [polypeptide binding]; other site 860228004782 substrate-cofactor binding pocket; other site 860228004783 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228004784 catalytic residue [active] 860228004785 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 860228004786 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 860228004787 FMN binding site [chemical binding]; other site 860228004788 substrate binding site [chemical binding]; other site 860228004789 putative catalytic residue [active] 860228004790 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 860228004791 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 860228004792 HflX GTPase family; Region: HflX; cd01878 860228004793 G1 box; other site 860228004794 GTP/Mg2+ binding site [chemical binding]; other site 860228004795 Switch I region; other site 860228004796 G2 box; other site 860228004797 G3 box; other site 860228004798 Switch II region; other site 860228004799 G4 box; other site 860228004800 G5 box; other site 860228004801 Uncharacterized conserved protein [Function unknown]; Region: COG3339 860228004802 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 860228004803 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 860228004804 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 860228004805 catalytic residue [active] 860228004806 lipoprotein signal peptidase; Provisional; Region: PRK14788 860228004807 lipoprotein signal peptidase; Provisional; Region: PRK14787 860228004808 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 860228004809 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 860228004810 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 860228004811 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 860228004812 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 860228004813 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228004814 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 860228004815 ApbE family; Region: ApbE; pfam02424 860228004816 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 860228004817 Phosphorylase superfamily; Region: PNP_UDP_1; pfam01048 860228004818 recombination factor protein RarA; Reviewed; Region: PRK13342 860228004819 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 860228004820 Walker A motif; other site 860228004821 ATP binding site [chemical binding]; other site 860228004822 Walker B motif; other site 860228004823 arginine finger; other site 860228004824 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 860228004825 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cl00298 860228004826 active site 860228004827 Rrf2 family protein; Region: rrf2_super; TIGR00738 860228004828 Transcriptional regulator; Region: Rrf2; pfam02082 860228004829 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 860228004830 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 860228004831 S-adenosylmethionine binding site [chemical binding]; other site 860228004832 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 860228004833 ATP binding site [chemical binding]; other site 860228004834 active site 860228004835 substrate binding site [chemical binding]; other site 860228004836 TM2 domain; Region: TM2; pfam05154 860228004837 Protein of unknown function (DUF2752); Region: DUF2752; pfam10825 860228004838 Tic20-like protein; Region: Tic20; pfam09685 860228004839 Peptidase family M48; Region: Peptidase_M48; cl12018 860228004840 Beta-lactamase; Region: Beta-lactamase; pfam00144 860228004841 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 860228004842 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 860228004843 tRNA adenylyltransferase; Region: tRNA_CCA_actino; TIGR02692 860228004844 active site 860228004845 NTP binding site [chemical binding]; other site 860228004846 metal binding triad [ion binding]; metal-binding site 860228004847 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 860228004848 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 860228004849 Zn2+ binding site [ion binding]; other site 860228004850 Mg2+ binding site [ion binding]; other site 860228004851 tRNA nucleotidyltransferase domain 2 putative; Region: tRNA_NucTran2_2; pfam13735 860228004852 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 860228004853 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 860228004854 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 860228004855 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 860228004856 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 860228004857 active site 860228004858 Zn binding site [ion binding]; other site 860228004859 Mannosyl oligosaccharide glucosidase; Region: Glyco_hydro_63; pfam03200 860228004860 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 860228004861 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 860228004862 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 860228004863 Substrate binding site; other site 860228004864 SprT homologues; Region: SprT; cl01182 860228004865 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 860228004866 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 860228004867 homodimer interface [polypeptide binding]; other site 860228004868 substrate-cofactor binding pocket; other site 860228004869 catalytic residue [active] 860228004870 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 860228004871 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 860228004872 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 860228004873 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 860228004874 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 860228004875 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 860228004876 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 860228004877 nicotinate phosphoribosyltransferase; Provisional; Region: PRK05321 860228004878 active site 860228004879 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 860228004880 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 860228004881 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 860228004882 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 860228004883 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 860228004884 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 860228004885 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 860228004886 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 860228004887 Predicted periplasmic protein (DUF2271); Region: DUF2271; pfam10029 860228004888 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 860228004889 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 860228004890 Flavodoxin; Region: Flavodoxin_1; pfam00258 860228004891 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 860228004892 FAD binding pocket [chemical binding]; other site 860228004893 conserved FAD binding motif [chemical binding]; other site 860228004894 phosphate binding motif [ion binding]; other site 860228004895 beta-alpha-beta structure motif; other site 860228004896 NAD binding pocket [chemical binding]; other site 860228004897 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 860228004898 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 860228004899 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 860228004900 salt bridge; other site 860228004901 non-specific DNA binding site [nucleotide binding]; other site 860228004902 sequence-specific DNA binding site [nucleotide binding]; other site 860228004903 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 860228004904 Glycosyl hydrolase family 20 (GH20) catalytic domain of dispersin B (DspB), lacto-N-biosidase (LnbB) and related proteins. Dispersin B is a soluble beta-N-acetylglucosamidase found in bacteria that hydrolyzes the beta-1,6-linkages of PGA (poly-beta-(1,6)...; Region: GH20_DspB_LnbB-like; cd06564 860228004905 active site 860228004906 Domain of unknown function (DUF4302); Region: DUF4302; pfam14135 860228004907 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 860228004908 starch binding outer