-- dump date 20140618_223414 -- class Genbank::misc_feature -- table misc_feature_note -- id note 439292000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 439292000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 439292000003 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 439292000004 Walker A motif; other site 439292000005 ATP binding site [chemical binding]; other site 439292000006 Walker B motif; other site 439292000007 arginine finger; other site 439292000008 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 439292000009 DnaA box-binding interface [nucleotide binding]; other site 439292000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 439292000011 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 439292000012 putative DNA binding surface [nucleotide binding]; other site 439292000013 dimer interface [polypeptide binding]; other site 439292000014 beta-clamp/clamp loader binding surface; other site 439292000015 beta-clamp/translesion DNA polymerase binding surface; other site 439292000016 S4 domain protein YaaA; Region: YaaA_near_RecF; TIGR02988 439292000017 recombination protein F; Reviewed; Region: recF; PRK00064 439292000018 ATP-binding cassette domain of RecF; Region: ABC_RecF; cd03242 439292000019 Walker A/P-loop; other site 439292000020 ATP binding site [chemical binding]; other site 439292000021 Q-loop/lid; other site 439292000022 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292000023 ABC transporter signature motif; other site 439292000024 Walker B; other site 439292000025 D-loop; other site 439292000026 H-loop/switch region; other site 439292000027 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 439292000028 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 439292000029 Mg2+ binding site [ion binding]; other site 439292000030 G-X-G motif; other site 439292000031 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 439292000032 anchoring element; other site 439292000033 dimer interface [polypeptide binding]; other site 439292000034 ATP binding site [chemical binding]; other site 439292000035 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 439292000036 active site 439292000037 putative metal-binding site [ion binding]; other site 439292000038 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 439292000039 DNA gyrase subunit A; Validated; Region: PRK05560 439292000040 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 439292000041 CAP-like domain; other site 439292000042 active site 439292000043 primary dimer interface [polypeptide binding]; other site 439292000044 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 439292000045 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 439292000046 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 439292000047 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 439292000048 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 439292000049 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 439292000050 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 439292000051 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292000052 Zn2+ binding site [ion binding]; other site 439292000053 Mg2+ binding site [ion binding]; other site 439292000054 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 439292000055 Predicted transcriptional regulators [Transcription]; Region: COG1695 439292000056 Transcriptional regulator PadR-like family; Region: PadR; cl17335 439292000057 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 439292000058 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 439292000059 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 439292000060 pyridoxal 5'-phosphate synthase, synthase subunit Pdx1; Region: TIGR00343 439292000061 PdxS is a subunit of the pyridoxal 5'-phosphate (PLP) synthase, an important enzyme in deoxyxylulose 5-phosphate (DXP)-independent pathway for de novo biosynthesis of PLP, present in some eubacteria, in archaea, fungi, plants, plasmodia, and some...; Region: pdxS; cd04727 439292000062 active site 439292000063 multimer interface [polypeptide binding]; other site 439292000064 imidazole glycerol phosphate synthase subunit hisH; Provisional; Region: hisH; CHL00188 439292000065 Glutamine Amidotransferase (GATase_I) involved in pyridoxine biosynthesis; Region: GATase1_PB; cd01749 439292000066 predicted active site [active] 439292000067 catalytic triad [active] 439292000068 seryl-tRNA synthetase; Provisional; Region: PRK05431 439292000069 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 439292000070 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 439292000071 dimer interface [polypeptide binding]; other site 439292000072 active site 439292000073 motif 1; other site 439292000074 motif 2; other site 439292000075 motif 3; other site 439292000076 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 439292000077 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 439292000078 Walker A/P-loop; other site 439292000079 ATP binding site [chemical binding]; other site 439292000080 Q-loop/lid; other site 439292000081 ABC transporter signature motif; other site 439292000082 Walker B; other site 439292000083 D-loop; other site 439292000084 H-loop/switch region; other site 439292000085 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 439292000086 ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]; Region: AppF; COG4608 439292000087 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 439292000088 Walker A/P-loop; other site 439292000089 ATP binding site [chemical binding]; other site 439292000090 Q-loop/lid; other site 439292000091 ABC transporter signature motif; other site 439292000092 Walker B; other site 439292000093 D-loop; other site 439292000094 H-loop/switch region; other site 439292000095 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 439292000096 The substrate binding component of an ABC-type lactococcal OppA-like transport system contains; Region: PBP2_Lactococcal_OppA_like; cd08510 439292000097 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 439292000098 peptide binding site [polypeptide binding]; other site 439292000099 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 439292000100 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 439292000101 dimer interface [polypeptide binding]; other site 439292000102 conserved gate region; other site 439292000103 putative PBP binding loops; other site 439292000104 ABC-ATPase subunit interface; other site 439292000105 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 439292000106 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 439292000107 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 439292000108 dimer interface [polypeptide binding]; other site 439292000109 conserved gate region; other site 439292000110 putative PBP binding loops; other site 439292000111 ABC-ATPase subunit interface; other site 439292000112 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 439292000113 nucleoside/Zn binding site; other site 439292000114 dimer interface [polypeptide binding]; other site 439292000115 catalytic motif [active] 439292000116 YycC-like protein; Region: YycC; pfam14174 439292000117 DNA polymerase III subunits gamma and tau; Validated; Region: PRK05563 439292000118 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 439292000119 Walker A motif; other site 439292000120 ATP binding site [chemical binding]; other site 439292000121 Walker B motif; other site 439292000122 arginine finger; other site 439292000123 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 439292000124 hypothetical protein; Validated; Region: PRK00153 439292000125 recombination protein RecR; Reviewed; Region: recR; PRK00076 439292000126 RecR protein; Region: RecR; pfam02132 439292000127 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 439292000128 putative active site [active] 439292000129 putative metal-binding site [ion binding]; other site 439292000130 tetramer interface [polypeptide binding]; other site 439292000131 Protein of unknown function (DUF2508); Region: DUF2508; pfam10704 439292000132 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 439292000133 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 439292000134 Hsp70 protein; Region: HSP70; pfam00012 439292000135 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 439292000136 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 439292000137 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 439292000138 catalytic residue [active] 439292000139 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 439292000140 thymidylate kinase; Validated; Region: tmk; PRK00698 439292000141 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 439292000142 TMP-binding site; other site 439292000143 ATP-binding site [chemical binding]; other site 439292000144 Protein of unknown function (DUF970); Region: DUF970; pfam06153 439292000145 DNA polymerase III subunit delta'; Validated; Region: PRK08058 439292000146 DNA polymerase III subunit delta'; Validated; Region: PRK08485 439292000147 Uncharacterized homolog of PSP1 [Function unknown]; Region: COG1774 439292000148 DNA replication intiation control protein YabA; Reviewed; Region: PRK13169 439292000149 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 439292000150 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 439292000151 S-adenosylmethionine binding site [chemical binding]; other site 439292000152 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 439292000153 GIY-YIG motif/motif A; other site 439292000154 putative active site [active] 439292000155 putative metal binding site [ion binding]; other site 439292000156 Predicted methyltransferases [General function prediction only]; Region: COG0313 439292000157 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 439292000158 putative SAM binding site [chemical binding]; other site 439292000159 putative homodimer interface [polypeptide binding]; other site 439292000160 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 439292000161 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 439292000162 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 439292000163 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 439292000164 active site 439292000165 HIGH motif; other site 439292000166 KMSKS motif; other site 439292000167 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 439292000168 tRNA binding surface [nucleotide binding]; other site 439292000169 anticodon binding site; other site 439292000170 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 439292000171 dimer interface [polypeptide binding]; other site 439292000172 putative tRNA-binding site [nucleotide binding]; other site 439292000173 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 439292000174 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 439292000175 active site 439292000176 Domain of unknown function (DUF348); Region: DUF348; pfam03990 439292000177 Domain of unknown function (DUF348); Region: DUF348; pfam03990 439292000178 Domain of unknown function (DUF348); Region: DUF348; pfam03990 439292000179 G5 domain; Region: G5; pfam07501 439292000180 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3584 439292000181 ribonuclease M5; Region: 5S_RNA_mat_M5; TIGR00334 439292000182 TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low...; Region: TOPRIM_RNase_M5_like; cd01027 439292000183 putative active site [active] 439292000184 putative metal binding site [ion binding]; other site 439292000185 Domain of unknown function (DUF4093); Region: DUF4093; pfam13331 439292000186 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 439292000187 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 439292000188 S-adenosylmethionine binding site [chemical binding]; other site 439292000189 Protein of unknown function (DUF1021); Region: DUF1021; pfam06257 439292000190 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00128 439292000191 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 439292000192 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 439292000193 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 439292000194 pur operon repressor; Provisional; Region: PRK09213 439292000195 Bacterial purine repressor, N-terminal; Region: PuR_N; pfam09182 439292000196 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 439292000197 active site 439292000198 regulatory protein SpoVG; Reviewed; Region: PRK13259 439292000199 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14354 439292000200 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 439292000201 Substrate binding site; other site 439292000202 Mg++ binding site; other site 439292000203 N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two...; Region: LbH_GlmU_C; cd03353 439292000204 active site 439292000205 substrate binding site [chemical binding]; other site 439292000206 CoA binding site [chemical binding]; other site 439292000207 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 439292000208 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 439292000209 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 439292000210 active site 439292000211 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 439292000212 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 439292000213 5S rRNA interface [nucleotide binding]; other site 439292000214 CTC domain interface [polypeptide binding]; other site 439292000215 L16 interface [polypeptide binding]; other site 439292000216 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 439292000217 putative active site [active] 439292000218 catalytic residue [active] 439292000219 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 439292000220 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 439292000221 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 439292000222 ATP binding site [chemical binding]; other site 439292000223 putative Mg++ binding site [ion binding]; other site 439292000224 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 439292000225 nucleotide binding region [chemical binding]; other site 439292000226 ATP-binding site [chemical binding]; other site 439292000227 TRCF domain; Region: TRCF; pfam03461 439292000228 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 439292000229 Stage V sporulation protein B, also known as Stage III sporulation protein F, and related proteins; Region: MATE_SpoVB_like; cd13124 439292000230 Protein containing tetrapyrrole methyltransferase domain and MazG-like (predicted pyrophosphatase) domain [General function prediction only]; Region: COG3956 439292000231 N-terminal S-AdoMet dependent methylase domain of Bacillus subtilis YabN and related proteins; Region: YabN_N; cd11723 439292000232 putative SAM binding site [chemical binding]; other site 439292000233 putative homodimer interface [polypeptide binding]; other site 439292000234 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 439292000235 homodimer interface [polypeptide binding]; other site 439292000236 metal binding site [ion binding]; metal-binding site 439292000237 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 439292000238 homodimer interface [polypeptide binding]; other site 439292000239 active site 439292000240 putative chemical substrate binding site [chemical binding]; other site 439292000241 metal binding site [ion binding]; metal-binding site 439292000242 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 439292000243 RNA binding surface [nucleotide binding]; other site 439292000244 Septum formation initiator; Region: DivIC; pfam04977 439292000245 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 439292000246 hypothetical protein; Provisional; Region: PRK08582 439292000247 S1_RPS1_repeat_hs4: 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_hs4; cd05692 439292000248 RNA binding site [nucleotide binding]; other site 439292000249 Uncharacterized conserved protein [Function unknown]; Region: COG2966 439292000250 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 439292000251 Protein of unknown function (DUF3815); Region: DUF3815; cl01118 439292000252 Protein of unknown function (DUF3815); Region: DUF3815; pfam12821 439292000253 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 439292000254 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 439292000255 Ligand Binding Site [chemical binding]; other site 439292000256 TilS substrate C-terminal domain; Region: TilS_C; smart00977 439292000257 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 439292000258 active site 439292000259 FtsH Extracellular; Region: FtsH_ext; pfam06480 439292000260 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 439292000261 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 439292000262 Walker A motif; other site 439292000263 ATP binding site [chemical binding]; other site 439292000264 Walker B motif; other site 439292000265 arginine finger; other site 439292000266 Peptidase family M41; Region: Peptidase_M41; pfam01434 439292000267 pantothenate kinase; Reviewed; Region: PRK13318 439292000268 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 439292000269 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat...; Region: Hsp33; cd00498 439292000270 dimerization interface [polypeptide binding]; other site 439292000271 domain crossover interface; other site 439292000272 redox-dependent activation switch; other site 439292000273 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 439292000274 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 439292000275 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 439292000276 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 439292000277 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 439292000278 glutamine binding [chemical binding]; other site 439292000279 catalytic triad [active] 439292000280 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 439292000281 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 439292000282 homodimer interface [polypeptide binding]; other site 439292000283 substrate-cofactor binding pocket; other site 439292000284 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292000285 catalytic residue [active] 439292000286 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 439292000287 dihydropteroate synthase; Region: DHPS; TIGR01496 439292000288 substrate binding pocket [chemical binding]; other site 439292000289 dimer interface [polypeptide binding]; other site 439292000290 inhibitor binding site; inhibition site 439292000291 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 439292000292 homooctamer interface [polypeptide binding]; other site 439292000293 active site 439292000294 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 439292000295 catalytic center binding site [active] 439292000296 ATP binding site [chemical binding]; other site 439292000297 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 439292000298 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 439292000299 FMN binding site [chemical binding]; other site 439292000300 active site 439292000301 catalytic residues [active] 439292000302 substrate binding site [chemical binding]; other site 439292000303 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 439292000304 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 439292000305 dimer interface [polypeptide binding]; other site 439292000306 putative anticodon binding site; other site 439292000307 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 439292000308 motif 1; other site 439292000309 active site 439292000310 motif 2; other site 439292000311 motif 3; other site 439292000312 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 439292000313 MgtC family; Region: MgtC; pfam02308 439292000314 Firmicute transcriptional repressor of class III stress genes (CtsR); Region: CtsR; pfam05848 439292000315 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]; Region: COG3880 439292000316 UvrB/uvrC motif; Region: UVR; pfam02151 439292000317 ATP:guanido phosphotransferase; Provisional; Region: PRK01059 439292000318 Phosphagen (guanidino) kinases found in bacteria; Region: bacterial_phosphagen_kinase; cd07930 439292000319 ADP binding site [chemical binding]; other site 439292000320 phosphagen binding site; other site 439292000321 substrate specificity loop; other site 439292000322 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 439292000323 Clp amino terminal domain; Region: Clp_N; pfam02861 439292000324 Clp amino terminal domain; Region: Clp_N; pfam02861 439292000325 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 439292000326 Walker A motif; other site 439292000327 ATP binding site [chemical binding]; other site 439292000328 Walker B motif; other site 439292000329 arginine finger; other site 439292000330 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 439292000331 Walker A motif; other site 439292000332 ATP binding site [chemical binding]; other site 439292000333 Walker B motif; other site 439292000334 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 439292000335 DNA repair protein RadA; Provisional; Region: PRK11823 439292000336 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 439292000337 Walker A motif/ATP binding site; other site 439292000338 ATP binding site [chemical binding]; other site 439292000339 Walker B motif; other site 439292000340 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 439292000341 DNA integrity scanning protein DisA; Provisional; Region: PRK13482 439292000342 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 439292000343 DisA bacterial checkpoint controller linker region; Region: DisA-linker; pfam10635 439292000344 Integral membrane protein (PIN domain superfamily) [General function prediction only]; Region: COG4956 439292000345 PIN domain of Thermus Thermophilus Hb8, uncharacterized Bacillus subtilis YacL, and other bacterial homologs; Region: PIN_YacL; cd09877 439292000346 putative active site [active] 439292000347 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 439292000348 substrate binding site; other site 439292000349 dimer interface; other site 439292000350 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 439292000351 homotrimer interaction site [polypeptide binding]; other site 439292000352 zinc binding site [ion binding]; other site 439292000353 CDP-binding sites; other site 439292000354 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 439292000355 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 439292000356 active site 439292000357 HIGH motif; other site 439292000358 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 439292000359 active site 439292000360 KMSKS motif; other site 439292000361 Serine acetyltransferase [Amino acid transport and metabolism]; Region: CysE; COG1045 439292000362 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 439292000363 trimer interface [polypeptide binding]; other site 439292000364 active site 439292000365 substrate binding site [chemical binding]; other site 439292000366 CoA binding site [chemical binding]; other site 439292000367 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 439292000368 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 439292000369 active site 439292000370 HIGH motif; other site 439292000371 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 439292000372 KMSKS motif; other site 439292000373 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 439292000374 tRNA binding surface [nucleotide binding]; other site 439292000375 anticodon binding site; other site 439292000376 Ribonuclease III family protein [Replication, recombination, and repair]; Region: COG1939 439292000377 dimerization interface [polypeptide binding]; other site 439292000378 active site 439292000379 metal binding site [ion binding]; metal-binding site 439292000380 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 439292000381 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 439292000382 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 439292000383 YacP-like NYN domain; Region: NYN_YacP; pfam05991 439292000384 RNA polymerase factor sigma-70; Validated; Region: PRK08295 439292000385 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 439292000386 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 439292000387 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 439292000388 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 439292000389 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 439292000390 DNA binding residues [nucleotide binding] 439292000391 50S ribosomal protein L33; Validated; Region: rpmG; PRK00504 439292000392 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; pfam00584 439292000393 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 439292000394 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 439292000395 putative homodimer interface [polypeptide binding]; other site 439292000396 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 439292000397 heterodimer interface [polypeptide binding]; other site 439292000398 homodimer interface [polypeptide binding]; other site 439292000399 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 439292000400 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 439292000401 23S rRNA interface [nucleotide binding]; other site 439292000402 L7/L12 interface [polypeptide binding]; other site 439292000403 putative thiostrepton binding site; other site 439292000404 L25 interface [polypeptide binding]; other site 439292000405 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 439292000406 mRNA/rRNA interface [nucleotide binding]; other site 439292000407 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 439292000408 23S rRNA interface [nucleotide binding]; other site 439292000409 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 439292000410 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 439292000411 core dimer interface [polypeptide binding]; other site 439292000412 peripheral dimer interface [polypeptide binding]; other site 439292000413 L10 interface [polypeptide binding]; other site 439292000414 L11 interface [polypeptide binding]; other site 439292000415 putative EF-Tu interaction site [polypeptide binding]; other site 439292000416 putative EF-G interaction site [polypeptide binding]; other site 439292000417 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 439292000418 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 439292000419 S-adenosylmethionine binding site [chemical binding]; other site 439292000420 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 439292000421 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 439292000422 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 439292000423 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 439292000424 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 439292000425 RPB10 interaction site [polypeptide binding]; other site 439292000426 RPB1 interaction site [polypeptide binding]; other site 439292000427 RPB11 interaction site [polypeptide binding]; other site 439292000428 RPB3 interaction site [polypeptide binding]; other site 439292000429 RPB12 interaction site [polypeptide binding]; other site 439292000430 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 439292000431 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 439292000432 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 439292000433 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 439292000434 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 439292000435 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 439292000436 Rpb1 (beta') - Rpb6 (omega) interaction site [polypeptide binding]; other site 439292000437 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 439292000438 G-loop; other site 439292000439 DNA binding site [nucleotide binding] 439292000440 putative ribosomal protein L7Ae-like; Provisional; Region: PRK13602 439292000441 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 439292000442 S17 interaction site [polypeptide binding]; other site 439292000443 S8 interaction site; other site 439292000444 16S rRNA interaction site [nucleotide binding]; other site 439292000445 streptomycin interaction site [chemical binding]; other site 439292000446 23S rRNA interaction site [nucleotide binding]; other site 439292000447 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 439292000448 30S ribosomal protein S7; Validated; Region: PRK05302 439292000449 elongation factor G; Reviewed; Region: PRK00007 439292000450 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 439292000451 G1 box; other site 439292000452 putative GEF interaction site [polypeptide binding]; other site 439292000453 GTP/Mg2+ binding site [chemical binding]; other site 439292000454 Switch I region; other site 439292000455 G2 box; other site 439292000456 G3 box; other site 439292000457 Switch II region; other site 439292000458 G4 box; other site 439292000459 G5 box; other site 439292000460 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 439292000461 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 439292000462 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 439292000463 elongation factor Tu; Reviewed; Region: PRK00049 439292000464 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 439292000465 G1 box; other site 439292000466 GEF interaction site [polypeptide binding]; other site 439292000467 GTP/Mg2+ binding site [chemical binding]; other site 439292000468 Switch I region; other site 439292000469 G2 box; other site 439292000470 G3 box; other site 439292000471 Switch II region; other site 439292000472 G4 box; other site 439292000473 G5 box; other site 439292000474 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 439292000475 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 439292000476 Antibiotic Binding Site [chemical binding]; other site 439292000477 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 439292000478 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 439292000479 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 439292000480 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 439292000481 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 439292000482 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 439292000483 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 439292000484 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 439292000485 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 439292000486 putative translocon binding site; other site 439292000487 protein-rRNA interface [nucleotide binding]; other site 439292000488 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 439292000489 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 439292000490 G-X-X-G motif; other site 439292000491 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 439292000492 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 439292000493 23S rRNA interface [nucleotide binding]; other site 439292000494 5S rRNA interface [nucleotide binding]; other site 439292000495 putative antibiotic binding site [chemical binding]; other site 439292000496 L25 interface [polypeptide binding]; other site 439292000497 L27 interface [polypeptide binding]; other site 439292000498 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 439292000499 23S rRNA interface [nucleotide binding]; other site 439292000500 putative translocon interaction site; other site 439292000501 signal recognition particle (SRP54) interaction site; other site 439292000502 L23 interface [polypeptide binding]; other site 439292000503 trigger factor interaction site; other site 439292000504 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 439292000505 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 439292000506 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 439292000507 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 439292000508 RNA binding site [nucleotide binding]; other site 439292000509 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 439292000510 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 439292000511 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 439292000512 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 439292000513 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 439292000514 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 439292000515 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 439292000516 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 439292000517 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 439292000518 5S rRNA interface [nucleotide binding]; other site 439292000519 L27 interface [polypeptide binding]; other site 439292000520 23S rRNA interface [nucleotide binding]; other site 439292000521 L5 interface [polypeptide binding]; other site 439292000522 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 439292000523 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 439292000524 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 439292000525 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 439292000526 23S rRNA binding site [nucleotide binding]; other site 439292000527 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 439292000528 adenylate kinase; Reviewed; Region: adk; PRK00279 439292000529 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 439292000530 AMP-binding site [chemical binding]; other site 439292000531 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 439292000532 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 439292000533 active site 439292000534 KOW motif of Ribosomal Protein L14; Region: KOW_RPL14; cd06088 439292000535 RNA binding site [nucleotide binding]; other site 439292000536 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 439292000537 rRNA binding site [nucleotide binding]; other site 439292000538 predicted 30S ribosome binding site; other site 439292000539 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 439292000540 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 439292000541 30S ribosomal protein S13; Region: bact_S13; TIGR03631 439292000542 30S ribosomal protein S11; Validated; Region: PRK05309 439292000543 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 439292000544 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 439292000545 alphaNTD - beta interaction site [polypeptide binding]; other site 439292000546 alphaNTD homodimer interface [polypeptide binding]; other site 439292000547 alphaNTD - beta' interaction site [polypeptide binding]; other site 439292000548 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 439292000549 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 439292000550 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13635 439292000551 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 439292000552 Walker A/P-loop; other site 439292000553 ATP binding site [chemical binding]; other site 439292000554 Q-loop/lid; other site 439292000555 ABC transporter signature motif; other site 439292000556 Walker B; other site 439292000557 D-loop; other site 439292000558 H-loop/switch region; other site 439292000559 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13634 439292000560 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 439292000561 Walker A/P-loop; other site 439292000562 ATP binding site [chemical binding]; other site 439292000563 Q-loop/lid; other site 439292000564 ABC transporter signature motif; other site 439292000565 Walker B; other site 439292000566 D-loop; other site 439292000567 H-loop/switch region; other site 439292000568 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 439292000569 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 439292000570 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 439292000571 dimerization interface 3.5A [polypeptide binding]; other site 439292000572 active site 439292000573 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 439292000574 23S rRNA interface [nucleotide binding]; other site 439292000575 L3 interface [polypeptide binding]; other site 439292000576 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 439292000577 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 439292000578 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 439292000579 putative active site [active] 439292000580 putative NTP binding site [chemical binding]; other site 439292000581 putative nucleic acid binding site [nucleotide binding]; other site 439292000582 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 439292000583 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 439292000584 Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins of...; Region: Band_7_flotillin; cd03399 439292000585 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: VanY; COG1876 439292000586 D-alanyl-D-alanine carboxypeptidase; Region: VanY; pfam02557 439292000587 Old yellow enzyme (OYE)-related FMN binding domain, group 4. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_4_FMN; cd04735 439292000588 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 439292000589 putative active site [active] 439292000590 putative FMN binding site [chemical binding]; other site 439292000591 putative substrate binding site [chemical binding]; other site 439292000592 putative catalytic residue [active] 439292000593 DNA photolyase; Region: DNA_photolyase; pfam00875 439292000594 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 439292000595 Purine catabolism regulatory protein-like family; Region: PucR; pfam07905 439292000596 Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]; Region: CdaR; COG3835 439292000597 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 439292000598 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 439292000599 Isochorismatase family; Region: Isochorismatase; pfam00857 439292000600 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 439292000601 catalytic triad [active] 439292000602 conserved cis-peptide bond; other site 439292000603 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 439292000604 nuc_hydro: Nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. This group contains eukaryotic, bacterial and archeal...; Region: nuc_hydro; cl00226 439292000605 Protein of unknown function (DUF2877); Region: DUF2877; pfam11392 439292000606 membrane protein FdrA; Validated; Region: PRK06091 439292000607 CoA binding domain; Region: CoA_binding; pfam02629 439292000608 CoA-ligase; Region: Ligase_CoA; pfam00549 439292000609 Protein of unknown function (DUF1116); Region: DUF1116; pfam06545 439292000610 carbamate kinase; Reviewed; Region: PRK12686 439292000611 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 439292000612 putative substrate binding site [chemical binding]; other site 439292000613 nucleotide binding site [chemical binding]; other site 439292000614 nucleotide binding site [chemical binding]; other site 439292000615 homodimer interface [polypeptide binding]; other site 439292000616 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 439292000617 Sodium Bile acid symporter family; Region: SBF; pfam01758 439292000618 choline dehydrogenase; Validated; Region: PRK02106 439292000619 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 439292000620 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 439292000621 Uncharacterized conserved protein [Function unknown]; Region: COG3391 439292000622 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 439292000623 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 439292000624 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 439292000625 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; cl17891 439292000626 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 439292000627 Predicted transcriptional regulators [Transcription]; Region: COG1510 439292000628 MarR family; Region: MarR_2; pfam12802 439292000629 Bacillus subtilis NAD+-dependent betaine aldehyde dehydrogenase-like; Region: ALDH_BADH-GbsA; cd07119 439292000630 glycine betaine aldehyde dehydrogenase; Region: BADH; TIGR01804 439292000631 tetramerization interface [polypeptide binding]; other site 439292000632 NAD(P) binding site [chemical binding]; other site 439292000633 catalytic residues [active] 439292000634 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292000635 Coenzyme A binding pocket [chemical binding]; other site 439292000636 Methyltransferase domain; Region: Methyltransf_31; pfam13847 439292000637 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 439292000638 S-adenosylmethionine binding site [chemical binding]; other site 439292000639 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 439292000640 MgtE intracellular N domain; Region: MgtE_N; pfam03448 439292000641 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 439292000642 Divalent cation transporter; Region: MgtE; pfam01769 439292000643 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 439292000644 active site 439292000645 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 439292000646 active site 439292000647 catalytic residues [active] 439292000648 hypothetical protein; Provisional; Region: PRK02947 439292000649 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 439292000650 putative active site [active] 439292000651 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 439292000652 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 439292000653 DNA-binding site [nucleotide binding]; DNA binding site 439292000654 UTRA domain; Region: UTRA; pfam07702 439292000655 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 439292000656 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 439292000657 active site 439292000658 trimer interface [polypeptide binding]; other site 439292000659 allosteric site; other site 439292000660 active site lid [active] 439292000661 hexamer (dimer of trimers) interface [polypeptide binding]; other site 439292000662 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 439292000663 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 439292000664 active site 439292000665 dimer interface [polypeptide binding]; other site 439292000666 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 439292000667 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 439292000668 DNA-binding site [nucleotide binding]; DNA binding site 439292000669 UTRA domain; Region: UTRA; pfam07702 439292000670 Enterococcus faecalis EF3048 and similar proteins; Region: YdjC_EF3048_like; cd10803 439292000671 putative active site [active] 439292000672 YdjC motif; other site 439292000673 Mg binding site [ion binding]; other site 439292000674 putative homodimer interface [polypeptide binding]; other site 439292000675 Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: CelF; COG1486 439292000676 Glycoside Hydrolases Family 4; Phospho-beta-glucosidase; Region: GH4_P_beta_glucosidase; cd05296 439292000677 NAD binding site [chemical binding]; other site 439292000678 sugar binding site [chemical binding]; other site 439292000679 divalent metal binding site [ion binding]; other site 439292000680 tetramer (dimer of dimers) interface [polypeptide binding]; other site 439292000681 dimer interface [polypeptide binding]; other site 439292000682 Phosphotransferase system cellobiose-specific component IIC [Carbohydrate transport and metabolism]; Region: CelB; COG1455 439292000683 cellobiose phosphotransferase system IIC component; Reviewed; Region: celD; PRK09592 439292000684 PTS_IIA, PTS system, lactose/cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_lac; cd00215 439292000685 methionine cluster; other site 439292000686 active site 439292000687 phosphorylation site [posttranslational modification] 439292000688 metal binding site [ion binding]; metal-binding site 439292000689 PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N; Region: PTS_IIB_chitobiose_lichenan; cd05564 439292000690 active site 439292000691 P-loop; other site 439292000692 phosphorylation site [posttranslational modification] 439292000693 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 439292000694 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 439292000695 nucleotide binding site [chemical binding]; other site 439292000696 Protein of unknown function (DUF1343); Region: DUF1343; pfam07075 439292000697 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 439292000698 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292000699 Coenzyme A binding pocket [chemical binding]; other site 439292000700 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292000701 Coenzyme A binding pocket [chemical binding]; other site 439292000702 N-acetylmuramic acid-6-phosphate etherase; Reviewed; Region: murQ; PRK05441 439292000703 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 439292000704 putative active site [active] 439292000705 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 439292000706 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 439292000707 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 439292000708 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 439292000709 dimer interface [polypeptide binding]; other site 439292000710 conserved gate region; other site 439292000711 putative PBP binding loops; other site 439292000712 ABC-ATPase subunit interface; other site 439292000713 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 439292000714 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 439292000715 dimer interface [polypeptide binding]; other site 439292000716 conserved gate region; other site 439292000717 putative PBP binding loops; other site 439292000718 ABC-ATPase subunit interface; other site 439292000719 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 439292000720 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 439292000721 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 439292000722 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 439292000723 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 439292000724 putative active site [active] 439292000725 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 439292000726 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 439292000727 HsdM N-terminal domain; Region: HsdM_N; pfam12161 439292000728 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 439292000729 Methyltransferase domain; Region: Methyltransf_26; pfam13659 439292000730 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 439292000731 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 439292000732 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 439292000733 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 439292000734 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 439292000735 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 439292000736 ATP binding site [chemical binding]; other site 439292000737 putative Mg++ binding site [ion binding]; other site 439292000738 Type I restriction and modification enzyme - subunit R C terminal; Region: EcoR124_C; pfam12008 439292000739 Helix-turn-helix domain; Region: HTH_17; pfam12728 439292000740 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 439292000741 Transposase; Region: HTH_Tnp_1; pfam01527 439292000742 putative transposase OrfB; Reviewed; Region: PHA02517 439292000743 HTH-like domain; Region: HTH_21; pfam13276 439292000744 Integrase core domain; Region: rve; pfam00665 439292000745 Integrase core domain; Region: rve_2; pfam13333 439292000746 Dynamin family; Region: Dynamin_N; pfam00350 439292000747 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 439292000748 G1 box; other site 439292000749 GTP/Mg2+ binding site [chemical binding]; other site 439292000750 G2 box; other site 439292000751 Switch I region; other site 439292000752 G3 box; other site 439292000753 Switch II region; other site 439292000754 G4 box; other site 439292000755 G5 box; other site 439292000756 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 439292000757 GTP/Mg2+ binding site [chemical binding]; other site 439292000758 G4 box; other site 439292000759 G5 box; other site 439292000760 GTPase SAR1 and related small G proteins [General function prediction only]; Region: COG1100 439292000761 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 439292000762 G1 box; other site 439292000763 G1 box; other site 439292000764 GTP/Mg2+ binding site [chemical binding]; other site 439292000765 Switch I region; other site 439292000766 G2 box; other site 439292000767 G2 box; other site 439292000768 Switch I region; other site 439292000769 G3 box; other site 439292000770 G3 box; other site 439292000771 Switch II region; other site 439292000772 Switch II region; other site 439292000773 G4 box; other site 439292000774 Uncharacterized protein/domain associated with GTPases [Function unknown]; Region: COG3597 439292000775 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 439292000776 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 439292000777 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 439292000778 DNA binding residues [nucleotide binding] 439292000779 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 439292000780 PIN domain; Region: PIN_Smg5-Smg6-like; cd09880 439292000781 putative active site [active] 439292000782 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 439292000783 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 439292000784 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292000785 Zn2+ binding site [ion binding]; other site 439292000786 Mg2+ binding site [ion binding]; other site 439292000787 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 439292000788 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 439292000789 Ligand Binding Site [chemical binding]; other site 439292000790 Sugar-specific transcriptional regulator TrmB; Region: TrmB; cl17775 439292000791 Predicted transcriptional regulators [Transcription]; Region: COG1695 439292000792 Transcriptional regulator PadR-like family; Region: PadR; cl17335 439292000793 Probable transposase; Region: OrfB_IS605; pfam01385 439292000794 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 439292000795 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 439292000796 Host cell surface-exposed lipoprotein; Region: Lipoprotein_Ltp; pfam07553 439292000797 Host cell surface-exposed lipoprotein; Region: Lipoprotein_Ltp; pfam07553 439292000798 Host cell surface-exposed lipoprotein; Region: Lipoprotein_Ltp; pfam07553 439292000799 ABC transporter transmembrane region; Region: ABC_membrane_3; pfam13748 439292000800 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 439292000801 Protein of unknown function (DUF2500); Region: DUF2500; pfam10694 439292000802 FtsX-like permease family; Region: FtsX; pfam02687 439292000803 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 439292000804 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 439292000805 Walker A/P-loop; other site 439292000806 ATP binding site [chemical binding]; other site 439292000807 Q-loop/lid; other site 439292000808 ABC transporter signature motif; other site 439292000809 Walker B; other site 439292000810 D-loop; other site 439292000811 H-loop/switch region; other site 439292000812 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 439292000813 M20 Peptidase Aminoacylase 1-like protein 2 aminobenzoyl-glutamate utilization protein B subfamily; Region: M20_Acy1L2_AbgB; cd05673 439292000814 amidohydrolase; Region: amidohydrolases; TIGR01891 439292000815 putative metal binding site [ion binding]; other site 439292000816 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 439292000817 nucleoside/Zn binding site; other site 439292000818 dimer interface [polypeptide binding]; other site 439292000819 catalytic motif [active] 439292000820 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 439292000821 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 439292000822 non-specific DNA binding site [nucleotide binding]; other site 439292000823 salt bridge; other site 439292000824 sequence-specific DNA binding site [nucleotide binding]; other site 439292000825 Predicted multitransmembrane protein [Function unknown]; Region: COG5438 439292000826 YibE/F-like protein; Region: YibE_F; pfam07907 439292000827 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 439292000828 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 439292000829 ATP binding site [chemical binding]; other site 439292000830 Mg++ binding site [ion binding]; other site 439292000831 motif III; other site 439292000832 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 439292000833 nucleotide binding region [chemical binding]; other site 439292000834 ATP-binding site [chemical binding]; other site 439292000835 RNA recognition motif (RRM) superfamily; Region: RRM_SF; cl17169 439292000836 Predicted drug exporters of the RND superfamily [General function prediction only]; Region: COG2409 439292000837 Predicted drug exporters of the RND superfamily [General function prediction only]; Region: COG2409 439292000838 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 439292000839 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 439292000840 catalytic site [active] 439292000841 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 439292000842 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 439292000843 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 439292000844 cxxc_20_cxxc protein; Region: cxxc_20_cxxc; TIGR04104 439292000845 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 439292000846 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 439292000847 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 439292000848 Bacterial PH domain; Region: DUF304; cl01348 439292000849 Iron-binding zinc finger CDGSH type; Region: zf-CDGSH; pfam09360 439292000850 Major membrane immunogen, membrane-anchored lipoprotein [Function unknown]; Region: COG4939 439292000851 FMN-binding domain; Region: FMN_bind; pfam04205 439292000852 FMN-binding domain; Region: FMN_bind; pfam04205 439292000853 FMN-binding domain; Region: FMN_bind; cl01081 439292000854 FMN-binding domain; Region: FMN_bind; pfam04205 439292000855 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 439292000856 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 439292000857 active site 439292000858 catalytic tetrad [active] 439292000859 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 439292000860 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 439292000861 active site 439292000862 phosphorylation site [posttranslational modification] 439292000863 intermolecular recognition site; other site 439292000864 dimerization interface [polypeptide binding]; other site 439292000865 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 439292000866 DNA binding site [nucleotide binding] 439292000867 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 439292000868 HAMP domain; Region: HAMP; pfam00672 439292000869 dimerization interface [polypeptide binding]; other site 439292000870 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 439292000871 dimer interface [polypeptide binding]; other site 439292000872 phosphorylation site [posttranslational modification] 439292000873 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 439292000874 ATP binding site [chemical binding]; other site 439292000875 Mg2+ binding site [ion binding]; other site 439292000876 G-X-G motif; other site 439292000877 shikimate kinase; Provisional; Region: PRK13948 439292000878 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 439292000879 active site 439292000880 Plasmid pRiA4b ORF-3-like protein; Region: PRiA4_ORF3; pfam07929 439292000881 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 439292000882 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 439292000883 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 439292000884 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 439292000885 active site 439292000886 metal binding site [ion binding]; metal-binding site 439292000887 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 439292000888 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 439292000889 S-adenosylmethionine binding site [chemical binding]; other site 439292000890 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 439292000891 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 439292000892 putative dimer interface [polypeptide binding]; other site 439292000893 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 439292000894 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 439292000895 transmembrane helices; other site 439292000896 SnoaL-like domain; Region: SnoaL_3; pfam13474 439292000897 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292000898 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292000899 metal binding site [ion binding]; metal-binding site 439292000900 active site 439292000901 I-site; other site 439292000902 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292000903 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292000904 metal binding site [ion binding]; metal-binding site 439292000905 active site 439292000906 I-site; other site 439292000907 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 439292000908 catalytic residues [active] 439292000909 dimer interface [polypeptide binding]; other site 439292000910 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 439292000911 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 439292000912 Walker A/P-loop; other site 439292000913 ATP binding site [chemical binding]; other site 439292000914 Q-loop/lid; other site 439292000915 ABC transporter signature motif; other site 439292000916 Walker B; other site 439292000917 D-loop; other site 439292000918 H-loop/switch region; other site 439292000919 Domain of unknown function (DUF4162); Region: DUF4162; pfam13732 439292000920 Putative exporter of polyketide antibiotics [Cell envelope biogenesis, outer membrane]; Region: TnrB3; COG3559 439292000921 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292000922 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292000923 metal binding site [ion binding]; metal-binding site 439292000924 active site 439292000925 I-site; other site 439292000926 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 439292000927 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 439292000928 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 439292000929 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 439292000930 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 439292000931 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 439292000932 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292000933 Walker A/P-loop; other site 439292000934 ATP binding site [chemical binding]; other site 439292000935 Q-loop/lid; other site 439292000936 ABC transporter signature motif; other site 439292000937 Walker B; other site 439292000938 D-loop; other site 439292000939 H-loop/switch region; other site 439292000940 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 439292000941 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 439292000942 active site 439292000943 phosphorylation site [posttranslational modification] 439292000944 intermolecular recognition site; other site 439292000945 dimerization interface [polypeptide binding]; other site 439292000946 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 439292000947 DNA binding residues [nucleotide binding] 439292000948 dimerization interface [polypeptide binding]; other site 439292000949 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 439292000950 Histidine kinase; Region: HisKA_3; pfam07730 439292000951 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 439292000952 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 439292000953 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 439292000954 active site 439292000955 phosphorylation site [posttranslational modification] 439292000956 intermolecular recognition site; other site 