membrane protein SusD; Region: SusD; cl17845 860228004909 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 860228004910 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228004911 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 860228004912 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228004913 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 860228004914 nudix motif; other site 860228004915 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 860228004916 DNA alkylation repair enzyme [DNA replication, recombination, and repair]; Region: COG4335 860228004917 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 860228004918 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 860228004919 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 860228004920 dimer interface [polypeptide binding]; other site 860228004921 motif 1; other site 860228004922 active site 860228004923 motif 2; other site 860228004924 motif 3; other site 860228004925 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 860228004926 Penicillinase repressor; Region: Pencillinase_R; pfam03965 860228004927 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 860228004928 nucleoside/Zn binding site; other site 860228004929 dimer interface [polypeptide binding]; other site 860228004930 catalytic motif [active] 860228004931 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 860228004932 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 860228004933 putative acyl-acceptor binding pocket; other site 860228004934 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 860228004935 4Fe-4S binding domain; Region: Fer4_5; pfam12801 860228004936 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 860228004937 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 860228004938 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 860228004939 Cytochrome c; Region: Cytochrom_C; pfam00034 860228004940 putative bifunctional cbb3-type cytochrome c oxidase subunit I/II; Provisional; Region: PRK14485 860228004941 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 860228004942 Low-spin heme binding site [chemical binding]; other site 860228004943 Putative water exit pathway; other site 860228004944 Binuclear center (active site) [active] 860228004945 Putative proton exit pathway; other site 860228004946 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; pfam02433 860228004947 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 860228004948 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 860228004949 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 860228004950 Heavy-metal-associated domain; Region: HMA; pfam00403 860228004951 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 860228004952 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 860228004953 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 860228004954 ligand binding site [chemical binding]; other site 860228004955 flexible hinge region; other site 860228004956 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 860228004957 putative switch regulator; other site 860228004958 non-specific DNA interactions [nucleotide binding]; other site 860228004959 DNA binding site [nucleotide binding] 860228004960 sequence specific DNA binding site [nucleotide binding]; other site 860228004961 putative cAMP binding site [chemical binding]; other site 860228004962 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 860228004963 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 860228004964 DNA primase; Validated; Region: dnaG; PRK05667 860228004965 CHC2 zinc finger; Region: zf-CHC2; cl17510 860228004966 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 860228004967 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 860228004968 active site 860228004969 metal binding site [ion binding]; metal-binding site 860228004970 interdomain interaction site; other site 860228004971 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 860228004972 Helix-turn-helix domain; Region: HTH_18; pfam12833 860228004973 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 860228004974 putative transporter; Validated; Region: PRK03818 860228004975 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 860228004976 TrkA-C domain; Region: TrkA_C; pfam02080 860228004977 TrkA-C domain; Region: TrkA_C; pfam02080 860228004978 AspT/YidE/YbjL antiporter duplication domain; Region: YidE_YbjL_dupl; TIGR01625 860228004979 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 860228004980 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 860228004981 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 860228004982 acyl-activating enzyme (AAE) consensus motif; other site 860228004983 putative AMP binding site [chemical binding]; other site 860228004984 putative active site [active] 860228004985 putative CoA binding site [chemical binding]; other site 860228004986 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 860228004987 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 860228004988 hexamer interface [polypeptide binding]; other site 860228004989 Walker A motif; other site 860228004990 ATP binding site [chemical binding]; other site 860228004991 Walker B motif; other site 860228004992 S-adenosylmethionine synthetase; Validated; Region: PRK05250 860228004993 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 860228004994 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 860228004995 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 860228004996 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 860228004997 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 860228004998 RNase E interface [polypeptide binding]; other site 860228004999 trimer interface [polypeptide binding]; other site 860228005000 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 860228005001 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 860228005002 RNase E interface [polypeptide binding]; other site 860228005003 trimer interface [polypeptide binding]; other site 860228005004 active site 860228005005 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 860228005006 putative nucleic acid binding region [nucleotide binding]; other site 860228005007 G-X-X-G motif; other site 860228005008 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 860228005009 RNA binding site [nucleotide binding]; other site 860228005010 domain interface; other site 860228005011 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 860228005012 16S/18S rRNA binding site [nucleotide binding]; other site 860228005013 S13e-L30e interaction site [polypeptide binding]; other site 860228005014 25S rRNA binding site [nucleotide binding]; other site 860228005015 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 860228005016 Galactose mutarotase-like; Region: Gal_mutarotas_2; pfam13802 860228005017 CPE1046 is an uncharacterized Clostridium perfringens protein with a glycosyl hydrolase family 31 (GH31) domain. The domain architecture of CPE1046 and its orthologs includes a C-terminal fibronectin type 3 (FN3) domain and a coagulation factor 5/8 type...; Region: GH31_CPE1046; cd06596 860228005018 putative active site [active] 860228005019 putative catalytic site [active] 860228005020 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 860228005021 Interdomain contacts; other site 860228005022 Cytokine receptor motif; other site 860228005023 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 860228005024 Domains similar to the eukaryotic reeler domain and bacterial cohesins; Region: Reeler_cohesin_like; cl14606 860228005025 thymidine kinase; Provisional; Region: PRK04296 860228005026 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 860228005027 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 860228005028 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 860228005029 TrkA-N domain; Region: TrkA_N; pfam02254 860228005030 TrkA-C domain; Region: TrkA_C; pfam02080 860228005031 Domain of unknown function (DUF4284); Region: DUF4284; pfam14112 860228005032 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 860228005033 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 860228005034 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 860228005035 catalytic residues [active] 860228005036 ferrochelatase; Reviewed; Region: hemH; PRK00035 860228005037 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 860228005038 C-terminal domain interface [polypeptide binding]; other site 860228005039 active site 860228005040 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 860228005041 active site 860228005042 N-terminal domain interface [polypeptide binding]; other site 860228005043 Flavodoxin domain; Region: Flavodoxin_5; cl17428 860228005044 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 860228005045 HAMP domain; Region: HAMP; pfam00672 860228005046 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 860228005047 dimer interface [polypeptide binding]; other site 860228005048 phosphorylation site [posttranslational modification] 860228005049 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 860228005050 ATP binding site [chemical binding]; other site 860228005051 Mg2+ binding site [ion binding]; other site 860228005052 G-X-G motif; other site 860228005053 DNA topoisomerase IV subunit A; Provisional; Region: PRK12758 860228005054 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cl00148 860228005055 CAP-like domain; other site 860228005056 active site 860228005057 triosephosphate isomerase; Provisional; Region: PRK14567 860228005058 Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually...; Region: TIM; cd00311 860228005059 substrate binding site [chemical binding]; other site 860228005060 dimer interface [polypeptide binding]; other site 860228005061 catalytic triad [active] 860228005062 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 860228005063 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 860228005064 substrate binding site [chemical binding]; other site 860228005065 active site 860228005066 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 860228005067 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 860228005068 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 860228005069 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 860228005070 nucleotide binding site/active site [active] 860228005071 HIT family signature motif; other site 860228005072 catalytic residue [active] 860228005073 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 860228005074 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 860228005075 Walker A motif; other site 860228005076 ATP binding site [chemical binding]; other site 860228005077 Walker B motif; other site 860228005078 arginine finger; other site 860228005079 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 860228005080 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 860228005081 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 860228005082 ligand binding site [chemical binding]; other site 860228005083 flexible hinge region; other site 860228005084 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 860228005085 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 860228005086 metal binding triad; other site 860228005087 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 860228005088 active site 860228005089 catalytic site [active] 860228005090 substrate binding site [chemical binding]; other site 860228005091 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 860228005092 purine nucleoside phosphorylase; Provisional; Region: PRK08202 860228005093 Vibrio parahaemolyticus Na(+)/galactose cotransporter (vSGLT) and related proteins; solute binding domain; Region: SLC5sbd_vSGLT; cd10325 860228005094 putative transporter; Provisional; Region: PRK10484 860228005095 Na binding site [ion binding]; other site 860228005096 substrate binding site [chemical binding]; other site 860228005097 Class I aldolases; Region: Aldolase_Class_I; cl17187 860228005098 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 860228005099 catalytic residue [active] 860228005100 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ACT14924; Region: LPLAT_ACT14924-like; cd07986 860228005101 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 860228005102 putative acyl-acceptor binding pocket; other site 860228005103 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 860228005104 Protein of unknown function (DUF2723); Region: DUF2723; pfam11028 860228005105 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 860228005106 active site 860228005107 GH3 auxin-responsive promoter; Region: GH3; pfam03321 860228005108 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 860228005109 Peptidase family M23; Region: Peptidase_M23; pfam01551 860228005110 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 860228005111 Shewanella-like phosphatases, metallophosphatase domain; Region: MPP_Shelphs; cd07425 860228005112 active site 860228005113 metal binding site [ion binding]; metal-binding site 860228005114 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 860228005115 DNA-binding site [nucleotide binding]; DNA binding site 860228005116 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 860228005117 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 860228005118 Walker A/P-loop; other site 860228005119 ATP binding site [chemical binding]; other site 860228005120 Q-loop/lid; other site 860228005121 ABC transporter signature motif; other site 860228005122 Walker B; other site 860228005123 D-loop; other site 860228005124 H-loop/switch region; other site 860228005125 MraZ protein; Region: MraZ; pfam02381 860228005126 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 860228005127 MraZ protein; Region: MraZ; pfam02381 860228005128 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 860228005129 MraW methylase family; Region: Methyltransf_5; cl17771 860228005130 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 860228005131 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 860228005132 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 860228005133 PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by...; Region: PASTA_Pbp2x-like_2; cd06575 860228005134 Domain of unknown function (DUF4298); Region: DUF4298; pfam14131 860228005135 CAAX protease self-immunity; Region: Abi; pfam02517 860228005136 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 860228005137 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 860228005138 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 860228005139 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 860228005140 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 860228005141 active site 860228005142 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 860228005143 Short-chain dehydrogenase involved in D-alanine esterification of lipoteichoic acid and wall teichoic acid (D-alanine transfer protein) [Cell envelope biogenesis, outer membrane]; Region: DltE; COG3967 860228005144 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 860228005145 NAD(P) binding site [chemical binding]; other site 860228005146 active site 860228005147 Bacteriocin-protection, YdeI or OmpD-Associated; Region: OmdA; pfam13376 860228005148 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 860228005149 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 860228005150 DNA alkylation repair enzyme [DNA replication, recombination, and repair]; Region: COG4335 860228005151 Protein of unknown function (DUF1697); Region: DUF1697; pfam08002 860228005152 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 860228005153 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 860228005154 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 860228005155 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 860228005156 CAAX protease self-immunity; Region: Abi; pfam02517 860228005157 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 860228005158 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 860228005159 Mg++ binding site [ion binding]; other site 860228005160 putative catalytic motif [active] 860228005161 putative substrate binding site [chemical binding]; other site 860228005162 UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]; Region: MurD; COG0771 860228005163 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 860228005164 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 860228005165 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 860228005166 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 860228005167 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 860228005168 active site 860228005169 homodimer interface [polypeptide binding]; other site 860228005170 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; pfam08780 860228005171 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 860228005172 active site 860228005173 NTP binding site [chemical binding]; other site 860228005174 metal binding triad [ion binding]; metal-binding site 860228005175 antibiotic binding site [chemical binding]; other site 860228005176 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 860228005177 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 860228005178 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 860228005179 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 860228005180 cell division protein FtsA; Region: ftsA; TIGR01174 860228005181 Cell division protein FtsA; Region: FtsA; smart00842 860228005182 Cell division protein FtsA; Region: FtsA; pfam14450 860228005183 cell division protein FtsZ; Validated; Region: PRK09330 860228005184 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 860228005185 nucleotide binding site [chemical binding]; other site 860228005186 SulA interaction site; other site 860228005187 Tetratricopeptide repeat; Region: TPR_12; pfam13424 860228005188 Tetratricopeptide repeat; Region: TPR_12; pfam13424 860228005189 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 860228005190 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 860228005191 dimer interface [polypeptide binding]; other site 860228005192 phosphorylation site [posttranslational modification] 860228005193 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 860228005194 ATP binding site [chemical binding]; other site 860228005195 Mg2+ binding site [ion binding]; other site 860228005196 G-X-G motif; other site 860228005197 Response regulator receiver domain; Region: Response_reg; pfam00072 860228005198 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 860228005199 active site 860228005200 phosphorylation site [posttranslational modification] 860228005201 intermolecular recognition site; other site 860228005202 dimerization interface [polypeptide binding]; other site 860228005203 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 860228005204 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 860228005205 Right handed beta helix region; Region: Beta_helix; pfam13229 860228005206 Collagen triple helix repeat (20 copies); Region: Collagen; pfam01391 860228005207 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 860228005208 cytochrome c oxidase subunit II; Validated; Region: COX2; MTH00098 860228005209 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 860228005210 ligand binding site [chemical binding]; other site 860228005211 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 860228005212 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 860228005213 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 860228005214 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 860228005215 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 860228005216 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 860228005217 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 860228005218 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 860228005219 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 860228005220 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 860228005221 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 860228005222 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 860228005223 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 860228005224 HIGH motif; other site 860228005225 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 860228005226 active site 860228005227 KMSKS motif; other site 860228005228 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 860228005229 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 860228005230 Walker A motif; other site 860228005231 ATP binding site [chemical binding]; other site 860228005232 Walker B motif; other site 860228005233 arginine finger; other site 860228005234 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 860228005235 Protein of unknown function (DUF4254); Region: DUF4254; pfam14063 860228005236 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 860228005237 putative catalytic site [active] 860228005238 putative metal binding site [ion binding]; other site 860228005239 putative phosphate binding site [ion binding]; other site 860228005240 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228005241 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228005242 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 860228005243 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 860228005244 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 860228005245 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 860228005246 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 860228005247 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 860228005248 rod shape-determining protein MreC; Provisional; Region: PRK13922 860228005249 Homeobox associated leucine zipper; Region: HALZ; cl02577 860228005250 rod shape-determining protein MreC; Region: MreC; pfam04085 860228005251 rod shape-determining protein MreB; Provisional; Region: PRK13927 860228005252 MreB and similar proteins; Region: MreB_like; cd10225 860228005253 nucleotide binding site [chemical binding]; other site 860228005254 Mg binding site [ion binding]; other site 860228005255 putative protofilament interaction site [polypeptide binding]; other site 860228005256 RodZ interaction site [polypeptide binding]; other site 860228005257 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 860228005258 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 860228005259 purine monophosphate binding site [chemical binding]; other site 860228005260 dimer interface [polypeptide binding]; other site 860228005261 putative catalytic residues [active] 860228005262 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 860228005263 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 860228005264 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 860228005265 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 860228005266 FtsX-like permease family; Region: FtsX; pfam02687 860228005267 Xanthomonas XOO_2897-like deaminase; Region: XOO_2897-deam; pfam14440 860228005268 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228005269 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228005270 Putative neutral zinc metallopeptidase; Region: Zn_peptidase_2; pfam04298 860228005271 GTPase CgtA; Reviewed; Region: obgE; PRK12299 860228005272 GTP1/OBG; Region: GTP1_OBG; pfam01018 860228005273 Obg GTPase; Region: Obg; cd01898 860228005274 G1 box; other site 860228005275 GTP/Mg2+ binding site [chemical binding]; other site 860228005276 Switch I region; other site 860228005277 G2 box; other site 860228005278 G3 box; other site 860228005279 Switch II region; other site 860228005280 G4 box; other site 860228005281 G5 box; other site 860228005282 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 860228005283 active site 860228005284 adenylate kinase; Reviewed; Region: adk; PRK00279 860228005285 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 860228005286 AMP-binding site [chemical binding]; other site 860228005287 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 860228005288 Nidogen, G2 