439292000957 dimerization interface [polypeptide binding]; other site 439292000958 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 439292000959 DNA binding residues [nucleotide binding] 439292000960 dimerization interface [polypeptide binding]; other site 439292000961 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 439292000962 Histidine kinase; Region: HisKA_3; pfam07730 439292000963 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 439292000964 ATP binding site [chemical binding]; other site 439292000965 Mg2+ binding site [ion binding]; other site 439292000966 G-X-G motif; other site 439292000967 Cell wall-active antibiotics response protein (DUF2154); Region: DUF2154; pfam09922 439292000968 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 439292000969 Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins; Region: GDPD_SaGlpQ_like; cd08601 439292000970 active site 439292000971 catalytic site [active] 439292000972 metal binding site [ion binding]; metal-binding site 439292000973 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 439292000974 methyl indole-3-acetate methyltransferase; Region: PLN02211; cl17657 439292000975 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 439292000976 RibD C-terminal domain; Region: RibD_C; cl17279 439292000977 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG; TIGR02491 439292000978 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 439292000979 FeS/SAM binding site; other site 439292000980 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK14704 439292000981 Class III ribonucleotide reductase; Region: RNR_III; cd01675 439292000982 effector binding site; other site 439292000983 active site 439292000984 Zn binding site [ion binding]; other site 439292000985 glycine loop; other site 439292000986 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 439292000987 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 439292000988 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 439292000989 dimer interface [polypeptide binding]; other site 439292000990 putative radical transfer pathway; other site 439292000991 diiron center [ion binding]; other site 439292000992 tyrosyl radical; other site 439292000993 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09209 439292000994 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 439292000995 Ribonucleotide reductase, barrel domain; Region: Ribonuc_red_lgC; pfam02867 439292000996 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 439292000997 Major Facilitator Superfamily; Region: MFS_1; pfam07690 439292000998 putative substrate translocation pore; other site 439292000999 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 439292001000 HicB family; Region: HicB; pfam05534 439292001001 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 439292001002 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 439292001003 Predicted membrane protein [Function unknown]; Region: COG3462 439292001004 Short C-terminal domain; Region: SHOCT; pfam09851 439292001005 Short C-terminal domain; Region: SHOCT; pfam09851 439292001006 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 439292001007 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292001008 dimerization interface [polypeptide binding]; other site 439292001009 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 439292001010 dimer interface [polypeptide binding]; other site 439292001011 phosphorylation site [posttranslational modification] 439292001012 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 439292001013 ATP binding site [chemical binding]; other site 439292001014 Mg2+ binding site [ion binding]; other site 439292001015 G-X-G motif; other site 439292001016 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 439292001017 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 439292001018 active site 439292001019 phosphorylation site [posttranslational modification] 439292001020 intermolecular recognition site; other site 439292001021 dimerization interface [polypeptide binding]; other site 439292001022 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 439292001023 DNA binding site [nucleotide binding] 439292001024 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 439292001025 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 439292001026 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 439292001027 DNA binding residues [nucleotide binding] 439292001028 Transcriptional regulators [Transcription]; Region: PurR; COG1609 439292001029 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 439292001030 DNA binding site [nucleotide binding] 439292001031 domain linker motif; other site 439292001032 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 439292001033 dimerization interface [polypeptide binding]; other site 439292001034 ligand binding site [chemical binding]; other site 439292001035 Protein of unknown function, DUF624; Region: DUF624; cl02369 439292001036 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 439292001037 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 439292001038 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 439292001039 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 439292001040 dimer interface [polypeptide binding]; other site 439292001041 putative PBP binding loops; other site 439292001042 ABC-ATPase subunit interface; other site 439292001043 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 439292001044 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 439292001045 dimer interface [polypeptide binding]; other site 439292001046 conserved gate region; other site 439292001047 putative PBP binding loops; other site 439292001048 ABC-ATPase subunit interface; other site 439292001049 Putative serine esterase (DUF676); Region: DUF676; pfam05057 439292001050 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 439292001051 PAS domain; Region: PAS_9; pfam13426 439292001052 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292001053 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292001054 metal binding site [ion binding]; metal-binding site 439292001055 active site 439292001056 I-site; other site 439292001057 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 439292001058 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 439292001059 metal-binding site [ion binding] 439292001060 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 439292001061 Soluble P-type ATPase [General function prediction only]; Region: COG4087 439292001062 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 439292001063 dimerization interface [polypeptide binding]; other site 439292001064 putative DNA binding site [nucleotide binding]; other site 439292001065 putative Zn2+ binding site [ion binding]; other site 439292001066 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292001067 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 439292001068 Walker A/P-loop; other site 439292001069 ATP binding site [chemical binding]; other site 439292001070 Q-loop/lid; other site 439292001071 ABC transporter signature motif; other site 439292001072 Walker B; other site 439292001073 D-loop; other site 439292001074 H-loop/switch region; other site 439292001075 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 439292001076 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 439292001077 dimer interface [polypeptide binding]; other site 439292001078 conserved gate region; other site 439292001079 putative PBP binding loops; other site 439292001080 ABC-ATPase subunit interface; other site 439292001081 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 439292001082 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 439292001083 Glycosyl hydrolase family 43; Region: GH43_ABN_1; cd08998 439292001084 substrate binding site [chemical binding]; other site 439292001085 active site 439292001086 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 439292001087 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 439292001088 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 439292001089 dimer interface [polypeptide binding]; other site 439292001090 conserved gate region; other site 439292001091 putative PBP binding loops; other site 439292001092 ABC-ATPase subunit interface; other site 439292001093 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 439292001094 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 439292001095 dimer interface [polypeptide binding]; other site 439292001096 conserved gate region; other site 439292001097 putative PBP binding loops; other site 439292001098 ABC-ATPase subunit interface; other site 439292001099 Protein of unknown function, DUF624; Region: DUF624; cl02369 439292001100 Alpha-L-arabinofuranosidase [Carbohydrate transport and metabolism]; Region: AbfA; COG3534 439292001101 Alpha-L-arabinofuranosidase C-terminus; Region: Alpha-L-AF_C; pfam06964 439292001102 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 439292001103 active site 439292001104 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 439292001105 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cd00398 439292001106 intersubunit interface [polypeptide binding]; other site 439292001107 active site 439292001108 Zn2+ binding site [ion binding]; other site 439292001109 ribulokinase; Provisional; Region: PRK04123 439292001110 Ribulokinases; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_RBK; cd07781 439292001111 N- and C-terminal domain interface [polypeptide binding]; other site 439292001112 active site 439292001113 MgATP binding site [chemical binding]; other site 439292001114 catalytic site [active] 439292001115 metal binding site [ion binding]; metal-binding site 439292001116 carbohydrate binding site [chemical binding]; other site 439292001117 homodimer interface [polypeptide binding]; other site 439292001118 L-arabinose isomerase; Provisional; Region: PRK02929 439292001119 L-Arabinose isomerase (AI) catalyzes the isomerization of L-arabinose to L-ribulose, the first reaction in its conversion into D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, which allows L-arabinose to be used as a carbon...; Region: L-arabinose_isomerase; cd03557 439292001120 putative hexamer (dimer of trimers) interface [polypeptide binding]; other site 439292001121 trimer interface [polypeptide binding]; other site 439292001122 putative substrate binding site [chemical binding]; other site 439292001123 putative metal binding site [ion binding]; other site 439292001124 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 439292001125 DNA-binding site [nucleotide binding]; DNA binding site 439292001126 Transcriptional regulators [Transcription]; Region: PurR; COG1609 439292001127 Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_AraR; cd01541 439292001128 putative dimerization interface [polypeptide binding]; other site 439292001129 putative ligand binding site [chemical binding]; other site 439292001130 Glycerol-1-phosphate dehydrogenase (G1PDH) catalyzes the reversible reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in an NADH-dependent manner; Region: G1PDH; cd08175 439292001131 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 439292001132 active site 439292001133 metal binding site [ion binding]; metal-binding site 439292001134 Selenophosphate synthase [Amino acid transport and metabolism]; Region: SelD; COG0709 439292001135 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 439292001136 dimerization interface [polypeptide binding]; other site 439292001137 putative ATP binding site [chemical binding]; other site 439292001138 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 439292001139 active site residue [active] 439292001140 Transcriptional regulator [Transcription]; Region: LysR; COG0583 439292001141 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 439292001142 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 439292001143 dimerization interface [polypeptide binding]; other site 439292001144 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 439292001145 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 439292001146 dimer interface [polypeptide binding]; other site 439292001147 conserved gate region; other site 439292001148 ABC-ATPase subunit interface; other site 439292001149 phosphonate ABC transporter, ATP-binding protein; Region: ABC_phnC; TIGR02315 439292001150 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 439292001151 Walker A/P-loop; other site 439292001152 ATP binding site [chemical binding]; other site 439292001153 Q-loop/lid; other site 439292001154 ABC transporter signature motif; other site 439292001155 Walker B; other site 439292001156 D-loop; other site 439292001157 H-loop/switch region; other site 439292001158 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; COG2113 439292001159 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 439292001160 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 439292001161 dimer interface [polypeptide binding]; other site 439292001162 conserved gate region; other site 439292001163 putative PBP binding loops; other site 439292001164 ABC-ATPase subunit interface; other site 439292001165 ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]; Region: ProV; COG4175 439292001166 ATP-binding cassette domain of the osmoprotectant proline/glycine betaine uptake system; Region: ABC_Pro_Gly_Betaine; cd03294 439292001167 Walker A/P-loop; other site 439292001168 ATP binding site [chemical binding]; other site 439292001169 Q-loop/lid; other site 439292001170 ABC transporter signature motif; other site 439292001171 Walker B; other site 439292001172 D-loop; other site 439292001173 H-loop/switch region; other site 439292001174 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 439292001175 Predicted transcriptional regulators [Transcription]; Region: COG1510 439292001176 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; cl17220 439292001177 putative DNA binding site [nucleotide binding]; other site 439292001178 putative Zn2+ binding site [ion binding]; other site 439292001179 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 439292001180 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 439292001181 putative multidrug transporter membrane\ATP-binding components; Provisional; Region: PRK10789 439292001182 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292001183 Walker A/P-loop; other site 439292001184 ATP binding site [chemical binding]; other site 439292001185 Q-loop/lid; other site 439292001186 ABC transporter signature motif; other site 439292001187 Walker B; other site 439292001188 D-loop; other site 439292001189 H-loop/switch region; other site 439292001190 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 439292001191 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 439292001192 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 439292001193 Walker A/P-loop; other site 439292001194 ATP binding site [chemical binding]; other site 439292001195 Q-loop/lid; other site 439292001196 ABC transporter signature motif; other site 439292001197 Walker B; other site 439292001198 D-loop; other site 439292001199 H-loop/switch region; other site 439292001200 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 439292001201 Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins; Region: CE4_SmPgdA_like; cd10944 439292001202 NodB motif; other site 439292001203 active site 439292001204 catalytic site [active] 439292001205 Zn binding site [ion binding]; other site 439292001206 Methyltransferase domain; Region: Methyltransf_23; pfam13489 439292001207 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 439292001208 S-adenosylmethionine binding site [chemical binding]; other site 439292001209 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 439292001210 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 439292001211 active site 439292001212 catalytic tetrad [active] 439292001213 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 439292001214 amino acid carrier protein; Region: agcS; TIGR00835 439292001215 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 439292001216 Domain of unknown function DUF59; Region: DUF59; pfam01883 439292001217 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 439292001218 KinB-signalling pathway activation in sporulation; Region: KbaA; pfam14089 439292001219 RNA polymerase sigma factor SigW; Provisional; Region: PRK09641 439292001220 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 439292001221 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 439292001222 DNA binding residues [nucleotide binding] 439292001223 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 439292001224 Putative zinc-finger; Region: zf-HC2; pfam13490 439292001225 Uncharacterized conserved protein [Function unknown]; Region: COG1624 439292001226 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 439292001227 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4856 439292001228 YbbR-like protein; Region: YbbR; pfam07949 439292001229 YbbR-like protein; Region: YbbR; pfam07949 439292001230 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14316 439292001231 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 439292001232 active site 439292001233 substrate binding site [chemical binding]; other site 439292001234 metal binding site [ion binding]; metal-binding site 439292001235 Predicted transcriptional regulators [Transcription]; Region: COG1725 439292001236 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 439292001237 DNA-binding site [nucleotide binding]; DNA binding site 439292001238 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 439292001239 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 439292001240 Walker A/P-loop; other site 439292001241 ATP binding site [chemical binding]; other site 439292001242 Q-loop/lid; other site 439292001243 ABC transporter signature motif; other site 439292001244 Walker B; other site 439292001245 D-loop; other site 439292001246 H-loop/switch region; other site 439292001247 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 439292001248 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 439292001249 glutaminase active site [active] 439292001250 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 439292001251 dimer interface [polypeptide binding]; other site 439292001252 active site 439292001253 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 439292001254 dimer interface [polypeptide binding]; other site 439292001255 active site 439292001256 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 439292001257 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 439292001258 Zn binding site [ion binding]; other site 439292001259 C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_C_like; cd08347 439292001260 Zn binding site [ion binding]; other site 439292001261 AbgT putative transporter family; Region: ABG_transport; pfam03806 439292001262 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 439292001263 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 439292001264 Heme-dependent peroxidases similar to plant peroxidases; Region: plant_peroxidase_like; cl00196 439292001265 heme binding site [chemical binding]; other site 439292001266 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 439292001267 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 439292001268 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 439292001269 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction...; Region: AhpF_NTD_N; cd02974 439292001270 catalytic residue [active] 439292001271 TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then...; Region: AhpF_NTD_C; cd03026 439292001272 catalytic residues [active] 439292001273 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 439292001274 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 439292001275 peroxiredoxin; Region: AhpC; TIGR03137 439292001276 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 439292001277 dimer interface [polypeptide binding]; other site 439292001278 decamer (pentamer of dimers) interface [polypeptide binding]; other site 439292001279 catalytic triad [active] 439292001280 peroxidatic and resolving cysteines [active] 439292001281 OsmC-like protein; Region: OsmC; pfam02566 439292001282 Domain of unknown function (DUF4317); Region: DUF4317; pfam14199 439292001283 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 439292001284 active site 439292001285 catalytic motif [active] 439292001286 Zn binding site [ion binding]; other site 439292001287 probable dihydroxyacetone kinase regulator; Region: DHAK_reg; TIGR02366 439292001288 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292001289 Transcriptional regulator C-terminal region; Region: TetR_C_8; pfam14278 439292001290 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 439292001291 Predicted membrane protein [Function unknown]; Region: COG1511 439292001292 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 439292001293 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 439292001294 Aminoglycoside 3-N-acetyltransferase; Region: Antibiotic_NAT; pfam02522 439292001295 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 439292001296 Protein of unknown function (DUF2804); Region: DUF2804; pfam10974 439292001297 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 439292001298 RNA polymerase factor sigma C; Reviewed; Region: PRK09415 439292001299 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 439292001300 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 439292001301 DNA binding residues [nucleotide binding] 439292001302 3-polyprenyl-4-hydroxybenzoate decarboxylase [Coenzyme metabolism]; Region: UbiX; COG0163 439292001303 Flavoprotein; Region: Flavoprotein; pfam02441 439292001304 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 439292001305 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 439292001306 putative active site [active] 439292001307 putative NTP binding site [chemical binding]; other site 439292001308 putative nucleic acid binding site [nucleotide binding]; other site 439292001309 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 439292001310 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 439292001311 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 439292001312 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 439292001313 NAD(P) binding site [chemical binding]; other site 439292001314 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 439292001315 Methyltransferase domain; Region: Methyltransf_11; pfam08241 439292001316 S-adenosylmethionine binding site [chemical binding]; other site 439292001317 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 439292001318 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292001319 Coenzyme A binding pocket [chemical binding]; other site 439292001320 Cache domain; Region: Cache_1; pfam02743 439292001321 HAMP domain; Region: HAMP; pfam00672 439292001322 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292001323 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292001324 dimer interface [polypeptide binding]; other site 439292001325 putative CheW interface [polypeptide binding]; other site 439292001326 heat shock protein HtpX; Provisional; Region: PRK04897 439292001327 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 439292001328 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 439292001329 dimerization interface [polypeptide binding]; other site 439292001330 putative DNA binding site [nucleotide binding]; other site 439292001331 putative Zn2+ binding site [ion binding]; other site 439292001332 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 439292001333 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 439292001334 nucleotide binding site [chemical binding]; other site 439292001335 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 439292001336 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 439292001337 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 439292001338 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 439292001339 dimer interface [polypeptide binding]; other site 439292001340 conserved gate region; other site 439292001341 putative PBP binding loops; other site 439292001342 ABC-ATPase subunit interface; other site 439292001343 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 439292001344 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 439292001345 dimer interface [polypeptide binding]; other site 439292001346 conserved gate region; other site 439292001347 putative PBP binding loops; other site 439292001348 ABC-ATPase subunit interface; other site 439292001349 beta-D-galactosidase; Reviewed; Region: lacZ; PRK09525 439292001350 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 439292001351 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 439292001352 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 439292001353 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 439292001354 DNA-binding transcriptional repressor EbgR; Provisional; Region: PRK10339 439292001355 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 439292001356 DNA binding site [nucleotide binding] 439292001357 domain linker motif; other site 439292001358 Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalR; cd01544 439292001359 putative dimerization interface [polypeptide binding]; other site 439292001360 putative ligand binding site [chemical binding]; other site 439292001361 Alpha-galactosidase [Carbohydrate transport and metabolism]; Region: GalA; COG3345 439292001362 Melibiase; Region: Melibiase; pfam02065 439292001363 galactokinase; Provisional; Region: PRK05322 439292001364 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 439292001365 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 439292001366 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 439292001367 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 439292001368 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 439292001369 NAD binding site [chemical binding]; other site 439292001370 homodimer interface [polypeptide binding]; other site 439292001371 active site 439292001372 substrate binding site [chemical binding]; other site 439292001373 galactose-1-phosphate uridylyltransferase; Provisional; Region: PRK05270 439292001374 Galactose-1-phosphate uridyl transferase, N-terminal domain; Region: GalP_UDP_transf; pfam01087 439292001375 Galactose-1-phosphate uridyl transferase, C-terminal domain; Region: GalP_UDP_tr_C; pfam02744 439292001376 Uncharacterized conserved protein [Function unknown]; Region: COG0398 439292001377 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 439292001378 Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]; Region: CheB; COG2201 439292001379 CheB methylesterase; Region: CheB_methylest; pfam01339 439292001380 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 439292001381 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 439292001382 PAS domain; Region: PAS_10; pfam13596 439292001383 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 439292001384 PAS fold; Region: PAS_3; pfam08447 439292001385 putative active site [active] 439292001386 heme pocket [chemical binding]; other site 439292001387 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 439292001388 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 439292001389 Zn binding site [ion binding]; other site 439292001390 C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_C_like; cd08347 439292001391 Zn binding site [ion binding]; other site 439292001392 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 439292001393 MarR family; Region: MarR; pfam01047 439292001394 MarR family; Region: MarR_2; cl17246 439292001395 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 439292001396 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 439292001397 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 439292001398 heat shock protein HtpX; Provisional; Region: PRK05457 439292001399 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 439292001400 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 439292001401 substrate binding pocket [chemical binding]; other site 439292001402 membrane-bound complex binding site; other site 439292001403 hinge residues; other site 439292001404 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 439292001405 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 439292001406 putative active site [active] 439292001407 heme pocket [chemical binding]; other site 439292001408 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 439292001409 dimer interface [polypeptide binding]; other site 439292001410 phosphorylation site [posttranslational modification] 439292001411 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 439292001412 ATP binding site [chemical binding]; other site 439292001413 Mg2+ binding site [ion binding]; other site 439292001414 G-X-G motif; other site 439292001415 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 439292001416 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 439292001417 active site 439292001418 phosphorylation site [posttranslational modification] 439292001419 intermolecular recognition site; other site 439292001420 dimerization interface [polypeptide binding]; other site 439292001421 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 439292001422 Walker A motif; other site 439292001423 ATP binding site [chemical binding]; other site 439292001424 Walker B motif; other site 439292001425 arginine finger; other site 439292001426 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 439292001427 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 439292001428 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 439292001429 Domain of unknown function (DUF1850); Region: DUF1850; cl01950 439292001430 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 439292001431 DctM-like transporters; Region: DctM; pfam06808 439292001432 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 439292001433 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 439292001434 active site 439292001435 catalytic tetrad [active] 439292001436 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 439292001437 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 439292001438 active site residue [active] 439292001439 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 439292001440 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 439292001441 high affinity sulphate transporter 1; Region: sulP; TIGR00815 439292001442 Sulfate transporter family; Region: Sulfate_transp; pfam00916 439292001443 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 439292001444 ribonuclease Z; Region: RNase_Z; TIGR02651 439292001445 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292001446 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292001447 metal binding site [ion binding]; metal-binding site 439292001448 active site 439292001449 I-site; other site 439292001450 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 439292001451 putative C-S lyase; Region: C_S_lyase_PatB; TIGR04350 439292001452 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 439292001453 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292001454 homodimer interface [polypeptide binding]; other site 439292001455 catalytic residue [active] 439292001456 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 439292001457 dimer interface [polypeptide binding]; other site 439292001458 conserved gate region; other site 439292001459 putative PBP binding loops; other site 439292001460 ABC-ATPase subunit interface; other site 439292001461 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 439292001462 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 439292001463 dimer interface [polypeptide binding]; other site 439292001464 conserved gate region; other site 439292001465 putative PBP binding loops; other site 439292001466 ABC-ATPase subunit interface; other site 439292001467 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 439292001468 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 439292001469 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 439292001470 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292001471 dimerization interface [polypeptide binding]; other site 439292001472 Histidine kinase; Region: His_kinase; pfam06580 439292001473 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 439292001474 ATP binding site [chemical binding]; other site 439292001475 Mg2+ binding site [ion binding]; other site 439292001476 G-X-G motif; other site 439292001477 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]; Region: COG4753 439292001478 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 439292001479 active site 439292001480 phosphorylation site [posttranslational modification] 439292001481 intermolecular recognition site; other site 439292001482 dimerization interface [polypeptide binding]; other site 439292001483 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 439292001484 Glycosyl Hydrolase Family 88; Region: Glyco_hydro_88; pfam07470 439292001485 Protein of unknown function, DUF624; Region: DUF624; cl02369 439292001486 Heparinase II/III-like protein; Region: Hepar_II_III; pfam07940 439292001487 1,3-beta-galactosyl-N-acetylhexosamine phosphorylase; Region: TIGR02336 439292001488 Lacto-N-biose phosphorylase; Region: Lact_bio_phlase; pfam09508 439292001489 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]; Region: Eda; COG0800 439292001490 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 439292001491 active site 439292001492 intersubunit interface [polypeptide binding]; other site 439292001493 catalytic residue [active] 439292001494 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 439292001495 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 439292001496 substrate binding site [chemical binding]; other site 439292001497 ATP binding site [chemical binding]; other site 439292001498 2-deoxy-D-gluconate 3-dehydrogenase; Region: kduD; TIGR01832 439292001499 gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs; Region: Ga5DH-like_SDR_c; cd05347 439292001500 NADP binding site [chemical binding]; other site 439292001501 homodimer interface [polypeptide binding]; other site 439292001502 active site 439292001503 5-keto-4-deoxyuronate isomerase; Provisional; Region: PRK00924 439292001504 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 439292001505 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 439292001506 Domain of unknown function (DUF1836); Region: DUF1836; pfam08876 439292001507 Predicted membrane protein [Function unknown]; Region: COG2860 439292001508 UPF0126 domain; Region: UPF0126; pfam03458 439292001509 UPF0126 domain; Region: UPF0126; pfam03458 439292001510 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 439292001511 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 439292001512 NAD(P) binding site [chemical binding]; other site 439292001513 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 439292001514 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 439292001515 active site 439292001516 metal binding site [ion binding]; metal-binding site 439292001517 mercuric reductase; Validated; Region: PRK06370 439292001518 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 439292001519 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 439292001520 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 439292001521 Uncharacterized conserved protein [Function unknown]; Region: COG0398 439292001522 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 439292001523 glycine reductase, selenoprotein B; Region: gly_red_sel_B; TIGR01917 439292001524 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 439292001525 DNA-binding site [nucleotide binding]; DNA binding site 439292001526 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 439292001527 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 439292001528 Walker A/P-loop; other site 439292001529 ATP binding site [chemical binding]; other site 439292001530 Q-loop/lid; other site 439292001531 ABC transporter signature motif; other site 439292001532 Walker B; other site 439292001533 D-loop; other site 439292001534 H-loop/switch region; other site 439292001535 Predicted transcriptional regulator [Transcription]; Region: COG2378 439292001536 HTH domain; Region: HTH_11; pfam08279 439292001537 WYL domain; Region: WYL; pfam13280 439292001538 Domain of unknown function (DUF3784); Region: DUF3784; pfam12650 439292001539 futalosine nucleosidase; Region: fut_nucase; TIGR03664 439292001540 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG2107 439292001541 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 439292001542 Major Facilitator Superfamily; Region: MFS_1; pfam07690 439292001543 putative substrate translocation pore; other site 439292001544 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 439292001545 putative substrate translocation pore; other site 439292001546 Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for...; Region: Sortase_E; cd05829 439292001547 active site 439292001548 putative catalytic site [active] 439292001549 Domain of unknown function (DUF4397); Region: DUF4397; pfam14344 439292001550 Domain of unknown function (DUF4397); Region: DUF4397; pfam14344 439292001551 cystathionine gamma-synthase; Reviewed; Region: PRK08247 439292001552 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 439292001553 homodimer interface [polypeptide binding]; other site 439292001554 substrate-cofactor binding pocket; other site 439292001555 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292001556 catalytic residue [active] 439292001557 cystathionine beta-lyase; Provisional; Region: PRK08064 439292001558 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 439292001559 homodimer interface [polypeptide binding]; other site 439292001560 substrate-cofactor binding pocket; other site 439292001561 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292001562 catalytic residue [active] 439292001563 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 439292001564 5-methyltetrahydrofolate--homocysteine methyltransferase; Region: metH; TIGR02082 439292001565 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 439292001566 substrate binding pocket [chemical binding]; other site 439292001567 dimer interface [polypeptide binding]; other site 439292001568 inhibitor binding site; inhibition site 439292001569 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 439292001570 B12 binding site [chemical binding]; other site 439292001571 cobalt ligand [ion binding]; other site 439292001572 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 439292001573 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK05427 439292001574 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 439292001575 DHHA2 domain; Region: DHHA2; pfam02833 439292001576 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 439292001577 catalytic residues [active] 439292001578 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 439292001579 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 439292001580 dimer interface [polypeptide binding]; other site 439292001581 conserved gate region; other site 439292001582 putative PBP binding loops; other site 439292001583 ABC-ATPase subunit interface; other site 439292001584 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 439292001585 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 439292001586 substrate binding pocket [chemical binding]; other site 439292001587 membrane-bound complex binding site; other site 439292001588 hinge residues; other site 439292001589 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 439292001590 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292001591 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 439292001592 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 439292001593 MgtE intracellular N domain; Region: MgtE_N; pfam03448 439292001594 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 439292001595 Divalent cation transporter; Region: MgtE; pfam01769 439292001596 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 439292001597 MgtE intracellular N domain; Region: MgtE_N; smart00924 439292001598 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 439292001599 Divalent cation transporter; Region: MgtE; pfam01769 439292001600 PAS domain; Region: PAS_9; pfam13426 439292001601 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 439292001602 putative active site [active] 439292001603 heme pocket [chemical binding]; other site 439292001604 Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation; Region: STAS_RsbR_RsbS_like; cd07041 439292001605 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 439292001606 MarR family; Region: MarR; pfam01047 439292001607 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 439292001608 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 439292001609 Methyltransferase domain; Region: Methyltransf_23; pfam13489 439292001610 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 439292001611 S-adenosylmethionine binding site [chemical binding]; other site 439292001612 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 439292001613 Ligand Binding Site [chemical binding]; other site 439292001614 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 439292001615 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 439292001616 Sulfate transporter family; Region: Sulfate_transp; pfam00916 439292001617 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 439292001618 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 439292001619 DNA-binding site [nucleotide binding]; DNA binding site 439292001620 RNA-binding motif; other site 439292001621 Transcriptional regulators [Transcription]; Region: PurR; COG1609 439292001622 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 439292001623 DNA binding site [nucleotide binding] 439292001624 domain linker motif; other site 439292001625 Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_TreR_like; cd01542 439292001626 dimerization interface [polypeptide binding]; other site 439292001627 ligand binding site [chemical binding]; other site 439292001628 PTS system, sucrose-specific IIBC component; Region: PTS-II-BC-sucr; TIGR01996 439292001629 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cd00212 439292001630 active site turn [active] 439292001631 phosphorylation site [posttranslational modification] 439292001632 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 439292001633 Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]; Region: CrcB; COG0239 439292001634 CrcB-like protein; Region: CRCB; cl09114 439292001635 BCCT family transporter; Region: BCCT; pfam02028 439292001636 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 439292001637 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 439292001638 PAS domain S-box; Region: sensory_box; TIGR00229 439292001639 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 439292001640 putative active site [active] 439292001641 heme pocket [chemical binding]; other site 439292001642 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292001643 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292001644 metal binding site [ion binding]; metal-binding site 439292001645 active site 439292001646 I-site; other site 439292001647 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292001648 Flavin reductase like domain; Region: Flavin_Reduct; pfam01613 439292001649 Sporulation and spore germination; Region: Germane; pfam10646 439292001650 RNA polymerase sigma factor SigX; Provisional; Region: PRK09639 439292001651 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 439292001652 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 439292001653 DNA binding residues [nucleotide binding] 439292001654 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 439292001655 Low-density lipoprotein-receptor YWTD domain; Region: LY; smart00135 439292001656 PAS fold; Region: PAS_4; pfam08448 439292001657 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 439292001658 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 439292001659 Walker A motif; other site 439292001660 ATP binding site [chemical binding]; other site 439292001661 Walker B motif; other site 439292001662 arginine finger; other site 439292001663 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 439292001664 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 439292001665 Delta(1)-pyrroline-5-carboxylate dehydrogenase, RocA; Region: ALDH_PutA-P5CDH-RocA; cd07124 439292001666 Glutamate binding site [chemical binding]; other site 439292001667 homodimer interface [polypeptide binding]; other site 439292001668 NAD binding site [chemical binding]; other site 439292001669 catalytic residues [active] 439292001670 ornithine--oxo-acid transaminase; Provisional; Region: rocD; PRK04073 439292001671 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 439292001672 inhibitor-cofactor binding pocket; inhibition site 439292001673 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292001674 catalytic residue [active] 439292001675 Proline dehydrogenase; Region: Pro_dh; cl03282 439292001676 Arginase family; Region: Arginase; cd09989 439292001677 agmatinase; Region: agmatinase; TIGR01230 439292001678 active site 439292001679 Mn binding site [ion binding]; other site 439292001680 oligomer interface [polypeptide binding]; other site 439292001681 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 439292001682 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292001683 Walker A/P-loop; other site 439292001684 ATP binding site [chemical binding]; other site 439292001685 Q-loop/lid; other site 439292001686 ABC transporter signature motif; other site 439292001687 Walker B; other site 439292001688 D-loop; other site 439292001689 H-loop/switch region; other site 439292001690 TOBE domain; Region: TOBE_2; pfam08402 439292001691 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 439292001692 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 439292001693 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 439292001694 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 439292001695 dimer interface [polypeptide binding]; other site 439292001696 conserved gate region; other site 439292001697 putative PBP binding loops; other site 439292001698 ABC-ATPase subunit interface; other site 439292001699 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 439292001700 dimer interface [polypeptide binding]; other site 439292001701 conserved gate region; other site 439292001702 putative PBP binding loops; other site 439292001703 ABC-ATPase subunit interface; other site 439292001704 Rhomboid family; Region: Rhomboid; pfam01694 439292001705 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 439292001706 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 439292001707 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 439292001708 putative substrate binding site [chemical binding]; other site 439292001709 putative ATP binding site [chemical binding]; other site 439292001710 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 439292001711 alanine racemase; Reviewed; Region: alr; PRK00053 439292001712 active site 439292001713 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 439292001714 dimer interface [polypeptide binding]; other site 439292001715 substrate binding site [chemical binding]; other site 439292001716 catalytic residues [active] 439292001717 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]; Region: NikR; COG0864 439292001718 PemK-like protein; Region: PemK; pfam02452 439292001719 Rsbr N terminal; Region: Rsbr_N; pfam08678 439292001720 Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation; Region: STAS_RsbR_RsbS_like; cd07041 439292001721 Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation; Region: STAS_RsbR_RsbS_like; cd07041 439292001722 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 439292001723 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 439292001724 ATP binding site [chemical binding]; other site 439292001725 Mg2+ binding site [ion binding]; other site 439292001726 G-X-G motif; other site 439292001727 Phosphoserine phosphatase RsbU, N-terminal domain; Region: RsbU_N; pfam08673 439292001728 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 439292001729 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 439292001730 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 439292001731 anti sigma factor interaction site; other site 439292001732 regulatory phosphorylation site [posttranslational modification]; other site 439292001733 serine-protein kinase RsbW; Provisional; Region: PRK04069 439292001734 Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms]; Region: RsbW; COG2172 439292001735 ATP binding site [chemical binding]; other site 439292001736 Mg2+ binding site [ion binding]; other site 439292001737 G-X-G motif; other site 439292001738 RNA polymerase sigma factor SigB; Validated; Region: PRK08583 439292001739 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 439292001740 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 439292001741 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 439292001742 DNA binding residues [nucleotide binding] 439292001743 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 439292001744 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 439292001745 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 439292001746 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 439292001747 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 439292001748 RNA binding site [nucleotide binding]; other site 439292001749 hypothetical protein; Provisional; Region: PRK04351 439292001750 SprT homologues; Region: SprT; cl01182 439292001751 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 439292001752 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 439292001753 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 439292001754 thiol reductant ABC exporter, CydD subunit; Region: CydD; TIGR02857 439292001755 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 439292001756 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292001757 Walker A/P-loop; other site 439292001758 ATP binding site [chemical binding]; other site 439292001759 Q-loop/lid; other site 439292001760 ABC transporter signature motif; other site 439292001761 Walker B; other site 439292001762 D-loop; other site 439292001763 H-loop/switch region; other site 439292001764 ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydC; COG4987 439292001765 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 439292001766 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 439292001767 Walker A/P-loop; other site 439292001768 ATP binding site [chemical binding]; other site 439292001769 Q-loop/lid; other site 439292001770 ABC transporter signature motif; other site 439292001771 Walker B; other site 439292001772 D-loop; other site 439292001773 H-loop/switch region; other site 439292001774 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 439292001775 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 439292001776 homodimer interface [polypeptide binding]; other site 439292001777 substrate-cofactor binding pocket; other site 439292001778 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292001779 catalytic residue [active] 439292001780 thiamine monophosphate kinase; Provisional; Region: PRK05731 439292001781 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 439292001782 ATP binding site [chemical binding]; other site 439292001783 dimerization interface [polypeptide binding]; other site 439292001784 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 439292001785 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 439292001786 Glycoprotease family; Region: Peptidase_M22; pfam00814 439292001787 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 439292001788 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292001789 Coenzyme A binding pocket [chemical binding]; other site 439292001790 RRXRR protein; Region: RRXRR; pfam14239 439292001791 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 439292001792 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 439292001793 active site 439292001794 UGMP family protein; Validated; Region: PRK09604 439292001795 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 439292001796 nucleotide binding site [chemical binding]; other site 439292001797 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 439292001798 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 439292001799 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 439292001800 ABC transporter; Region: ABC_tran_2; pfam12848 439292001801 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 439292001802 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 439292001803 trimer interface [polypeptide binding]; other site 439292001804 dimer interface [polypeptide binding]; other site 439292001805 putative active site [active] 439292001806 redox-sensing transcriptional repressor Rex; Provisional; Region: PRK05472 439292001807 Putative DNA-binding protein N-terminus; Region: Put_DNA-bind_N; pfam06971 439292001808 CoA binding domain; Region: CoA_binding; pfam02629 439292001809 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 439292001810 Major Facilitator Superfamily; Region: MFS_1; pfam07690 439292001811 putative substrate translocation pore; other site 439292001812 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 439292001813 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292001814 dimerization interface [polypeptide binding]; other site 439292001815 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 439292001816 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 439292001817 dimer interface [polypeptide binding]; other site 439292001818 phosphorylation site [posttranslational modification] 439292001819 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 439292001820 ATP binding site [chemical binding]; other site 439292001821 Mg2+ binding site [ion binding]; other site 439292001822 G-X-G motif; other site 439292001823 PEP-CTERM-box response regulator transcription factor; Region: PEP_resp_reg; TIGR02915 439292001824 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 439292001825 active site 439292001826 phosphorylation site [posttranslational modification] 439292001827 intermolecular recognition site; other site 439292001828 dimerization interface [polypeptide binding]; other site 439292001829 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 439292001830 Walker A motif; other site 439292001831 ATP binding site [chemical binding]; other site 439292001832 Walker B motif; other site 439292001833 arginine finger; other site 439292001834 twin arginine translocase protein A; Provisional; Region: tatA; PRK14861 439292001835 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 439292001836 4Fe-4S binding domain; Region: Fer4_6; pfam12837 439292001837 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 439292001838 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 439292001839 tetrathionate reductase subunit A; Provisional; Region: PRK14991 439292001840 The MopB_Tetrathionate-Ra CD contains tetrathionate reductase, subunit A, (TtrA) and other related proteins. The Salmonella enterica tetrathionate reductase catalyses the reduction of trithionate but not sulfur or thiosulfate. Members of this CD belong...; Region: MopB_Tetrathionate-Ra; cd02758 439292001841 putative [Fe4-S4] binding site [ion binding]; other site 439292001842 putative molybdopterin cofactor binding site [chemical binding]; other site 439292001843 Molybdopterin-Binding, C-terminal (MopB_CT) 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-...; Region: MopB_CT; cl09929 439292001844 molybdopterin cofactor binding site; other site 439292001845 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 439292001846 Domain of unknown function (DUF4305); Region: DUF4305; pfam14146 439292001847 CAAX protease self-immunity; Region: Abi; pfam02517 439292001848 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 439292001849 oligomerisation interface [polypeptide binding]; other site 439292001850 mobile loop; other site 439292001851 roof hairpin; other site 439292001852 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 439292001853 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 439292001854 ring oligomerisation interface [polypeptide binding]; other site 439292001855 ATP/Mg binding site [chemical binding]; other site 439292001856 stacking interactions; other site 439292001857 hinge regions; other site 439292001858 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 439292001859 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292001860 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292001861 metal binding site [ion binding]; metal-binding site 439292001862 active site 439292001863 I-site; other site 439292001864 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 439292001865 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 439292001866 FMN binding site [chemical binding]; other site 439292001867 active site 439292001868 catalytic residues [active] 439292001869 substrate binding site [chemical binding]; other site 439292001870 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 439292001871 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 439292001872 Purine catabolism regulatory protein-like family; Region: PucR; pfam07905 439292001873 DRTGG domain; Region: DRTGG; pfam07085 439292001874 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 439292001875 Amidase; Region: Amidase; cl11426 439292001876 indole-3-acetamide amidohydrolase; Region: PLN02722 439292001877 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 439292001878 allantoinase; Region: allantoinase; TIGR03178 439292001879 active site 439292001880 xanthine dehydrogenase C subunit; Region: pucC; TIGR03199 439292001881 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 439292001882 xanthine dehydrogenase D subunit; Region: pucD; TIGR03196 439292001883 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 439292001884 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 439292001885 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 439292001886 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 439292001887 catalytic loop [active] 439292001888 iron binding site [ion binding]; other site 439292001889 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 439292001890 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 439292001891 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 439292001892 XdhC Rossmann domain; Region: XdhC_C; pfam13478 439292001893 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 439292001894 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 439292001895 Ligand binding site; other site 439292001896 metal-binding site 439292001897 N-ethylammeline chlorohydrolase; Provisional; Region: PRK07228 439292001898 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 439292001899 active site 439292001900 putative substrate binding pocket [chemical binding]; other site 439292001901 OHCU decarboxylase; Region: OHCU_decarbox; cl01251 439292001902 Uricase (urate oxidase) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3648 439292001903 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 439292001904 active site 439292001905 HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU); Region: TLP_HIUase; cd05822 439292001906 active site 439292001907 homotetramer interface [polypeptide binding]; other site 439292001908 allantoate amidohydrolase; Reviewed; Region: PRK09290 439292001909 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 439292001910 active site 439292001911 metal binding site [ion binding]; metal-binding site 439292001912 dimer interface [polypeptide binding]; other site 439292001913 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 439292001914 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 439292001915 catalytic residue [active] 439292001916 Ferritin-like domain; Region: Ferritin; pfam00210 439292001917 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 439292001918 dimerization interface [polypeptide binding]; other site 439292001919 DPS ferroxidase diiron center [ion binding]; other site 439292001920 ion pore; other site 439292001921 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 439292001922 active site residue [active] 439292001923 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 439292001924 active site residue [active] 439292001925 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 439292001926 Low molecular weight phosphatase family; Region: LMWPc; cd00115 439292001927 active site 439292001928 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 439292001929 dimerization interface [polypeptide binding]; other site 439292001930 putative DNA binding site [nucleotide binding]; other site 439292001931 putative Zn2+ binding site [ion binding]; other site 439292001932 Methyltransferase domain; Region: Methyltransf_23; pfam13489 439292001933 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 439292001934 S-adenosylmethionine binding site [chemical binding]; other site 439292001935 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292001936 Coenzyme A binding pocket [chemical binding]; other site 439292001937 DoxX-like family; Region: DoxX_2; pfam13564 439292001938 coenzyme A disulfide reductase; Reviewed; Region: PRK09564 439292001939 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 439292001940 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 439292001941 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 439292001942 Protein of unknown function (DUF2805); Region: DUF2805; pfam10985 439292001943 cryptochrome, DASH family; Region: crypto_DASH; TIGR02765 439292001944 DNA photolyase; Region: DNA_photolyase; pfam00875 439292001945 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 439292001946 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 439292001947 Probable transposase; Region: OrfB_IS605; pfam01385 439292001948 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 439292001949 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 439292001950 (2R,3R)-2,3-butanediol dehydrogenase; Region: butanediol_DH_like; cd08233 439292001951 putative NAD(P) binding site [chemical binding]; other site 439292001952 catalytic Zn binding site [ion binding]; other site 439292001953 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 439292001954 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 439292001955 E3 interaction surface; other site 439292001956 lipoyl attachment site [posttranslational modification]; other site 439292001957 e3 binding domain; Region: E3_binding; pfam02817 439292001958 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 439292001959 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 439292001960 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 439292001961 alpha subunit interface [polypeptide binding]; other site 439292001962 TPP binding site [chemical binding]; other site 439292001963 heterodimer interface [polypeptide binding]; other site 439292001964 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 439292001965 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 439292001966 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 439292001967 tetramer interface [polypeptide binding]; other site 439292001968 TPP-binding site [chemical binding]; other site 439292001969 heterodimer interface [polypeptide binding]; other site 439292001970 phosphorylation loop region [posttranslational modification] 439292001971 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 439292001972 GAF domain; Region: GAF; pfam01590 439292001973 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 439292001974 Walker A motif; other site 439292001975 ATP binding site [chemical binding]; other site 439292001976 Walker B motif; other site 439292001977 arginine finger; other site 439292001978 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 439292001979 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]; Region: COG3947 439292001980 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 439292001981 active site 439292001982 phosphorylation site [posttranslational modification] 439292001983 intermolecular recognition site; other site 439292001984 dimerization interface [polypeptide binding]; other site 439292001985 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 439292001986 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 439292001987 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 439292001988 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 439292001989 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 439292001990 dimer interface [polypeptide binding]; other site 439292001991 phosphorylation site [posttranslational modification] 439292001992 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 439292001993 ATP binding site [chemical binding]; other site 439292001994 Mg2+ binding site [ion binding]; other site 439292001995 G-X-G motif; other site 439292001996 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 439292001997 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 439292001998 active site 439292001999 phosphorylation site [posttranslational modification] 439292002000 intermolecular recognition site; other site 439292002001 dimerization interface [polypeptide binding]; other site 439292002002 Histidine kinase; Region: His_kinase; pfam06580 439292002003 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 439292002004 ATP binding site [chemical binding]; other site 439292002005 Mg2+ binding site [ion binding]; other site 439292002006 G-X-G motif; other site 439292002007 Predicted outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG4932 439292002008 Collagen binding domain; Region: Collagen_bind; pfam05737 439292002009 Collagen binding domain; Region: Collagen_bind; pfam05737 439292002010 Collagen binding domain; Region: Collagen_bind; pfam05737 439292002011 Collagen binding domain; Region: Collagen_bind; pfam05737 439292002012 Collagen binding domain; Region: Collagen_bind; pfam05737 439292002013 Cna protein B-type domain; Region: Cna_B; pfam05738 439292002014 Cna protein B-type domain; Region: Cna_B; pfam05738 439292002015 Cna protein B-type domain; Region: Cna_B; pfam05738 439292002016 Cna protein B-type domain; Region: Cna_B; pfam05738 439292002017 Cna protein B-type domain; Region: Cna_B; pfam05738 439292002018 Cna protein B-type domain; Region: Cna_B; pfam05738 439292002019 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002020 domain interaction interfaces [polypeptide binding]; other site 439292002021 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002022 domain interaction interfaces [polypeptide binding]; other site 439292002023 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002024 domain interaction interfaces [polypeptide binding]; other site 439292002025 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002026 domain interaction interfaces [polypeptide binding]; other site 439292002027 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002028 domain interaction interfaces [polypeptide binding]; other site 439292002029 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002030 domain interaction interfaces [polypeptide binding]; other site 439292002031 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002032 domain interaction interfaces [polypeptide binding]; other site 439292002033 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002034 domain interaction interfaces [polypeptide binding]; other site 439292002035 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002036 domain interaction interfaces [polypeptide binding]; other site 439292002037 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002038 domain interaction interfaces [polypeptide binding]; other site 439292002039 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002040 domain interaction interfaces [polypeptide binding]; other site 439292002041 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002042 domain interaction interfaces [polypeptide binding]; other site 439292002043 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002044 domain interaction interfaces [polypeptide binding]; other site 439292002045 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002046 domain interaction interfaces [polypeptide binding]; other site 439292002047 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002048 domain interaction interfaces [polypeptide binding]; other site 439292002049 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 439292002050 domain interaction interfaces [polypeptide binding]; other site 439292002051 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved...; Region: Sortase_D_4; cd05828 439292002052 active site 439292002053 catalytic site [active] 439292002054 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 439292002055 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 439292002056 active site 439292002057 phosphorylation site [posttranslational modification] 439292002058 intermolecular recognition site; other site 439292002059 dimerization interface [polypeptide binding]; other site 439292002060 YcbB domain; Region: YcbB; pfam08664 439292002061 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 439292002062 ATP binding site [chemical binding]; other site 439292002063 G-X-G motif; other site 439292002064 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 439292002065 active site 439292002066 homodimer interface [polypeptide binding]; other site 439292002067 homotetramer interface [polypeptide binding]; other site 439292002068 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 439292002069 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 439292002070 Aspartase; Region: Aspartase; cd01357 439292002071 active sites [active] 439292002072 tetramer interface [polypeptide binding]; other site 439292002073 succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family; Region: sdhC_b558_fam; TIGR02046 439292002074 Succinate:quinone oxidoreductase (SQR) Type B subfamily 1, transmembrane subunit; composed of proteins similar to Bacillus subtilis SQR. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Bacillus subtilis...; Region: SQR_TypeB_1_TM; cd03497 439292002075 putative Iron-sulfur protein interface [polypeptide binding]; other site 439292002076 proximal heme binding site [chemical binding]; other site 439292002077 distal heme binding site [chemical binding]; other site 439292002078 putative dimer interface [polypeptide binding]; other site 439292002079 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08641 439292002080 L-aspartate oxidase; Provisional; Region: PRK06175 439292002081 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 439292002082 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK08640 439292002083 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 439292002084 Transcriptional regulators [Transcription]; Region: MarR; COG1846 439292002085 MarR family; Region: MarR; pfam01047 439292002086 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 439292002087 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 439292002088 active site 439292002089 phosphorylation site [posttranslational modification] 439292002090 dimerization interface [polypeptide binding]; other site 439292002091 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292002092 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292002093 metal binding site [ion binding]; metal-binding site 439292002094 active site 439292002095 I-site; other site 439292002096 Response regulator receiver domain; Region: Response_reg; pfam00072 439292002097 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 439292002098 active site 439292002099 phosphorylation site [posttranslational modification] 439292002100 intermolecular recognition site; other site 439292002101 dimerization interface [polypeptide binding]; other site 439292002102 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 439292002103 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 439292002104 active site 439292002105 phosphorylation site [posttranslational modification] 439292002106 intermolecular recognition site; other site 439292002107 dimerization interface [polypeptide binding]; other site 439292002108 HAMP domain; Region: HAMP; pfam00672 439292002109 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 439292002110 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 439292002111 dimer interface [polypeptide binding]; other site 439292002112 phosphorylation site [posttranslational modification] 439292002113 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 439292002114 ATP binding site [chemical binding]; other site 439292002115 Mg2+ binding site [ion binding]; other site 439292002116 G-X-G motif; other site 439292002117 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 439292002118 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292002119 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 439292002120 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292002121 Coenzyme A binding pocket [chemical binding]; other site 439292002122 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 439292002123 ligand binding site [chemical binding]; other site 439292002124 active site 439292002125 UGI interface [polypeptide binding]; other site 439292002126 catalytic site [active] 439292002127 endonuclease VIII; Provisional; Region: PRK10445 439292002128 N-terminal domain of Escherichia coli Nei/endonuclease VIII and related DNA glycosylases; Region: EcNei-like_N; cd08965 439292002129 DNA binding site [nucleotide binding] 439292002130 catalytic residue [active] 439292002131 putative catalytic residues [active] 439292002132 H2TH interface [polypeptide binding]; other site 439292002133 intercalation triad [nucleotide binding]; other site 439292002134 substrate specificity determining residue; other site 439292002135 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 439292002136 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 439292002137 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 439292002138 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 439292002139 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 439292002140 S-adenosylmethionine binding site [chemical binding]; other site 439292002141 Protein of unknown function (DUF2922); Region: DUF2922; pfam11148 439292002142 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 439292002143 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 439292002144 anti sigma factor interaction site; other site 439292002145 regulatory phosphorylation site [posttranslational modification]; other site 439292002146 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 439292002147 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 439292002148 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 439292002149 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292002150 dimerization interface [polypeptide binding]; other site 439292002151 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292002152 dimer interface [polypeptide binding]; other site 439292002153 putative CheW interface [polypeptide binding]; other site 439292002154 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 439292002155 cytochrome c nitrite reductase, Fe-S protein; Region: cyt_nit_nrfC; TIGR03149 439292002156 4Fe-4S binding domain; Region: Fer4; pfam00037 439292002157 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 439292002158 ApbE family; Region: ApbE; pfam02424 439292002159 hopene-associated glycosyltransferase HpnB; Region: HpnB; TIGR03469 439292002160 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 439292002161 DXD motif; other site 439292002162 Dehydroquinase class II; Region: DHquinase_II; pfam01220 439292002163 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 439292002164 trimer interface [polypeptide binding]; other site 439292002165 active site 439292002166 dimer interface [polypeptide binding]; other site 439292002167 shikimate kinase; Reviewed; Region: aroK; PRK00131 439292002168 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 439292002169 ADP binding site [chemical binding]; other site 439292002170 magnesium binding site [ion binding]; other site 439292002171 putative shikimate binding site; other site 439292002172 Predicted small molecule binding protein (contains 3H domain) [General function prediction only]; Region: COG1827 439292002173 HTH domain; Region: HTH_11; pfam08279 439292002174 3H domain; Region: 3H; pfam02829 439292002175 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 439292002176 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 439292002177 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH5; cd08189 439292002178 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 439292002179 putative active site [active] 439292002180 metal binding site [ion binding]; metal-binding site 439292002181 Domain of unknown function (DUF1858); Region: DUF1858; pfam08984 439292002182 Uncharacterized conserved protein [Function unknown]; Region: COG2461 439292002183 Family of unknown function (DUF438); Region: DUF438; pfam04282 439292002184 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 439292002185 Domain of Unknown function (DUF542); Region: ScdA_N; pfam04405 439292002186 iron-sulfur cluster repair di-iron protein; Region: FeS_repair_RIC; TIGR03652 439292002187 Hemerythrin-like domain; Region: Hr-like; cd12108 439292002188 Fe binding site [ion binding]; other site 439292002189 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 439292002190 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 439292002191 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 439292002192 DNA binding residues [nucleotide binding] 439292002193 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 439292002194 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 439292002195 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 439292002196 active site residue [active] 439292002197 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 439292002198 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292002199 dimerization interface [polypeptide binding]; other site 439292002200 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 439292002201 dimer interface [polypeptide binding]; other site 439292002202 phosphorylation site [posttranslational modification] 439292002203 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 439292002204 ATP binding site [chemical binding]; other site 439292002205 Mg2+ binding site [ion binding]; other site 439292002206 G-X-G motif; other site 439292002207 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 439292002208 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 439292002209 active site 439292002210 phosphorylation site [posttranslational modification] 439292002211 intermolecular recognition site; other site 439292002212 dimerization interface [polypeptide binding]; other site 439292002213 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 439292002214 DNA binding site [nucleotide binding] 439292002215 PAS domain S-box; Region: sensory_box; TIGR00229 439292002216 PAS domain; Region: PAS; smart00091 439292002217 putative active site [active] 439292002218 heme pocket [chemical binding]; other site 439292002219 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292002220 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292002221 metal binding site [ion binding]; metal-binding site 439292002222 active site 439292002223 I-site; other site 439292002224 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 439292002225 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 439292002226 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292002227 Walker A/P-loop; other site 439292002228 ATP binding site [chemical binding]; other site 439292002229 Q-loop/lid; other site 439292002230 ABC transporter signature motif; other site 439292002231 Walker B; other site 439292002232 D-loop; other site 439292002233 H-loop/switch region; other site 439292002234 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 439292002235 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 439292002236 ligand binding site [chemical binding]; other site 439292002237 flexible hinge region; other site 439292002238 B12 binding domain; Region: B12-binding_2; pfam02607 439292002239 methyltransferase cognate corrinoid proteins, Methanosarcina family; Region: pyl_corrinoid; TIGR02370 439292002240 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cd02065 439292002241 B12 binding site [chemical binding]; other site 439292002242 Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation; Region: STAS_RsbR_RsbS_like; cd07041 439292002243 CHASE2 domain; Region: CHASE2; pfam05226 439292002244 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 439292002245 cyclase homology domain; Region: CHD; cd07302 439292002246 nucleotidyl binding site; other site 439292002247 metal binding site [ion binding]; metal-binding site 439292002248 dimer interface [polypeptide binding]; other site 439292002249 FecR protein; Region: FecR; pfam04773 439292002250 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 439292002251 Interdomain contacts; other site 439292002252 Cytokine receptor motif; other site 439292002253 NHL repeat; Region: NHL; pfam01436 439292002254 Protein of unknown function (DUF3307); Region: DUF3307; pfam11750 439292002255 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 439292002256 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 439292002257 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292002258 Zn2+ binding site [ion binding]; other site 439292002259 Mg2+ binding site [ion binding]; other site 439292002260 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 439292002261 Major Facilitator Superfamily; Region: MFS_1; pfam07690 439292002262 putative substrate translocation pore; other site 439292002263 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 439292002264 Glycerophosphodiester phosphodiesterase domain of Thermoanaerobacter tengcongensis and similar proteins; Region: GDPD_TtGDE_like; cd08563 439292002265 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 439292002266 active site 439292002267 catalytic site [active] 439292002268 metal binding site [ion binding]; metal-binding site 439292002269 dimer interface [polypeptide binding]; other site 439292002270 YpjP-like protein; Region: YpjP; pfam14005 439292002271 Nitrate and nitrite sensing; Region: NIT; pfam08376 439292002272 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292002273 dimerization interface [polypeptide binding]; other site 439292002274 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 439292002275 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 439292002276 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292002277 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292002278 metal binding site [ion binding]; metal-binding site 439292002279 active site 439292002280 I-site; other site 439292002281 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292002282 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 439292002283 ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydD; COG4988 439292002284 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292002285 Walker A/P-loop; other site 439292002286 ATP binding site [chemical binding]; other site 439292002287 Q-loop/lid; other site 439292002288 ABC transporter signature motif; other site 439292002289 Walker B; other site 439292002290 D-loop; other site 439292002291 H-loop/switch region; other site 439292002292 ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydC; COG4987 439292002293 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 439292002294 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 439292002295 Walker A/P-loop; other site 439292002296 ATP binding site [chemical binding]; other site 439292002297 Q-loop/lid; other site 439292002298 ABC transporter signature motif; other site 439292002299 Walker B; other site 439292002300 D-loop; other site 439292002301 H-loop/switch region; other site 439292002302 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 439292002303 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 439292002304 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 439292002305 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 439292002306 Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar...; Region: RHOD_Pyr_redox; cd01524 439292002307 active site residue [active] 439292002308 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cl00436 439292002309 CPxP motif; other site 439292002310 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 439292002311 FMN binding site [chemical binding]; other site 439292002312 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 439292002313 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 439292002314 nucleoside/Zn binding site; other site 439292002315 dimer interface [polypeptide binding]; other site 439292002316 catalytic motif [active] 439292002317 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 439292002318 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292002319 dimerization interface [polypeptide binding]; other site 439292002320 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292002321 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292002322 metal binding site [ion binding]; metal-binding site 439292002323 active site 439292002324 I-site; other site 439292002325 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292002326 MoxR-like ATPases [General function prediction only]; Region: COG0714 439292002327 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 439292002328 Walker A motif; other site 439292002329 ATP binding site [chemical binding]; other site 439292002330 Walker B motif; other site 439292002331 arginine finger; other site 439292002332 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 439292002333 Protein of unknown function DUF58; Region: DUF58; pfam01882 439292002334 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 439292002335 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 439292002336 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 439292002337 GMP synthase; Reviewed; Region: guaA; PRK00074 439292002338 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 439292002339 AMP/PPi binding site [chemical binding]; other site 439292002340 candidate oxyanion hole; other site 439292002341 catalytic triad [active] 439292002342 potential glutamine specificity residues [chemical binding]; other site 439292002343 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 439292002344 ATP Binding subdomain [chemical binding]; other site 439292002345 Ligand Binding sites [chemical binding]; other site 439292002346 Dimerization subdomain; other site 439292002347 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 439292002348 FeoA domain; Region: FeoA; pfam04023 439292002349 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 439292002350 ferrous iron transporter FeoB; Region: feoB; TIGR00437 439292002351 G1 box; other site 439292002352 GTP/Mg2+ binding site [chemical binding]; other site 439292002353 G2 box; other site 439292002354 Switch I region; other site 439292002355 G3 box; other site 439292002356 Switch II region; other site 439292002357 G4 box; other site 439292002358 G5 box; other site 439292002359 Nucleoside recognition; Region: Gate; pfam07670 439292002360 Nucleoside recognition; Region: Gate; pfam07670 439292002361 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 439292002362 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 439292002363 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 439292002364 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 439292002365 Walker A motif; other site 439292002366 ATP binding site [chemical binding]; other site 439292002367 Walker B motif; other site 439292002368 arginine finger; other site 439292002369 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 439292002370 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 439292002371 Walker A motif; other site 439292002372 ATP binding site [chemical binding]; other site 439292002373 Walker B motif; other site 439292002374 arginine finger; other site 439292002375 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 439292002376 Protein of unknown function (DUF1499); Region: DUF1499; pfam07386 439292002377 NETI protein; Region: NETI; pfam14044 439292002378 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 439292002379 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 439292002380 ATP-grasp domain; Region: ATP-grasp; pfam02222 439292002381 adenylosuccinate lyase; Provisional; Region: PRK07492 439292002382 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 439292002383 tetramer interface [polypeptide binding]; other site 439292002384 active site 439292002385 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 439292002386 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 439292002387 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 439292002388 ATP binding site [chemical binding]; other site 439292002389 active site 439292002390 substrate binding site [chemical binding]; other site 439292002391 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; pfam02700 439292002392 phosphoribosylformylglycinamidine synthase I; Provisional; Region: PRK03619 439292002393 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 439292002394 putative active site [active] 439292002395 catalytic triad [active] 439292002396 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 439292002397 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 439292002398 dimerization interface [polypeptide binding]; other site 439292002399 ATP binding site [chemical binding]; other site 439292002400 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 439292002401 dimerization interface [polypeptide binding]; other site 439292002402 ATP binding site [chemical binding]; other site 439292002403 amidophosphoribosyltransferase; Provisional; Region: PRK07631 439292002404 Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the...; Region: GPATase_N; cd00715 439292002405 active site 439292002406 tetramer interface [polypeptide binding]; other site 439292002407 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 439292002408 active site 439292002409 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 439292002410 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 439292002411 dimerization interface [polypeptide binding]; other site 439292002412 putative ATP binding site [chemical binding]; other site 439292002413 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 439292002414 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 439292002415 active site 439292002416 substrate binding site [chemical binding]; other site 439292002417 cosubstrate binding site; other site 439292002418 catalytic site [active] 439292002419 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 439292002420 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 439292002421 purine monophosphate binding site [chemical binding]; other site 439292002422 dimer interface [polypeptide binding]; other site 439292002423 putative catalytic residues [active] 439292002424 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 439292002425 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 439292002426 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 439292002427 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 439292002428 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 439292002429 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 439292002430 FOG: CBS domain [General function prediction only]; Region: COG0517 439292002431 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the BON (bacterial OsmY and nodulation domain) domain. BON is a putative phospholipid-binding domain found in a family of osmotic shock protection...; Region: CBS_pair_BON_assoc; cd04586 439292002432 YcxB-like protein; Region: YcxB; pfam14317 439292002433 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 439292002434 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 439292002435 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 439292002436 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 439292002437 ATP-grasp domain; Region: ATP-grasp_4; cl17255 439292002438 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 439292002439 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 439292002440 metal binding site [ion binding]; metal-binding site 439292002441 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 439292002442 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 439292002443 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 439292002444 GAF domain; Region: GAF_3; pfam13492 439292002445 Histidine kinase; Region: His_kinase; pfam06580 439292002446 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 439292002447 ATP binding site [chemical binding]; other site 439292002448 Mg2+ binding site [ion binding]; other site 439292002449 G-X-G motif; other site 439292002450 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 439292002451 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 439292002452 active site 439292002453 phosphorylation site [posttranslational modification] 439292002454 intermolecular recognition site; other site 439292002455 dimerization interface [polypeptide binding]; other site 439292002456 LytTr DNA-binding domain; Region: LytTR; smart00850 439292002457 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 439292002458 Carbon starvation protein CstA; Region: CstA; pfam02554 439292002459 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 439292002460 Carbon starvation protein CstA; Region: CstA; pfam02554 439292002461 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 439292002462 Uncharacterized protein conserved in bacteria (DUF2200); Region: DUF2200; pfam09966 439292002463 Adenine deaminase [Nucleotide transport and metabolism]; Region: AdeC; COG1001 439292002464 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 439292002465 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 439292002466 active site 439292002467 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 439292002468 Protein of unknown function (DUF3048); Region: DUF3048; pfam11258 439292002469 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4496 439292002470 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 439292002471 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292002472 Walker A/P-loop; other site 439292002473 ATP binding site [chemical binding]; other site 439292002474 Q-loop/lid; other site 439292002475 ABC transporter signature motif; other site 439292002476 Walker B; other site 439292002477 D-loop; other site 439292002478 H-loop/switch region; other site 439292002479 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 439292002480 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 439292002481 TM-ABC transporter signature motif; other site 439292002482 Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_uncharacterized_transporter; cd06325 439292002483 zinc binding site [ion binding]; other site 439292002484 putative ligand binding site [chemical binding]; other site 439292002485 peroxiredoxin; Provisional; Region: PRK13189 439292002486 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 439292002487 dimer interface [polypeptide binding]; other site 439292002488 decamer (pentamer of dimers) interface [polypeptide binding]; other site 439292002489 catalytic triad [active] 439292002490 phenylalanyl-tRNA synthetase subunit alpha; Provisional; Region: pheS; PRK04172 439292002491 BCCT family transporter; Region: BCCT; pfam02028 439292002492 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 439292002493 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 439292002494 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; smart00833 439292002495 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 439292002496 FAD-NAD(P)-binding; Region: NAD_binding_9; pfam13454 439292002497 L-lysine 6-monooxygenase (NADPH-requiring); Region: K_oxygenase; pfam13434 439292002498 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 439292002499 Cytochrome P450; Region: p450; cl12078 439292002500 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_b2; cd09204 439292002501 PLD-like domain; Region: PLDc_2; pfam13091 439292002502 putative homodimer interface [polypeptide binding]; other site 439292002503 putative active site [active] 439292002504 catalytic site [active] 439292002505 DEAD-like helicases superfamily; Region: DEXDc; smart00487 439292002506 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 439292002507 ATP binding site [chemical binding]; other site 439292002508 putative Mg++ binding site [ion binding]; other site 439292002509 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 439292002510 nucleotide binding region [chemical binding]; other site 439292002511 ATP-binding site [chemical binding]; other site 439292002512 Domain of unknown function (DUF3427); Region: DUF3427; pfam11907 439292002513 The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic...; Region: MutT_pyrophosphohydrolase; cd03425 439292002514 active site 439292002515 8-oxo-dGMP binding site [chemical binding]; other site 439292002516 nudix motif; other site 439292002517 metal binding site [ion binding]; metal-binding site 439292002518 Protein of unknown function (DUF1648); Region: DUF1648; pfam07853 439292002519 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 439292002520 dimerization interface [polypeptide binding]; other site 439292002521 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292002522 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292002523 dimer interface [polypeptide binding]; other site 439292002524 putative CheW interface [polypeptide binding]; other site 439292002525 PAS domain; Region: PAS_9; pfam13426 439292002526 PAS domain S-box; Region: sensory_box; TIGR00229 439292002527 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 439292002528 putative active site [active] 439292002529 heme pocket [chemical binding]; other site 439292002530 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 439292002531 PAS domain; Region: PAS_9; pfam13426 439292002532 putative active site [active] 439292002533 heme pocket [chemical binding]; other site 439292002534 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292002535 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292002536 metal binding site [ion binding]; metal-binding site 439292002537 active site 439292002538 I-site; other site 439292002539 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292002540 PAS domain S-box; Region: sensory_box; TIGR00229 439292002541 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 439292002542 putative active site [active] 439292002543 heme pocket [chemical binding]; other site 439292002544 PAS domain S-box; Region: sensory_box; TIGR00229 439292002545 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 439292002546 PAS domain; Region: PAS_9; pfam13426 439292002547 putative active site [active] 439292002548 heme pocket [chemical binding]; other site 439292002549 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292002550 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292002551 metal binding site [ion binding]; metal-binding site 439292002552 active site 439292002553 I-site; other site 439292002554 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292002555 Zn2+ binding site [ion binding]; other site 439292002556 Mg2+ binding site [ion binding]; other site 439292002557 PcrB family; Region: PcrB; pfam01884 439292002558 PcrB_like proteins. One member of this family, a protein from Archaeoglobus fulgidus, has been characterized as a (S)-3-O-geranylgeranylglyceryl phosphate synthase (AfGGGPS). AfGGGPS catalyzes the formation of an ether linkage between...; Region: PcrB_like; cd02812 439292002559 substrate binding site [chemical binding]; other site 439292002560 putative active site [active] 439292002561 dimer interface [polypeptide binding]; other site 439292002562 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 439292002563 Part of AAA domain; Region: AAA_19; pfam13245 439292002564 Family description; Region: UvrD_C_2; pfam13538 439292002565 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 439292002566 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 439292002567 nucleotide binding pocket [chemical binding]; other site 439292002568 K-X-D-G motif; other site 439292002569 catalytic site [active] 439292002570 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 439292002571 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 439292002572 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 439292002573 Dimer interface [polypeptide binding]; other site 439292002574 N-terminal repeat domain of CamS sex pheromone cAM373 precursor; Region: CamS_repeat_1; cd13441 439292002575 putative dimer interface [polypeptide binding]; other site 439292002576 CamS sex pheromone cAM373 precursor; Region: CamS; pfam07537 439292002577 C-terminal repeat domain of CamS sex pheromone cAM373 precursor; Region: CamS_repeat_2; cd13440 439292002578 putative dimer interface [polypeptide binding]; other site 439292002579 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 439292002580 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 439292002581 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 439292002582 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 439292002583 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 439292002584 GatB domain; Region: GatB_Yqey; pfam02637 439292002585 putative lipid kinase; Reviewed; Region: PRK13337 439292002586 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 439292002587 Bacterial protein of unknown function (DUF948); Region: DUF948; pfam06103 439292002588 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 439292002589 intersubunit interface [polypeptide binding]; other site 439292002590 active site 439292002591 catalytic residue [active] 439292002592 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 439292002593 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 439292002594 tetramer interface [polypeptide binding]; other site 439292002595 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292002596 catalytic residue [active] 439292002597 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 439292002598 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 439292002599 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 439292002600 P loop; other site 439292002601 Nucleotide binding site [chemical binding]; other site 439292002602 DTAP/Switch II; other site 439292002603 Switch I; other site 439292002604 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 439292002605 DTAP/Switch II; other site 439292002606 Switch I; other site 439292002607 arsenical pump membrane protein; Provisional; Region: PRK15445 439292002608 Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a...; Region: ArsB_permease; cd01118 439292002609 transmembrane helices; other site 439292002610 Predicted NAD/FAD-dependent oxidoreductase [General function prediction only]; Region: COG3380 439292002611 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 439292002612 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 439292002613 TRAM domain; Region: TRAM; pfam01938 439292002614 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 439292002615 S-adenosylmethionine binding site [chemical binding]; other site 439292002616 Bromovirus movement protein; Region: Bromo_MP; pfam01573 439292002617 Type II restriction enzyme, methylase subunits [Defense mechanisms]; Region: COG1002 439292002618 Methyltransferase domain; Region: Methyltransf_26; pfam13659 439292002619 DEAD-like helicases superfamily; Region: DEXDc; smart00487 439292002620 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 439292002621 ATP binding site [chemical binding]; other site 439292002622 putative Mg++ binding site [ion binding]; other site 439292002623 T5orf172 domain; Region: T5orf172; pfam10544 439292002624 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria and archaea; Region: GIY-YIG_unchar_2; cd10447 439292002625 GIY-YIG motif/motif A; other site 439292002626 putative active site [active] 439292002627 putative metal binding site [ion binding]; other site 439292002628 Domain of unknown function (DUF4357); Region: DUF4357; pfam14267 439292002629 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 439292002630 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 439292002631 DNA binding residues [nucleotide binding] 439292002632 Protein of unknown function (DUF2800); Region: DUF2800; pfam10926 439292002633 Protein of unknown function (DUF2815); Region: DUF2815; pfam10991 439292002634 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_A; cd08642 439292002635 DNA binding site [nucleotide binding] 439292002636 active site 439292002637 catalytic site [active] 439292002638 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 439292002639 BRO family, N-terminal domain; Region: Bro-N; smart01040 439292002640 Phage antirepressor protein KilAC domain; Region: ANT; pfam03374 439292002641 Virulence-associated protein E; Region: VirE; pfam05272 439292002642 VRR-NUC domain; Region: VRR_NUC; pfam08774 439292002643 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 439292002644 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 439292002645 ATP binding site [chemical binding]; other site 439292002646 putative Mg++ binding site [ion binding]; other site 439292002647 Protein of unknown function (DUF1492); Region: DUF1492; pfam07374 439292002648 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 439292002649 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; cl17393 439292002650 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 439292002651 ParB-like nuclease domain; Region: ParBc; pfam02195 439292002652 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 439292002653 DNA methylase; Region: N6_N4_Mtase; pfam01555 439292002654 Protein of unknown function (DUF4065); Region: DUF4065; pfam13274 439292002655 Phage terminase, small subunit; Region: Terminase_4; pfam05119 439292002656 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl17442 439292002657 Hom_end-associated Hint; Region: Hom_end_hint; pfam05203 439292002658 Phage Terminase; Region: Terminase_1; pfam03354 439292002659 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 439292002660 Phage-related protein [Function unknown]; Region: COG4695 439292002661 Phage portal protein; Region: Phage_portal; pfam04860 439292002662 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 439292002663 oligomer interface [polypeptide binding]; other site 439292002664 active site residues [active] 439292002665 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 439292002666 Phage capsid family; Region: Phage_capsid; pfam05065 439292002667 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 439292002668 oligomerization interface [polypeptide binding]; other site 439292002669 Phage head-tail joining protein; Region: Phage_H_T_join; pfam05521 439292002670 phage protein, HK97 gp10 family; Region: phge_HK97_gp10; TIGR01725 439292002671 phage major tail protein, phi13 family; Region: maj_tail_phi13; TIGR01603 439292002672 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 439292002673 Phage-related protein [Function unknown]; Region: COG4722 439292002674 Phage tail protein; Region: Sipho_tail; cl17486 439292002675 Prophage endopeptidase tail; Region: Prophage_tail; cl12123 439292002676 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 439292002677 Holin family; Region: Phage_holin_4; pfam05105 439292002678 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 439292002679 amidase catalytic site [active] 439292002680 Zn binding residues [ion binding]; other site 439292002681 substrate binding site [chemical binding]; other site 439292002682 Sporulation related domain; Region: SPOR; pfam05036 439292002683 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 439292002684 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 439292002685 catalytic residues [active] 439292002686 catalytic nucleophile [active] 439292002687 Recombinase; Region: Recombinase; pfam07508 439292002688 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 439292002689 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 439292002690 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 439292002691 catalytic residues [active] 439292002692 catalytic nucleophile [active] 439292002693 Recombinase; Region: Recombinase; pfam07508 439292002694 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 439292002695 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 439292002696 catalytic residues [active] 439292002697 catalytic nucleophile [active] 439292002698 Recombinase; Region: Recombinase; pfam07508 439292002699 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 439292002700 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 439292002701 catalytic residues [active] 439292002702 catalytic nucleophile [active] 439292002703 Recombinase; Region: Recombinase; pfam07508 439292002704 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 439292002705 Interdomain contacts; other site 439292002706 Cytokine receptor motif; other site 439292002707 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 439292002708 S-layer homology domain; Region: SLH; pfam00395 439292002709 S-layer homology domain; Region: SLH; pfam00395 439292002710 S-layer homology domain; Region: SLH; pfam00395 439292002711 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 439292002712 The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold; Region: PBP2_Ylib_like; cd08499 439292002713 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 439292002714 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 439292002715 active site 439292002716 metal binding site [ion binding]; metal-binding site 439292002717 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 439292002718 S-layer homology domain; Region: SLH; pfam00395 439292002719 S-layer homology domain; Region: SLH; pfam00395 439292002720 Predicted hydrolases of the HAD superfamily [General function prediction only]; Region: Cof; COG0561 439292002721 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 439292002722 active site 439292002723 motif I; other site 439292002724 motif II; other site 439292002725 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 439292002726 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292002727 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292002728 dimer interface [polypeptide binding]; other site 439292002729 putative CheW interface [polypeptide binding]; other site 439292002730 Cache domain; Region: Cache_1; pfam02743 439292002731 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 439292002732 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 439292002733 Probable transposase; Region: OrfB_IS605; pfam01385 439292002734 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 439292002735 S-layer homology domain; Region: SLH; pfam00395 439292002736 S-layer homology domain; Region: SLH; pfam00395 439292002737 S-layer homology domain; Region: SLH; pfam00395 439292002738 S-layer homology domain; Region: SLH; pfam00395 439292002739 S-layer homology domain; Region: SLH; pfam00395 439292002740 S-layer homology domain; Region: SLH; pfam00395 439292002741 putative transposase OrfB; Reviewed; Region: PHA02517 439292002742 HTH-like domain; Region: HTH_21; pfam13276 439292002743 Integrase core domain; Region: rve; pfam00665 439292002744 Integrase core domain; Region: rve_2; pfam13333 439292002745 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 439292002746 Transposase; Region: HTH_Tnp_1; pfam01527 439292002747 Bacterial Ig-like domain (group 4); Region: Big_4; pfam07532 439292002748 Bacterial Ig-like domain (group 4); Region: Big_4; pfam07532 439292002749 S-layer homology domain; Region: SLH; pfam00395 439292002750 S-layer homology domain; Region: SLH; pfam00395 439292002751 S-layer homology domain; Region: SLH; pfam00395 439292002752 Predicted membrane protein [Function unknown]; Region: COG4640 439292002753 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 439292002754 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 439292002755 Double zinc ribbon; Region: DZR; pfam12773 439292002756 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 439292002757 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 439292002758 S-layer homology domain; Region: SLH; pfam00395 439292002759 S-layer homology domain; Region: SLH; pfam00395 439292002760 S-layer homology domain; Region: SLH; pfam00395 439292002761 Predicted membrane protein [Function unknown]; Region: COG4640 439292002762 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 439292002763 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 439292002764 Transposase; Region: HTH_Tnp_1; pfam01527 439292002765 putative transposase OrfB; Reviewed; Region: PHA02517 439292002766 HTH-like domain; Region: HTH_21; pfam13276 439292002767 Integrase core domain; Region: rve; pfam00665 439292002768 Integrase core domain; Region: rve_2; pfam13333 439292002769 Double zinc ribbon; Region: DZR; pfam12773 439292002770 Uncharacterized protein family UPF0547; Region: UPF0547; pfam10571 439292002771 Double zinc ribbon; Region: DZR; pfam12773 439292002772 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 439292002773 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 439292002774 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 439292002775 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 439292002776 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 439292002777 Glycosaminoglycan (GAG) polysaccharide lyase family. This family consists of a group of secreted bacterial lyase enzymes capable of acting on glycosaminoglycans, such as hyaluronan and chondroitin, in the extracellular matrix of host tissues; Region: GAG_Lyase; cd01083 439292002778 substrate binding site [chemical binding]; other site 439292002779 catalytic residues [active] 439292002780 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 439292002781 S-layer homology domain; Region: SLH; pfam00395 439292002782 S-layer homology domain; Region: SLH; pfam00395 439292002783 S-layer homology domain; Region: SLH; pfam00395 439292002784 S-layer homology domain; Region: SLH; pfam00395 439292002785 S-layer homology domain; Region: SLH; pfam00395 439292002786 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 439292002787 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 439292002788 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292002789 Zn2+ binding site [ion binding]; other site 439292002790 Mg2+ binding site [ion binding]; other site 439292002791 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 439292002792 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 439292002793 Peptidase S8 family domain in Subtilisin proteins; Region: Peptidases_S8_Subtilisin_subset; cd07477 439292002794 active site 439292002795 catalytic residues [active] 439292002796 S-layer homology domain; Region: SLH; pfam00395 439292002797 S-layer homology domain; Region: SLH; pfam00395 439292002798 S-layer homology domain; Region: SLH; pfam00395 439292002799 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 439292002800 NlpC/P60 family; Region: NLPC_P60; pfam00877 439292002801 Predicted membrane protein [Function unknown]; Region: COG2855 439292002802 LysR transcriptional regulator; Provisional; Region: rbcR; CHL00180 439292002803 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 439292002804 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 439292002805 putative dimerization interface [polypeptide binding]; other site 439292002806 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 439292002807 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 439292002808 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 439292002809 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 439292002810 putative active site [active] 439292002811 putative metal binding site [ion binding]; other site 439292002812 Capsule biosynthesis CapC; Region: Caps_synth_CapC; pfam14102 439292002813 poly-gamma-glutamate synthase PgsB/CapB; Region: poly_gGlu_PgsB; TIGR04012 439292002814 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 439292002815 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 439292002816 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 439292002817 Probable transposase; Region: OrfB_IS605; pfam01385 439292002818 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 439292002819 Helix-turn-helix domain; Region: HTH_17; pfam12728 439292002820 histidyl-tRNA synthetase; Provisional; Region: PRK12420 439292002821 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 439292002822 dimer interface [polypeptide binding]; other site 439292002823 motif 1; other site 439292002824 active site 439292002825 motif 2; other site 439292002826 motif 3; other site 439292002827 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 439292002828 anticodon binding site; other site 439292002829 S-layer homology domain; Region: SLH; pfam00395 439292002830 S-layer homology domain; Region: SLH; pfam00395 439292002831 Probable transposase; Region: OrfB_IS605; pfam01385 439292002832 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 439292002833 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 439292002834 Response regulator receiver domain; Region: Response_reg; pfam00072 439292002835 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 439292002836 active site 439292002837 phosphorylation site [posttranslational modification] 439292002838 intermolecular recognition site; other site 439292002839 dimerization interface [polypeptide binding]; other site 439292002840 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 439292002841 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 439292002842 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 439292002843 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 439292002844 dimer interface [polypeptide binding]; other site 439292002845 phosphorylation site [posttranslational modification] 439292002846 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 439292002847 ATP binding site [chemical binding]; other site 439292002848 Mg2+ binding site [ion binding]; other site 439292002849 G-X-G motif; other site 439292002850 Response regulator receiver domain; Region: Response_reg; pfam00072 439292002851 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 439292002852 active site 439292002853 phosphorylation site [posttranslational modification] 439292002854 intermolecular recognition site; other site 439292002855 dimerization interface [polypeptide binding]; other site 439292002856 Histidine kinase; Region: His_kinase; pfam06580 439292002857 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 439292002858 ATP binding site [chemical binding]; other site 439292002859 Mg2+ binding site [ion binding]; other site 439292002860 G-X-G motif; other site 439292002861 Domain of unknown function DUF11; Region: DUF11; pfam01345 