domain; Nidogen is an important component of the basement membrane, an extracellular sheet-like matrix. Nidogen is a multifunctional protein that interacts with many other basement membrane proteins, like collagen, perlecan, lamin, and has a...; Region: nidG2; cl00186 860228005289 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228005290 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228005291 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 860228005292 Domain of unknown function (DUF4249); Region: DUF4249; pfam14054 860228005293 Transposase and inactivated derivatives, IS1 family [DNA replication, recombination, and repair]; Region: InsB; COG1662 860228005294 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 860228005295 L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of...; Region: L-Ala-DL-Glu_epimerase; cd03319 860228005296 active site 860228005297 Tetratricopeptide repeat; Region: TPR_12; pfam13424 860228005298 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 860228005299 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 860228005300 cell surface protein SprA; Region: surface_SprA; TIGR04189 860228005301 Motility related/secretion protein; Region: SprA_N; pfam14349 860228005302 Motility related/secretion protein; Region: SprA_N; pfam14349 860228005303 Motility related/secretion protein; Region: SprA_N; pfam14349 860228005304 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 860228005305 RuvA N terminal domain; Region: RuvA_N; pfam01330 860228005306 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 860228005307 Sporulation related domain; Region: SPOR; pfam05036 860228005308 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 860228005309 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 860228005310 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 860228005311 iron-sulfur cluster [ion binding]; other site 860228005312 [2Fe-2S] cluster binding site [ion binding]; other site 860228005313 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 860228005314 active site 860228005315 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 860228005316 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 860228005317 NAD(P) binding site [chemical binding]; other site 860228005318 active site 860228005319 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 860228005320 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 860228005321 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 860228005322 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 860228005323 dimer interface [polypeptide binding]; other site 860228005324 anticodon binding site; other site 860228005325 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 860228005326 homodimer interface [polypeptide binding]; other site 860228005327 motif 1; other site 860228005328 active site 860228005329 motif 2; other site 860228005330 GAD domain; Region: GAD; pfam02938 860228005331 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 860228005332 active site 860228005333 motif 3; other site 860228005334 Lipocalin-like domain; Region: Lipocalin_4; pfam13648 860228005335 Lipocalin-like domain; Region: Lipocalin_4; pfam13648 860228005336 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 860228005337 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 860228005338 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 860228005339 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 860228005340 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 860228005341 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 860228005342 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 860228005343 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 860228005344 DKNYY family; Region: DKNYY; pfam13644 860228005345 DKNYY family; Region: DKNYY; pfam13644 860228005346 Transposase domain (DUF772); Region: DUF772; pfam05598 860228005347 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 860228005348 Alpha amylase catalytic domain found in an uncharacterized protein family; Region: AmyAc_3; cd11349 860228005349 active site 860228005350 catalytic site [active] 860228005351 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 860228005352 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 860228005353 S23 ribosomal protein; Region: Ribosomal_S23p; cl05287 860228005354 four helix bundle protein; Region: TIGR02436 860228005355 cytoplasmic alpha-amylase; Reviewed; Region: PRK09441 860228005356 Alpha amylase catalytic domain found in archaeal, bacterial, and plant Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_arch_bac_plant_AmyA; cd11314 860228005357 active site 860228005358 Ca binding site [ion binding]; other site 860228005359 catalytic site [active] 860228005360 Domain of unknown function (DUF1939); Region: DUF1939; pfam09154 860228005361 SusE outer membrane protein; Region: SusE; pfam14292 860228005362 carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins; Region: CBM_SusE-F_like; cd12956 860228005363 starch binding site [chemical binding]; other site 860228005364 carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins; Region: CBM_SusE-F_like; cd12956 860228005365 starch binding site [chemical binding]; other site 860228005366 starch binding outer membrane protein SusD; Region: SusD; cd08977 860228005367 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 860228005368 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228005369 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 860228005370 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 860228005371 Transcriptional regulators [Transcription]; Region: PurR; COG1609 860228005372 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 860228005373 DNA binding site [nucleotide binding] 860228005374 domain linker motif; other site 860228005375 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 860228005376 ligand binding site [chemical binding]; other site 860228005377 dimerization interface [polypeptide binding]; other site 860228005378 Cyclomaltodextrinase, N-terminal; Region: Cyc-maltodext_N; pfam09087 860228005379 Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins; Region: AmyAc_bac_CMD_like_3; cd11340 860228005380 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 860228005381 Ca binding site [ion binding]; other site 860228005382 active site 860228005383 homodimer interface [polypeptide binding]; other site 860228005384 catalytic site [active] 860228005385 Cyclo-malto-dextrinase C-terminal domain; Region: Cyc-maltodext_C; pfam10438 860228005386 maltose phosphorylase; Provisional; Region: PRK13807 860228005387 Glycosyl hydrolase family 65, N-terminal domain; Region: Glyco_hydro_65N; pfam03636 860228005388 Glycosyl hydrolase family 65 central catalytic domain; Region: Glyco_hydro_65m; pfam03632 860228005389 Glycosyl hydrolase family 65, C-terminal domain; Region: Glyco_hydro_65C; pfam03633 860228005390 Protein of unknown function with HXXEE motif; Region: HXXEE; pfam13787 860228005391 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 860228005392 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 860228005393 Coenzyme A binding pocket [chemical binding]; other site 860228005394 beta-phosphoglucomutase; Region: bPGM; TIGR01990 860228005395 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 860228005396 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 860228005397 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 860228005398 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 860228005399 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 860228005400 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 860228005401 Alpha amylase catalytic domain found in an uncharacterized protein family; Region: AmyAc_3; cd11349 860228005402 active site 860228005403 catalytic site [active] 860228005404 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 860228005405 Uncharacterized protein family UPF0102; Region: UPF0102; cl00516 860228005406 putative recombination protein RecB; Provisional; Region: PRK13909 860228005407 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 860228005408 Bacterial SH3 domain homologues; Region: SH3b; smart00287 860228005409 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 860228005410 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 860228005411 Coenzyme A binding pocket [chemical binding]; other site 860228005412 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 860228005413 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228005414 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 860228005415 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 860228005416 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 860228005417 starch binding outer membrane protein SusD; Region: SusD; cd08977 860228005418 SusD family; Region: SusD; pfam07980 860228005419 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 860228005420 active site 860228005421 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 860228005422 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 860228005423 protein binding site [polypeptide binding]; other site 860228005424 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 860228005425 putative substrate binding region [chemical binding]; other site 860228005426 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 860228005427 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 860228005428 trimer interface [polypeptide binding]; other site 860228005429 active site 860228005430 substrate binding site [chemical binding]; other site 860228005431 CoA binding site [chemical binding]; other site 860228005432 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 860228005433 active site 860228005434 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 860228005435 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 860228005436 dimer interface [polypeptide binding]; other site 860228005437 motif 1; other site 860228005438 active site 860228005439 motif 2; other site 860228005440 motif 3; other site 860228005441 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 860228005442 anticodon binding site; other site 860228005443 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 860228005444 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 860228005445 FeS/SAM binding site; other site 860228005446 sialate_O-acetylesterase_like subfamily of the SGNH-hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: sialate_O-acetylesterase_like2; cd01828 860228005447 active site 860228005448 catalytic triad [active] 860228005449 oxyanion hole [active] 860228005450 NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the...; Region: NTR_like; cl02512 860228005451 Uncharacterized protein family UPF0054; Region: UPF0054; pfam02130 860228005452 exonuclease subunit SbcD; Provisional; Region: PRK10966 860228005453 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 860228005454 active site 860228005455 metal binding site [ion binding]; metal-binding site 860228005456 DNA binding site [nucleotide binding] 860228005457 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 860228005458 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228005459 AAA domain; Region: AAA_23; pfam13476 860228005460 Walker A/P-loop; other site 860228005461 ATP binding site [chemical binding]; other site 860228005462 Q-loop/lid; other site 860228005463 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228005464 ABC transporter signature motif; other site 860228005465 Walker B; other site 860228005466 D-loop; other site 860228005467 H-loop/switch region; other site 860228005468 Transposase and inactivated derivatives, IS1 family [DNA replication, recombination, and repair]; Region: InsB; COG1662 860228005469 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 860228005470 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 860228005471 NAD binding site [chemical binding]; other site 860228005472 substrate binding site [chemical binding]; other site 860228005473 homodimer interface [polypeptide binding]; other site 860228005474 active site 860228005475 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 860228005476 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 860228005477 DNA-binding interface [nucleotide binding]; DNA binding site 860228005478 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 860228005479 AAA domain; Region: AAA_28; pfam13521 860228005480 Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]; Region: NadR; COG3172 860228005481 Domain of unknown function (DUF4301); Region: DUF4301; pfam14134 860228005482 Uncharacterized conserved protein [Function unknown]; Region: COG5276 860228005483 Uncharacterized conserved protein [Function unknown]; Region: COG5276 860228005484 Protein of unknown function (DUF2931); Region: DUF2931; pfam11153 860228005485 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 860228005486 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 860228005487 homodimer interface [polypeptide binding]; other site 860228005488 NAD binding pocket [chemical binding]; other site 860228005489 ATP binding pocket [chemical binding]; other site 860228005490 Mg binding site [ion binding]; other site 860228005491 active-site loop [active] 860228005492 DOMON-like type 9 carbohydrate binding module; Region: CBM9_like_3; cd09620 860228005493 putative ligand binding site [chemical binding]; other site 860228005494 Domain of unknown function (DUF377); Region: DUF377; pfam04041 860228005495 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 860228005496 active site 860228005497 hypothetical protein; Provisional; Region: PRK08201 860228005498 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_3; cd05680 860228005499 metal binding site [ion binding]; metal-binding site 860228005500 putative dimer interface [polypeptide binding]; other site 860228005501 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 860228005502 PGAP1-like protein; Region: PGAP1; pfam07819 860228005503 putative calcium/sodium:proton antiporter; Provisional; Region: PRK10734 860228005504 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 860228005505 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 860228005506 Uncharacterized conserved protein [Function unknown]; Region: COG1284 860228005507 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 860228005508 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 860228005509 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 860228005510 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 860228005511 Cyclomaltodextrinase, N-terminal; Region: Cyc-maltodext_N; pfam09087 860228005512 maltose phosphorylase; Provisional; Region: PRK13807 860228005513 Glycosyl hydrolase family 65, N-terminal domain; Region: Glyco_hydro_65N; pfam03636 860228005514 Glycosyl hydrolase family 65 central catalytic domain; Region: Glyco_hydro_65m; pfam03632 860228005515 Glycosyl hydrolase family 65, C-terminal domain; Region: Glyco_hydro_65C; pfam03633 860228005516 beta-phosphoglucomutase; Region: bPGM; TIGR01990 860228005517 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 860228005518 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 860228005519 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 860228005520 Fe-S metabolism associated domain; Region: SufE; cl00951 860228005521 FeS assembly SUF system protein; Region: SUF_assoc; TIGR02945 860228005522 Protein of unknown function (DUF2480); Region: DUF2480; pfam10652 860228005523 Protein of unknown function (DUF3078); Region: DUF3078; pfam11276 860228005524 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_1; cd08352 860228005525 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 860228005526 putative metal binding site [ion binding]; other site 860228005527 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 860228005528 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 860228005529 active site 860228005530 interdomain interaction site; other site 860228005531 putative metal-binding site [ion