439292002862 conserved repeat domain; Region: B_ant_repeat; TIGR01451 439292002863 conserved repeat domain; Region: B_ant_repeat; TIGR01451 439292002864 conserved repeat domain; Region: B_ant_repeat; TIGR01451 439292002865 conserved repeat domain; Region: B_ant_repeat; TIGR01451 439292002866 conserved repeat domain; Region: B_ant_repeat; TIGR01451 439292002867 conserved repeat domain; Region: B_ant_repeat; TIGR01451 439292002868 conserved repeat domain; Region: B_ant_repeat; TIGR01451 439292002869 conserved repeat domain; Region: B_ant_repeat; TIGR01451 439292002870 conserved repeat domain; Region: B_ant_repeat; TIGR01451 439292002871 Cna protein B-type domain; Region: Cna_B; pfam05738 439292002872 Cache domain; Region: Cache_1; pfam02743 439292002873 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292002874 dimerization interface [polypeptide binding]; other site 439292002875 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292002876 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292002877 dimer interface [polypeptide binding]; other site 439292002878 putative CheW interface [polypeptide binding]; other site 439292002879 Transposase; Region: HTH_Tnp_1; pfam01527 439292002880 Winged helix-turn helix; Region: HTH_29; pfam13551 439292002881 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]; Region: COG3947 439292002882 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 439292002883 active site 439292002884 phosphorylation site [posttranslational modification] 439292002885 intermolecular recognition site; other site 439292002886 dimerization interface [polypeptide binding]; other site 439292002887 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 439292002888 Cache domain; Region: Cache_1; pfam02743 439292002889 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 439292002890 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292002891 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292002892 metal binding site [ion binding]; metal-binding site 439292002893 active site 439292002894 I-site; other site 439292002895 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292002896 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292002897 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292002898 dimer interface [polypeptide binding]; other site 439292002899 putative CheW interface [polypeptide binding]; other site 439292002900 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the...; Region: Sortase_A_1; cd06165 439292002901 active site 439292002902 catalytic site [active] 439292002903 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]; Region: COG3947 439292002904 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 439292002905 active site 439292002906 phosphorylation site [posttranslational modification] 439292002907 intermolecular recognition site; other site 439292002908 dimerization interface [polypeptide binding]; other site 439292002909 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 439292002910 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 439292002911 Uncharacterized protein with SCP/PR1 domains [Function unknown]; Region: COG2340 439292002912 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 439292002913 Thymidine kinase from herpesvirus; Region: Herpes_TK; cl17264 439292002914 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 439292002915 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 439292002916 DXD motif; other site 439292002917 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 439292002918 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 439292002919 substrate binding site [chemical binding]; other site 439292002920 dimer interface [polypeptide binding]; other site 439292002921 ATP binding site [chemical binding]; other site 439292002922 Phosphotransferase enzyme family; Region: APH; pfam01636 439292002923 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 439292002924 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 439292002925 amidase catalytic site [active] 439292002926 Zn binding residues [ion binding]; other site 439292002927 substrate binding site [chemical binding]; other site 439292002928 Sporulation related domain; Region: SPOR; pfam05036 439292002929 DctM-like transporters; Region: DctM; pfam06808 439292002930 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 439292002931 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 439292002932 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 439292002933 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 439292002934 allantoate amidohydrolase; Reviewed; Region: PRK09290 439292002935 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 439292002936 active site 439292002937 metal binding site [ion binding]; metal-binding site 439292002938 dimer interface [polypeptide binding]; other site 439292002939 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 439292002940 GAF domain; Region: GAF_3; pfam13492 439292002941 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 439292002942 Transcriptional antiterminator [Transcription]; Region: BglG; COG3711 439292002943 PTS_IIB_bgl_like: the PTS (phosphotransferase system) IIB domain of a family of sensory systems composed of a membrane-bound sugar-sensor (similar to BglF) and a transcription antiterminator (similar to BglG) which regulate expression of genes involved...; Region: PTS_IIB_bgl_like; cd05568 439292002944 active site 439292002945 P-loop; other site 439292002946 phosphorylation site [posttranslational modification] 439292002947 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cl00163 439292002948 active site 439292002949 phosphorylation site [posttranslational modification] 439292002950 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 439292002951 active site 439292002952 phosphorylation site [posttranslational modification] 439292002953 PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a...; Region: PTS_IIB_ascorbate; cd05563 439292002954 active site 439292002955 P-loop; other site 439292002956 phosphorylation site [posttranslational modification] 439292002957 PTS system ascorbate-specific transporter subunit IIC; Reviewed; Region: ulaA; PRK09410 439292002958 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 439292002959 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 439292002960 active site 439292002961 motif I; other site 439292002962 motif II; other site 439292002963 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 439292002964 Transcriptional regulators [Transcription]; Region: PurR; COG1609 439292002965 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 439292002966 DNA binding site [nucleotide binding] 439292002967 domain linker motif; other site 439292002968 Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs; Region: PBP1_Qymf_like; cd06291 439292002969 dimerization interface [polypeptide binding]; other site 439292002970 ligand binding site [chemical binding]; other site 439292002971 sodium binding site [ion binding]; other site 439292002972 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 439292002973 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 439292002974 substrate binding site [chemical binding]; other site 439292002975 dimer interface [polypeptide binding]; other site 439292002976 ATP binding site [chemical binding]; other site 439292002977 D-ribose pyranase; Provisional; Region: PRK11797 439292002978 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 439292002979 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 439292002980 Walker A/P-loop; other site 439292002981 ATP binding site [chemical binding]; other site 439292002982 Q-loop/lid; other site 439292002983 ABC transporter signature motif; other site 439292002984 Walker B; other site 439292002985 D-loop; other site 439292002986 H-loop/switch region; other site 439292002987 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 439292002988 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 439292002989 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 439292002990 TM-ABC transporter signature motif; other site 439292002991 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 439292002992 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 439292002993 ligand binding site [chemical binding]; other site 439292002994 dimerization interface [polypeptide binding]; other site 439292002995 Predicted transcriptional regulators [Transcription]; Region: COG1695 439292002996 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 439292002997 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 439292002998 PAS fold; Region: PAS_3; pfam08447 439292002999 putative active site [active] 439292003000 heme pocket [chemical binding]; other site 439292003001 PAS fold; Region: PAS_4; pfam08448 439292003002 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; cl02459 439292003003 putative active site [active] 439292003004 heme pocket [chemical binding]; other site 439292003005 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292003006 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292003007 metal binding site [ion binding]; metal-binding site 439292003008 active site 439292003009 I-site; other site 439292003010 AhpC/TSA antioxidant enzyme; Region: AhpC-TSA_2; pfam13911 439292003011 Transposase IS200 like; Region: Y1_Tnp; pfam01797 439292003012 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 439292003013 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 439292003014 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 439292003015 catalytic residues [active] 439292003016 Predicted dehydrogenase [General function prediction only]; Region: COG0579 439292003017 hydroxyglutarate oxidase; Provisional; Region: PRK11728 439292003018 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 439292003019 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 439292003020 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 439292003021 Uncharacterized protein with conserved CXXC pairs [Function unknown]; Region: COG3862 439292003022 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 439292003023 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 439292003024 DNA binding residues [nucleotide binding] 439292003025 dimerization interface [polypeptide binding]; other site 439292003026 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 439292003027 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 439292003028 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 439292003029 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 439292003030 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 439292003031 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 439292003032 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 439292003033 putative substrate binding site [chemical binding]; other site 439292003034 putative ATP binding site [chemical binding]; other site 439292003035 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional; Region: PRK09765 439292003036 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 439292003037 active site 439292003038 phosphorylation site [posttranslational modification] 439292003039 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 439292003040 active site 439292003041 P-loop; other site 439292003042 phosphorylation site [posttranslational modification] 439292003043 Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism]; Region: FruA; COG1299 439292003044 Demethylmenaquinone methyltransferase [Coenzyme metabolism]; Region: MenG; COG0684 439292003045 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 439292003046 active site 439292003047 catalytic triad [active] 439292003048 oxyanion hole [active] 439292003049 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 439292003050 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292003051 Walker A/P-loop; other site 439292003052 ATP binding site [chemical binding]; other site 439292003053 Q-loop/lid; other site 439292003054 ABC transporter signature motif; other site 439292003055 Walker B; other site 439292003056 D-loop; other site 439292003057 H-loop/switch region; other site 439292003058 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 439292003059 ABC-type transport system involved in multi-copper enzyme maturation, permease component [General function prediction only]; Region: NosY; COG1277 439292003060 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481 439292003061 Dihydroxyacetone kinase [Carbohydrate transport and metabolism]; Region: DAK1; COG2376 439292003062 dihydroxyacetone kinase, phosphoprotein-dependent, L subunit; Region: dha_L_ycgS; TIGR02365 439292003063 phosphotransferase mannnose-specific family component IIA; Provisional; Region: PRK14484 439292003064 probable dihydroxyacetone kinase regulator; Region: DHAK_reg; TIGR02366 439292003065 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292003066 Transcriptional regulator C-terminal region; Region: TetR_C_8; pfam14278 439292003067 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481; cl10557 439292003068 Dihydroxyacetone kinase [Carbohydrate transport and metabolism]; Region: DAK1; COG2376 439292003069 S-layer homology domain; Region: SLH; pfam00395 439292003070 S-layer homology domain; Region: SLH; pfam00395 439292003071 Uncharacterized protein with SCP/PR1 domains [Function unknown]; Region: COG2340 439292003072 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 439292003073 Domains similar to the eukaryotic reeler domain and bacterial cohesins; Region: Reeler_cohesin_like; cl14606 439292003074 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 439292003075 N-terminal domain interface [polypeptide binding]; other site 439292003076 substrate binding pocket (H-site) [chemical binding]; other site 439292003077 Putative Ig domain; Region: He_PIG; pfam05345 439292003078 Bacterial Ig-like domain (group 4); Region: Big_4; pfam07532 439292003079 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 439292003080 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 439292003081 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 439292003082 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 439292003083 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 439292003084 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 439292003085 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 439292003086 N-terminal Early set domain, a glycogen binding domain, associated with the catalytic domain of AMP-activated protein kinase beta subunit; Region: E_set_AMPKbeta_like_N; cd02859 439292003087 glycogen binding site [chemical binding]; other site 439292003088 N-terminal Early set domain, a glycogen binding domain, associated with the catalytic domain of AMP-activated protein kinase beta subunit; Region: E_set_AMPKbeta_like_N; cd02859 439292003089 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 439292003090 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 439292003091 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 439292003092 metal ion-dependent adhesion site (MIDAS); other site 439292003093 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 439292003094 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 439292003095 Predicted integral membrane protein [Function unknown]; Region: COG5652 439292003096 Peptidase S8 family domain in Streptococcal C5a peptidases; Region: Peptidases_S8_C5a_Peptidase; cd07475 439292003097 putative active site [active] 439292003098 catalytic triad [active] 439292003099 PA_C5a_like: Protease-associated domain containing proteins like Streptococcus pyogenes C5a peptidase. This group contains various PA domain-containing proteins similar to S. pyogenes C5a, including, i) Vpr, a minor extracellular serine protease from...; Region: PA_C5a_like; cd02133 439292003100 PA/protease domain interface [polypeptide binding]; other site 439292003101 putative integrin binding motif; other site 439292003102 Peptidase S8 family domain in Streptococcal C5a peptidases; Region: Peptidases_S8_C5a_Peptidase; cd07475 439292003103 Fn3-like domain (DUF1034); Region: DUF1034; pfam06280 439292003104 S-layer homology domain; Region: SLH; pfam00395 439292003105 S-layer homology domain; Region: SLH; pfam00395 439292003106 S-layer homology domain; Region: SLH; pfam00395 439292003107 Beta-glucanase/Beta-glucan synthetase [Carbohydrate transport and metabolism]; Region: SKN1; COG2273 439292003108 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 439292003109 active site 439292003110 catalytic residues [active] 439292003111 S-layer homology domain; Region: SLH; pfam00395 439292003112 S-layer homology domain; Region: SLH; pfam00395 439292003113 S-layer homology domain; Region: SLH; pfam00395 439292003114 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 439292003115 classical (c) SDRs; Region: SDR_c; cd05233 439292003116 NAD(P) binding site [chemical binding]; other site 439292003117 active site 439292003118 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 439292003119 classical (c) SDRs; Region: SDR_c; cd05233 439292003120 NAD(P) binding site [chemical binding]; other site 439292003121 active site 439292003122 Bacterial SNF2 helicase associated; Region: SNF2_assoc; pfam08455 439292003123 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 439292003124 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 439292003125 ATP binding site [chemical binding]; other site 439292003126 putative Mg++ binding site [ion binding]; other site 439292003127 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 439292003128 nucleotide binding region [chemical binding]; other site 439292003129 ATP-binding site [chemical binding]; other site 439292003130 PAS domain; Region: PAS; smart00091 439292003131 PAS fold; Region: PAS; pfam00989 439292003132 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 439292003133 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 439292003134 Walker A motif; other site 439292003135 ATP binding site [chemical binding]; other site 439292003136 Walker B motif; other site 439292003137 arginine finger; other site 439292003138 isoaspartyl dipeptidase; Provisional; Region: PRK10657 439292003139 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 439292003140 active site 439292003141 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 439292003142 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 439292003143 Walker A/P-loop; other site 439292003144 ATP binding site [chemical binding]; other site 439292003145 Q-loop/lid; other site 439292003146 ABC transporter signature motif; other site 439292003147 Walker B; other site 439292003148 D-loop; other site 439292003149 H-loop/switch region; other site 439292003150 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 439292003151 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 439292003152 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 439292003153 Walker A/P-loop; other site 439292003154 ATP binding site [chemical binding]; other site 439292003155 Q-loop/lid; other site 439292003156 ABC transporter signature motif; other site 439292003157 Walker B; other site 439292003158 D-loop; other site 439292003159 H-loop/switch region; other site 439292003160 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 439292003161 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 439292003162 dimer interface [polypeptide binding]; other site 439292003163 conserved gate region; other site 439292003164 putative PBP binding loops; other site 439292003165 ABC-ATPase subunit interface; other site 439292003166 glutathione ABC transporter permease GsiC; Provisional; Region: PRK15081 439292003167 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 439292003168 dimer interface [polypeptide binding]; other site 439292003169 conserved gate region; other site 439292003170 putative PBP binding loops; other site 439292003171 ABC-ATPase subunit interface; other site 439292003172 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 439292003173 The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold; Region: PBP2_Ylib_like; cd08499 439292003174 Domain of unknown function (DUF1980); Region: DUF1980; cl01492 439292003175 Predicted permeases [General function prediction only]; Region: COG0701 439292003176 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 439292003177 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 439292003178 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 439292003179 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cl17315 439292003180 DNA binding residues [nucleotide binding] 439292003181 dimerization interface [polypeptide binding]; other site 439292003182 pyruvate phosphate dikinase; Provisional; Region: PRK09279 439292003183 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 439292003184 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 439292003185 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 439292003186 PEP synthetase regulatory protein; Provisional; Region: PRK05339 439292003187 Predicted acetamidase/formamidase [Energy production and conversion]; Region: COG2421 439292003188 S-layer homology domain; Region: SLH; pfam00395 439292003189 S-layer homology domain; Region: SLH; pfam00395 439292003190 S-layer homology domain; Region: SLH; pfam00395 439292003191 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3786 439292003192 L-lactate permease; Region: Lactate_perm; cl00701 439292003193 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 439292003194 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 439292003195 Cache domain; Region: Cache_1; pfam02743 439292003196 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292003197 dimerization interface [polypeptide binding]; other site 439292003198 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292003199 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292003200 dimer interface [polypeptide binding]; other site 439292003201 putative CheW interface [polypeptide binding]; other site 439292003202 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 439292003203 Sodium Bile acid symporter family; Region: SBF; cl17470 439292003204 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 439292003205 Acetyl xylan esterase (AXE1); Region: AXE1; pfam05448 439292003206 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 439292003207 DinB family; Region: DinB; cl17821 439292003208 DinB superfamily; Region: DinB_2; pfam12867 439292003209 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 439292003210 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; COG2049 439292003211 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 439292003212 LamB/YcsF family of lactam utilization protein; Region: LamB_YcsF_like; cd10787 439292003213 putative active site [active] 439292003214 Allophanate hydrolase subunit 2; Region: AHS2; pfam02626 439292003215 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 439292003216 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 439292003217 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 439292003218 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292003219 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 439292003220 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 439292003221 Bacterial SH3 domain; Region: SH3_3; pfam08239 439292003222 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 439292003223 active site 439292003224 Zn binding site [ion binding]; other site 439292003225 S-layer homology domain; Region: SLH; pfam00395 439292003226 S-layer homology domain; Region: SLH; pfam00395 439292003227 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 439292003228 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 439292003229 active site 439292003230 metal binding site [ion binding]; metal-binding site 439292003231 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 439292003232 Fn3 associated; Region: Fn3_assoc; pfam13287 439292003233 YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate...; Region: YhcR_OBF_like; cd04486 439292003234 generic binding surface I; other site 439292003235 generic binding surface II; other site 439292003236 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 439292003237 putative catalytic site [active] 439292003238 putative metal binding site [ion binding]; other site 439292003239 putative phosphate binding site [ion binding]; other site 439292003240 generic binding surface II; other site 439292003241 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 439292003242 generic binding surface I; other site 439292003243 S-layer homology domain; Region: SLH; pfam00395 439292003244 S-layer homology domain; Region: SLH; pfam00395 439292003245 Family 41 Carbohydrate-Binding Module from pullulanase-like enzymes; Region: CBM41_pullulanase; cd10315 439292003246 carbohydrate binding site [chemical binding]; other site 439292003247 Family 41 Carbohydrate-Binding Module from pullulanase-like enzymes; Region: CBM41_pullulanase; cd10315 439292003248 carbohydrate binding site [chemical binding]; other site 439292003249 Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins; Region: AmyAc_bac_CMD_like_2; cd11339 439292003250 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 439292003251 active site 439292003252 catalytic site [active] 439292003253 pullulanase, extracellular, Gram-positive; Region: pullulan_Gpos; TIGR02102 439292003254 Family 41 Carbohydrate-Binding Module from pullulanase-like enzymes; Region: CBM41_pullulanase; cd10315 439292003255 carbohydrate binding site [chemical binding]; other site 439292003256 Family 41 Carbohydrate-Binding Module from pullulanase-like enzymes; Region: CBM41_pullulanase; cd10315 439292003257 carbohydrate binding site [chemical binding]; other site 439292003258 Early set domain associated with the catalytic domain of pullulanase (also called dextrinase and alpha-dextrin endo-1,6-alpha glucosidase); Region: E_set_Pullulanase; cd02860 439292003259 Alpha amylase catalytic domain found in Pullulanase (also called dextrinase; alpha-dextrin endo-1,6-alpha glucosidase), limit dextrinase, and related proteins; Region: AmyAc_Pullulanase_LD-like; cd11341 439292003260 Ca binding site [ion binding]; other site 439292003261 active site 439292003262 catalytic site [active] 439292003263 S-layer homology domain; Region: SLH; pfam00395 439292003264 S-layer homology domain; Region: SLH; pfam00395 439292003265 S-layer homology domain; Region: SLH; pfam00395 439292003266 Predicted permeases [General function prediction only]; Region: COG0730 439292003267 heat shock protein 90; Provisional; Region: PRK05218 439292003268 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 439292003269 ATP binding site [chemical binding]; other site 439292003270 Mg2+ binding site [ion binding]; other site 439292003271 G-X-G motif; other site 439292003272 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 439292003273 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 439292003274 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 439292003275 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 439292003276 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 439292003277 M42 Peptidase, Endoglucanase-like subfamily; Region: M42_glucanase_like; cd05657 439292003278 putative oligomer interface [polypeptide binding]; other site 439292003279 putative active site [active] 439292003280 metal binding site [ion binding]; metal-binding site 439292003281 DoxX; Region: DoxX; cl17842 439292003282 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 439292003283 Phosphoenolpyruvate carboxylase; Region: PEPcase; pfam00311 439292003284 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 439292003285 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 439292003286 Na binding site [ion binding]; other site 439292003287 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 439292003288 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 439292003289 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 439292003290 HAMP domain; Region: HAMP; pfam00672 439292003291 dimerization interface [polypeptide binding]; other site 439292003292 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 439292003293 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 439292003294 dimer interface [polypeptide binding]; other site 439292003295 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 439292003296 ATP binding site [chemical binding]; other site 439292003297 Mg2+ binding site [ion binding]; other site 439292003298 G-X-G motif; other site 439292003299 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 439292003300 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 439292003301 S-layer homology domain; Region: SLH; pfam00395 439292003302 S-layer homology domain; Region: SLH; pfam00395 439292003303 S-layer homology domain; Region: SLH; pfam00395 439292003304 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 439292003305 trimer interface [polypeptide binding]; other site 439292003306 active site 439292003307 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 439292003308 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 439292003309 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 439292003310 O-Antigen ligase; Region: Wzy_C; pfam04932 439292003311 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 439292003312 Cell envelope-related transcriptional attenuator domain; Region: LytR_cpsA_psr; cl00581 439292003313 Uncharacterized conserved protein [Function unknown]; Region: COG1739 439292003314 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 439292003315 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 439292003316 Sensor protein DegS; Region: DegS; pfam05384 439292003317 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 439292003318 Histidine kinase; Region: HisKA_3; pfam07730 439292003319 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 439292003320 ATP binding site [chemical binding]; other site 439292003321 Mg2+ binding site [ion binding]; other site 439292003322 G-X-G motif; other site 439292003323 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 439292003324 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 439292003325 active site 439292003326 phosphorylation site [posttranslational modification] 439292003327 intermolecular recognition site; other site 439292003328 dimerization interface [polypeptide binding]; other site 439292003329 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 439292003330 DNA binding residues [nucleotide binding] 439292003331 dimerization interface [polypeptide binding]; other site 439292003332 EDD domain protein, DegV family; Region: DegV; TIGR00762 439292003333 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 439292003334 Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]; Region: comFA; COG4098 439292003335 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 439292003336 ATP binding site [chemical binding]; other site 439292003337 putative Mg++ binding site [ion binding]; other site 439292003338 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 439292003339 nucleotide binding region [chemical binding]; other site 439292003340 ATP-binding site [chemical binding]; other site 439292003341 Nuclease-related domain; Region: NERD; pfam08378 439292003342 comF family protein; Region: comF; TIGR00201 439292003343 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 439292003344 active site 439292003345 flagellar operon protein TIGR03826; Region: YvyF 439292003346 Anti-sigma-28 factor, FlgM; Region: FlgM; pfam04316 439292003347 FlgN protein; Region: FlgN; pfam05130 439292003348 Flagellar hook-associated protein [Cell motility and secretion]; Region: FlgK; COG1256 439292003349 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 439292003350 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 439292003351 flagellar hook-associated protein FlgL; Validated; Region: PRK06663 439292003352 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 439292003353 flagellar assembly protein FliW; Provisional; Region: PRK13285 439292003354 carbon storage regulator; Provisional; Region: PRK01712 439292003355 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 439292003356 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 439292003357 DNA binding residues [nucleotide binding] 439292003358 dimerization interface [polypeptide binding]; other site 439292003359 flagellin; Provisional; Region: PRK12804 439292003360 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 439292003361 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 439292003362 insertion element IS2 transposase InsD; Provisional; Region: PRK14702 439292003363 Integrase core domain; Region: rve; pfam00665 439292003364 Integrase core domain; Region: rve_3; pfam13683 439292003365 flagellin; Reviewed; Region: PRK08869 439292003366 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 439292003367 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 439292003368 putative substrate translocation pore; other site 439292003369 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 439292003370 PAS domain; Region: PAS_9; pfam13426 439292003371 putative active site [active] 439292003372 heme pocket [chemical binding]; other site 439292003373 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292003374 dimer interface [polypeptide binding]; other site 439292003375 putative CheW interface [polypeptide binding]; other site 439292003376 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 439292003377 thiamine phosphate binding site [chemical binding]; other site 439292003378 active site 439292003379 pyrophosphate binding site [ion binding]; other site 439292003380 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 439292003381 dimer interface [polypeptide binding]; other site 439292003382 substrate binding site [chemical binding]; other site 439292003383 ATP binding site [chemical binding]; other site 439292003384 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine...; Region: THZ_kinase; cd01170 439292003385 substrate binding site [chemical binding]; other site 439292003386 multimerization interface [polypeptide binding]; other site 439292003387 ATP binding site [chemical binding]; other site 439292003388 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 439292003389 DNA-binding site [nucleotide binding]; DNA binding site 439292003390 RNA-binding motif; other site 439292003391 Predicted membrane protein [Function unknown]; Region: COG1511 439292003392 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 439292003393 Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; Region: SPEC; cl02488 439292003394 linker region; other site 439292003395 Predicted membrane protein [Function unknown]; Region: COG1511 439292003396 YhgE/Pip C-terminal domain; Region: pip_yhgE_Cterm; TIGR03062 439292003397 PAS domain; Region: PAS_9; pfam13426 439292003398 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 439292003399 putative active site [active] 439292003400 heme pocket [chemical binding]; other site 439292003401 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292003402 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292003403 metal binding site [ion binding]; metal-binding site 439292003404 active site 439292003405 I-site; other site 439292003406 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292003407 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 439292003408 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 439292003409 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 439292003410 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 439292003411 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 439292003412 Probable transposase; Region: OrfB_IS605; pfam01385 439292003413 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 439292003414 Putative motility protein; Region: YjfB_motility; pfam14070 439292003415 atypical (a) SDRs, subgroup 5; Region: SDR_a5; cd05243 439292003416 NADH(P)-binding; Region: NAD_binding_10; pfam13460 439292003417 NAD(P) binding site [chemical binding]; other site 439292003418 putative active site [active] 439292003419 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 439292003420 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292003421 Zn2+ binding site [ion binding]; other site 439292003422 Mg2+ binding site [ion binding]; other site 439292003423 NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Region: LDH_MDH_like; cl17195 439292003424 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292003425 dimer interface [polypeptide binding]; other site 439292003426 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 439292003427 putative CheW interface [polypeptide binding]; other site 439292003428 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 439292003429 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292003430 Zn2+ binding site [ion binding]; other site 439292003431 Mg2+ binding site [ion binding]; other site 439292003432 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292003433 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292003434 metal binding site [ion binding]; metal-binding site 439292003435 active site 439292003436 I-site; other site 439292003437 flagellar capping protein; Validated; Region: fliD; PRK07737 439292003438 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 439292003439 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 439292003440 flagellar capping protein; Validated; Region: fliD; PRK07737 439292003441 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 439292003442 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 439292003443 Flagellar protein FliT; Region: FliT; pfam05400 439292003444 FlaG protein; Region: FlaG; pfam03646 439292003445 Flagellar protein FliS; Region: FliS; cl00654 439292003446 S-layer homology domain; Region: SLH; pfam00395 439292003447 S-layer homology domain; Region: SLH; pfam00395 439292003448 S-layer homology domain; Region: SLH; pfam00395 439292003449 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 439292003450 Escherichia coli UshA-like family, N-terminal metallophosphatase domain; Region: MPP_UshA_N_like; cd00845 439292003451 active site 439292003452 metal binding site [ion binding]; metal-binding site 439292003453 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 439292003454 S-layer homology domain; Region: SLH; pfam00395 439292003455 S-layer homology domain; Region: SLH; pfam00395 439292003456 maltodextrin glucosidase; Provisional; Region: PRK10785 439292003457 N-terminal Early set domain associated with the catalytic domain of cyclomaltodextrinase and pullulan-degrading enzymes; Region: E_set_CDase_PDE_N; cd02857 439292003458 homodimer interface [polypeptide binding]; other site 439292003459 Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins; Region: AmyAc_CMD; cd11338 439292003460 active site 439292003461 homodimer interface [polypeptide binding]; other site 439292003462 catalytic site [active] 439292003463 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 439292003464 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 439292003465 dimer interface [polypeptide binding]; other site 439292003466 ssDNA binding site [nucleotide binding]; other site 439292003467 tetramer (dimer of dimers) interface [polypeptide binding]; other site 439292003468 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 439292003469 DNA-binding site [nucleotide binding]; DNA binding site 439292003470 RNA-binding motif; other site 439292003471 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 439292003472 30S subunit binding site; other site 439292003473 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 439292003474 PTS system, glucose-specific IIBC component; Region: PTS-II-BC-glcB; TIGR02002 439292003475 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cd00212 439292003476 active site turn [active] 439292003477 phosphorylation site [posttranslational modification] 439292003478 PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_glc; cd00210 439292003479 HPr interaction site; other site 439292003480 glycerol kinase (GK) interaction site [polypeptide binding]; other site 439292003481 active site 439292003482 phosphorylation site [posttranslational modification] 439292003483 transcriptional antiterminator BglG; Provisional; Region: PRK09772 439292003484 CAT RNA binding domain; Region: CAT_RBD; smart01061 439292003485 PRD domain; Region: PRD; pfam00874 439292003486 PRD domain; Region: PRD; pfam00874 439292003487 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 439292003488 DEAD/DEAH box helicase; Region: DEAD; pfam00270 439292003489 ATP binding site [chemical binding]; other site 439292003490 putative Mg++ binding site [ion binding]; other site 439292003491 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 439292003492 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 439292003493 nucleotide binding region [chemical binding]; other site 439292003494 ATP-binding site [chemical binding]; other site 439292003495 SEC-C motif; Region: SEC-C; pfam02810 439292003496 peptide chain release factor 2; Validated; Region: prfB; PRK00578 439292003497 This domain is found in peptide chain release factors; Region: PCRF; smart00937 439292003498 RF-1 domain; Region: RF-1; pfam00472 439292003499 Uncharacterized conserved protein [Function unknown]; Region: COG1284 439292003500 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 439292003501 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 439292003502 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 439292003503 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 439292003504 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 439292003505 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 439292003506 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292003507 Walker A/P-loop; other site 439292003508 ATP binding site [chemical binding]; other site 439292003509 Q-loop/lid; other site 439292003510 ABC transporter signature motif; other site 439292003511 Walker B; other site 439292003512 D-loop; other site 439292003513 H-loop/switch region; other site 439292003514 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 439292003515 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 439292003516 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 439292003517 Peptidase family M23; Region: Peptidase_M23; pfam01551 439292003518 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 439292003519 C-terminal peptidase (prc); Region: prc; TIGR00225 439292003520 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 439292003521 protein binding site [polypeptide binding]; other site 439292003522 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 439292003523 Catalytic dyad [active] 439292003524 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 439292003525 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 439292003526 excinuclease ABC subunit B; Provisional; Region: PRK05298 439292003527 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 439292003528 ATP binding site [chemical binding]; other site 439292003529 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 439292003530 nucleotide binding region [chemical binding]; other site 439292003531 ATP-binding site [chemical binding]; other site 439292003532 Ultra-violet resistance protein B; Region: UvrB; pfam12344 439292003533 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 439292003534 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 439292003535 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 439292003536 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 439292003537 Uncharacterized conserved protein [Function unknown]; Region: COG3595 439292003538 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 439292003539 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 439292003540 PspC domain; Region: PspC; pfam04024 439292003541 Membrane protein of unknown function; Region: DUF360; cl00850 439292003542 HPr kinase/phosphorylase; Provisional; Region: PRK05428 439292003543 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 439292003544 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 439292003545 Hpr binding site; other site 439292003546 active site 439292003547 homohexamer subunit interaction site [polypeptide binding]; other site 439292003548 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK12437 439292003549 Nucleoside recognition; Region: Gate; pfam07670 439292003550 Nucleoside recognition; Region: Gate; pfam07670 439292003551 pyrophosphatase PpaX; Provisional; Region: PRK13288 439292003552 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 439292003553 motif II; other site 439292003554 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 439292003555 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 439292003556 trimer interface [polypeptide binding]; other site 439292003557 CoA binding site [chemical binding]; other site 439292003558 active site 439292003559 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12292 439292003560 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 439292003561 dimer interface [polypeptide binding]; other site 439292003562 motif 1; other site 439292003563 active site 439292003564 motif 2; other site 439292003565 motif 3; other site 439292003566 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 439292003567 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 439292003568 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 439292003569 histidinol dehydrogenase; Region: hisD; TIGR00069 439292003570 NAD binding site [chemical binding]; other site 439292003571 dimerization interface [polypeptide binding]; other site 439292003572 product binding site; other site 439292003573 substrate binding site [chemical binding]; other site 439292003574 zinc binding site [ion binding]; other site 439292003575 catalytic residues [active] 439292003576 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 439292003577 putative active site pocket [active] 439292003578 4-fold oligomerization interface [polypeptide binding]; other site 439292003579 metal binding residues [ion binding]; metal-binding site 439292003580 3-fold/trimer interface [polypeptide binding]; other site 439292003581 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 439292003582 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 439292003583 putative active site [active] 439292003584 oxyanion strand; other site 439292003585 catalytic triad [active] 439292003586 HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1...; Region: HisA; cd04732 439292003587 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 439292003588 catalytic residues [active] 439292003589 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 439292003590 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 439292003591 substrate binding site [chemical binding]; other site 439292003592 glutamase interaction surface [polypeptide binding]; other site 439292003593 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 439292003594 Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]; Region: HisI; COG0139 439292003595 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 439292003596 metal binding site [ion binding]; metal-binding site 439292003597 phytoene desaturase; Region: crtI_fam; TIGR02734 439292003598 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 439292003599 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 439292003600 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 439292003601 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 439292003602 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 439292003603 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 439292003604 conserved hypothetical protein, cofD-related; Region: CofD_related; TIGR01826 439292003605 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 439292003606 phosphate binding site [ion binding]; other site 439292003607 putative substrate binding pocket [chemical binding]; other site 439292003608 dimer interface [polypeptide binding]; other site 439292003609 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1481 439292003610 Sporulation Regulator WhiA N terminal; Region: WhiA_N; pfam10298 439292003611 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 439292003612 dimerization domain swap beta strand [polypeptide binding]; other site 439292003613 regulatory protein interface [polypeptide binding]; other site 439292003614 active site 439292003615 regulatory phosphorylation site [posttranslational modification]; other site 439292003616 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 439292003617 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 439292003618 oligomer interface [polypeptide binding]; other site 439292003619 active site residues [active] 439292003620 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 439292003621 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 439292003622 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 439292003623 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 439292003624 Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]; Region: DeoR; COG2390 439292003625 Putative sugar-binding domain; Region: Sugar-bind; pfam04198 439292003626 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 439292003627 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 439292003628 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 439292003629 Phosphoglycerate kinase; Region: PGK; pfam00162 439292003630 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 439292003631 substrate binding site [chemical binding]; other site 439292003632 hinge regions; other site 439292003633 ADP binding site [chemical binding]; other site 439292003634 catalytic site [active] 439292003635 triosephosphate isomerase; Provisional; Region: PRK14567 439292003636 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 439292003637 substrate binding site [chemical binding]; other site 439292003638 dimer interface [polypeptide binding]; other site 439292003639 catalytic triad [active] 439292003640 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 439292003641 phosphoglyceromutase; Provisional; Region: PRK05434 439292003642 enolase; Provisional; Region: eno; PRK00077 439292003643 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 439292003644 dimer interface [polypeptide binding]; other site 439292003645 metal binding site [ion binding]; metal-binding site 439292003646 substrate binding pocket [chemical binding]; other site 439292003647 Transcriptional regulator [Transcription]; Region: LysR; COG0583 439292003648 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 439292003649 putative DNA binding site [nucleotide binding]; other site 439292003650 putative Zn2+ binding site [ion binding]; other site 439292003651 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 439292003652 dimerization interface [polypeptide binding]; other site 439292003653 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 439292003654 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292003655 Walker A/P-loop; other site 439292003656 ATP binding site [chemical binding]; other site 439292003657 Q-loop/lid; other site 439292003658 ABC transporter signature motif; other site 439292003659 Walker B; other site 439292003660 D-loop; other site 439292003661 H-loop/switch region; other site 439292003662 TOBE domain; Region: TOBE_2; pfam08402 439292003663 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 439292003664 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 439292003665 dimer interface [polypeptide binding]; other site 439292003666 conserved gate region; other site 439292003667 putative PBP binding loops; other site 439292003668 ABC-ATPase subunit interface; other site 439292003669 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 439292003670 dimer interface [polypeptide binding]; other site 439292003671 conserved gate region; other site 439292003672 putative PBP binding loops; other site 439292003673 ABC-ATPase subunit interface; other site 439292003674 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 439292003675 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 439292003676 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 439292003677 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 439292003678 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 439292003679 Esterase/lipase [General function prediction only]; Region: COG1647 439292003680 BAAT / Acyl-CoA thioester hydrolase C terminal; Region: BAAT_C; pfam08840 439292003681 Esterase/lipase [General function prediction only]; Region: COG1647 439292003682 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 439292003683 ribonuclease R; Region: RNase_R; TIGR02063 439292003684 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 439292003685 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 439292003686 RNB domain; Region: RNB; pfam00773 439292003687 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 439292003688 RNA binding site [nucleotide binding]; other site 439292003689 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 439292003690 SmpB-tmRNA interface; other site 439292003691 hypothetical protein; Provisional; Region: PRK08201 439292003692 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_3; cd05680 439292003693 metal binding site [ion binding]; metal-binding site 439292003694 putative dimer interface [polypeptide binding]; other site 439292003695 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 439292003696 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 439292003697 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 439292003698 ATP binding site [chemical binding]; other site 439292003699 Mg2+ binding site [ion binding]; other site 439292003700 G-X-G motif; other site 439292003701 PAS domain; Region: PAS_9; pfam13426 439292003702 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 439292003703 putative active site [active] 439292003704 heme pocket [chemical binding]; other site 439292003705 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 439292003706 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 439292003707 anti sigma factor interaction site; other site 439292003708 regulatory phosphorylation site [posttranslational modification]; other site 439292003709 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292003710 dimerization interface [polypeptide binding]; other site 439292003711 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 439292003712 dimer interface [polypeptide binding]; other site 439292003713 phosphorylation site [posttranslational modification] 439292003714 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 439292003715 ATP binding site [chemical binding]; other site 439292003716 Mg2+ binding site [ion binding]; other site 439292003717 G-X-G motif; other site 439292003718 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 439292003719 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 439292003720 active site 439292003721 phosphorylation site [posttranslational modification] 439292003722 intermolecular recognition site; other site 439292003723 dimerization interface [polypeptide binding]; other site 439292003724 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 439292003725 DNA binding site [nucleotide binding] 439292003726 Uncharacterized conserved protein [Function unknown]; Region: COG3391 439292003727 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 439292003728 SecY translocase; Region: SecY; pfam00344 439292003729 3-hydroxyacyl-CoA dehydrogenase; Validated; Region: PRK06035 439292003730 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 439292003731 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 439292003732 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 439292003733 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 439292003734 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 439292003735 substrate binding site [chemical binding]; other site 439292003736 oxyanion hole (OAH) forming residues; other site 439292003737 trimer interface [polypeptide binding]; other site 439292003738 acetyl-CoA acetyltransferase; Provisional; Region: PRK07661 439292003739 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 439292003740 dimer interface [polypeptide binding]; other site 439292003741 active site 439292003742 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 439292003743 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 439292003744 active site 439292003745 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 439292003746 lipoyl attachment site [posttranslational modification]; other site 439292003747 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 439292003748 Major Facilitator Superfamily; Region: MFS_1; pfam07690 439292003749 putative substrate translocation pore; other site 439292003750 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 439292003751 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 439292003752 Walker A/P-loop; other site 439292003753 ATP binding site [chemical binding]; other site 439292003754 Q-loop/lid; other site 439292003755 ABC transporter signature motif; other site 439292003756 Walker B; other site 439292003757 D-loop; other site 439292003758 H-loop/switch region; other site 439292003759 NIL domain; Region: NIL; pfam09383 439292003760 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 439292003761 dimer interface [polypeptide binding]; other site 439292003762 ABC-ATPase subunit interface; other site 439292003763 putative PBP binding loops; other site 439292003764 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 439292003765 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 439292003766 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292003767 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292003768 metal binding site [ion binding]; metal-binding site 439292003769 active site 439292003770 I-site; other site 439292003771 Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]; Region: sufC; COG0396 439292003772 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 439292003773 Walker A/P-loop; other site 439292003774 ATP binding site [chemical binding]; other site 439292003775 Q-loop/lid; other site 439292003776 ABC transporter signature motif; other site 439292003777 Walker B; other site 439292003778 D-loop; other site 439292003779 H-loop/switch region; other site 439292003780 Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]; Region: SufB; COG0719 439292003781 FeS assembly protein SufD; Region: sufD; TIGR01981 439292003782 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 439292003783 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 439292003784 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 439292003785 catalytic residue [active] 439292003786 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 439292003787 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 439292003788 trimerization site [polypeptide binding]; other site 439292003789 active site 439292003790 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 439292003791 FeS assembly protein SufB; Region: sufB; TIGR01980 439292003792 Uncharacterized conserved protein [Function unknown]; Region: COG1801 439292003793 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 439292003794 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 439292003795 Escherichia coli UshA-like family, N-terminal metallophosphatase domain; Region: MPP_UshA_N_like; cd00845 439292003796 active site 439292003797 metal binding site [ion binding]; metal-binding site 439292003798 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 439292003799 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 