binding]; other site 860228005532 nucleotide binding site [chemical binding]; other site 860228005533 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 860228005534 domain I; other site 860228005535 DNA binding groove [nucleotide binding] 860228005536 phosphate binding site [ion binding]; other site 860228005537 domain II; other site 860228005538 domain III; other site 860228005539 nucleotide binding site [chemical binding]; other site 860228005540 catalytic site [active] 860228005541 domain IV; other site 860228005542 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 860228005543 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 860228005544 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 860228005545 ATP-grasp domain; Region: ATP-grasp; pfam02222 860228005546 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 860228005547 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 860228005548 Cu(I) binding site [ion binding]; other site 860228005549 Protein of unknown function (DUF420); Region: DUF420; pfam04238 860228005550 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 860228005551 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 860228005552 catalytic residue [active] 860228005553 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 860228005554 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 860228005555 ATP binding site [chemical binding]; other site 860228005556 putative Mg++ binding site [ion binding]; other site 860228005557 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 860228005558 nucleotide binding region [chemical binding]; other site 860228005559 ATP-binding site [chemical binding]; other site 860228005560 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 860228005561 This domain contains a conserved N-terminal (F/Y)RG motif. It is functionally uncharacterised; Region: FRG; smart00901 860228005562 GTP-binding protein LepA; Provisional; Region: PRK05433 860228005563 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 860228005564 G1 box; other site 860228005565 putative GEF interaction site [polypeptide binding]; other site 860228005566 GTP/Mg2+ binding site [chemical binding]; other site 860228005567 Switch I region; other site 860228005568 G2 box; other site 860228005569 G3 box; other site 860228005570 Switch II region; other site 860228005571 G4 box; other site 860228005572 G5 box; other site 860228005573 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 860228005574 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 860228005575 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 860228005576 CYTH-like Clostridium thermocellum TTM-like subgroup 1; Region: CYTH-like_CthTTM-like_1; cd07891 860228005577 putative active site [active] 860228005578 putative metal binding residues [ion binding]; other site 860228005579 signature motif; other site 860228005580 putative dimer interface [polypeptide binding]; other site 860228005581 putative phosphate binding site [ion binding]; other site 860228005582 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 860228005583 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 860228005584 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 860228005585 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 860228005586 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 860228005587 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 860228005588 putative NAD(P) binding site [chemical binding]; other site 860228005589 active site 860228005590 putative substrate binding site [chemical binding]; other site 860228005591 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 860228005592 Polysaccharide biosynthesis protein; Region: Polysacc_synt; pfam01943 860228005593 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 860228005594 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 860228005595 Glycosyl transferase family 8; Region: Glyco_transf_8; pfam01501 860228005596 active site 860228005597 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 860228005598 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 860228005599 pyridoxal 5'-phosphate binding site [chemical binding]; other site 860228005600 homodimer interface [polypeptide binding]; other site 860228005601 catalytic residue [active] 860228005602 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 860228005603 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 860228005604 TupA-like ATPgrasp; Region: ATPgrasp_TupA; pfam14305 860228005605 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 860228005606 active site 860228005607 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 860228005608 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 860228005609 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 860228005610 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 860228005611 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 860228005612 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 860228005613 active site 860228005614 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 860228005615 S23 ribosomal protein; Region: Ribosomal_S23p; pfam05635 860228005616 four helix bundle protein; Region: TIGR02436 860228005617 WxcM-like, C-terminal; Region: FdtA; pfam05523 860228005618 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 860228005619 AAA domain; Region: AAA_21; pfam13304 860228005620 Walker A/P-loop; other site 860228005621 ATP binding site [chemical binding]; other site 860228005622 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 860228005623 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 860228005624 NAD(P) binding site [chemical binding]; other site 860228005625 active site 860228005626 dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfbC; COG1898 860228005627 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 860228005628 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 860228005629 active site 860228005630 homodimer interface [polypeptide binding]; other site 860228005631 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 860228005632 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 860228005633 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 860228005634 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 860228005635 NAD(P) binding site [chemical binding]; other site 860228005636 active site 860228005637 Sugar transferases involved in lipopolysaccharide synthesis [Cell envelope biogenesis, outer membrane]; Region: WcaJ; COG2148 860228005638 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 860228005639 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 860228005640 NAD(P) binding site [chemical binding]; other site 860228005641 homodimer interface [polypeptide binding]; other site 860228005642 substrate binding site [chemical binding]; other site 860228005643 active site 860228005644 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 860228005645 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 860228005646 substrate binding site; other site 860228005647 tetramer interface; other site 860228005648 Archaeal ATPase; Region: Arch_ATPase; pfam01637 860228005649 AAA ATPase domain; Region: AAA_16; pfam13191 860228005650 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 860228005651 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 860228005652 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 860228005653 NADP binding site [chemical binding]; other site 860228005654 active site 860228005655 putative substrate binding site [chemical binding]; other site 860228005656 Predicted membrane protein [Function unknown]; Region: COG1288 860228005657 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 860228005658 Cna protein B-type domain; Region: Cna_B_2; pfam13715 860228005659 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 860228005660 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228005661 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 860228005662 Phytase; Region: Phytase; cl17685 