439292003800 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292003801 Zn2+ binding site [ion binding]; other site 439292003802 Mg2+ binding site [ion binding]; other site 439292003803 thymidylate synthase; Reviewed; Region: thyA; PRK01827 439292003804 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 439292003805 dimerization interface [polypeptide binding]; other site 439292003806 active site 439292003807 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 439292003808 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 439292003809 folate binding site [chemical binding]; other site 439292003810 NADP+ binding site [chemical binding]; other site 439292003811 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 439292003812 Protein of unknown function (DUF3055); Region: DUF3055; pfam11256 439292003813 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 439292003814 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 439292003815 putative active site [active] 439292003816 Uncharacterized conserved protein [Function unknown]; Region: COG2445 439292003817 Predicted transcriptional regulator [Transcription]; Region: COG2345 439292003818 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 439292003819 putative DNA binding site [nucleotide binding]; other site 439292003820 putative Zn2+ binding site [ion binding]; other site 439292003821 HAD-superfamily subfamily IIA hydrolase, TIGR01457; Region: HAD-SF-IIA-hyp2 439292003822 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 439292003823 active site 439292003824 motif I; other site 439292003825 motif II; other site 439292003826 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 439292003827 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 439292003828 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 439292003829 dimerization interface [polypeptide binding]; other site 439292003830 ligand binding site [chemical binding]; other site 439292003831 NADP binding site [chemical binding]; other site 439292003832 catalytic site [active] 439292003833 NifU-like domain; Region: NifU; cl00484 439292003834 Protein of unknown function (DUF1462); Region: DUF1462; pfam07315 439292003835 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 439292003836 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 439292003837 hypothetical protein; Provisional; Region: PRK13669 439292003838 putative menaquinone biosynthesis protein, SCO4494 family; Region: mena_SCO4494; TIGR03700 439292003839 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 439292003840 FeS/SAM binding site; other site 439292003841 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 439292003842 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 439292003843 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 439292003844 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 439292003845 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 439292003846 Putative membrane protein; Region: YuiB; pfam14068 439292003847 Divergent PAP2 family; Region: DUF212; pfam02681 439292003848 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 439292003849 DctM-like transporters; Region: DctM; pfam06808 439292003850 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 439292003851 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 439292003852 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 439292003853 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 439292003854 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 439292003855 Ligand binding site [chemical binding]; other site 439292003856 Electron transfer flavoprotein domain; Region: ETF; pfam01012 439292003857 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 439292003858 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 439292003859 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 439292003860 oxidoreductase; Provisional; Region: PRK10015 439292003861 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 439292003862 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 439292003863 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 439292003864 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 439292003865 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 439292003866 AsnC family; Region: AsnC_trans_reg; pfam01037 439292003867 hypothetical protein; Validated; Region: PRK07682 439292003868 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 439292003869 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292003870 homodimer interface [polypeptide binding]; other site 439292003871 catalytic residue [active] 439292003872 general stress protein 13; Validated; Region: PRK08059 439292003873 S1_RPS1_repeat_hs4: 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_hs4; cd05692 439292003874 RNA binding site [nucleotide binding]; other site 439292003875 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 439292003876 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 439292003877 dimer interface [polypeptide binding]; other site 439292003878 active site 439292003879 metal binding site [ion binding]; metal-binding site 439292003880 glucose-6-phosphate isomerase; Provisional; Region: pgi; PRK14097 439292003881 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 439292003882 active site 439292003883 dimer interface [polypeptide binding]; other site 439292003884 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 439292003885 dimer interface [polypeptide binding]; other site 439292003886 active site 439292003887 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 439292003888 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 439292003889 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 439292003890 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 439292003891 Soluble P-type ATPase [General function prediction only]; Region: COG4087 439292003892 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 439292003893 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 439292003894 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 439292003895 Na2 binding site [ion binding]; other site 439292003896 putative substrate binding site 1 [chemical binding]; other site 439292003897 Na binding site 1 [ion binding]; other site 439292003898 putative substrate binding site 2 [chemical binding]; other site 439292003899 Trehalose and maltose hydrolases (possible phosphorylases) [Carbohydrate transport and metabolism]; Region: ATH1; COG1554 439292003900 Glycosyl hydrolase family 65, N-terminal domain; Region: Glyco_hydro_65N; pfam03636 439292003901 Glycosyl hydrolase family 65 central catalytic domain; Region: Glyco_hydro_65m; pfam03632 439292003902 Glycosyl hydrolase family 65, C-terminal domain; Region: Glyco_hydro_65C; pfam03633 439292003903 DsrE/DsrF/DrsH-like family; Region: DrsE_2; pfam13686 439292003904 Uncharacterized protein YrkD from Bacillus subtilis and related domains; this domain superfamily was previously known as part of DUF156; Region: BsYrkD-like_DUF156; cd10155 439292003905 putative homodimer interface [polypeptide binding]; other site 439292003906 putative homotetramer interface [polypeptide binding]; other site 439292003907 putative metal binding site [ion binding]; other site 439292003908 putative homodimer-homodimer interface [polypeptide binding]; other site 439292003909 putative allosteric switch controlling residues; other site 439292003910 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 439292003911 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 439292003912 motif II; other site 439292003913 Uncharacterized conserved protein [Function unknown]; Region: COG1284 439292003914 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 439292003915 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 439292003916 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 439292003917 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 439292003918 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 439292003919 homodimer interface [polypeptide binding]; other site 439292003920 substrate-cofactor binding pocket; other site 439292003921 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292003922 catalytic residue [active] 439292003923 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 439292003924 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292003925 dimerization interface [polypeptide binding]; other site 439292003926 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292003927 dimer interface [polypeptide binding]; other site 439292003928 putative CheW interface [polypeptide binding]; other site 439292003929 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 439292003930 Ligand Binding Site [chemical binding]; other site 439292003931 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 439292003932 formate dehydrogenase, alpha subunit, proteobacterial-type; Region: formate-DH-alph; TIGR01553 439292003933 Tat (twin-arginine translocation) pathway signal sequence; Region: TAT_signal_seq; TIGR01409 439292003934 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 439292003935 [4Fe-4S] binding site [ion binding]; other site 439292003936 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 439292003937 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 439292003938 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 439292003939 molybdopterin cofactor binding site; other site 439292003940 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 439292003941 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 439292003942 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 439292003943 Protein involved in formate dehydrogenase formation; Region: FdhE; pfam04216 439292003944 formate dehydrogenase accessory protein FdhE; Region: FdhE; TIGR01562 439292003945 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 439292003946 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 439292003947 GTP binding site; other site 439292003948 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 439292003949 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 439292003950 dimer interface [polypeptide binding]; other site 439292003951 putative functional site; other site 439292003952 putative MPT binding site; other site 439292003953 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional; Region: PRK14498 439292003954 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 439292003955 dimer interface [polypeptide binding]; other site 439292003956 putative functional site; other site 439292003957 putative MPT binding site; other site 439292003958 PBP superfamily domain; Region: PBP_like; pfam12727 439292003959 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 439292003960 nucleoside triphosphatase YtkD; Region: nudix_YtkD; TIGR02705 439292003961 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 439292003962 nudix motif; other site 439292003963 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 439292003964 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 439292003965 S-adenosylmethionine synthetase; Validated; Region: PRK05250 439292003966 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 439292003967 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 439292003968 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 439292003969 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 439292003970 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 439292003971 trimer interface [polypeptide binding]; other site 439292003972 putative metal binding site [ion binding]; other site 439292003973 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 439292003974 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 439292003975 Protein of unknown function (DUF2600); Region: DUF2600; pfam10776 439292003976 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 439292003977 S-adenosylmethionine binding site [chemical binding]; other site 439292003978 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 439292003979 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 439292003980 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 439292003981 HIGH motif; other site 439292003982 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 439292003983 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 439292003984 active site 439292003985 KMSKS motif; other site 439292003986 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 439292003987 tRNA binding surface [nucleotide binding]; other site 439292003988 HI0933-like protein; Region: HI0933_like; pfam03486 439292003989 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK07634 439292003990 Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]; Region: ProC; COG0345 439292003991 Uncharacterized protein family UPF0047; Region: UPF0047; cl00439 439292003992 cell division protein FtsW; Region: ftsW; TIGR02614 439292003993 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 439292003994 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 439292003995 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 439292003996 RNA binding surface [nucleotide binding]; other site 439292003997 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 439292003998 active site 439292003999 uracil binding [chemical binding]; other site 439292004000 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; cl17531 439292004001 sugar efflux transporter; Region: 2A0120; TIGR00899 439292004002 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 439292004003 putative substrate translocation pore; other site 439292004004 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 439292004005 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 439292004006 dimer interface [polypeptide binding]; other site 439292004007 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292004008 catalytic residue [active] 439292004009 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 439292004010 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 439292004011 ABC transporter; Region: ABC_tran_2; pfam12848 439292004012 Integral membrane protein (DUF2244); Region: DUF2244; cl02302 439292004013 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 439292004014 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 439292004015 active site pocket [active] 439292004016 glycogen synthase; Provisional; Region: glgA; PRK00654 439292004017 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 439292004018 ADP-binding pocket [chemical binding]; other site 439292004019 homodimer interface [polypeptide binding]; other site 439292004020 glucose-1-phosphate adenylyltransferase, GlgD subunit; Region: glgD; TIGR02092 439292004021 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 439292004022 ligand binding site; other site 439292004023 oligomer interface; other site 439292004024 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 439292004025 dimer interface [polypeptide binding]; other site 439292004026 N-terminal domain interface [polypeptide binding]; other site 439292004027 sulfate 1 binding site; other site 439292004028 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK05293 439292004029 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 439292004030 ligand binding site; other site 439292004031 oligomer interface; other site 439292004032 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 439292004033 dimer interface [polypeptide binding]; other site 439292004034 N-terminal domain interface [polypeptide binding]; other site 439292004035 sulfate 1 binding site; other site 439292004036 glycogen branching enzyme; Provisional; Region: PRK12313 439292004037 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 439292004038 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 439292004039 active site 439292004040 catalytic site [active] 439292004041 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 439292004042 pullulanase, type I; Region: pulA_typeI; TIGR02104 439292004043 Early set domain associated with the catalytic domain of pullulanase (also called dextrinase and alpha-dextrin endo-1,6-alpha glucosidase); Region: E_set_Pullulanase; cd02860 439292004044 Alpha amylase catalytic domain found in Pullulanase (also called dextrinase; alpha-dextrin endo-1,6-alpha glucosidase), limit dextrinase, and related proteins; Region: AmyAc_Pullulanase_LD-like; cd11341 439292004045 Ca binding site [ion binding]; other site 439292004046 active site 439292004047 catalytic site [active] 439292004048 Phosphotransferase enzyme family; Region: APH; pfam01636 439292004049 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 439292004050 active site 439292004051 substrate binding site [chemical binding]; other site 439292004052 ATP binding site [chemical binding]; other site 439292004053 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 439292004054 S-adenosylmethionine binding site [chemical binding]; other site 439292004055 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 439292004056 Predicted small secreted protein [Function unknown]; Region: COG5584 439292004057 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 439292004058 M42 Peptidase, Endoglucanases; Region: M42_Frv; cd05656 439292004059 oligomer interface [polypeptide binding]; other site 439292004060 active site 439292004061 metal binding site [ion binding]; metal-binding site 439292004062 YtoQ family protein; Region: YtoQ_fam; TIGR03646 439292004063 Predicted membrane protein, putative toxin regulator [General function prediction only]; Region: PfoR; COG3641 439292004064 Phosphotransferase system, EIIC; Region: PTS_EIIC_2; pfam13303 439292004065 hypothetical protein; Provisional; Region: PRK13668 439292004066 nicotinate phosphoribosyltransferase; Provisional; Region: PRK07188 439292004067 Nicotinate phosphoribosyltransferase (NAPRTase), subgroup B. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction...; Region: NAPRTase_B; cd01571 439292004068 active site 439292004069 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 439292004070 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 439292004071 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 439292004072 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 439292004073 Leucyl aminopeptidase (aminopeptidase T) [Amino acid transport and metabolism]; Region: AmpS; COG2309 439292004074 Thermophilic metalloprotease (M29); Region: Peptidase_M29; pfam02073 439292004075 Uncharacterized protein containing a divergent version of the methyl-accepting chemotaxis-like domain [General function prediction only]; Region: COG4768 439292004076 YtxH-like protein; Region: YtxH; pfam12732 439292004077 bacillithiol system protein YtxJ; Region: B_thiol_YtxJ; TIGR04019 439292004078 cell division protein FtsA; Region: ftsA; TIGR01174 439292004079 Cell division protein FtsA; Region: FtsA; smart00842 439292004080 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 439292004081 nucleotide binding site [chemical binding]; other site 439292004082 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed; Region: PRK12595 439292004083 Chorismate mutase type II; Region: CM_2; cl00693 439292004084 phospho-2-dehydro-3-deoxyheptonate aldolase; Region: DAHP_synth_Bsub; TIGR01361 439292004085 catabolite control protein A; Region: ccpA; TIGR01481 439292004086 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 439292004087 DNA binding site [nucleotide binding] 439292004088 domain linker motif; other site 439292004089 Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation; Region: PBP1_CcpA_like; cd06298 439292004090 dimerization interface [polypeptide binding]; other site 439292004091 effector binding site; other site 439292004092 flagellar motor protein MotP; Reviewed; Region: PRK06926 439292004093 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 439292004094 flagellar motor protein MotS; Reviewed; Region: PRK06925 439292004095 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 439292004096 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 439292004097 ligand binding site [chemical binding]; other site 439292004098 FOG: CBS domain [General function prediction only]; Region: COG0517 439292004099 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms. They produce...; Region: CBS_pair_ACT_assoc; cd04584 439292004100 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 439292004101 Class I histone deacetylase AcuC (Acetoin utilization protein)-like enzymes; Region: HDAC_AcuC_like; cd09994 439292004102 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 439292004103 active site 439292004104 Zn binding site [ion binding]; other site 439292004105 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 439292004106 Transglycosylase; Region: Transgly; pfam00912 439292004107 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 439292004108 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 439292004109 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 439292004110 active site 439292004111 HIGH motif; other site 439292004112 dimer interface [polypeptide binding]; other site 439292004113 KMSKS motif; other site 439292004114 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 439292004115 RNA binding surface [nucleotide binding]; other site 439292004116 DGC domain; Region: DGC; pfam08859 439292004117 Putative exporter of polyketide antibiotics [Cell envelope biogenesis, outer membrane]; Region: TnrB3; COG3559 439292004118 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 439292004119 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 439292004120 Walker A/P-loop; other site 439292004121 ATP binding site [chemical binding]; other site 439292004122 Q-loop/lid; other site 439292004123 ABC transporter signature motif; other site 439292004124 Walker B; other site 439292004125 D-loop; other site 439292004126 H-loop/switch region; other site 439292004127 Domain of unknown function (DUF4162); Region: DUF4162; pfam13732 439292004128 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 439292004129 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292004130 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 439292004131 Domain of unknown function DUF20; Region: UPF0118; pfam01594 439292004132 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 439292004133 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_Nitrate-R-NarG-like; cd02750 439292004134 [4Fe-4S] binding site [ion binding]; other site 439292004135 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 439292004136 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 439292004137 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 439292004138 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 439292004139 molybdopterin cofactor binding site; other site 439292004140 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 439292004141 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 439292004142 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 439292004143 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; pfam02665 439292004144 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 439292004145 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 439292004146 nitrite extrusion protein (nitrite facilitator); Region: 2A0108; TIGR00886 439292004147 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 439292004148 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 439292004149 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 439292004150 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 439292004151 Walker A/P-loop; other site 439292004152 ATP binding site [chemical binding]; other site 439292004153 Q-loop/lid; other site 439292004154 ABC transporter signature motif; other site 439292004155 Walker B; other site 439292004156 D-loop; other site 439292004157 H-loop/switch region; other site 439292004158 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 439292004159 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 439292004160 dimer interface [polypeptide binding]; other site 439292004161 conserved gate region; other site 439292004162 putative PBP binding loops; other site 439292004163 ABC-ATPase subunit interface; other site 439292004164 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 439292004165 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 439292004166 substrate binding pocket [chemical binding]; other site 439292004167 membrane-bound complex binding site; other site 439292004168 hinge residues; other site 439292004169 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 439292004170 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 439292004171 ligand binding site [chemical binding]; other site 439292004172 flexible hinge region; other site 439292004173 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 439292004174 non-specific DNA interactions [nucleotide binding]; other site 439292004175 DNA binding site [nucleotide binding] 439292004176 sequence specific DNA binding site [nucleotide binding]; other site 439292004177 putative cAMP binding site [chemical binding]; other site 439292004178 Cytochrome c552; Region: Cytochrom_C552; pfam02335 439292004179 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 439292004180 Cytochrome c552; Region: Cytochrom_C552; pfam02335 439292004181 CcmE; Region: CcmE; cl00994 439292004182 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 439292004183 Cytochrome C biogenesis protein; Region: CcmH; cl01179 439292004184 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 439292004185 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 439292004186 Walker A/P-loop; other site 439292004187 ATP binding site [chemical binding]; other site 439292004188 Q-loop/lid; other site 439292004189 ABC transporter signature motif; other site 439292004190 Walker B; other site 439292004191 D-loop; other site 439292004192 H-loop/switch region; other site 439292004193 ABC-type transport system involved in cytochrome c biogenesis, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CcmB; COG2386 439292004194 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 439292004195 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 439292004196 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 439292004197 catalytic residues [active] 439292004198 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 439292004199 active site 439292004200 putative catalytic site [active] 439292004201 DNA binding site [nucleotide binding] 439292004202 putative phosphate binding site [ion binding]; other site 439292004203 metal binding site A [ion binding]; metal-binding site 439292004204 AP binding site [nucleotide binding]; other site 439292004205 metal binding site B [ion binding]; metal-binding site 439292004206 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 439292004207 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 439292004208 S-adenosylmethionine binding site [chemical binding]; other site 439292004209 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 439292004210 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 439292004211 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 439292004212 RNA binding surface [nucleotide binding]; other site 439292004213 GAF domain; Region: GAF_2; pfam13185 439292004214 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 439292004215 GAF domain; Region: GAF_3; pfam13492 439292004216 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292004217 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292004218 metal binding site [ion binding]; metal-binding site 439292004219 active site 439292004220 I-site; other site 439292004221 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 439292004222 GAF domain; Region: GAF_2; pfam13185 439292004223 histidinol-phosphatase; Reviewed; Region: PRK08123 439292004224 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like; Region: PHP_HisPPase_Hisj_like; cd12110 439292004225 active site 439292004226 dimer interface [polypeptide binding]; other site 439292004227 septation ring formation regulator EzrA; Provisional; Region: PRK04778 439292004228 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 439292004229 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 439292004230 active site 439292004231 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03501 439292004232 ATP-NAD kinase; Region: NAD_kinase; pfam01513 439292004233 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 439292004234 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 439292004235 tandem repeat interface [polypeptide binding]; other site 439292004236 oligomer interface [polypeptide binding]; other site 439292004237 active site residues [active] 439292004238 RDD family; Region: RDD; pfam06271 439292004239 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 439292004240 dimer interface [polypeptide binding]; other site 439292004241 catalytic triad [active] 439292004242 peroxidatic and resolving cysteines [active] 439292004243 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 439292004244 Methyltransferase domain; Region: Methyltransf_26; pfam13659 439292004245 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 439292004246 propionate/acetate kinase; Provisional; Region: PRK12379 439292004247 Domain of unknown function (DUF4391); Region: DUF4391; pfam14335 439292004248 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 439292004249 Ligand Binding Site [chemical binding]; other site 439292004250 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK12825 439292004251 classical (c) SDRs; Region: SDR_c; cd05233 439292004252 NAD(P) binding site [chemical binding]; other site 439292004253 active site 439292004254 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 439292004255 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 439292004256 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 439292004257 active site 439292004258 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 439292004259 metal-dependent hydrolase; Provisional; Region: PRK00685 439292004260 Predicted transcriptional regulator containing CBS domains [Transcription]; Region: COG4109 439292004261 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 439292004262 DNA-binding site [nucleotide binding]; DNA binding site 439292004263 DRTGG domain; Region: DRTGG; pfam07085 439292004264 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a DRTGG domain upstream. The function of the DRTGG domain, named after its conserved residues, is unknown. CBS is a small domain originally...; Region: CBS_pair_DRTGG_assoc; cd04596 439292004265 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cd03440 439292004266 active site 2 [active] 439292004267 active site 1 [active] 439292004268 YtpI-like protein; Region: YtpI; pfam14007 439292004269 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 439292004270 DHH family; Region: DHH; pfam01368 439292004271 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 439292004272 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 439292004273 active site 439292004274 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 439292004275 generic binding surface II; other site 439292004276 generic binding surface I; other site 439292004277 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 439292004278 Malic enzyme, N-terminal domain; Region: malic; pfam00390 439292004279 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 439292004280 putative NAD(P) binding site [chemical binding]; other site 439292004281 phosphonate utilization associated transcriptional regulator; Region: phnR_burk; TIGR03338 439292004282 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 439292004283 DNA-binding site [nucleotide binding]; DNA binding site 439292004284 FCD domain; Region: FCD; pfam07729 439292004285 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 439292004286 RNA polymerases M/15 Kd subunit; Region: RNA_POL_M_15KD; cl02717 439292004287 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 439292004288 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 439292004289 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 439292004290 6-phosphofructokinase; Provisional; Region: PRK03202 439292004291 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 439292004292 active site 439292004293 ADP/pyrophosphate binding site [chemical binding]; other site 439292004294 dimerization interface [polypeptide binding]; other site 439292004295 allosteric effector site; other site 439292004296 fructose-1,6-bisphosphate binding site; other site 439292004297 pyruvate kinase; Provisional; Region: PRK06354 439292004298 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; cd00288 439292004299 domain interfaces; other site 439292004300 active site 439292004301 Phosphohistidine swiveling domain [Signal transduction mechanisms]; Region: COG3848 439292004302 FxsA cytoplasmic membrane protein; Region: FxsA; pfam04186 439292004303 Protein of unknown function (DUF441); Region: DUF441; pfam04284 439292004304 Bacillus subtilis (Bs) citrate synthase (CS)-II_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). 2MCS catalyzes the...; Region: BSuCS-II_like; cd06110 439292004305 dimer interface [polypeptide binding]; other site 439292004306 active site 439292004307 citrylCoA binding site [chemical binding]; other site 439292004308 Citrate synthase; Region: Citrate_synt; pfam00285 439292004309 oxalacetate/citrate binding site [chemical binding]; other site 439292004310 coenzyme A binding site [chemical binding]; other site 439292004311 catalytic triad [active] 439292004312 isocitrate dehydrogenase; Reviewed; Region: PRK07006 439292004313 isocitrate dehydrogenase; Validated; Region: PRK07362 439292004314 malate dehydrogenase; Reviewed; Region: PRK06223 439292004315 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 439292004316 dimer interface [polypeptide binding]; other site 439292004317 NAD(P) binding site [chemical binding]; other site 439292004318 tetramer (dimer of dimers) interface [polypeptide binding]; other site 439292004319 substrate binding site [chemical binding]; other site 439292004320 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 439292004321 dimer interaction site [polypeptide binding]; other site 439292004322 substrate-binding tunnel; other site 439292004323 active site 439292004324 catalytic site [active] 439292004325 substrate binding site [chemical binding]; other site 439292004326 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 439292004327 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 439292004328 active site 439292004329 phosphorylation site [posttranslational modification] 439292004330 intermolecular recognition site; other site 439292004331 dimerization interface [polypeptide binding]; other site 439292004332 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 439292004333 DNA binding site [nucleotide binding] 439292004334 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292004335 dimerization interface [polypeptide binding]; other site 439292004336 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 439292004337 PAS domain; Region: PAS; smart00091 439292004338 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 439292004339 dimer interface [polypeptide binding]; other site 439292004340 phosphorylation site [posttranslational modification] 439292004341 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 439292004342 ATP binding site [chemical binding]; other site 439292004343 Mg2+ binding site [ion binding]; other site 439292004344 G-X-G motif; other site 439292004345 DNA polymerase I; Provisional; Region: PRK05755 439292004346 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 439292004347 active site 439292004348 metal binding site 1 [ion binding]; metal-binding site 439292004349 putative 5' ssDNA interaction site; other site 439292004350 metal binding site 3; metal-binding site 439292004351 metal binding site 2 [ion binding]; metal-binding site 439292004352 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 439292004353 putative DNA binding site [nucleotide binding]; other site 439292004354 putative metal binding site [ion binding]; other site 439292004355 inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases; Region: DNA_polA_I_Bacillus_like_exo; cd06140 439292004356 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 439292004357 active site 439292004358 DNA binding site [nucleotide binding] 439292004359 catalytic site [active] 439292004360 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 439292004361 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 439292004362 DNA binding site [nucleotide binding] 439292004363 catalytic residue [active] 439292004364 H2TH interface [polypeptide binding]; other site 439292004365 putative catalytic residues [active] 439292004366 turnover-facilitating residue; other site 439292004367 intercalation triad [nucleotide binding]; other site 439292004368 8OG recognition residue [nucleotide binding]; other site 439292004369 putative reading head residues; other site 439292004370 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 439292004371 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 439292004372 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 439292004373 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 439292004374 CoA-binding site [chemical binding]; other site 439292004375 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK07729 439292004376 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 439292004377 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 439292004378 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 439292004379 ATP cone domain; Region: ATP-cone; pfam03477 439292004380 Replication initiation/membrane attachment protein [DNA replication, recombination, and repair]; Region: DnaB; COG3611 439292004381 Replication initiation and membrane attachment; Region: DnaB_2; pfam07261 439292004382 primosomal protein DnaI; Reviewed; Region: PRK08939 439292004383 Primosomal protein DnaI N-terminus; Region: DnaI_N; pfam07319 439292004384 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 439292004385 Walker A motif; other site 439292004386 ATP binding site [chemical binding]; other site 439292004387 Walker B motif; other site 439292004388 menaquinone biosynthesis protein, SCO4550 family; Region: mena_SCO4550; TIGR03699 439292004389 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 439292004390 FeS/SAM binding site; other site 439292004391 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 439292004392 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 439292004393 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 439292004394 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 439292004395 active site 439292004396 dimer interface [polypeptide binding]; other site 439292004397 motif 1; other site 439292004398 motif 2; other site 439292004399 motif 3; other site 439292004400 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 439292004401 anticodon binding site; other site 439292004402 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 439292004403 PAS domain; Region: PAS_9; pfam13426 439292004404 putative active site [active] 439292004405 heme pocket [chemical binding]; other site 439292004406 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292004407 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292004408 metal binding site [ion binding]; metal-binding site 439292004409 active site 439292004410 I-site; other site 439292004411 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292004412 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 439292004413 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 439292004414 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 439292004415 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 439292004416 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 439292004417 23S rRNA binding site [nucleotide binding]; other site 439292004418 L21 binding site [polypeptide binding]; other site 439292004419 L13 binding site [polypeptide binding]; other site 439292004420 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 439292004421 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 439292004422 dUTPase; Region: dUTPase_2; pfam08761 439292004423 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in dimeric 2-Deoxyuridine 5'-triphosphate nucleotidohydrolase and similar proteins; Region: NTP-PPase_dUTPase; cd11527 439292004424 active site 439292004425 homodimer interface [polypeptide binding]; other site 439292004426 metal binding site [ion binding]; metal-binding site 439292004427 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 439292004428 M42 Peptidase, Endoglucanases; Region: M42_Frv; cd05656 439292004429 oligomer interface [polypeptide binding]; other site 439292004430 active site 439292004431 metal binding site [ion binding]; metal-binding site 439292004432 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; COG2113 439292004433 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 439292004434 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 439292004435 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 439292004436 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 439292004437 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 439292004438 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 439292004439 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 439292004440 dimer interface [polypeptide binding]; other site 439292004441 motif 1; other site 439292004442 active site 439292004443 motif 2; other site 439292004444 motif 3; other site 439292004445 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 439292004446 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 439292004447 putative tRNA-binding site [nucleotide binding]; other site 439292004448 B3/4 domain; Region: B3_4; pfam03483 439292004449 tRNA synthetase B5 domain; Region: B5; smart00874 439292004450 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 439292004451 dimer interface [polypeptide binding]; other site 439292004452 motif 1; other site 439292004453 motif 3; other site 439292004454 motif 2; other site 439292004455 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 439292004456 ribonuclease HIII; Provisional; Region: PRK00996 439292004457 Domain of unknown function (DUF3378); Region: DUF3378; pfam11858 439292004458 bacterial Ribonuclease HIII-like; Region: RNase_HII_bacteria_HIII_like; cd06590 439292004459 RNA/DNA hybrid binding site [nucleotide binding]; other site 439292004460 active site 439292004461 Cell division protein ZapA; Region: ZapA; cl01146 439292004462 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 439292004463 Colicin V production protein; Region: Colicin_V; pfam02674 439292004464 hypothetical protein; Provisional; Region: PRK08609 439292004465 Nucleotidyltransferase (NT) domain of family X DNA Polymerases; Region: NT_POLXc; cd00141 439292004466 active site 439292004467 primer binding site [nucleotide binding]; other site 439292004468 NTP binding site [chemical binding]; other site 439292004469 metal binding triad [ion binding]; metal-binding site 439292004470 Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; Region: PHP_PolX; cd07436 439292004471 active site 439292004472 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 439292004473 MutS domain III; Region: MutS_III; pfam05192 439292004474 ATP-binding cassette domain of MutS2; Region: ABC_MutS2; cd03280 439292004475 Walker A/P-loop; other site 439292004476 ATP binding site [chemical binding]; other site 439292004477 Q-loop/lid; other site 439292004478 ABC transporter signature motif; other site 439292004479 Walker B; other site 439292004480 D-loop; other site 439292004481 H-loop/switch region; other site 439292004482 Smr domain; Region: Smr; pfam01713 439292004483 Predicted membrane protein [Function unknown]; Region: COG3766 439292004484 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 439292004485 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 439292004486 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06710 439292004487 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 439292004488 acyl-activating enzyme (AAE) consensus motif; other site 439292004489 putative AMP binding site [chemical binding]; other site 439292004490 putative active site [active] 439292004491 putative CoA binding site [chemical binding]; other site 439292004492 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06710 439292004493 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 439292004494 acyl-activating enzyme (AAE) consensus motif; other site 439292004495 putative AMP binding site [chemical binding]; other site 439292004496 putative active site [active] 439292004497 putative CoA binding site [chemical binding]; other site 439292004498 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 439292004499 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292004500 YsiA-like protein, C-terminal region; Region: TetR_C_4; pfam08359 439292004501 enoyl-CoA hydratase; Provisional; Region: PRK07658 439292004502 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 439292004503 substrate binding site [chemical binding]; other site 439292004504 oxyanion hole (OAH) forming residues; other site 439292004505 trimer interface [polypeptide binding]; other site 439292004506 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 439292004507 Ligand binding site [chemical binding]; other site 439292004508 Electron transfer flavoprotein domain; Region: ETF; pfam01012 439292004509 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 439292004510 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 439292004511 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 439292004512 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 439292004513 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 439292004514 catalytic residues [active] 439292004515 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 439292004516 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 439292004517 GIY-YIG motif/motif A; other site 439292004518 active site 439292004519 catalytic site [active] 439292004520 putative DNA binding site [nucleotide binding]; other site 439292004521 metal binding site [ion binding]; metal-binding site 439292004522 UvrB/uvrC motif; Region: UVR; pfam02151 439292004523 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 439292004524 aspartate kinase; Reviewed; Region: PRK06635 439292004525 AAK_AK-DapG-like: Amino Acid Kinase Superfamily (AAK), AK-DapG-like; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the diaminopimelate-sensitive aspartokinase isoenzyme AKI (DapG), a monofunctional enzymes found in Bacilli; Region: AAK_AK-DapG-like; cd04246 439292004526 putative catalytic residues [active] 439292004527 putative nucleotide binding site [chemical binding]; other site 439292004528 putative aspartate binding site [chemical binding]; other site 439292004529 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 439292004530 putative allosteric regulatory site; other site 439292004531 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AK-LysC-DapG-like_2; cd04923 439292004532 Protein of unknown function (DUF2507); Region: DUF2507; pfam10702 439292004533 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 439292004534 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 439292004535 Succinate:quinone oxidoreductase (SQR) Type B subfamily 1, transmembrane subunit; composed of proteins similar to Bacillus subtilis SQR. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Bacillus subtilis...; Region: SQR_TypeB_1_TM; cd03497 439292004536 putative Iron-sulfur protein interface [polypeptide binding]; other site 439292004537 succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family; Region: sdhC_b558_fam; TIGR02046 439292004538 proximal heme binding site [chemical binding]; other site 439292004539 distal heme binding site [chemical binding]; other site 439292004540 putative dimer interface [polypeptide binding]; other site 439292004541 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08641 439292004542 L-aspartate oxidase; Provisional; Region: PRK06175 439292004543 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 439292004544 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK08640 439292004545 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 439292004546 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 439292004547 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 439292004548 active site 439292004549 CAT RNA binding domain; Region: CAT_RBD; smart01061 439292004550 PRD domain; Region: PRD; pfam00874 439292004551 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 439292004552 dimerization domain swap beta strand [polypeptide binding]; other site 439292004553 regulatory protein interface [polypeptide binding]; other site 439292004554 active site 439292004555 regulatory phosphorylation site [posttranslational modification]; other site 439292004556 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 439292004557 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 439292004558 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 439292004559 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 439292004560 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 439292004561 MarR family; Region: MarR; pfam01047 439292004562 glutamate racemase; Provisional; Region: PRK00865 439292004563 ribonuclease PH; Reviewed; Region: rph; PRK00173 439292004564 Ribonuclease PH; Region: RNase_PH_bact; cd11362 439292004565 hexamer interface [polypeptide binding]; other site 439292004566 active site 439292004567 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 439292004568 active site 439292004569 dimerization interface [polypeptide binding]; other site 439292004570 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 439292004571 active site 439292004572 metal binding site [ion binding]; metal-binding site 439292004573 homotetramer interface [polypeptide binding]; other site 439292004574 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 439292004575 TPR motif; other site 439292004576 Tetratricopeptide repeat; Region: TPR_16; pfam13432 439292004577 binding surface 439292004578 trigger factor; Provisional; Region: tig; PRK01490 439292004579 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 439292004580 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 439292004581 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 439292004582 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 439292004583 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 439292004584 Walker A motif; other site 439292004585 ATP binding site [chemical binding]; other site 439292004586 Walker B motif; other site 439292004587 arginine finger; other site 439292004588 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 439292004589 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 439292004590 Found in ATP-dependent protease La (LON); Region: LON; smart00464 439292004591 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 439292004592 Walker A motif; other site 439292004593 ATP binding site [chemical binding]; other site 439292004594 Walker B motif; other site 439292004595 arginine finger; other site 439292004596 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 439292004597 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 439292004598 G1 box; other site 439292004599 GTP/Mg2+ binding site [chemical binding]; other site 439292004600 Switch I region; other site 439292004601 G2 box; other site 439292004602 G3 box; other site 439292004603 Switch II region; other site 439292004604 G4 box; other site 439292004605 G5 box; other site 439292004606 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 439292004607 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 439292004608 tRNA; other site 439292004609 putative tRNA binding site [nucleotide binding]; other site 439292004610 putative NADP binding site [chemical binding]; other site 439292004611 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 439292004612 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 439292004613 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 439292004614 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 439292004615 domain interfaces; other site 439292004616 active site 439292004617 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 439292004618 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 439292004619 active site 439292004620 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS; cd00384 439292004621 dimer interface [polypeptide binding]; other site 439292004622 active site 439292004623 Schiff base residues; other site 439292004624 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 439292004625 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 439292004626 inhibitor-cofactor binding pocket; inhibition site 439292004627 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292004628 catalytic residue [active] 439292004629 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 439292004630 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 439292004631 Cell wall-active antibiotics response protein (DUF2154); Region: DUF2154; pfam09922 439292004632 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 439292004633 Histidine kinase; Region: HisKA_3; pfam07730 439292004634 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 439292004635 ATP binding site [chemical binding]; other site 439292004636 Mg2+ binding site [ion binding]; other site 439292004637 G-X-G motif; other site 439292004638 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 439292004639 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 439292004640 active site 439292004641 phosphorylation site [posttranslational modification] 439292004642 intermolecular recognition site; other site 439292004643 dimerization interface [polypeptide binding]; other site 439292004644 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 439292004645 DNA binding residues [nucleotide binding] 439292004646 dimerization interface [polypeptide binding]; other site 439292004647 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 439292004648 ATP-grasp domain; Region: ATP-grasp_4; cl17255 439292004649 ATP-grasp domain; Region: ATP-grasp_4; cl17255 439292004650 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 439292004651 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 439292004652 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 439292004653 Domain of unknown function (DUF4271); Region: DUF4271; pfam14093 439292004654 GAF domain; Region: GAF_3; pfam13492 439292004655 GAF domain; Region: GAF_2; pfam13185 439292004656 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292004657 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292004658 metal binding site [ion binding]; metal-binding site 439292004659 active site 439292004660 I-site; other site 439292004661 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; cl02915 439292004662 VanW like protein; Region: VanW; pfam04294 439292004663 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 439292004664 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 439292004665 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 439292004666 Walker A motif; other site 439292004667 ATP binding site [chemical binding]; other site 439292004668 Walker B motif; other site 439292004669 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 439292004670 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 439292004671 Walker A motif; other site 439292004672 ATP binding site [chemical binding]; other site 439292004673 Walker B motif; other site 439292004674 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 439292004675 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 439292004676 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 439292004677 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 439292004678 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 439292004679 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 439292004680 type IV pilus assembly protein PilM; Region: pilM; TIGR01175 439292004681 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 439292004682 Aspartase; Region: Aspartase; cd01357 439292004683 active sites [active] 439292004684 tetramer interface [polypeptide binding]; other site 439292004685 Maf-like protein; Region: Maf; pfam02545 439292004686 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 439292004687 active site 439292004688 dimer interface [polypeptide binding]; other site 439292004689 hypothetical protein; Reviewed; Region: PRK00024 439292004690 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 439292004691 helix-hairpin-helix signature motif; other site 439292004692 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 439292004693 MPN+ (JAMM) motif; other site 439292004694 Zinc-binding site [ion binding]; other site 439292004695 rod shape-determining protein MreB; Provisional; Region: PRK13927 439292004696 MreB and similar proteins; Region: MreB_like; cd10225 439292004697 nucleotide binding site [chemical binding]; other site 439292004698 Mg binding site [ion binding]; other site 439292004699 putative protofilament interaction site [polypeptide binding]; other site 439292004700 RodZ interaction site [polypeptide binding]; other site 439292004701 rod shape-determining protein MreC; Provisional; Region: PRK13922 439292004702 rod shape-determining protein MreC; Region: MreC; pfam04085 439292004703 rod shape-determining protein MreD; Region: MreD; cl01087 439292004704 septum formation inhibitor; Reviewed; Region: minC; PRK00513 439292004705 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 439292004706 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 439292004707 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 439292004708 Switch I; other site 439292004709 Switch II; other site 439292004710 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 439292004711 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 439292004712 Transcriptional regulators [Transcription]; Region: PurR; COG1609 439292004713 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 439292004714 DNA binding site [nucleotide binding] 439292004715 domain linker motif; other site 439292004716 Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species; Region: PBP1_CcpB_like; cd06286 439292004717 putative dimerization interface [polypeptide binding]; other site 439292004718 putative ligand binding site [chemical binding]; other site 439292004719 ABC-type sugar transport systems, permease components [Carbohydrate transport and metabolism]; Region: UgpA; COG1175 439292004720 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 439292004721 dimer interface [polypeptide binding]; other site 439292004722 conserved gate region; other site 439292004723 putative PBP binding loops; other site 439292004724 ABC-ATPase subunit interface; other site 439292004725 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 439292004726 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 439292004727 dimer interface [polypeptide binding]; other site 439292004728 conserved gate region; other site 439292004729 putative PBP binding loops; other site 439292004730 ABC-ATPase subunit interface; other site 439292004731 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 439292004732 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 439292004733 homodimer interface [polypeptide binding]; other site 439292004734 oligonucleotide binding site [chemical binding]; other site 439292004735 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 439292004736 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 439292004737 hypothetical protein; Provisional; Region: PRK14553 439292004738 