860228005663 Mevalonate kinase [Lipid metabolism]; Region: ERG12; COG1577 860228005664 Class II hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR); Region: HMG-CoA_reductase_classII; cd00644 860228005665 homodimer interface [polypeptide binding]; other site 860228005666 catalytic residues [active] 860228005667 NAD binding site [chemical binding]; other site 860228005668 substrate binding pocket [chemical binding]; other site 860228005669 flexible flap; other site 860228005670 thiamine-monophosphate kinase; Region: thiL; TIGR01379 860228005671 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 860228005672 ATP binding site [chemical binding]; other site 860228005673 dimerization interface [polypeptide binding]; other site 860228005674 Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA); Region: CE4_PuuE_HpPgdA_like_2; cd10941 860228005675 putative active site [active] 860228005676 putative catalytic site [active] 860228005677 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 860228005678 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 860228005679 Ligand binding site; other site 860228005680 Putative Catalytic site; other site 860228005681 DXD motif; other site 860228005682 Protein of unknown function (DUF2029); Region: DUF2029; pfam09594 860228005683 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 860228005684 heme-binding site [chemical binding]; other site 860228005685 Cupin domain; Region: Cupin_2; cl17218 860228005686 Rrf2 family protein; Region: rrf2_super; TIGR00738 860228005687 Transcriptional regulator; Region: Rrf2; pfam02082 860228005688 Transcriptional regulator; Region: Rrf2; cl17282 860228005689 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 860228005690 active site 860228005691 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 860228005692 putative active site [active] 860228005693 dimerization interface [polypeptide binding]; other site 860228005694 putative tRNAtyr binding site [nucleotide binding]; other site 860228005695 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 860228005696 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 860228005697 GIY-YIG motif/motif A; other site 860228005698 active site 860228005699 catalytic site [active] 860228005700 putative DNA binding site [nucleotide binding]; other site 860228005701 metal binding site [ion binding]; metal-binding site 860228005702 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 860228005703 H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Region: H3TH_StructSpec-5'-nucleases; cl14815 860228005704 DNA binding site [nucleotide binding] 860228005705 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 860228005706 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 860228005707 substrate binding pocket [chemical binding]; other site 860228005708 chain length determination region; other site 860228005709 substrate-Mg2+ binding site; other site 860228005710 catalytic residues [active] 860228005711 aspartate-rich region 1; other site 860228005712 active site lid residues [active] 860228005713 aspartate-rich region 2; other site 860228005714 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 860228005715 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 860228005716 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 860228005717 Competence protein CoiA-like family; Region: CoiA; cl11541 860228005718 Transposase, Mutator family; Region: Transposase_mut; pfam00872 860228005719 biotin synthase; Region: bioB; TIGR00433 860228005720 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 860228005721 FeS/SAM binding site; other site 860228005722 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 860228005723 Helix-turn-helix domain; Region: HTH_38; pfam13936 860228005724 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 860228005725 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 860228005726 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 860228005727 HlyD family secretion protein; Region: HlyD_3; pfam13437 860228005728 BRO family, N-terminal domain; Region: Bro-N; smart01040 860228005729 Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_1; cd02137 860228005730 dimer interface [polypeptide binding]; other site 860228005731 FMN binding site [chemical binding]; other site 860228005732 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 860228005733 dimer interface [polypeptide binding]; other site 860228005734 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 860228005735 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 860228005736 Coenzyme A binding pocket [chemical binding]; other site 860228005737 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 860228005738 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 860228005739 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 860228005740 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 860228005741 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 860228005742 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 860228005743 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 860228005744 putative oxidoreductase; Provisional; Region: PRK10206 860228005745 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 860228005746 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 860228005747 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 860228005748 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 860228005749 DNA-binding site [nucleotide binding]; DNA binding site 860228005750 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 860228005751 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 860228005752 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 860228005753 active site 860228005754 HIGH motif; other site 860228005755 dimer interface [polypeptide binding]; other site 860228005756 KMSKS motif; other site 860228005757 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 860228005758 Integrase core domain; Region: rve; pfam00665 860228005759 DNA/RNA non-specific endonuclease; Region: Endonuclea_NS_2; cl17626 860228005760 Immunoglobulin domain; Region: Ig; cl11960 860228005761 A nuclease family of the HNH/ENDO VII superfamily with conserved AHH; Region: AHH; pfam14412 860228005762 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 860228005763 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 860228005764 hexamer interface [polypeptide binding]; other site 860228005765 ligand binding site [chemical binding]; other site 860228005766 putative active site [active] 860228005767 NAD(P) binding site [chemical binding]; other site 860228005768 Uncharacterized conserved protein (COG2071); Region: DUF2071; cl01329 860228005769 Acyl-protein synthetase, LuxE; Region: LuxE; pfam04443 860228005770 Acyl-protein synthetase, LuxE; Region: LuxE; pfam04443 860228005771 Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from...; Region: ArsC_family; cd02977 860228005772 ArsC family; Region: ArsC; pfam03960 860228005773 catalytic residue [active] 860228005774 Domain of unknown function (DUF4163); Region: DUF4163; pfam13739 860228005775 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 860228005776 Mn-dependent transcriptional regulator [Transcription]; Region: TroR; COG1321 860228005777 Iron dependent repressor, N-terminal DNA binding domain; Region: Fe_dep_repress; pfam01325 860228005778 Iron dependent repressor, metal binding and dimerisation domain; Region: Fe_dep_repr_C; pfam02742 860228005779 FeoA domain; Region: FeoA; pfam04023 860228005780 bis(5'-nucleosyl)-tetraphosphatase (symmetrical); Region: apaH; TIGR00668 860228005781 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 860228005782 active site 860228005783 metal binding site [ion binding]; metal-binding site 860228005784 Divergent AAA domain; Region: AAA_4; pfam04326 860228005785 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 860228005786 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 860228005787 DNA binding site [nucleotide binding] 860228005788 active site