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 439292004739 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 439292004740 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 439292004741 PBP superfamily domain; Region: PBP_like_2; cl17296 439292004742 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 439292004743 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 439292004744 dimer interface [polypeptide binding]; other site 439292004745 conserved gate region; other site 439292004746 putative PBP binding loops; other site 439292004747 ABC-ATPase subunit interface; other site 439292004748 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 439292004749 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 439292004750 dimer interface [polypeptide binding]; other site 439292004751 conserved gate region; other site 439292004752 putative PBP binding loops; other site 439292004753 ABC-ATPase subunit interface; other site 439292004754 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 439292004755 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 439292004756 Walker A/P-loop; other site 439292004757 ATP binding site [chemical binding]; other site 439292004758 Q-loop/lid; other site 439292004759 ABC transporter signature motif; other site 439292004760 Walker B; other site 439292004761 D-loop; other site 439292004762 H-loop/switch region; other site 439292004763 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 439292004764 PhoU domain; Region: PhoU; pfam01895 439292004765 PhoU domain; Region: PhoU; pfam01895 439292004766 Protein of unknown function (DUF1516); Region: DUF1516; cl11654 439292004767 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 439292004768 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; cl17736 439292004769 active site 439292004770 phosphorylation site [posttranslational modification] 439292004771 intermolecular recognition site; other site 439292004772 dimerization interface [polypeptide binding]; other site 439292004773 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 439292004774 DNA binding residues [nucleotide binding] 439292004775 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 439292004776 active site residue [active] 439292004777 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292004778 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292004779 dimer interface [polypeptide binding]; other site 439292004780 putative CheW interface [polypeptide binding]; other site 439292004781 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 439292004782 active site residue [active] 439292004783 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 439292004784 active site residue [active] 439292004785 thiosulfate reductase PhsA; Provisional; Region: PRK15488 439292004786 The MopB_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme...; Region: MopB_Thiosulfate-R-like; cd02755 439292004787 putative [Fe4-S4] binding site [ion binding]; other site 439292004788 putative molybdopterin cofactor binding site [chemical binding]; other site 439292004789 The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme...; Region: MopB_CT_Thiosulfate-R-like; cd02778 439292004790 putative molybdopterin cofactor binding site; other site 439292004791 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 439292004792 4Fe-4S binding domain; Region: Fer4; pfam00037 439292004793 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 439292004794 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 439292004795 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 439292004796 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 439292004797 active site residue [active] 439292004798 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 439292004799 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 439292004800 active site residue [active] 439292004801 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 439292004802 active site residue [active] 439292004803 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 439292004804 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 439292004805 hexamer interface [polypeptide binding]; other site 439292004806 ligand binding site [chemical binding]; other site 439292004807 putative active site [active] 439292004808 NAD(P) binding site [chemical binding]; other site 439292004809 KTSC domain; Region: KTSC; pfam13619 439292004810 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 439292004811 PAS domain; Region: PAS_9; pfam13426 439292004812 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292004813 metal binding site [ion binding]; metal-binding site 439292004814 active site 439292004815 I-site; other site 439292004816 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292004817 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 439292004818 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 439292004819 active site 439292004820 phosphorylation site [posttranslational modification] 439292004821 intermolecular recognition site; other site 439292004822 dimerization interface [polypeptide binding]; other site 439292004823 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 439292004824 DNA binding site [nucleotide binding] 439292004825 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292004826 dimerization interface [polypeptide binding]; other site 439292004827 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 439292004828 dimer interface [polypeptide binding]; other site 439292004829 phosphorylation site [posttranslational modification] 439292004830 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 439292004831 ATP binding site [chemical binding]; other site 439292004832 Mg2+ binding site [ion binding]; other site 439292004833 G-X-G motif; other site 439292004834 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 439292004835 MarR family; Region: MarR_2; pfam12802 439292004836 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 439292004837 Protein export membrane protein; Region: SecD_SecF; cl14618 439292004838 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 439292004839 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292004840 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 439292004841 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 439292004842 ligand binding site [chemical binding]; other site 439292004843 flexible hinge region; other site 439292004844 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 439292004845 non-specific DNA interactions [nucleotide binding]; other site 439292004846 DNA binding site [nucleotide binding] 439292004847 sequence specific DNA binding site [nucleotide binding]; other site 439292004848 putative cAMP binding site [chemical binding]; other site 439292004849 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cd00501 439292004850 putative substrate binding pocket [chemical binding]; other site 439292004851 AC domain interface; other site 439292004852 catalytic triad [active] 439292004853 AB domain interface; other site 439292004854 interchain disulfide; other site 439292004855 GIY-YIG domain of hypothetical proteins from archaea and their bacterial homologs; Region: GIY-YIG_COG1833; cd10441 439292004856 putative active site [active] 439292004857 GIY-YIG motif/motif A; other site 439292004858 putative metal binding site [ion binding]; other site 439292004859 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH; cd00488 439292004860 aromatic arch; other site 439292004861 DCoH dimer interaction site [polypeptide binding]; other site 439292004862 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 439292004863 DCoH tetramer interaction site [polypeptide binding]; other site 439292004864 substrate binding site [chemical binding]; other site 439292004865 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292004866 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 439292004867 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 439292004868 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 439292004869 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 439292004870 FeS/SAM binding site; other site 439292004871 Protein of unknown function (DUF4080); Region: DUF4080; pfam13311 439292004872 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 439292004873 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 439292004874 FeS/SAM binding site; other site 439292004875 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 439292004876 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 439292004877 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 439292004878 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 439292004879 putative active site [active] 439292004880 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 439292004881 DctM-like transporters; Region: DctM; pfam06808 439292004882 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 439292004883 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 439292004884 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_8; cd13134 439292004885 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 439292004886 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 439292004887 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292004888 dimer interface [polypeptide binding]; other site 439292004889 putative CheW interface [polypeptide binding]; other site 439292004890 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 439292004891 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 439292004892 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 439292004893 dimer interface [polypeptide binding]; other site 439292004894 conserved gate region; other site 439292004895 putative PBP binding loops; other site 439292004896 ABC-ATPase subunit interface; other site 439292004897 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 439292004898 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 439292004899 dimer interface [polypeptide binding]; other site 439292004900 conserved gate region; other site 439292004901 putative PBP binding loops; other site 439292004902 ABC-ATPase subunit interface; other site 439292004903 Transcriptional regulators [Transcription]; Region: PurR; COG1609 439292004904 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 439292004905 DNA binding site [nucleotide binding] 439292004906 domain linker motif; other site 439292004907 Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors; Region: PBP1_ycjW_transcription_regulator_like; cd06294 439292004908 putative dimerization interface [polypeptide binding]; other site 439292004909 putative ligand binding site [chemical binding]; other site 439292004910 Domain of unknown function DUF20; Region: UPF0118; pfam01594 439292004911 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 439292004912 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 439292004913 active site residue [active] 439292004914 Intracellular proteinase inhibitor; Region: BsuPI; pfam12690 439292004915 SNF2 Helicase protein; Region: DUF3670; pfam12419 439292004916 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 439292004917 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 439292004918 ATP binding site [chemical binding]; other site 439292004919 putative Mg++ binding site [ion binding]; other site 439292004920 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 439292004921 nucleotide binding region [chemical binding]; other site 439292004922 ATP-binding site [chemical binding]; other site 439292004923 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 439292004924 AzlC protein; Region: AzlC; cl00570 439292004925 Branched-chain amino acid transport protein (AzlD); Region: AzlD; pfam05437 439292004926 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292004927 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 439292004928 Coenzyme A binding pocket [chemical binding]; other site 439292004929 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 439292004930 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 439292004931 motif II; other site 439292004932 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 439292004933 Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG); Region: Caa3_CtaG; cl09173 439292004934 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 439292004935 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 439292004936 Cu(I) binding site [ion binding]; other site 439292004937 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 439292004938 MoaE interaction surface [polypeptide binding]; other site 439292004939 MoeB interaction surface [polypeptide binding]; other site 439292004940 thiocarboxylated glycine; other site 439292004941 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 439292004942 MoaE homodimer interface [polypeptide binding]; other site 439292004943 MoaD interaction [polypeptide binding]; other site 439292004944 active site residues [active] 439292004945 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 439292004946 Walker A motif; other site 439292004947 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 439292004948 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 439292004949 dimer interface [polypeptide binding]; other site 439292004950 putative functional site; other site 439292004951 putative MPT binding site; other site 439292004952 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 439292004953 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 439292004954 ligand binding site [chemical binding]; other site 439292004955 flexible hinge region; other site 439292004956 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 439292004957 putative switch regulator; other site 439292004958 non-specific DNA interactions [nucleotide binding]; other site 439292004959 DNA binding site [nucleotide binding] 439292004960 sequence specific DNA binding site [nucleotide binding]; other site 439292004961 putative cAMP binding site [chemical binding]; other site 439292004962 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 439292004963 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 439292004964 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 439292004965 ligand binding site [chemical binding]; other site 439292004966 flexible hinge region; other site 439292004967 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 439292004968 putative switch regulator; other site 439292004969 non-specific DNA interactions [nucleotide binding]; other site 439292004970 DNA binding site [nucleotide binding] 439292004971 sequence specific DNA binding site [nucleotide binding]; other site 439292004972 putative cAMP binding site [chemical binding]; other site 439292004973 YwiC-like protein; Region: YwiC; pfam14256 439292004974 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 439292004975 Probable transposase; Region: OrfB_IS605; pfam01385 439292004976 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 439292004977 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 439292004978 Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria; Region: PBP1_BmpA_like; cd06304 439292004979 ligand binding site [chemical binding]; other site 439292004980 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 439292004981 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 439292004982 dimer interface [polypeptide binding]; other site 439292004983 active site 439292004984 CoA binding pocket [chemical binding]; other site 439292004985 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 439292004986 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 439292004987 dimer interface [polypeptide binding]; other site 439292004988 active site 439292004989 radical SAM protein, BA_1875 family; Region: sam_11; TIGR04053 439292004990 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 439292004991 FeS/SAM binding site; other site 439292004992 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 439292004993 Transcriptional regulator [Transcription]; Region: LytR; COG1316 439292004994 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 439292004995 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 439292004996 ligand binding site [chemical binding]; other site 439292004997 flexible hinge region; other site 439292004998 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 439292004999 putative switch regulator; other site 439292005000 non-specific DNA interactions [nucleotide binding]; other site 439292005001 DNA binding site [nucleotide binding] 439292005002 sequence specific DNA binding site [nucleotide binding]; other site 439292005003 putative cAMP binding site [chemical binding]; other site 439292005004 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 439292005005 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 439292005006 active site 439292005007 HIGH motif; other site 439292005008 dimer interface [polypeptide binding]; other site 439292005009 KMSKS motif; other site 439292005010 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 439292005011 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 439292005012 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 439292005013 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292005014 Zn2+ binding site [ion binding]; other site 439292005015 Mg2+ binding site [ion binding]; other site 439292005016 Putative glycosyl hydrolase domain; Region: DUF4015; pfam13200 439292005017 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292005018 Coenzyme A binding pocket [chemical binding]; other site 439292005019 Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex...; Region: ArsC_Spx; cd03032 439292005020 ArsC family; Region: ArsC; pfam03960 439292005021 putative catalytic residues [active] 439292005022 thiol/disulfide switch; other site 439292005023 adaptor protein; Provisional; Region: PRK02315 439292005024 Competence protein CoiA-like family; Region: CoiA; cl11541 439292005025 oligoendopeptidase F; Region: pepF; TIGR00181 439292005026 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_3; cd09608 439292005027 active site 439292005028 Zn binding site [ion binding]; other site 439292005029 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 439292005030 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 439292005031 catalytic residues [active] 439292005032 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 439292005033 apolar tunnel; other site 439292005034 heme binding site [chemical binding]; other site 439292005035 dimerization interface [polypeptide binding]; other site 439292005036 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 439292005037 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 439292005038 N-acetyl-D-glucosamine binding site [chemical binding]; other site 439292005039 catalytic residue [active] 439292005040 Uncharacterized subgroup 1 of the CYTH-like superfamily; Region: CYTH-like_Pase_1; cd07762 439292005041 putative active site [active] 439292005042 putative metal binding residues [ion binding]; other site 439292005043 signature motif; other site 439292005044 putative triphosphate binding site [ion binding]; other site 439292005045 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 439292005046 synthetase active site [active] 439292005047 NTP binding site [chemical binding]; other site 439292005048 metal binding site [ion binding]; metal-binding site 439292005049 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK04885 439292005050 ATP-NAD kinase; Region: NAD_kinase; pfam01513 439292005051 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 439292005052 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 439292005053 active site 439292005054 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08594 439292005055 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 439292005056 NAD binding site [chemical binding]; other site 439292005057 homotetramer interface [polypeptide binding]; other site 439292005058 homodimer interface [polypeptide binding]; other site 439292005059 substrate binding site [chemical binding]; other site 439292005060 active site 439292005061 Predicted flavoprotein [General function prediction only]; Region: COG0431 439292005062 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 439292005063 radical SAM protein, BA_1875 family; Region: sam_11; TIGR04053 439292005064 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 439292005065 FeS/SAM binding site; other site 439292005066 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 439292005067 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292005068 dimerization interface [polypeptide binding]; other site 439292005069 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292005070 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292005071 dimer interface [polypeptide binding]; other site 439292005072 putative CheW interface [polypeptide binding]; other site 439292005073 Domain of unknown function (DUF373); Region: DUF373; cl12079 439292005074 PAS domain S-box; Region: sensory_box; TIGR00229 439292005075 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292005076 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292005077 metal binding site [ion binding]; metal-binding site 439292005078 active site 439292005079 I-site; other site 439292005080 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292005081 Peptide methionine sulfoxide reductase; Region: PMSR; pfam01625 439292005082 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 439292005083 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 439292005084 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 439292005085 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 439292005086 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292005087 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292005088 dimer interface [polypeptide binding]; other site 439292005089 putative CheW interface [polypeptide binding]; other site 439292005090 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 439292005091 malate synthase G; Provisional; Region: PRK02999 439292005092 active site 439292005093 isocitrate lyase; Provisional; Region: PRK15063 439292005094 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 439292005095 tetramer interface [polypeptide binding]; other site 439292005096 active site 439292005097 Mg2+/Mn2+ binding site [ion binding]; other site 439292005098 BCCT family transporter; Region: BCCT; pfam02028 439292005099 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 439292005100 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 439292005101 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 439292005102 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 439292005103 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 439292005104 active site 439292005105 catalytic tetrad [active] 439292005106 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 439292005107 DEAD-like helicases superfamily; Region: DEXDc; smart00487 439292005108 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 439292005109 ATP binding site [chemical binding]; other site 439292005110 putative Mg++ binding site [ion binding]; other site 439292005111 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 439292005112 nucleotide binding region [chemical binding]; other site 439292005113 ATP-binding site [chemical binding]; other site 439292005114 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 439292005115 tetramer interfaces [polypeptide binding]; other site 439292005116 binuclear metal-binding site [ion binding]; other site 439292005117 hypothetical protein; Provisional; Region: PRK13679 439292005118 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 439292005119 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 439292005120 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 439292005121 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292005122 Coenzyme A binding pocket [chemical binding]; other site 439292005123 S-ribosylhomocysteinase; Provisional; Region: PRK02260 439292005124 This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH as...; Region: NfsA_FRP; cd02146 439292005125 dimer interface [polypeptide binding]; other site 439292005126 FMN binding site [chemical binding]; other site 439292005127 NADPH bind site [chemical binding]; other site 439292005128 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 439292005129 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292005130 Walker A/P-loop; other site 439292005131 ATP binding site [chemical binding]; other site 439292005132 Q-loop/lid; other site 439292005133 ABC transporter signature motif; other site 439292005134 Walker B; other site 439292005135 D-loop; other site 439292005136 H-loop/switch region; other site 439292005137 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 439292005138 TrkA-N domain; Region: TrkA_N; pfam02254 439292005139 TrkA-C domain; Region: TrkA_C; pfam02080 439292005140 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 439292005141 Ligand Binding Site [chemical binding]; other site 439292005142 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 439292005143 Mechanosensitive ion channel; Region: MS_channel; pfam00924 439292005144 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 439292005145 catalytic residues [active] 439292005146 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292005147 Zn2+ binding site [ion binding]; other site 439292005148 Mg2+ binding site [ion binding]; other site 439292005149 Tetrahydrodipicolinate succinyltransferase N-terminal; Region: DapH_N; pfam08503 439292005150 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; Region: DapD_Ac; TIGR03532 439292005151 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 439292005152 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 439292005153 putative CoA binding site [chemical binding]; other site 439292005154 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 439292005155 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 439292005156 metal binding site [ion binding]; metal-binding site 439292005157 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 439292005158 Mechanosensitive ion channel; Region: MS_channel; pfam00924 439292005159 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 439292005160 TrkA-N domain; Region: TrkA_N; pfam02254 439292005161 TrkA-C domain; Region: TrkA_C; pfam02080 439292005162 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 439292005163 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 439292005164 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 439292005165 Protein of unknown function (DUF1447); Region: DUF1447; cl11492 439292005166 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 439292005167 active site 439292005168 catalytic residues [active] 439292005169 metal binding site [ion binding]; metal-binding site 439292005170 Putative cell-wall binding lipoprotein; Region: YkyA; pfam10368 439292005171 Protein of unknown function (DUF342); Region: DUF342; pfam03961 439292005172 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_x; TIGR03181 439292005173 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 439292005174 TPP-binding site [chemical binding]; other site 439292005175 heterodimer interface [polypeptide binding]; other site 439292005176 tetramer interface [polypeptide binding]; other site 439292005177 phosphorylation loop region [posttranslational modification] 439292005178 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 439292005179 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 439292005180 alpha subunit interface [polypeptide binding]; other site 439292005181 TPP binding site [chemical binding]; other site 439292005182 heterodimer interface [polypeptide binding]; other site 439292005183 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 439292005184 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 439292005185 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 439292005186 E3 interaction surface; other site 439292005187 lipoyl attachment site [posttranslational modification]; other site 439292005188 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 439292005189 E3 interaction surface; other site 439292005190 lipoyl attachment site [posttranslational modification]; other site 439292005191 e3 binding domain; Region: E3_binding; pfam02817 439292005192 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 439292005193 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 439292005194 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 439292005195 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 439292005196 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 439292005197 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 439292005198 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 439292005199 NodB motif; other site 439292005200 active site 439292005201 catalytic site [active] 439292005202 metal binding site [ion binding]; metal-binding site 439292005203 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 439292005204 Peptidase family M23; Region: Peptidase_M23; pfam01551 439292005205 Protein of unknown function (DUF3055); Region: DUF3055; pfam11256 439292005206 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 439292005207 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine...; Region: Orn_deC_like; cd00615 439292005208 homodimer interface [polypeptide binding]; other site 439292005209 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292005210 catalytic residue [active] 439292005211 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 439292005212 hypothetical protein; Provisional; Region: PRK04387 439292005213 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4493 439292005214 Protein of unknown function (DUF1054); Region: DUF1054; pfam06335 439292005215 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 439292005216 Inositol-monophosphatase-like domains. This family of phosphatases is dependent on bivalent metal ions such as Mg++, and many members are inhibited by Li+ (which is thought to displace a bivalent ion in the active site). Substrates include fructose-1; Region: IMPase_like; cd01637 439292005217 active site 439292005218 YlaH-like protein; Region: YlaH; pfam14036 439292005219 Uncharacterized protein conserved in bacteria (DUF2197); Region: DUF2197; pfam09963 439292005220 hypothetical protein; Provisional; Region: PRK06733 439292005221 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 439292005222 hypothetical protein; Provisional; Region: PRK13666 439292005223 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 439292005224 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 439292005225 dimerization interface [polypeptide binding]; other site 439292005226 DPS ferroxidase diiron center [ion binding]; other site 439292005227 ion pore; other site 439292005228 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 439292005229 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 439292005230 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 439292005231 UbiA prenyltransferase family; Region: UbiA; pfam01040 439292005232 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 439292005233 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 439292005234 Cytochrome c; Region: Cytochrom_C; pfam00034 439292005235 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 439292005236 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 439292005237 D-pathway; other site 439292005238 Putative ubiquinol binding site [chemical binding]; other site 439292005239 Low-spin heme (heme b) binding site [chemical binding]; other site 439292005240 Putative water exit pathway; other site 439292005241 Binuclear center (heme o3/CuB) [ion binding]; other site 439292005242 K-pathway; other site 439292005243 Putative proton exit pathway; other site 439292005244 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 439292005245 Protein of unknown function (DUF420); Region: DUF420; pfam04238 439292005246 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 439292005247 Domain of unknown function DUF20; Region: UPF0118; pfam01594 439292005248 YugN-like family; Region: YugN; pfam08868 439292005249 Uncharacterized protein with SCP/PR1 domains [Function unknown]; Region: COG2340 439292005250 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 439292005251 Regulatory protein involved in competence development and sporulation [Replication, recombination and repair; Signal transduction mechanisms]; Region: COG3679 439292005252 Uncharacterized protein conserved in bacteria (DUF2129); Region: DUF2129; cl11453 439292005253 Conserved hypothetical protein 95; Region: Cons_hypoth95; pfam03602 439292005254 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 439292005255 S-adenosylmethionine binding site [chemical binding]; other site 439292005256 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 439292005257 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 439292005258 active site 439292005259 (T/H)XGH motif; other site 439292005260 Predicted secreted protein containing a PDZ domain [Signal transduction mechanisms]; Region: SdrC; COG3480 439292005261 PDZ domain of ATP-dependent LON serine proteases. Most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this bacterial subfamily of protease-associated PDZ...; Region: PDZ_LON_protease; cd00986 439292005262 protein binding site [polypeptide binding]; other site 439292005263 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 439292005264 hypothetical protein; Provisional; Region: PRK13670 439292005265 HIGH Nucleotidyl Transferase; Region: HIGH_NTase1; cl17673 439292005266 Predicted metal-binding, possibly nucleic acid-binding protein [General function prediction only]; Region: COG1399 439292005267 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 439292005268 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 439292005269 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 439292005270 substrate binding site [chemical binding]; other site 439292005271 oxyanion hole (OAH) forming residues; other site 439292005272 trimer interface [polypeptide binding]; other site 439292005273 hypothetical protein; Provisional; Region: PRK13688 439292005274 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292005275 Coenzyme A binding pocket [chemical binding]; other site 439292005276 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 439292005277 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 439292005278 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 439292005279 Uncharacterized protein conserved in bacteria (DUF2317); Region: DUF2317; pfam10079 439292005280 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4365 439292005281 cell division protein MraZ; Reviewed; Region: PRK00326 439292005282 MraZ protein; Region: MraZ; pfam02381 439292005283 MraZ protein; Region: MraZ; pfam02381 439292005284 MraW methylase family; Region: Methyltransf_5; pfam01795 439292005285 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 439292005286 Cell division protein FtsL; Region: FtsL; cl11433 439292005287 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 439292005288 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 439292005289 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 439292005290 PASTA domain of PBP2x-like proteins, first 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_1; cd06576 439292005291 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 439292005292 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 439292005293 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 439292005294 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 439292005295 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 439292005296 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 439292005297 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 439292005298 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 439292005299 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 439292005300 Mg++ binding site [ion binding]; other site 439292005301 putative catalytic motif [active] 439292005302 putative substrate binding site [chemical binding]; other site 439292005303 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02472 439292005304 TrkA-N domain; Region: TrkA_N; pfam02254 439292005305 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 439292005306 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 439292005307 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 439292005308 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 439292005309 active site 439292005310 homodimer interface [polypeptide binding]; other site 439292005311 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 439292005312 FAD binding domain; Region: FAD_binding_4; pfam01565 439292005313 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 439292005314 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 439292005315 Cell division protein FtsQ; Region: FtsQ; pfam03799 439292005316 Bacterial protein of unknown function (DUF881); Region: DUF881; pfam05949 439292005317 Bacterial protein of unknown function (DUF881); Region: DUF881; pfam05949 439292005318 Protein of unknown function (DUF1290); Region: DUF1290; pfam06947 439292005319 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 439292005320 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 439292005321 nucleotide binding site [chemical binding]; other site 439292005322 SHS2 domain inserted in FTSA; Region: SHS2_FTSA; pfam02491 439292005323 Cell division protein FtsA; Region: FtsA; pfam14450 439292005324 cell division protein FtsZ; Validated; Region: PRK09330 439292005325 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 439292005326 nucleotide binding site [chemical binding]; other site 439292005327 SulA interaction site; other site 439292005328 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 439292005329 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 439292005330 catalytic residue [active] 439292005331 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1799 439292005332 YGGT family; Region: YGGT; pfam02325 439292005333 DivIVA protein; Region: DivIVA; pfam05103 439292005334 DivIVA domain; Region: DivI1A_domain; TIGR03544 439292005335 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 439292005336 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 439292005337 HIGH motif; other site 439292005338 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 439292005339 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 439292005340 active site 439292005341 KMSKS motif; other site 439292005342 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 439292005343 tRNA binding surface [nucleotide binding]; other site 439292005344 anticodon binding site; other site 439292005345 DsrH like protein; Region: DsrH; cl17347 439292005346 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 439292005347 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 439292005348 lipoprotein signal peptidase; Provisional; Region: PRK14787 439292005349 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 439292005350 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 439292005351 RNA binding surface [nucleotide binding]; other site 439292005352 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 439292005353 active site 439292005354 Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Region: PyrR; COG2065 439292005355 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 439292005356 active site 439292005357 uracil transporter; Provisional; Region: PRK10720 439292005358 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 439292005359 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 439292005360 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 439292005361 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 439292005362 dihydroorotase; Validated; Region: pyrC; PRK09357 439292005363 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 439292005364 active site 439292005365 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 439292005366 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 439292005367 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 439292005368 catalytic site [active] 439292005369 subunit interface [polypeptide binding]; other site 439292005370 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 439292005371 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 439292005372 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 439292005373 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 439292005374 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 439292005375 ATP-grasp domain; Region: ATP-grasp_4; cl17255 439292005376 Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways...; Region: MGS_CPS_II; cd01424 439292005377 IMP binding site; other site 439292005378 dimer interface [polypeptide binding]; other site 439292005379 interdomain contacts; other site 439292005380 partial ornithine binding site; other site 439292005381 dihydroorotate dehydrogenase electron transfer subunit; Reviewed; Region: PRK00054 439292005382 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to...; Region: DHOD_e_trans; cd06218 439292005383 FAD binding pocket [chemical binding]; other site 439292005384 FAD binding motif [chemical binding]; other site 439292005385 phosphate binding motif [ion binding]; other site 439292005386 beta-alpha-beta structure motif; other site 439292005387 NAD binding pocket [chemical binding]; other site 439292005388 Iron coordination center [ion binding]; other site 439292005389 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 439292005390 Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. 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...; Region: DHOD_1B_like; cd04740 439292005391 heterodimer interface [polypeptide binding]; other site 439292005392 active site 439292005393 FMN binding site [chemical binding]; other site 439292005394 homodimer interface [polypeptide binding]; other site 439292005395 substrate binding site [chemical binding]; other site 439292005396 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 439292005397 active site 439292005398 dimer interface [polypeptide binding]; other site 439292005399 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 439292005400 active site 439292005401 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 439292005402 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 439292005403 putative active site [active] 439292005404 putative NTP binding site [chemical binding]; other site 439292005405 putative nucleic acid binding site [nucleotide binding]; other site 439292005406 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 439292005407 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 439292005408 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 439292005409 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292005410 Walker A/P-loop; other site 439292005411 ATP binding site [chemical binding]; other site 439292005412 Q-loop/lid; other site 439292005413 ABC transporter signature motif; other site 439292005414 Walker B; other site 439292005415 D-loop; other site 439292005416 H-loop/switch region; other site 439292005417 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 439292005418 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 439292005419 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 439292005420 Walker A/P-loop; other site 439292005421 ATP binding site [chemical binding]; other site 439292005422 Q-loop/lid; other site 439292005423 ABC transporter signature motif; other site 439292005424 Walker B; other site 439292005425 D-loop; other site 439292005426 H-loop/switch region; other site 439292005427 Fibronectin-binding protein A N-terminus (FbpA); Region: FbpA; pfam05833 439292005428 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 439292005429 NAD binding pocket [chemical binding]; other site 439292005430 Domain of unknown function (DUF814); Region: DUF814; pfam05670 439292005431 hypothetical protein; Provisional; Region: PRK11820 439292005432 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 439292005433 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 439292005434 hypothetical protein; Provisional; Region: PRK04323 439292005435 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 439292005436 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 439292005437 catalytic site [active] 439292005438 G-X2-G-X-G-K; other site 439292005439 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 439292005440 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 439292005441 Flavoprotein; Region: Flavoprotein; pfam02441 439292005442 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 439292005443 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 439292005444 primosomal protein N' Region: priA; TIGR00595 439292005445 ATP binding site [chemical binding]; other site 439292005446 helicase superfamily c-terminal domain; Region: HELICc; smart00490 439292005447 ATP-binding site [chemical binding]; other site 439292005448 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 439292005449 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 439292005450 putative active site [active] 439292005451 substrate binding site [chemical binding]; other site 439292005452 putative cosubstrate binding site; other site 439292005453 catalytic site [active] 439292005454 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 439292005455 substrate binding site [chemical binding]; other site 439292005456 16S rRNA methyltransferase B; Provisional; Region: PRK14902 439292005457 NusB family; Region: NusB; pfam01029 439292005458 putative RNA binding site [nucleotide binding]; other site 439292005459 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 439292005460 S-adenosylmethionine binding site [chemical binding]; other site 439292005461 Protein phosphatase 2C; Region: PP2C; pfam00481 439292005462 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 439292005463 active site 439292005464 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 439292005465 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 439292005466 active site 439292005467 ATP binding site [chemical binding]; other site 439292005468 substrate binding site [chemical binding]; other site 439292005469 activation loop (A-loop); other site 439292005470 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 439292005471 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 439292005472 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 439292005473 GTPase RsgA; Reviewed; Region: PRK00098 439292005474 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 439292005475 RNA binding site [nucleotide binding]; other site 439292005476 homodimer interface [polypeptide binding]; other site 439292005477 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 439292005478 GTPase/Zn-binding domain interface [polypeptide binding]; other site 439292005479 GTP/Mg2+ binding site [chemical binding]; other site 439292005480 G4 box; other site 439292005481 G5 box; other site 439292005482 G1 box; other site 439292005483 Switch I region; other site 439292005484 G2 box; other site 439292005485 G3 box; other site 439292005486 Switch II region; other site 439292005487 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 439292005488 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 439292005489 substrate binding site [chemical binding]; other site 439292005490 hexamer interface [polypeptide binding]; other site 439292005491 metal binding site [ion binding]; metal-binding site 439292005492 Thiamine transporter protein (Thia_YuaJ); Region: Thia_YuaJ; pfam09515 439292005493 Thiamine pyrophosphokinase; Region: TPK; cd07995 439292005494 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 439292005495 active site 439292005496 dimerization interface [polypeptide binding]; other site 439292005497 thiamine binding site [chemical binding]; other site 439292005498 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 439292005499 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1302 439292005500 DAK2 domain fusion protein YloV; Region: YloV; TIGR03599 439292005501 DAK2 domain; Region: Dak2; pfam02734 439292005502 EDD domain protein, DegV family; Region: DegV; TIGR00762 439292005503 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 439292005504 L-serine dehydratase, iron-sulfur-dependent, beta subunit; Region: sda_beta; TIGR00719 439292005505 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 439292005506 C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit; Region: ACT_LSD; cd04903 439292005507 putative L-serine binding site [chemical binding]; other site 439292005508 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 439292005509 L-serine deaminase [Amino acid transport and metabolism]; Region: SdaA; COG1760 439292005510 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 439292005511 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 439292005512 generic binding surface II; other site 439292005513 ssDNA binding site; other site 439292005514 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 439292005515 ATP binding site [chemical binding]; other site 439292005516 putative Mg++ binding site [ion binding]; other site 439292005517 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 439292005518 nucleotide binding region [chemical binding]; other site 439292005519 ATP-binding site [chemical binding]; other site 439292005520 fatty acid biosynthesis transcriptional regulator; Provisional; Region: PRK04424 439292005521 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cd03440 439292005522 active site 2 [active] 439292005523 active site 1 [active] 439292005524 putative phosphate acyltransferase; Provisional; Region: PRK05331 439292005525 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 439292005526 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 439292005527 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 439292005528 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 439292005529 NAD(P) binding site [chemical binding]; other site 439292005530 homotetramer interface [polypeptide binding]; other site 439292005531 homodimer interface [polypeptide binding]; other site 439292005532 active site 439292005533 acyl carrier protein; Provisional; Region: acpP; PRK00982 439292005534 ribonuclease III; Reviewed; Region: rnc; PRK00102 439292005535 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 439292005536 dimerization interface [polypeptide binding]; other site 439292005537 active site 439292005538 metal binding site [ion binding]; metal-binding site 439292005539 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 439292005540 dsRNA binding site [nucleotide binding]; other site 439292005541 Kinase associated protein B; Region: KapB; pfam08810 439292005542 Protein of unknown function (DUF1128); Region: DUF1128; cl11553 439292005543 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 439292005544 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 439292005545 Walker A/P-loop; other site 439292005546 ATP binding site [chemical binding]; other site 439292005547 Q-loop/lid; other site 439292005548 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 439292005549 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 439292005550 ABC transporter signature motif; other site 439292005551 Walker B; other site 439292005552 D-loop; other site 439292005553 H-loop/switch region; other site 439292005554 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 439292005555 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 439292005556 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 439292005557 P loop; other site 439292005558 GTP binding site [chemical binding]; other site 439292005559 putative DNA-binding protein; Validated; Region: PRK00118 439292005560 Putative helix-turn-helix protein, YlxM / p13 like; Region: UPF0122; pfam04297 439292005561 signal recognition particle protein; Provisional; Region: PRK10867 439292005562 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 439292005563 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 439292005564 P loop; other site 439292005565 GTP binding site [chemical binding]; other site 439292005566 Signal peptide binding domain; Region: SRP_SPB; pfam02978 439292005567 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 439292005568 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 439292005569 hypothetical protein; Provisional; Region: PRK00468 439292005570 G-X-X-G motif; other site 439292005571 Protein of unknown function (DUF2869); Region: DUF2869; pfam11068 439292005572 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 439292005573 RimM N-terminal domain; Region: RimM; pfam01782 439292005574 PRC-barrel domain; Region: PRC; pfam05239 439292005575 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 439292005576 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 439292005577 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 439292005578 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 439292005579 Catalytic site [active] 439292005580 GTPase YlqF; Reviewed; Region: rbgA; PRK09563 439292005581 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 439292005582 GTP/Mg2+ binding site [chemical binding]; other site 439292005583 G4 box; other site 439292005584 G5 box; other site 439292005585 G1 box; other site 439292005586 Switch I region; other site 439292005587 G2 box; other site 439292005588 G3 box; other site 439292005589 Switch II region; other site 439292005590 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 439292005591 RNA/DNA hybrid binding site [nucleotide binding]; other site 439292005592 active site 439292005593 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 439292005594 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 439292005595 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 439292005596 CoA-ligase; Region: Ligase_CoA; pfam00549 439292005597 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 439292005598 CoA binding domain; Region: CoA_binding; smart00881 439292005599 CoA-ligase; Region: Ligase_CoA; pfam00549 439292005600 DNA protecting protein DprA; Region: dprA; TIGR00732 439292005601 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 439292005602 DNA topoisomerase I; Validated; Region: PRK05582 439292005603 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 439292005604 active site 439292005605 interdomain interaction site; other site 439292005606 putative metal-binding site [ion binding]; other site 439292005607 nucleotide binding site [chemical binding]; other site 439292005608 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 439292005609 domain I; other site 439292005610 DNA binding groove [nucleotide binding] 439292005611 phosphate binding site [ion binding]; other site 439292005612 domain II; other site 439292005613 domain III; other site 439292005614 nucleotide binding site [chemical binding]; other site 439292005615 catalytic site [active] 439292005616 domain IV; other site 439292005617 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 439292005618 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 439292005619 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 439292005620 active site 439292005621 DNA binding site [nucleotide binding] 439292005622 Int/Topo IB signature motif; other site 439292005623 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 439292005624 active site 439292005625 HslU subunit interaction site [polypeptide binding]; other site 439292005626 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 439292005627 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 439292005628 Walker A motif; other site 439292005629 ATP binding site [chemical binding]; other site 439292005630 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 439292005631 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 439292005632 transcriptional repressor CodY; Validated; Region: PRK04158 439292005633 CodY GAF-like domain; Region: CodY; pfam06018 439292005634 CodY helix-turn-helix domain; Region: HTH_CodY; pfam08222 439292005635 flagellar basal-body rod protein FlgB; Region: FlgB; TIGR01396 439292005636 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 439292005637 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgC; COG1558 439292005638 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 439292005639 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 439292005640 flagellar hook-basal body protein FliE; Provisional; Region: fliE; PRK12728 439292005641 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 439292005642 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 439292005643 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 439292005644 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 439292005645 FliG C-terminal domain; Region: FliG_C; pfam01706 439292005646 flagellar assembly protein FliH; Region: FliH_bacil; TIGR03825 439292005647 Flagellar assembly protein FliH; Region: FliH; pfam02108 439292005648 flagellum-specific ATP synthase; Validated; Region: fliI; PRK07721 439292005649 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 439292005650 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 439292005651 Walker A motif/ATP binding site; other site 439292005652 Walker B motif; other site 439292005653 Flagellar biosynthesis chaperone [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]; Region: FliJ; COG2882 439292005654 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK07720 439292005655 Uncharacterized conserved protein [Function unknown]; Region: COG3334 439292005656 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 439292005657 flagellar basal body rod modification protein; Provisional; Region: flgD; PRK09618 439292005658 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 439292005659 Protein of unknown function (DUF3766); Region: DUF3766; cl11797 439292005660 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 439292005661 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 439292005662 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 439292005663 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 439292005664 Flagellar protein (FlbD); Region: FlbD; pfam06289 439292005665 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 439292005666 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK07718 439292005667 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 439292005668 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 439292005669 flagellar motor switch protein; Validated; Region: PRK08119 439292005670 CheC-like family; Region: CheC; pfam04509 439292005671 CheC-like family; Region: CheC; pfam04509 439292005672 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 439292005673 Response regulator receiver domain; Region: Response_reg; pfam00072 439292005674 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 439292005675 active site 439292005676 phosphorylation site [posttranslational modification] 439292005677 intermolecular recognition site; other site 439292005678 dimerization interface [polypeptide binding]; other site 439292005679 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 439292005680 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 439292005681 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 439292005682 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 439292005683 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 439292005684 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 439292005685 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 439292005686 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 439292005687 FHIPEP family; Region: FHIPEP; pfam00771 439292005688 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 439292005689 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 439292005690 P-loop; other site 439292005691 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 439292005692 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 439292005693 active site 439292005694 phosphorylation site [posttranslational modification] 439292005695 intermolecular recognition site; other site 439292005696 dimerization interface [polypeptide binding]; other site 439292005697 CheB methylesterase; Region: CheB_methylest; pfam01339 439292005698 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 439292005699 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 439292005700 putative binding surface; other site 439292005701 active site 439292005702 P2 response regulator binding domain; Region: P2; pfam07194 439292005703 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 439292005704 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 439292005705 ATP binding site [chemical binding]; other site 439292005706 Mg2+ binding site [ion binding]; other site 439292005707 G-X-G motif; other site 439292005708 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 439292005709 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 439292005710 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 439292005711 CheC-like family; Region: CheC; pfam04509 439292005712 CheC-like family; Region: CheC; pfam04509 439292005713 Chemotaxis protein; stimulates methylation of MCP proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheD; COG1871 439292005714 RNA polymerase sigma factor SigD; Validated; Region: PRK07670 439292005715 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 439292005716 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 439292005717 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 439292005718 DNA binding residues [nucleotide binding] 439292005719 Protein of unknown function (DUF342); Region: DUF342; pfam03961 439292005720 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 439292005721 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 439292005722 rRNA interaction site [nucleotide binding]; other site 439292005723 S8 interaction site; other site 439292005724 putative laminin-1 binding site; other site 439292005725 elongation factor Ts; Provisional; Region: tsf; PRK09377 439292005726 UBA/TS-N domain; Region: UBA; pfam00627 439292005727 Elongation factor TS; Region: EF_TS; pfam00889 439292005728 Elongation factor TS; Region: EF_TS; pfam00889 439292005729 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 439292005730 putative nucleotide binding site [chemical binding]; other site 439292005731 uridine monophosphate binding site [chemical binding]; other site 439292005732 homohexameric interface [polypeptide binding]; other site 439292005733 ribosome recycling factor; Reviewed; Region: frr; PRK00083 439292005734 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 439292005735 hinge region; other site 439292005736 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 439292005737 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 439292005738 catalytic residue [active] 439292005739 putative FPP diphosphate binding site; other site 439292005740 putative FPP binding hydrophobic cleft; other site 439292005741 dimer interface [polypeptide binding]; other site 439292005742 putative IPP diphosphate binding site; other site 439292005743 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 439292005744 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 439292005745 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 439292005746 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 439292005747 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 439292005748 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 439292005749 RIP metalloprotease RseP; Region: TIGR00054 439292005750 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 439292005751 active site 439292005752 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 439292005753 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 439292005754 protein binding site [polypeptide binding]; other site 439292005755 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 439292005756 putative substrate binding region [chemical binding]; other site 439292005757 prolyl-tRNA synthetase; Provisional; Region: PRK09194 439292005758 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 439292005759 dimer interface [polypeptide binding]; other site 439292005760 motif 1; other site 439292005761 active site 439292005762 motif 2; other site 439292005763 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 439292005764 putative deacylase active site [active] 439292005765 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 439292005766 active site 439292005767 motif 3; other site 439292005768 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 439292005769 anticodon binding site; other site 439292005770 DNA polymerase III PolC; Validated; Region: polC; PRK00448 439292005771 DNA polymerase III polC-type N-terminus; Region: DNA_pol3_alph_N; pfam11490 439292005772 polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two...; Region: polC_OBF; cd04484 439292005773 generic binding surface I; other site 439292005774 generic binding surface II; other site 439292005775 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 439292005776 active site 439292005777 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 439292005778 active site 439292005779 catalytic site [active] 439292005780 substrate binding site [chemical binding]; other site 439292005781 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at PolC gene; Region: PHP_PolIIIA_POLC; cd07435 439292005782 ribosome maturation protein RimP; Reviewed; Region: PRK00092 439292005783 Sm and related proteins; Region: Sm_like; cl00259 439292005784 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 439292005785 putative oligomer interface [polypeptide binding]; other site 439292005786 putative RNA binding site [nucleotide binding]; other site 439292005787 transcription elongation factor NusA; Provisional; Region: nusA; PRK12327 439292005788 NusA N-terminal domain; Region: NusA_N; pfam08529 439292005789 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 439292005790 RNA binding site [nucleotide binding]; other site 439292005791 homodimer interface [polypeptide binding]; other site 439292005792 NusA-like KH domain; Region: KH_5; pfam13184 439292005793 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 439292005794 G-X-X-G motif; other site 439292005795 Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation; Region: YlxR; cd00279 439292005796 putative RNA binding cleft [nucleotide binding]; other site 439292005797 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 439292005798 translation initiation factor IF-2; Validated; Region: infB; PRK05306 439292005799 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 439292005800 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 439292005801 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 439292005802 G1 box; other site 439292005803 putative GEF interaction site [polypeptide binding]; other site 439292005804 GTP/Mg2+ binding site [chemical binding]; other site 439292005805 Switch I region; other site 439292005806 G2 box; other site 439292005807 G3 box; other site 439292005808 Switch II region; other site 439292005809 G4 box; other site 439292005810 G5 box; other site 439292005811 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 439292005812 Translation-initiation factor 2; Region: IF-2; pfam11987 439292005813 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 439292005814 Protein of unknown function (DUF503); Region: DUF503; pfam04456 439292005815 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 439292005816 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK01550 439292005817 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 439292005818 RNA binding site [nucleotide binding]; other site 439292005819 active site 439292005820 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 439292005821 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 439292005822 active site 439292005823 Riboflavin kinase; Region: Flavokinase; pfam01687 439292005824 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 439292005825 16S/18S rRNA binding site [nucleotide binding]; other site 439292005826 S13e-L30e interaction site [polypeptide binding]; other site 439292005827 25S rRNA binding site [nucleotide binding]; other site 439292005828 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 439292005829 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 439292005830 RNase E interface [polypeptide binding]; other site 439292005831 trimer interface [polypeptide binding]; other site 439292005832 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 439292005833 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 439292005834 RNase E interface [polypeptide binding]; other site 439292005835 trimer interface [polypeptide binding]; other site 439292005836 active site 439292005837 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 439292005838 putative nucleic acid binding region [nucleotide binding]; other site 439292005839 G-X-X-G motif; other site 439292005840 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 439292005841 RNA binding site [nucleotide binding]; other site 439292005842 domain interface; other site 439292005843 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 439292005844 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 439292005845 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 439292005846 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 439292005847 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 439292005848 aspartate kinase I; Reviewed; Region: PRK08210 439292005849 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 439292005850 nucleotide binding site [chemical binding]; other site 439292005851 substrate binding site [chemical binding]; other site 439292005852 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 439292005853 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 439292005854 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 439292005855 dihydrodipicolinate synthase; Region: dapA; TIGR00674 439292005856 dimer interface [polypeptide binding]; other site 439292005857 active site 439292005858 catalytic residue [active] 439292005859 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 439292005860 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 439292005861 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 439292005862 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 439292005863 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 439292005864 putative active site [active] 439292005865 putative NTP binding site [chemical binding]; other site 439292005866 putative nucleic acid binding site [nucleotide binding]; other site 439292005867 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 439292005868 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 439292005869 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 439292005870 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 439292005871 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 439292005872 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 439292005873 DNA-binding site [nucleotide binding]; DNA binding site 439292005874 UTRA domain; Region: UTRA; pfam07702 439292005875 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 439292005876 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 439292005877 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 439292005878 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 439292005879 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 439292005880 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 439292005881 classical (c) SDRs; Region: SDR_c; cd05233 439292005882 NAD(P) binding site [chemical binding]; other site 439292005883 active site 439292005884 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 439292005885 Protein of unknown function (DUF3388); Region: DUF3388; pfam11868 439292005886 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 439292005887 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 439292005888 non-specific DNA binding site [nucleotide binding]; other site 439292005889 salt bridge; other site 439292005890 sequence-specific DNA binding site [nucleotide binding]; other site 439292005891 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase; Region: pgsA; TIGR00560 439292005892 competence damage-inducible protein A; Provisional; Region: PRK00549 439292005893 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 439292005894 putative MPT binding site; other site 439292005895 Competence-damaged protein; Region: CinA; pfam02464 439292005896 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 439292005897 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 439292005898 ATP binding site [chemical binding]; other site 439292005899 Mg++ binding site [ion binding]; other site 439292005900 motif III; other site 439292005901 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 439292005902 nucleotide binding region [chemical binding]; other site 439292005903 ATP-binding site [chemical binding]; other site 439292005904 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 439292005905 RNA binding site [nucleotide binding]; other site 439292005906 recombinase A; Provisional; Region: recA; PRK09354 439292005907 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 439292005908 hexamer interface [polypeptide binding]; other site 439292005909 Walker A motif; other site 439292005910 ATP binding site [chemical binding]; other site 439292005911 Walker B motif; other site 439292005912 phosphodiesterase; Provisional; Region: PRK12704 439292005913 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292005914 Zn2+ binding site [ion binding]; other site 439292005915 Mg2+ binding site [ion binding]; other site 439292005916 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 439292005917 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 439292005918 putative active site [active] 439292005919 metal binding site [ion binding]; metal-binding site 439292005920 homodimer binding site [polypeptide binding]; other site 439292005921 Stage V sporulation protein S (SpoVS); Region: SpoVS; pfam04232 439292005922 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 439292005923 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 439292005924 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 439292005925 dimer interface [polypeptide binding]; other site 439292005926 PYR/PP interface [polypeptide binding]; other site 439292005927 TPP binding site [chemical binding]; other site 439292005928 substrate binding site [chemical binding]; other site 439292005929 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 439292005930 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 439292005931 TPP-binding site [chemical binding]; other site 439292005932 Pyruvate ferredoxin oxidoreductase beta subunit C terminal; Region: PFO_beta_C; pfam12367 439292005933 Threonine dehydrogenase; Region: TDH; cd05281 439292005934 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 439292005935 structural Zn binding site [ion binding]; other site 439292005936 catalytic Zn binding site [ion binding]; other site 439292005937 tetramer interface [polypeptide binding]; other site 439292005938 NADP binding site [chemical binding]; other site 439292005939 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 439292005940 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 439292005941 substrate-cofactor binding pocket; other site 439292005942 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292005943 catalytic residue [active] 439292005944 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14327 439292005945 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 439292005946 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 439292005947 FeS/SAM binding site; other site 439292005948 TRAM domain; Region: TRAM; pfam01938 439292005949 Predicted membrane protein [Function unknown]; Region: COG4550 439292005950 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 439292005951 MutS domain I; Region: MutS_I; pfam01624 439292005952 MutS domain II; Region: MutS_II; pfam05188 439292005953 MutS domain III; Region: MutS_III; pfam05192 439292005954 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 439292005955 Walker A/P-loop; other site 439292005956 ATP binding site [chemical binding]; other site 439292005957 Q-loop/lid; other site 439292005958 ABC transporter signature motif; other site 439292005959 Walker B; other site 439292005960 D-loop; other site 439292005961 H-loop/switch region; other site 439292005962 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 439292005963 Transposase; Region: HTH_Tnp_1; pfam01527 439292005964 putative transposase OrfB; Reviewed; Region: PHA02517 439292005965 HTH-like domain; Region: HTH_21; pfam13276 439292005966 Integrase core domain; Region: rve; pfam00665 439292005967 Integrase core domain; Region: rve_2; pfam13333 439292005968 Putative SAM-dependent methyltransferase; Region: SAM_MT; cl17517 439292005969 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 439292005970 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 439292005971 bacterial Hfq-like; Region: Hfq; cd01716 439292005972 hexamer interface [polypeptide binding]; other site 439292005973 Sm1 motif; other site 439292005974 RNA binding site [nucleotide binding]; other site 439292005975 Sm2 motif; other site 439292005976 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 439292005977 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 439292005978 HflX GTPase family; Region: HflX; cd01878 439292005979 G1 box; other site 439292005980 GTP/Mg2+ binding site [chemical binding]; other site 439292005981 Switch I region; other site 439292005982 G2 box; other site 439292005983 G3 box; other site 439292005984 Switch II region; other site 439292005985 G4 box; other site 439292005986 Cystathionine beta-lyase family protein involved in aluminum resistance [Inorganic ion transport and metabolism]; Region: COG4100 439292005987 Aluminium resistance protein; Region: Alum_res; pfam06838 439292005988 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 439292005989 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 439292005990 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 439292005991 LexA repressor; Validated; Region: PRK00215 439292005992 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 439292005993 putative DNA binding site [nucleotide binding]; other site 439292005994 putative Zn2+ binding site [ion binding]; other site 439292005995 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 439292005996 Catalytic site [active] 439292005997 LysM domain; Region: LysM; pfam01476 439292005998 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 439292005999 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 439292006000 catalytic residues [active] 439292006001 catalytic nucleophile [active] 439292006002 Bacterial protein of unknown function (DUF896); Region: DUF896; pfam05979 439292006003 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 439292006004 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 439292006005 TPP-binding site [chemical binding]; other site 439292006006 dimer interface [polypeptide binding]; other site 439292006007 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 439292006008 PYR/PP interface [polypeptide binding]; other site 439292006009 dimer interface [polypeptide binding]; other site 439292006010 TPP binding site [chemical binding]; other site 439292006011 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 439292006012 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3763 439292006013 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 439292006014 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 439292006015 active site residue [active] 439292006016 Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156; Region: CsoR-like_DUF156; cl00846 439292006017 putative homodimer interface [polypeptide binding]; other site 439292006018 putative homotetramer interface [polypeptide binding]; other site 439292006019 putative allosteric switch controlling residues; other site 439292006020 putative metal binding site [ion binding]; other site 439292006021 putative homodimer-homodimer interface [polypeptide binding]; other site 439292006022 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 439292006023 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 439292006024 metal-binding site [ion binding] 439292006025 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 439292006026 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 439292006027 metal-binding site [ion binding] 439292006028 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 439292006029 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 439292006030 motif II; other site 439292006031 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 439292006032 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 439292006033 metal-binding site [ion binding] 439292006034 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 439292006035 catalytic residues [active] 439292006036 Protein of unknown function (DUF1453); Region: DUF1453; pfam07301 439292006037 Protein of unknown function (DUF2621); Region: DUF2621; pfam11084 439292006038 Uncharacterized homolog of PrgY (pheromone shutdown protein) [Function unknown]; Region: COG1916 439292006039 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 439292006040 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 439292006041 D-ala D-ala ligase C-terminus; Region: Dala_Dala_lig_C; pfam07478 439292006042 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 439292006043 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 439292006044 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 439292006045 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 439292006046 Glyoxalase-like domain; Region: Glyoxalase_3; pfam13468 439292006047 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 439292006048 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 439292006049 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292006050 dimer interface [polypeptide binding]; other site 439292006051 putative CheW interface [polypeptide binding]; other site 439292006052 RDD family; Region: RDD; pfam06271 439292006053 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 439292006054 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 439292006055 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292006056 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292006057 metal binding site [ion binding]; metal-binding site 439292006058 active site 439292006059 I-site; other site 439292006060 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292006061 Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]; Region: CdaR; COG3835 439292006062 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 439292006063 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 439292006064 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 439292006065 molybdopterin cofactor binding site; other site 439292006066 Molybdopterin-Binding, C-terminal (MopB_CT) 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-...; Region: MopB_CT; cd02775 439292006067 molybdopterin cofactor binding site; other site 439292006068 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 439292006069 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 439292006070 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 439292006071 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 439292006072 anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family; Region: dmsA_ynfE; TIGR02166 439292006073 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 439292006074 molybdopterin cofactor binding site; other site 439292006075 Molybdopterin-Binding, C-terminal (MopB_CT) 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-...; Region: MopB_CT; cl09929 439292006076 molybdopterin cofactor binding site; other site 439292006077 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 439292006078 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 439292006079 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl17519 439292006080 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit; Region: F420_cofH; TIGR03551 439292006081 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 439292006082 FeS/SAM binding site; other site 439292006083 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit; Region: F420_cofG; TIGR03550 439292006084 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 439292006085 FeS/SAM binding site; other site 439292006086 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292006087 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292006088 dimer interface [polypeptide binding]; other site 439292006089 putative CheW interface [polypeptide binding]; other site 439292006090 Sensory domain found in DIguanylate Cyclases & Two-component systems; Region: DICT; pfam10069 439292006091 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 439292006092 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 439292006093 selenocysteine-specific elongation factor SelB; Region: selB; TIGR00475 439292006094 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 439292006095 G1 box; other site 439292006096 putative GEF interaction site [polypeptide binding]; other site 439292006097 GTP/Mg2+ binding site [chemical binding]; other site 439292006098 Switch I region; other site 439292006099 G2 box; other site 439292006100 G3 box; other site 439292006101 Switch II region; other site 439292006102 G4 box; other site 439292006103 G5 box; other site 439292006104 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 439292006105 This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements:...; Region: selB_III; cd04094 439292006106 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 439292006107 Rdx family; Region: Rdx; pfam10262 439292006108 selenocysteine synthase; Provisional; Region: PRK04311 439292006109 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 439292006110 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 439292006111 catalytic residue [active] 439292006112 aconitate hydratase; Validated; Region: PRK09277 439292006113 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 439292006114 substrate binding site [chemical binding]; other site 439292006115 ligand binding site [chemical binding]; other site 439292006116 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 439292006117 substrate binding site [chemical binding]; other site 439292006118 VanZ like family; Region: VanZ; pfam04892 439292006119 potential frameshift: common BLAST hit: gi|15614852|ref|NP_243155.1| stage V sporulation protein K 439292006120 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 439292006121 AAA domain; Region: AAA_22; pfam13401 439292006122 Walker A motif; other site 439292006123 ATP binding site [chemical binding]; other site 439292006124 Walker B motif; other site 439292006125 arginine finger; other site 439292006126 stage V sporulation protein K; Region: spore_V_K; TIGR02881 439292006127 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 439292006128 Walker A motif; other site 439292006129 ATP binding site [chemical binding]; other site 439292006130 Walker B motif; other site 439292006131 arginine finger; other site 439292006132 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 439292006133 active site 439292006134 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 439292006135 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 439292006136 homodimer interface [polypeptide binding]; other site 439292006137 NAD binding pocket [chemical binding]; other site 439292006138 ATP binding pocket [chemical binding]; other site 439292006139 Mg binding site [ion binding]; other site 439292006140 active-site loop [active] 439292006141 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 439292006142 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 439292006143 active site 439292006144 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 439292006145 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292006146 EAL-domain associated signalling protein domain; Region: YkuI_C; pfam10388 439292006147 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 439292006148 Predicted membrane protein (DUF2207); Region: DUF2207; pfam09972 439292006149 YwpF-like protein; Region: YwpF; pfam14183 439292006150 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; cd01292 439292006151 active site 439292006152 Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones]; Region: PpiB; COG0652 439292006153 active site 439292006154 trehalose synthase; Region: treS_nterm; TIGR02456 439292006155 Alpha amylase catalytic domain found in bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_bac2_AmyA; cd11316 439292006156 Ca binding site [ion binding]; other site 439292006157 active site 439292006158 catalytic site [active] 439292006159 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 439292006160 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292006161 Walker A/P-loop; other site 439292006162 ATP binding site [chemical binding]; other site 439292006163 Q-loop/lid; other site 439292006164 ABC transporter signature motif; other site 439292006165 Walker B; other site 439292006166 D-loop; other site 439292006167 H-loop/switch region; other site 439292006168 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 439292006169 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 439292006170 Predicted transcriptional regulators [Transcription]; Region: COG1725 439292006171 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 439292006172 DNA-binding site [nucleotide binding]; DNA binding site 439292006173 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 439292006174 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 439292006175 Walker A/P-loop; other site 439292006176 ATP binding site [chemical binding]; other site 439292006177 Q-loop/lid; other site 439292006178 ABC transporter signature motif; other site 439292006179 Walker B; other site 439292006180 D-loop; other site 439292006181 H-loop/switch region; other site 439292006182 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 439292006183 putative CheA interaction surface; other site 439292006184 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 439292006185 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 439292006186 active site 439292006187 phosphorylation site [posttranslational modification] 439292006188 intermolecular recognition site; other site 439292006189 dimerization interface [polypeptide binding]; other site 439292006190 YhfH-like protein; Region: YhfH; pfam14149 439292006191 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 439292006192 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 439292006193 dimer interface [polypeptide binding]; other site 439292006194 PYR/PP interface [polypeptide binding]; other site 439292006195 TPP binding site [chemical binding]; other site 439292006196 substrate binding site [chemical binding]; other site 439292006197 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 439292006198 Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea...; Region: TPP_PFOR_porB_like; cd03376 439292006199 TPP-binding site [chemical binding]; other site 439292006200 putative dimer interface [polypeptide binding]; other site 439292006201 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 439292006202 pyruvate ferredoxin oxidoreductase subunit gamma/delta; Provisional; Region: PRK14028 439292006203 4Fe-4S binding domain; Region: Fer4; pfam00037 439292006204 Predicted HD superfamily hydrolase [General function prediction only]; Region: COG1418 439292006205 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292006206 Zn2+ binding site [ion binding]; other site 439292006207 Mg2+ binding site [ion binding]; other site 439292006208 intracellular protease, PfpI family; Region: PfpI; TIGR01382 439292006209 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 439292006210 proposed catalytic triad [active] 439292006211 conserved cys residue [active] 439292006212 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 439292006213 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 439292006214 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 439292006215 Major Facilitator Superfamily; Region: MFS_1; pfam07690 439292006216 putative substrate translocation pore; other site 439292006217 Acetamidase/Formamidase family; Region: FmdA_AmdA; pfam03069 439292006218 helicase/secretion neighborhood putative DEAH-box helicase; Region: DECH_helic; TIGR03817 439292006219 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 439292006220 ATP binding site [chemical binding]; other site 439292006221 putative Mg++ binding site [ion binding]; other site 439292006222 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 439292006223 nucleotide binding region [chemical binding]; other site 439292006224 ATP-binding site [chemical binding]; other site 439292006225 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 439292006226 Predicted exonuclease [DNA replication, recombination, and repair]; Region: COG3359 439292006227 RNase_H superfamily; Region: RNase_H_2; pfam13482 439292006228 active site 439292006229 substrate binding site [chemical binding]; other site 439292006230 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 439292006231 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 439292006232 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 439292006233 ligand binding site [chemical binding]; other site 439292006234 flexible hinge region; other site 439292006235 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 439292006236 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 439292006237 metal binding triad; other site 439292006238 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 439292006239 active site 439292006240 catalytic site [active] 439292006241 substrate binding site [chemical binding]; other site 439292006242 hypothetical protein; Provisional; Region: PRK13660 439292006243 cell division protein GpsB; Provisional; Region: PRK14127 439292006244 DivIVA domain; Region: DivI1A_domain; TIGR03544 439292006245 RNAse HI family that includes Archaeal RNase HI; Region: RNase_HI_archaeal_like; cd09279 439292006246 RNA/DNA hybrid binding site [nucleotide binding]; other site 439292006247 active site 439292006248 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 439292006249 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 439292006250 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 439292006251 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 439292006252 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 439292006253 FeS/SAM binding site; other site 439292006254 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 439292006255 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 439292006256 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 439292006257 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 439292006258 active site 439292006259 Zn binding site [ion binding]; other site 439292006260 ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]; Region: OpuBA; COG1125 439292006261 ATP-binding cassette domain of the osmoprotectant transporter; Region: ABC_OpuCA_Osmoprotection; cd03295 439292006262 Walker A/P-loop; other site 439292006263 ATP binding site [chemical binding]; other site 439292006264 Q-loop/lid; other site 439292006265 ABC transporter signature motif; other site 439292006266 Walker B; other site 439292006267 D-loop; other site 439292006268 H-loop/switch region; other site 439292006269 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 439292006270 dimer interface [polypeptide binding]; other site 439292006271 conserved gate region; other site 439292006272 ABC-ATPase subunit interface; other site 439292006273 Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]; Region: OpuBC; COG1732 439292006274 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 439292006275 Ligand Binding Site [chemical binding]; other site 439292006276 Predicted CoA-binding protein [General function prediction only]; Region: COG1832 439292006277 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 439292006278 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 439292006279 ATP binding site [chemical binding]; other site 439292006280 Mg2+ binding site [ion binding]; other site 439292006281 G-X-G motif; other site 439292006282 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 439292006283 anchoring element; other site 439292006284 dimer interface [polypeptide binding]; other site 439292006285 ATP binding site [chemical binding]; other site 439292006286 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 439292006287 active site 439292006288 putative metal-binding site [ion binding]; other site 439292006289 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 439292006290 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 439292006291 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 439292006292 CAP-like domain; other site 439292006293 active site 439292006294 primary dimer interface [polypeptide binding]; other site 439292006295 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 439292006296 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 439292006297 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 439292006298 Uncharacterized conserved protein (DUF2203); Region: DUF2203; pfam09969 439292006299 Predicted hydrolases of the HAD superfamily [General function prediction only]; Region: Cof; COG0561 439292006300 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 439292006301 active site 439292006302 motif I; other site 439292006303 motif II; other site 439292006304 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 439292006305 S-adenosylmethionine decarboxylase; Provisional; Region: PRK05462 439292006306 Flavodoxin domain; Region: Flavodoxin_5; pfam12724 439292006307 KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); Region: KOW; cl00354 439292006308 MOSC domain; Region: MOSC; pfam03473 439292006309 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 439292006310 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 439292006311 putative active site [active] 439292006312 putative metal binding site [ion binding]; other site 439292006313 DNA topoisomerase III; Provisional; Region: PRK07726 439292006314 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 439292006315 active site 439292006316 putative interdomain interaction site [polypeptide binding]; other site 439292006317 putative metal-binding site [ion binding]; other site 439292006318 putative nucleotide binding site [chemical binding]; other site 439292006319 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 439292006320 domain I; other site 439292006321 DNA binding groove [nucleotide binding] 439292006322 phosphate binding site [ion binding]; other site 439292006323 domain II; other site 439292006324 domain III; other site 439292006325 nucleotide binding site [chemical binding]; other site 439292006326 catalytic site [active] 439292006327 domain IV; other site 439292006328 PADR1 (NUC008) domain; Region: PADR1; pfam08063 439292006329 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 439292006330 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 439292006331 S1 domain; Region: S1_2; pfam13509 439292006332 threonine dehydratase; Validated; Region: PRK08639 439292006333 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 439292006334 tetramer interface [polypeptide binding]; other site 439292006335 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292006336 catalytic residue [active] 439292006337 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 439292006338 putative Ile/Val binding site [chemical binding]; other site 439292006339 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 439292006340 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 439292006341 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 439292006342 active site 439292006343 NAD binding site [chemical binding]; other site 439292006344 metal binding site [ion binding]; metal-binding site 439292006345 hypothetical protein; Provisional; Region: PRK07740 439292006346 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 439292006347 active site 439292006348 catalytic site [active] 439292006349 substrate binding site [chemical binding]; other site 439292006350 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 439292006351 metal binding triad; other site 439292006352 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 439292006353 EamA-like transporter family; Region: EamA; pfam00892 439292006354 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 439292006355 EamA-like transporter family; Region: EamA; pfam00892 439292006356 Protein involved in polysaccharide intercellular adhesin (PIA) synthesis/biofilm formation [Carbohydrate transport and metabolism]; Region: COG3936 439292006357 Acyltransferase family; Region: Acyl_transf_3; pfam01757 439292006358 Beta-lactamase; Region: Beta-lactamase; pfam00144 439292006359 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 439292006360 ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein; Region: ACT_1ZPV; cd04872 439292006361 Uncharacterized proteins with similarity to Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL_like_DUF711; cd08025 439292006362 gamma-glutamyl kinase; Provisional; Region: PRK05429 439292006363 AAK_G5K_ProB: Glutamate-5-kinase (G5K) catalyzes glutamate-dependent ATP cleavage; G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, in the first and controlling step of proline (and, in mammals, ornithine)...; Region: AAK_G5K_ProB; cd04242 439292006364 nucleotide binding site [chemical binding]; other site 439292006365 homotetrameric interface [polypeptide binding]; other site 439292006366 putative phosphate binding site [ion binding]; other site 439292006367 putative allosteric binding site; other site 439292006368 PUA domain; Region: PUA; pfam01472 439292006369 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 439292006370 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 439292006371 putative catalytic cysteine [active] 439292006372 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 439292006373 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 439292006374 G1 box; other site 439292006375 putative GEF interaction site [polypeptide binding]; other site 439292006376 GTP/Mg2+ binding site [chemical binding]; other site 439292006377 Switch I region; other site 439292006378 G2 box; other site 439292006379 G3 box; other site 439292006380 Switch II region; other site 439292006381 G4 box; other site 439292006382 G5 box; other site 439292006383 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 439292006384 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 439292006385 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 439292006386 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292006387 Coenzyme A binding pocket [chemical binding]; other site 439292006388 diaminobutyrate--2-oxoglutarate aminotransferase; Validated; Region: PRK09264 439292006389 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 439292006390 inhibitor-cofactor binding pocket; inhibition site 439292006391 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292006392 catalytic residue [active] 439292006393 Ectoine synthase; Region: Ectoine_synth; pfam06339 439292006394 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 439292006395 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 439292006396 INT_SG3, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 3, catalytic domain. The CD contains various predicted bacterial and phage integrase/recombinase sequences for which not much experimental characterization is available; Region: INT_SG3_C; cd01186 439292006397 Int/Topo IB signature motif; other site 439292006398 Predicted thiol-disulfide oxidoreductase [General function prediction only]; Region: COG3011 439292006399 5'-3' exonuclease; Region: 53EXOc; smart00475 439292006400 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 439292006401 active site 439292006402 metal binding site 1 [ion binding]; metal-binding site 439292006403 putative 5' ssDNA interaction site; other site 439292006404 metal binding site 3; metal-binding site 439292006405 metal binding site 2 [ion binding]; metal-binding site 439292006406 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 439292006407 putative DNA binding site [nucleotide binding]; other site 439292006408 putative metal binding site [ion binding]; other site 439292006409 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 439292006410 putative active site [active] 439292006411 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 439292006412 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 439292006413 homodimer interface [polypeptide binding]; other site 439292006414 substrate-cofactor binding pocket; other site 439292006415 catalytic residue [active] 439292006416 argininosuccinate lyase; Provisional; Region: PRK00855 439292006417 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 439292006418 active sites [active] 439292006419 tetramer interface [polypeptide binding]; other site 439292006420 argininosuccinate synthase; Provisional; Region: PRK13820 439292006421 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 439292006422 ANP binding site [chemical binding]; other site 439292006423 Substrate Binding Site II [chemical binding]; other site 439292006424 Substrate Binding Site I [chemical binding]; other site 439292006425 ornithine carbamoyltransferase; Provisional; Region: PRK00779 439292006426 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 439292006427 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 439292006428 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 439292006429 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 439292006430 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 439292006431 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 439292006432 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 439292006433 ATP-grasp domain; Region: ATP-grasp_4; cl17255 439292006434 MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate...; Region: MGS-like; cl00245 439292006435 substrate binding site [chemical binding]; other site 439292006436 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12838 439292006437 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 439292006438 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 439292006439 catalytic site [active] 439292006440 subunit interface [polypeptide binding]; other site 439292006441 acetylornithine aminotransferase; Provisional; Region: PRK02627 439292006442 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 439292006443 inhibitor-cofactor binding pocket; inhibition site 439292006444 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292006445 catalytic residue [active] 439292006446 AAK_NAGK-like: N-Acetyl-L-glutamate kinase (NAGK)-like . Included in this CD are the Escherichia coli and Pseudomonas aeruginosa type NAGKs which catalyze the phosphorylation of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine...; Region: AAK_NAGK-like; cd04238 439292006447 nucleotide binding site [chemical binding]; other site 439292006448 N-acetyl-L-glutamate binding site [chemical binding]; other site 439292006449 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 439292006450 heterotetramer interface [polypeptide binding]; other site 439292006451 active site pocket [active] 439292006452 cleavage site 439292006453 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 439292006454 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 439292006455 cardiolipin synthase; Region: bac_cardiolipin; TIGR04265 439292006456 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 439292006457 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 439292006458 putative active site [active] 439292006459 catalytic site [active] 439292006460 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 439292006461 putative active site [active] 439292006462 catalytic site [active] 439292006463 Beta-lactamase; Region: Beta-lactamase; pfam00144 439292006464 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 439292006465 methionine sulfoxide reductase A; Provisional; Region: PRK14054 439292006466 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 439292006467 Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_2_FMN; cd04733 439292006468 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 439292006469 putative active site [active] 439292006470 putative FMN binding site [chemical binding]; other site 439292006471 putative substrate binding site [chemical binding]; other site 439292006472 putative catalytic residue [active] 439292006473 Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase; Region: AAT; pfam03417 439292006474 Choloylglycine hydrolase (CGH)_like. This family of choloylglycine hydrolase-like proteins includes conjugated bile acid hydrolase (CBAH), penicillin V acylase (PVA), acid ceramidase (AC), and N-acylethanolamine-hydrolyzing acid amidase (NAAA) which...; Region: Ntn_CGH_like; cd01935 439292006475 active site 439292006476 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 439292006477 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 439292006478 putative catalytic cysteine [active] 439292006479 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 439292006480 putative active site [active] 439292006481 metal binding site [ion binding]; metal-binding site 439292006482 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 439292006483 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292006484 Walker A/P-loop; other site 439292006485 ATP binding site [chemical binding]; other site 439292006486 Q-loop/lid; other site 439292006487 ABC transporter signature motif; other site 439292006488 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 439292006489 Walker B; other site 439292006490 D-loop; other site 439292006491 H-loop/switch region; other site 439292006492 ABC transporter; Region: ABC_tran_2; pfam12848 439292006493 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 439292006494 Protein of unknown function (DUF952); Region: DUF952; cl01393 439292006495 exonuclease SbcC; Region: sbcc; TIGR00618 439292006496 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 439292006497 Walker A/P-loop; other site 439292006498 ATP binding site [chemical binding]; other site 439292006499 Q-loop/lid; other site 439292006500 ABC transporter signature motif; other site 439292006501 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292006502 ABC transporter signature motif; other site 439292006503 Walker B; other site 439292006504 D-loop; other site 439292006505 H-loop/switch region; other site 439292006506 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 439292006507 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 439292006508 active site 439292006509 metal binding site [ion binding]; metal-binding site 439292006510 DNA binding site [nucleotide binding] 439292006511 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 439292006512 helicase-exonuclease AddAB, AddA subunit, Firmicutes type; Region: addA_Gpos; TIGR02785 439292006513 Part of AAA domain; Region: AAA_19; pfam13245 439292006514 Family description; Region: UvrD_C_2; pfam13538 439292006515 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 439292006516 helicase-exonuclease AddAB, AddB subunit; Region: addB_Gpos; TIGR02773 439292006517 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 439292006518 Predicted membrane protein [Function unknown]; Region: COG4129 439292006519 Bacterial protein of unknown function (DUF939); Region: DUF939; pfam06081 439292006520 Uncharacterized conserved protein [Function unknown]; Region: COG0398 439292006521 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 439292006522 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 439292006523 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 439292006524 dihydrodipicolinate synthase; Region: dapA; TIGR00674 439292006525 dimer interface [polypeptide binding]; other site 439292006526 active site 439292006527 catalytic residue [active] 439292006528 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 439292006529 Pyruvate formate lyase 1; Region: PFL1; cd01678 439292006530 coenzyme A binding site [chemical binding]; other site 439292006531 active site 439292006532 catalytic residues [active] 439292006533 glycine loop; other site 439292006534 pyruvate formate-lyase 1-activating enzyme; Region: PFLA; TIGR02493 439292006535 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 439292006536 FeS/SAM binding site; other site 439292006537 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 439292006538 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 439292006539 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 439292006540 active site 439292006541 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 439292006542 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 439292006543 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14455 439292006544 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 439292006545 FeS/SAM binding site; other site 439292006546 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 439292006547 EamA-like transporter family; Region: EamA; pfam00892 439292006548 EamA-like transporter family; Region: EamA; pfam00892 439292006549 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 439292006550 active site residue [active] 439292006551 amidase; Provisional; Region: PRK06529 439292006552 Amidase; Region: Amidase; cl11426 439292006553 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 439292006554 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 439292006555 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 439292006556 sn-glycerol-3-phosphate dehydrogenase subunit C; Provisional; Region: glpC; PRK11168 439292006557 Cysteine-rich domain; Region: CCG; pfam02754 439292006558 Cysteine-rich domain; Region: CCG; pfam02754 439292006559 anaerobic glycerol-3-phosphate dehydrogenase subunit B; Validated; Region: PRK05329 439292006560 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 439292006561 glycerol-3-phosphate dehydrogenase, anaerobic, A subunit; Region: glycerol3P_GlpA; TIGR03377 439292006562 hydroxyglutarate oxidase; Provisional; Region: PRK11728 439292006563 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 439292006564 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 439292006565 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 439292006566 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 439292006567 Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]; Region: COG1765 439292006568 6-phosphofructokinase; Provisional; Region: PRK03202 439292006569 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 439292006570 active site 439292006571 ADP/pyrophosphate binding site [chemical binding]; other site 439292006572 dimerization interface [polypeptide binding]; other site 439292006573 allosteric effector site; other site 439292006574 fructose-1,6-bisphosphate binding site; other site 439292006575 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 439292006576 Predicted permease [General function prediction only]; Region: COG2056 439292006577 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 439292006578 AbgT putative transporter family; Region: ABG_transport; cl17431 439292006579 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 439292006580 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 439292006581 homodimer interface [polypeptide binding]; other site 439292006582 substrate-cofactor binding pocket; other site 439292006583 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292006584 catalytic residue [active] 439292006585 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 439292006586 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 439292006587 active site 439292006588 HIGH motif; other site 439292006589 nucleotide binding site [chemical binding]; other site 439292006590 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 439292006591 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 439292006592 active site 439292006593 KMSKS motif; other site 439292006594 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 439292006595 tRNA binding surface [nucleotide binding]; other site 439292006596 anticodon binding site; other site 439292006597 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 439292006598 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 439292006599 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4152 439292006600 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292006601 Walker A/P-loop; other site 439292006602 ATP binding site [chemical binding]; other site 439292006603 Q-loop/lid; other site 439292006604 ABC transporter signature motif; other site 439292006605 Walker B; other site 439292006606 D-loop; other site 439292006607 H-loop/switch region; other site 439292006608 Domain of unknown function (DUF4162); Region: DUF4162; pfam13732 439292006609 Domain of unknown function (DUF4349); Region: DUF4349; pfam14257 439292006610 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 439292006611 Predicted transcriptional regulators [Transcription]; Region: COG1695 439292006612 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 439292006613 Protein of unknown function (DUF2812); Region: DUF2812; pfam11193 439292006614 YolD-like protein; Region: YolD; pfam08863 439292006615 DNA polymerase IV; Reviewed; Region: PRK03103 439292006616 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 439292006617 active site 439292006618 DNA binding site [nucleotide binding] 439292006619 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 439292006620 Response regulator receiver domain; Region: Response_reg; pfam00072 439292006621 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 439292006622 active site 439292006623 phosphorylation site [posttranslational modification] 439292006624 intermolecular recognition site; other site 439292006625 dimerization interface [polypeptide binding]; other site 439292006626 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292006627 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292006628 metal binding site [ion binding]; metal-binding site 439292006629 active site 439292006630 I-site; other site 439292006631 Response regulator receiver domain; Region: Response_reg; pfam00072 439292006632 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 439292006633 active site 439292006634 phosphorylation site [posttranslational modification] 439292006635 intermolecular recognition site; other site 439292006636 dimerization interface [polypeptide binding]; other site 439292006637 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 439292006638 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 439292006639 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292006640 catalytic residue [active] 439292006641 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 439292006642 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 439292006643 Protein of unknown function (DUF342); Region: DUF342; pfam03961 439292006644 BCCT family transporter; Region: BCCT; pfam02028 439292006645 AAA domain; Region: AAA_32; pfam13654 439292006646 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 439292006647 PAS domain S-box; Region: sensory_box; TIGR00229 439292006648 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 439292006649 putative active site [active] 439292006650 heme pocket [chemical binding]; other site 439292006651 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 439292006652 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 439292006653 PAS domain; Region: PAS_9; pfam13426 439292006654 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292006655 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292006656 metal binding site [ion binding]; metal-binding site 439292006657 active site 439292006658 I-site; other site 439292006659 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292006660 methionine gamma-lyase; Provisional; Region: PRK06767 439292006661 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 439292006662 homodimer interface [polypeptide binding]; other site 439292006663 substrate-cofactor binding pocket; other site 439292006664 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292006665 catalytic residue [active] 439292006666 Major Facilitator Superfamily; Region: MFS_1; pfam07690 439292006667 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 439292006668 putative substrate translocation pore; other site 439292006669 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 439292006670 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 439292006671 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 439292006672 putative active site [active] 439292006673 putative NTP binding site [chemical binding]; other site 439292006674 putative nucleic acid binding site [nucleotide binding]; other site 439292006675 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 439292006676 C-3',4' desaturase CrtD; Region: desat_CrtD; TIGR02733 439292006677 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 439292006678 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 439292006679 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 439292006680 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 439292006681 dimer interface [polypeptide binding]; other site 439292006682 phosphorylation site [posttranslational modification] 439292006683 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 439292006684 ATP binding site [chemical binding]; other site 439292006685 Mg2+ binding site [ion binding]; other site 439292006686 G-X-G motif; other site 439292006687 glutamate dehydrogenase; Provisional; Region: PRK09414 439292006688 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 439292006689 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 439292006690 NAD(P) binding pocket [chemical binding]; other site 439292006691 Transcriptional regulator [Transcription]; Region: LysR; COG0583 439292006692 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 439292006693 The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; Region: PBP2_GltC_like; cd08434 439292006694 putative dimerization interface [polypeptide binding]; other site 439292006695 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 439292006696 S-adenosylmethionine binding site [chemical binding]; other site 439292006697 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 439292006698 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 439292006699 TraB family; Region: TraB; pfam01963 439292006700 Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; Region: DLP_2; cd09912 439292006701 Dynamin family; Region: Dynamin_N; pfam00350 439292006702 G1 box; other site 439292006703 GTP/Mg2+ binding site [chemical binding]; other site 439292006704 G2 box; other site 439292006705 Switch I region; other site 439292006706 G3 box; other site 439292006707 Switch II region; other site 439292006708 G4 box; other site 439292006709 G5 box; other site 439292006710 Dynamin family; Region: Dynamin_N; pfam00350 439292006711 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 439292006712 G1 box; other site 439292006713 GTP/Mg2+ binding site [chemical binding]; other site 439292006714 G2 box; other site 439292006715 Switch I region; other site 439292006716 Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; Region: DLP_2; cd09912 439292006717 G3 box; other site 439292006718 Switch II region; other site 439292006719 GTP/Mg2+ binding site [chemical binding]; other site 439292006720 G4 box; other site 439292006721 G5 box; other site 439292006722 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 439292006723 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 439292006724 E3 interaction surface; other site 439292006725 lipoyl attachment site [posttranslational modification]; other site 439292006726 e3 binding domain; Region: E3_binding; pfam02817 439292006727 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 439292006728 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 439292006729 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 439292006730 TPP-binding site [chemical binding]; other site 439292006731 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 439292006732 aminotransferase A; Validated; Region: PRK07683 439292006733 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 439292006734 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292006735 homodimer interface [polypeptide binding]; other site 439292006736 catalytic residue [active] 439292006737 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 439292006738 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 439292006739 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 439292006740 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 439292006741 methionine sulfoxide reductase B; Provisional; Region: PRK00222 439292006742 SelR domain; Region: SelR; pfam01641 439292006743 methionine sulfoxide reductase A; Provisional; Region: PRK14054 439292006744 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]; Region: COG2355 439292006745 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics; Region: rDP_like; cd01301 439292006746 active site 439292006747 dimer interface [polypeptide binding]; other site 439292006748 fumarate hydratase; Reviewed; Region: fumC; PRK00485 439292006749 Class II fumarases; Region: Fumarase_classII; cd01362 439292006750 active site 439292006751 tetramer interface [polypeptide binding]; other site 439292006752 acetyl-CoA synthetase; Provisional; Region: PRK04319 439292006753 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 439292006754 Uncharacterized subfamily of Acetyl-CoA synthetase like family (ACS); Region: MACS_like_4; cd05969 439292006755 active site 439292006756 acyl-activating enzyme (AAE) consensus motif; other site 439292006757 putative CoA binding site [chemical binding]; other site 439292006758 AMP binding site [chemical binding]; other site 439292006759 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 439292006760 Uncharacterized ALDH (y4uC) with similarity to Tortula ruralis aldehyde dehydrogenase ALDH21A1; Region: ALDH_y4uC; cd07149 439292006761 NAD(P) binding site [chemical binding]; other site 439292006762 catalytic residues [active] 439292006763 maltose phosphorylase; Provisional; Region: PRK13807 439292006764 Glycosyl hydrolase family 65, N-terminal domain; Region: Glyco_hydro_65N; pfam03636 439292006765 Glycosyl hydrolase family 65 central catalytic domain; Region: Glyco_hydro_65m; pfam03632 439292006766 Glycosyl hydrolase family 65, C-terminal domain; Region: Glyco_hydro_65C; pfam03633 439292006767 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); Region: NT5C; cl17836 439292006768 beta-phosphoglucomutase; Region: bPGM; TIGR01990 439292006769 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 439292006770 Predicted membrane protein [Function unknown]; Region: COG2322 439292006771 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 439292006772 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 439292006773 putative substrate translocation pore; other site 439292006774 drug efflux system protein MdtG; Provisional; Region: PRK09874 439292006775 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 439292006776 putative substrate translocation pore; other site 439292006777 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 439292006778 nucleophile elbow; other site 439292006779 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 439292006780 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 439292006781 [4Fe-4S] binding site [ion binding]; other site 439292006782 molybdopterin cofactor binding site; other site 439292006783 Molybdopterin-Binding, C-terminal (MopB_CT) 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-...; Region: MopB_CT; cl09929 439292006784 molybdopterin cofactor binding site; other site 439292006785 EDD domain protein, DegV family; Region: DegV; TIGR00762 439292006786 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 439292006787 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 439292006788 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 439292006789 Substrate-binding site [chemical binding]; other site 439292006790 Substrate specificity [chemical binding]; other site 439292006791 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 439292006792 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 439292006793 Substrate-binding site [chemical binding]; other site 439292006794 Substrate specificity [chemical binding]; other site 439292006795 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 439292006796 dinuclear metal binding motif [ion binding]; other site 439292006797 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 439292006798 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 439292006799 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 439292006800 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 439292006801 NRDE protein; Region: NRDE; cl01315 439292006802 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 439292006803 GAF domain; Region: GAF_2; pfam13185 439292006804 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292006805 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292006806 metal binding site [ion binding]; metal-binding site 439292006807 active site 439292006808 I-site; other site 439292006809 Toxic anion resistance protein (TelA); Region: TelA; pfam05816 439292006810 Protein of unknown function (DUF2777); Region: DUF2777; pfam10949 439292006811 Predicted membrane protein [Function unknown]; Region: COG3428 439292006812 Bacterial PH domain; Region: DUF304; pfam03703 439292006813 Bacterial PH domain; Region: DUF304; pfam03703 439292006814 Bacterial PH domain; Region: DUF304; pfam03703 439292006815 Uncharacterized conserved protein [Function unknown]; Region: COG3402 439292006816 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 439292006817 Virulence factor; Region: Virulence_fact; pfam13769 439292006818 HEAT repeats; Region: HEAT_2; pfam13646 439292006819 Predicted phosphoesterases, related to the Icc protein [General function prediction only]; Region: COG2129 439292006820 Calcineurin-like phosphoesterase superfamily domain; Region: Metallophos_2; pfam12850 439292006821 active site 439292006822 metal binding site [ion binding]; metal-binding site 439292006823 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 439292006824 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 439292006825 catalytic residues [active] 439292006826 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 439292006827 catalytic residues [active] 439292006828 Isochorismatase family; Region: Isochorismatase; pfam00857 439292006829 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 439292006830 catalytic triad [active] 439292006831 conserved cis-peptide bond; other site 439292006832 FOG: CBS domain [General function prediction only]; Region: COG0517 439292006833 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 439292006834 Bacterial domain of unknown function (DUF1798); Region: DUF1798; pfam08807 439292006835 Holliday junction-specific endonuclease; Reviewed; Region: recU; PRK02234 439292006836 Transglycosylase; Region: Transgly; pfam00912 439292006837 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 439292006838 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 439292006839 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 439292006840 Interdomain contacts; other site 439292006841 Cytokine receptor motif; other site 439292006842 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 439292006843 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 439292006844 minor groove reading motif; other site 439292006845 helix-hairpin-helix signature motif; other site 439292006846 substrate binding pocket [chemical binding]; other site 439292006847 active site 439292006848 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 439292006849 Putative primosome component and related proteins [DNA replication, recombination, and repair]; Region: DnaD; COG3935 439292006850 Replication initiation and membrane attachment; Region: DnaB_2; pfam07261 439292006851 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 439292006852 AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a...; Region: AsnRS_cyto_like_N; cd04323 439292006853 putative dimer interface [polypeptide binding]; other site 439292006854 putative anticodon binding site; other site 439292006855 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 439292006856 homodimer interface [polypeptide binding]; other site 439292006857 motif 1; other site 439292006858 motif 2; other site 439292006859 active site 439292006860 motif 3; other site 439292006861 aspartate aminotransferase; Provisional; Region: PRK05764 439292006862 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 439292006863 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292006864 homodimer interface [polypeptide binding]; other site 439292006865 catalytic residue [active] 439292006866 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5353 439292006867 N-ethylammeline chlorohydrolase; Provisional; Region: PRK06038 439292006868 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 439292006869 active site 439292006870 putative substrate binding pocket [chemical binding]; other site 439292006871 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated; Region: PRK08074 439292006872 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 439292006873 active site 439292006874 catalytic site [active] 439292006875 substrate binding site [chemical binding]; other site 439292006876 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 439292006877 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 439292006878 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 439292006879 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 439292006880 tetramerization interface [polypeptide binding]; other site 439292006881 active site 439292006882 pantoate--beta-alanine ligase; Region: panC; TIGR00018 439292006883 Pantoate-beta-alanine ligase; Region: PanC; cd00560 439292006884 active site 439292006885 ATP-binding site [chemical binding]; other site 439292006886 pantoate-binding site; other site 439292006887 HXXH motif; other site 439292006888 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 439292006889 oligomerization interface [polypeptide binding]; other site 439292006890 active site 439292006891 metal binding site [ion binding]; metal-binding site 439292006892 Biotin operon repressor [Transcription]; Region: BirA; COG1654 439292006893 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 439292006894 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 439292006895 tRNA CCA-pyrophosphorylase; Provisional; Region: PRK13299 439292006896 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 439292006897 active site 439292006898 NTP binding site [chemical binding]; other site 439292006899 metal binding triad [ion binding]; metal-binding site 439292006900 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 439292006901 tRNA nucleotidyltransferase domain 2 putative; Region: tRNA_NucTran2_2; pfam13735 439292006902 N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA; Region: thiol_BshA; TIGR03999 439292006903 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 439292006904 bacillithiol biosynthesis deacetylase BshB1; Region: thiol_BshB1; TIGR04001 439292006905 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 439292006906 active site 439292006907 dimer interfaces [polypeptide binding]; other site 439292006908 catalytic residues [active] 439292006909 dihydrodipicolinate reductase; Provisional; Region: PRK00048 439292006910 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 439292006911 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 439292006912 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 439292006913 homodimer interface [polypeptide binding]; other site 439292006914 metal binding site [ion binding]; metal-binding site 439292006915 Uncharacterized conserved protein [Function unknown]; Region: COG1284 439292006916 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 439292006917 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 439292006918 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 439292006919 Putative neutral zinc metallopeptidase; Region: Zn_peptidase_2; pfam04298 439292006920 Protein of unknown function (DUF1405); Region: DUF1405; cl01798 439292006921 interchain domain interface [polypeptide binding]; other site 439292006922 intrachain domain interface; other site 439292006923 Qi binding site; other site 439292006924 Qo binding site; other site 439292006925 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 439292006926 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 439292006927 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 439292006928 cytochrome b6; Provisional; Region: PRK03735 439292006929 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 439292006930 interchain domain interface [polypeptide binding]; other site 439292006931 intrachain domain interface; other site 439292006932 heme bH binding site [chemical binding]; other site 439292006933 Qi binding site; other site 439292006934 heme bL binding site [chemical binding]; other site 439292006935 Qo binding site; other site 439292006936 Rieske Fe-S protein [Energy production and conversion]; Region: QcrA; COG0723 439292006937 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; cd03467 439292006938 iron-sulfur cluster [ion binding]; other site 439292006939 [2Fe-2S] cluster binding site [ion binding]; other site 439292006940 Protein of unknown function (DUF2487); Region: DUF2487; pfam10673 439292006941 hypothetical protein; Provisional; Region: PRK03636 439292006942 UPF0302 domain; Region: UPF0302; pfam08864 439292006943 IDEAL domain; Region: IDEAL; cl07452 439292006944 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 439292006945 TPR motif; other site 439292006946 binding surface 439292006947 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 439292006948 binding surface 439292006949 TPR motif; other site 439292006950 TPR repeat; Region: TPR_11; pfam13414 439292006951 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 439292006952 binding surface 439292006953 TPR motif; other site 439292006954 TPR repeat; Region: TPR_11; pfam13414 439292006955 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 439292006956 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 439292006957 hinge; other site 439292006958 active site 439292006959 prephenate dehydrogenase; Validated; Region: PRK06545 439292006960 prephenate dehydrogenase; Validated; Region: PRK08507 439292006961 C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH); Region: ACT_PDH-BS; cd04909 439292006962 histidinol-phosphate aminotransferase; Provisional; Region: PRK03158 439292006963 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 439292006964 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292006965 homodimer interface [polypeptide binding]; other site 439292006966 catalytic residue [active] 439292006967 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 439292006968 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 439292006969 substrate binding site [chemical binding]; other site 439292006970 active site 439292006971 catalytic residues [active] 439292006972 heterodimer interface [polypeptide binding]; other site 439292006973 bifunctional phosphoribosylanthranilate isomerase/tryptophan synthase subunit beta; Provisional; Region: PRK13803 439292006974 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 439292006975 active site 439292006976 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 439292006977 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292006978 catalytic residue [active] 439292006979 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 439292006980 active site 439292006981 ribulose/triose binding site [chemical binding]; other site 439292006982 phosphate binding site [ion binding]; other site 439292006983 substrate (anthranilate) binding pocket [chemical binding]; other site 439292006984 product (indole) binding pocket [chemical binding]; other site 439292006985 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 439292006986 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 439292006987 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 439292006988 anthranilate synthase component I; Provisional; Region: PRK13569 439292006989 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 439292006990 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 439292006991 Chorismate mutase (AroH) is one of at least five chorismate-utilizing enzymes present in microorganisms that catalyze the rearrangement of chorismate to prephenic acid, the first committed step in the biosynthesis of aromatic amino acids. In prokaryotes; Region: AroH; cd02185 439292006992 homotrimer interaction site [polypeptide binding]; other site 439292006993 active site 439292006994 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 439292006995 active site 439292006996 dimer interface [polypeptide binding]; other site 439292006997 metal binding site [ion binding]; metal-binding site 439292006998 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 439292006999 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 439292007000 Tetramer interface [polypeptide binding]; other site 439292007001 active site 439292007002 FMN-binding site [chemical binding]; other site 439292007003 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 439292007004 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 439292007005 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 439292007006 S-adenosylmethionine binding site [chemical binding]; other site 439292007007 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 439292007008 active site 439292007009 multimer interface [polypeptide binding]; other site 439292007010 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 439292007011 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 439292007012 substrate binding pocket [chemical binding]; other site 439292007013 chain length determination region; other site 439292007014 substrate-Mg2+ binding site; other site 439292007015 catalytic residues [active] 439292007016 aspartate-rich region 1; other site 439292007017 active site lid residues [active] 439292007018 aspartate-rich region 2; other site 439292007019 Menaquinone biosynthesis; Region: VitK2_biosynth; pfam02621 439292007020 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]; Region: UbiA; cl00337 439292007021 UbiA prenyltransferase family; Region: UbiA; pfam01040 439292007022 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 439292007023 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 439292007024 S-adenosylmethionine binding site [chemical binding]; other site 439292007025 Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1; Region: HEPPP_synt_1; pfam07307 439292007026 transcription attenuation protein MtrB; Provisional; Region: PRK13251 439292007027 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 439292007028 homodecamer interface [polypeptide binding]; other site 439292007029 GTP cyclohydrolase I; Provisional; Region: PLN03044 439292007030 active site 439292007031 putative catalytic site residues [active] 439292007032 zinc binding site [ion binding]; other site 439292007033 GTP-CH-I/GFRP interaction surface; other site 439292007034 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 439292007035 IHF dimer interface [polypeptide binding]; other site 439292007036 IHF - DNA interface [nucleotide binding]; other site 439292007037 Protein of unknown function (DUF2768); Region: DUF2768; pfam10966 439292007038 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 439292007039 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 439292007040 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 439292007041 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; cl00410 439292007042 GTP-binding protein Der; Reviewed; Region: PRK00093 439292007043 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 439292007044 G1 box; other site 439292007045 GTP/Mg2+ binding site [chemical binding]; other site 439292007046 Switch I region; other site 439292007047 G2 box; other site 439292007048 Switch II region; other site 439292007049 G3 box; other site 439292007050 G4 box; other site 439292007051 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 439292007052 G1 box; other site 439292007053 GTP/Mg2+ binding site [chemical binding]; other site 439292007054 Switch I region; other site 439292007055 G2 box; other site 439292007056 G3 box; other site 439292007057 Switch II region; other site 439292007058 G4 box; other site 439292007059 G5 box; other site 439292007060 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 439292007061 Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal; Region: IDI-2_FMN; cd02811 439292007062 homotetramer interface [polypeptide binding]; other site 439292007063 FMN binding site [chemical binding]; other site 439292007064 homodimer contacts [polypeptide binding]; other site 439292007065 putative active site [active] 439292007066 putative substrate binding site [chemical binding]; other site 439292007067 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06676 439292007068 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 439292007069 RNA binding site [nucleotide binding]; other site 439292007070 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 439292007071 RNA binding site [nucleotide binding]; other site 439292007072 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 439292007073 RNA binding site [nucleotide binding]; other site 439292007074 S1_RPS1_repeat_hs4: 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_hs4; cd05692 439292007075 RNA binding site [nucleotide binding]; other site 439292007076 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 439292007077 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 439292007078 putative acyl-acceptor binding pocket; other site 439292007079 cytidylate kinase; Provisional; Region: cmk; PRK00023 439292007080 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 439292007081 CMP-binding site; other site 439292007082 The sites determining sugar specificity; other site 439292007083 c-di-GMP-binding protein [Signal transduction mechanisms]; Region: COG5581 439292007084 Flagellar protein YcgR; Region: YcgR_2; pfam12945 439292007085 PilZ domain; Region: PilZ; pfam07238 439292007086 Protease prsW family; Region: PrsW-protease; pfam13367 439292007087 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 439292007088 active site 439292007089 homotetramer interface [polypeptide binding]; other site 439292007090 homodimer interface [polypeptide binding]; other site 439292007091 putative bacillithiol system oxidoreductase, YpdA family; Region: Bthiol_YpdA; TIGR04018 439292007092 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 439292007093 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 439292007094 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 439292007095 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 439292007096 NAD(P) binding site [chemical binding]; other site 439292007097 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 439292007098 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 439292007099 DNA binding residues [nucleotide binding] 439292007100 B12 binding domain; Region: B12-binding_2; pfam02607 439292007101 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cd02065 439292007102 B12 binding site [chemical binding]; other site 439292007103 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 439292007104 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 439292007105 Potassium binding sites [ion binding]; other site 439292007106 Cesium cation binding sites [ion binding]; other site 439292007107 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 439292007108 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; pfam01558 439292007109 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit [Energy production and conversion]; Region: PorB; COG1013 439292007110 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 439292007111 TPP-binding site [chemical binding]; other site 439292007112 2-ketoisovalerate ferredoxin reductase; Validated; Region: PRK07119 439292007113 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 439292007114 dimer interface [polypeptide binding]; other site 439292007115 PYR/PP interface [polypeptide binding]; other site 439292007116 TPP binding site [chemical binding]; other site 439292007117 substrate binding site [chemical binding]; other site 439292007118 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 439292007119 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 439292007120 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 439292007121 CAAX protease self-immunity; Region: Abi; pfam02517 439292007122 DEAD-like helicases superfamily; Region: DEXDc; smart00487 439292007123 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 439292007124 ATP binding site [chemical binding]; other site 439292007125 putative Mg++ binding site [ion binding]; other site 439292007126 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 439292007127 nucleotide binding region [chemical binding]; other site 439292007128 ATP-binding site [chemical binding]; other site 439292007129 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4955 439292007130 Ferredoxin [Energy production and conversion]; Region: Fer; COG1141 439292007131 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 439292007132 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 439292007133 ligand binding site [chemical binding]; other site 439292007134 flexible hinge region; other site 439292007135 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 439292007136 putative switch regulator; other site 439292007137 non-specific DNA interactions [nucleotide binding]; other site 439292007138 DNA binding site [nucleotide binding] 439292007139 sequence specific DNA binding site [nucleotide binding]; other site 439292007140 putative cAMP binding site [chemical binding]; other site 439292007141 FCD domain; Region: FCD; cl11656 439292007142 Transcriptional regulators [Transcription]; Region: FadR; COG2186 439292007143 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 439292007144 DNA-binding site [nucleotide binding]; DNA binding site 439292007145 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 439292007146 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 439292007147 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 439292007148 ligand binding site [chemical binding]; other site 439292007149 NAD binding site [chemical binding]; other site 439292007150 dimerization interface [polypeptide binding]; other site 439292007151 catalytic site [active] 439292007152 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 439292007153 putative L-serine binding site [chemical binding]; other site 439292007154 SurA N-terminal domain; Region: SurA_N_3; cl07813 439292007155 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 439292007156 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 439292007157 MPT binding site; other site 439292007158 trimer interface [polypeptide binding]; other site 439292007159 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 439292007160 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292007161 dimerization interface [polypeptide binding]; other site 439292007162 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 439292007163 dimer interface [polypeptide binding]; other site 439292007164 phosphorylation site [posttranslational modification] 439292007165 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 439292007166 ATP binding site [chemical binding]; other site 439292007167 Mg2+ binding site [ion binding]; other site 439292007168 G-X-G motif; other site 439292007169 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 439292007170 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 439292007171 active site 439292007172 phosphorylation site [posttranslational modification] 439292007173 intermolecular recognition site; other site 439292007174 dimerization interface [polypeptide binding]; other site 439292007175 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 439292007176 DNA binding site [nucleotide binding] 439292007177 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 439292007178 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 439292007179 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 439292007180 ResB-like family; Region: ResB; pfam05140 439292007181 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 439292007182 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 439292007183 catalytic residues [active] 439292007184 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 439292007185 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 439292007186 RNA binding surface [nucleotide binding]; other site 439292007187 Pseudouridine synthases, RsuA subfamily; Region: PseudoU_synth_RsuA_like; cd02870 439292007188 active site 439292007189 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 439292007190 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 439292007191 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 439292007192 Protein of unknown function (DUF3907); Region: DUF3907; pfam13047 439292007193 segregation and condensation protein B; Reviewed; Region: scpB; PRK00135 439292007194 segregation and condensation protein A; Reviewed; Region: scpA; PRK00104 439292007195 Domain of unknown function (DUF309); Region: DUF309; pfam03745 439292007196 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 439292007197 homopentamer interface [polypeptide binding]; other site 439292007198 active site 439292007199 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 439292007200 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 439292007201 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 439292007202 dimerization interface [polypeptide binding]; other site 439292007203 active site 439292007204 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 439292007205 Lumazine binding domain; Region: Lum_binding; pfam00677 439292007206 Lumazine binding domain; Region: Lum_binding; pfam00677 439292007207 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 439292007208 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 439292007209 catalytic motif [active] 439292007210 Zn binding site [ion binding]; other site 439292007211 RibD C-terminal domain; Region: RibD_C; cl17279 439292007212 Fic/DOC family; Region: Fic; cl00960 439292007213 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 439292007214 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cd03440 439292007215 active site 2 [active] 439292007216 active site 1 [active] 439292007217 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 439292007218 active site 439292007219 diaminopimelate decarboxylase; Region: lysA; TIGR01048 439292007220 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 439292007221 active site 439292007222 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 439292007223 substrate binding site [chemical binding]; other site 439292007224 catalytic residues [active] 439292007225 dimer interface [polypeptide binding]; other site 439292007226 pyrimidine-nucleoside phosphorylase; Reviewed; Region: PRK06078 439292007227 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 439292007228 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 439292007229 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; pfam07831 439292007230 purine nucleoside phosphorylase; Provisional; Region: PRK08202 439292007231 purine nucleoside phosphorylase; Provisional; Region: PRK08202 439292007232 phosphopentomutase; Provisional; Region: PRK05362 439292007233 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 439292007234 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 439292007235 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 439292007236 active site 439292007237 Int/Topo IB signature motif; other site 439292007238 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 439292007239 metal binding site 2 [ion binding]; metal-binding site 439292007240 putative DNA binding helix; other site 439292007241 metal binding site 1 [ion binding]; metal-binding site 439292007242 dimer interface [polypeptide binding]; other site 439292007243 structural Zn2+ binding site [ion binding]; other site 439292007244 nudix-type nucleoside diphosphatase, YffH/AdpP family; Region: TIGR00052 439292007245 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 439292007246 dimer interface [polypeptide binding]; other site 439292007247 ADP-ribose binding site [chemical binding]; other site 439292007248 active site 439292007249 nudix motif; other site 439292007250 metal binding site [ion binding]; metal-binding site 439292007251 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 439292007252 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 439292007253 active site 439292007254 catalytic tetrad [active] 439292007255 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 439292007256 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 439292007257 catalytic residues [active] 439292007258 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK12554 439292007259 Phosphotransferase system IIA components [Carbohydrate transport and metabolism]; Region: NagE; COG2190 439292007260 HPr interaction site; other site 439292007261 glycerol kinase (GK) interaction site [polypeptide binding]; other site 439292007262 active site 439292007263 phosphorylation site [posttranslational modification] 439292007264 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 439292007265 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 439292007266 active site 439292007267 motif I; other site 439292007268 motif II; other site 439292007269 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 439292007270 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 439292007271 classical (c) SDRs; Region: SDR_c; cd05233 439292007272 NAD(P) binding site [chemical binding]; other site 439292007273 active site 439292007274 Protein of unknown function (DUF422); Region: DUF422; cl00991 439292007275 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 439292007276 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cd06551 439292007277 putative acyl-acceptor binding pocket; other site 439292007278 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 439292007279 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 439292007280 DXD motif; other site 439292007281 phytoene desaturase; Region: crtI_fam; TIGR02734 439292007282 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 439292007283 active site lid residues [active] 439292007284 substrate binding pocket [chemical binding]; other site 439292007285 catalytic residues [active] 439292007286 substrate-Mg2+ binding site; other site 439292007287 aspartate-rich region 1; other site 439292007288 aspartate-rich region 2; other site 439292007289 phytoene desaturase; Region: crtI_fam; TIGR02734 439292007290 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 439292007291 hydroxyglutarate oxidase; Provisional; Region: PRK11728 439292007292 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 439292007293 phytoene desaturase; Region: crtI_fam; TIGR02734 439292007294 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 439292007295 MoaE interaction surface [polypeptide binding]; other site 439292007296 MoeB interaction surface [polypeptide binding]; other site 439292007297 thiocarboxylated glycine; other site 439292007298 Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]; Region: COG2414 439292007299 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; pfam02730 439292007300 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 439292007301 Methyltransferase domain; Region: Methyltransf_23; pfam13489 439292007302 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 439292007303 S-adenosylmethionine binding site [chemical binding]; other site 439292007304 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 439292007305 Low molecular weight phosphatase family; Region: LMWPc; cd00115 439292007306 active site 439292007307 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 439292007308 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 439292007309 NAD(P) binding site [chemical binding]; other site 439292007310 active site 439292007311 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 439292007312 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 439292007313 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 439292007314 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 439292007315 DTW domain; Region: DTW; cl01221 439292007316 Ion transport protein; Region: Ion_trans; pfam00520 439292007317 Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Region: HTH_GlnR-like; cd01105 439292007318 DNA binding residues [nucleotide binding] 439292007319 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 439292007320 putative dimer interface [polypeptide binding]; other site 439292007321 OsmC-like protein; Region: OsmC; pfam02566 439292007322 Sodium Bile acid symporter family; Region: SBF; cl17470 439292007323 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 439292007324 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_30; cd04643 439292007325 FOG: CBS domain [General function prediction only]; Region: COG0517 439292007326 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 439292007327 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 439292007328 active site 439292007329 FMN binding site [chemical binding]; other site 439292007330 substrate binding site [chemical binding]; other site 439292007331 homotetramer interface [polypeptide binding]; other site 439292007332 catalytic residue [active] 439292007333 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 439292007334 hydrophobic ligand binding site; other site 439292007335 Protein of unknown function (DUF4236); Region: DUF4236; pfam14020 439292007336 Transcriptional regulators [Transcription]; Region: PurR; COG1609 439292007337 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 439292007338 DNA binding site [nucleotide binding] 439292007339 domain linker motif; other site 439292007340 Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs; Region: PBP1_Qymf_like; cd06291 439292007341 dimerization interface [polypeptide binding]; other site 439292007342 ligand binding site [chemical binding]; other site 439292007343 sodium binding site [ion binding]; other site 439292007344 Alpha amylase catalytic domain found in sucrose phosphorylase (also called sucrose glucosyltransferase, disaccharide glucosyltransferase, and sucrose-phosphate alpha-D glucosyltransferase); Region: AmyAc_Sucrose_phosphorylase; cd11355 439292007345 sucrose phosphorylase; Region: sucrose_gtfA; TIGR03852 439292007346 active site 439292007347 homodimer interface [polypeptide binding]; other site 439292007348 catalytic site [active] 439292007349 Protein of unknown function (DUF327); Region: DUF327; pfam03885 439292007350 Flagellin and related hook-associated proteins [Cell motility and secretion]; Region: FlgL; COG1344 439292007351 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 439292007352 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 439292007353 Flagellar protein FliS; Region: FliS; cl00654 439292007354 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 439292007355 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 439292007356 DNA polymerase IV; Validated; Region: PRK01810 439292007357 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 439292007358 active site 439292007359 DNA binding site [nucleotide binding] 439292007360 RNA polymerase sigma-B factor; Region: Sigma_B; TIGR02941 439292007361 Transcriptional regulators [Transcription]; Region: MarR; COG1846 439292007362 MarR family; Region: MarR_2; pfam12802 439292007363 M20 Peptidase T like enzymes specifically cleave tripeptides; Region: M20_peptT_like; cd05683 439292007364 peptidase T-like protein; Region: PepT-like; TIGR01883 439292007365 metal binding site [ion binding]; metal-binding site 439292007366 putative dimer interface [polypeptide binding]; other site 439292007367 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 439292007368 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 439292007369 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 439292007370 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 439292007371 B12 binding site [chemical binding]; other site 439292007372 cobalt ligand [ion binding]; other site 439292007373 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 439292007374 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 439292007375 dimer interface [polypeptide binding]; other site 439292007376 substrate binding site [chemical binding]; other site 439292007377 metal binding site [ion binding]; metal-binding site 439292007378 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, isobutyryl-CoA mutase (ICM)-like subfamily; contains archaeal and bacterial proteins similar to the large subunit of Streptomyces cinnamonensis coenzyme B12-dependent ICM. ICM...; Region: MM_CoA_mutase_ICM_like; cd03680 439292007379 Predicted membrane protein [Function unknown]; Region: COG4129 439292007380 Bacterial protein of unknown function (DUF939); Region: DUF939; pfam06081 439292007381 DUF939 C-terminal domain; Region: DUF939_C; pfam11728 439292007382 F420-0:Gamma-glutamyl ligase; Region: F420_ligase; cl00644 439292007383 Disulphide isomerase; Region: Disulph_isomer; pfam06491 439292007384 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 439292007385 intersubunit interface [polypeptide binding]; other site 439292007386 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 439292007387 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 439292007388 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 439292007389 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 439292007390 E3 interaction surface; other site 439292007391 lipoyl attachment site [posttranslational modification]; other site 439292007392 e3 binding domain; Region: E3_binding; pfam02817 439292007393 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 439292007394 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 439292007395 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 439292007396 alpha subunit interface [polypeptide binding]; other site 439292007397 TPP binding site [chemical binding]; other site 439292007398 heterodimer interface [polypeptide binding]; other site 439292007399 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 439292007400 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 439292007401 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 439292007402 tetramer interface [polypeptide binding]; other site 439292007403 TPP-binding site [chemical binding]; other site 439292007404 heterodimer interface [polypeptide binding]; other site 439292007405 phosphorylation loop region [posttranslational modification] 439292007406 dihydrolipoamide dehydrogenase; Validated; Region: PRK05976 439292007407 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 439292007408 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 439292007409 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 439292007410 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 439292007411 nucleotide binding site [chemical binding]; other site 439292007412 Acetokinase family; Region: Acetate_kinase; cl17229 439292007413 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 439292007414 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 439292007415 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 439292007416 NAD binding site [chemical binding]; other site 439292007417 Phe binding site; other site 439292007418 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 439292007419 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 439292007420 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 439292007421 putative active site [active] 439292007422 heme pocket [chemical binding]; other site 439292007423 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 439292007424 putative active site [active] 439292007425 heme pocket [chemical binding]; other site 439292007426 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 439292007427 Walker A motif; other site 439292007428 ATP binding site [chemical binding]; other site 439292007429 Walker B motif; other site 439292007430 arginine finger; other site 439292007431 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 439292007432 Protein of unknown function (DUF2627); Region: DUF2627; pfam11118 439292007433 sporulation transcription factor Spo0A; Region: spore_0_A; TIGR02875 439292007434 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 439292007435 active site 439292007436 phosphorylation site [posttranslational modification] 439292007437 intermolecular recognition site; other site 439292007438 dimerization interface [polypeptide binding]; other site 439292007439 Sporulation initiation factor Spo0A C terminal; Region: Spo0A_C; pfam08769 439292007440 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 439292007441 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 439292007442 Walker A/P-loop; other site 439292007443 ATP binding site [chemical binding]; other site 439292007444 Q-loop/lid; other site 439292007445 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 439292007446 ABC transporter signature motif; other site 439292007447 Walker B; other site 439292007448 D-loop; other site 439292007449 H-loop/switch region; other site 439292007450 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 439292007451 arginine repressor; Provisional; Region: PRK04280 439292007452 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 439292007453 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 439292007454 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 439292007455 RNA binding surface [nucleotide binding]; other site 439292007456 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 439292007457 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 439292007458 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 439292007459 TPP-binding site; other site 439292007460 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 439292007461 PYR/PP interface [polypeptide binding]; other site 439292007462 dimer interface [polypeptide binding]; other site 439292007463 TPP binding site [chemical binding]; other site 439292007464 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 439292007465 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 439292007466 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 439292007467 substrate binding pocket [chemical binding]; other site 439292007468 chain length determination region; other site 439292007469 substrate-Mg2+ binding site; other site 439292007470 catalytic residues [active] 439292007471 aspartate-rich region 1; other site 439292007472 active site lid residues [active] 439292007473 aspartate-rich region 2; other site 439292007474 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 439292007475 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 439292007476 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 439292007477 generic binding surface II; other site 439292007478 generic binding surface I; other site 439292007479 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14190 439292007480 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 439292007481 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 439292007482 homodimer interface [polypeptide binding]; other site 439292007483 NADP binding site [chemical binding]; other site 439292007484 substrate binding site [chemical binding]; other site 439292007485 transcription antitermination factor NusB; Region: nusB; TIGR01951 439292007486 putative RNA binding site [nucleotide binding]; other site 439292007487 Asp23 family; Region: Asp23; pfam03780 439292007488 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 439292007489 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 439292007490 ATP-grasp domain; Region: ATP-grasp_4; cl17255 439292007491 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 439292007492 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 439292007493 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 439292007494 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 439292007495 carboxyltransferase (CT) interaction site; other site 439292007496 biotinylation site [posttranslational modification]; other site 439292007497 elongation factor P; Validated; Region: PRK00529 439292007498 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 439292007499 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 439292007500 RNA binding site [nucleotide binding]; other site 439292007501 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 439292007502 RNA binding site [nucleotide binding]; other site 439292007503 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 439292007504 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 439292007505 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 439292007506 active site 439292007507 manganese transport transcriptional regulator; Provisional; Region: PRK03902 439292007508 Iron dependent repressor, N-terminal DNA binding domain; Region: Fe_dep_repress; pfam01325 439292007509 Iron dependent repressor, metal binding and dimerisation domain; Region: Fe_dep_repr_C; pfam02742 439292007510 Uncharacterized conserved protein [Function unknown]; Region: COG3595 439292007511 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 439292007512 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08115 439292007513 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 439292007514 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 439292007515 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 439292007516 active site 439292007517 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 439292007518 active site residue [active] 439292007519 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 439292007520 tetramer interface [polypeptide binding]; other site 439292007521 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292007522 catalytic residue [active] 439292007523 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 439292007524 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 439292007525 tetramer interface [polypeptide binding]; other site 439292007526 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292007527 catalytic residue [active] 439292007528 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 439292007529 Sarcosine oxidase, gamma subunit family; Region: SoxG; cl01893 439292007530 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 439292007531 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 439292007532 Competence protein ComGF [Intracellular trafficking and secretion]; Region: ComGF; COG4940 439292007533 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 439292007534 Competence protein ComGC [Intracellular trafficking and secretion]; Region: ComGC; COG4537 439292007535 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 439292007536 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 439292007537 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 439292007538 Walker A motif; other site 439292007539 ATP binding site [chemical binding]; other site 439292007540 Walker B motif; other site 439292007541 YtxH-like protein; Region: YtxH; pfam12732 439292007542 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 439292007543 putative DNA binding site [nucleotide binding]; other site 439292007544 Predicted transcriptional regulator [Transcription]; Region: COG2345 439292007545 putative Zn2+ binding site [ion binding]; other site 439292007546 Protein of unknown function (DUF2626); Region: DUF2626; pfam11117 439292007547 Uncharacterized conserved protein [Function unknown]; Region: COG1565 439292007548 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 439292007549 Probable transposase; Region: OrfB_IS605; pfam01385 439292007550 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 439292007551 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 439292007552 Protein of unknown function (DUF2759); Region: DUF2759; pfam10958 439292007553 Protein of unknown function (DUF1385); Region: DUF1385; cl01595 439292007554 Domain of unknown function DUF77; Region: DUF77; pfam01910 439292007555 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG0390 439292007556 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 439292007557 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 439292007558 Walker A/P-loop; other site 439292007559 ATP binding site [chemical binding]; other site 439292007560 Q-loop/lid; other site 439292007561 ABC transporter signature motif; other site 439292007562 Walker B; other site 439292007563 D-loop; other site 439292007564 H-loop/switch region; other site 439292007565 ROK family protein (putative glucokinase); Region: ROK_glcA_fam; TIGR00744 439292007566 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 439292007567 nucleotide binding site [chemical binding]; other site 439292007568 Bacterial protein of unknown function (DUF910); Region: DUF910; cl11543 439292007569 Protein of unknown function (DUF1694); Region: DUF1694; pfam07997 439292007570 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 439292007571 TPR repeat; Region: TPR_11; pfam13414 439292007572 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 439292007573 binding surface 439292007574 TPR motif; other site 439292007575 L-lactate dehydrogenase; Reviewed; Region: ldh; PRK00066 439292007576 A subgroup of L-lactate dehydrogenases; Region: LDH_2; cd05292 439292007577 NAD binding site [chemical binding]; other site 439292007578 dimer interface [polypeptide binding]; other site 439292007579 substrate binding site [chemical binding]; other site 439292007580 tetramer (dimer of dimers) interface [polypeptide binding]; other site 439292007581 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated; Region: PRK07688 439292007582 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 439292007583 ATP binding site [chemical binding]; other site 439292007584 substrate interface [chemical binding]; other site 439292007585 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 439292007586 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 439292007587 3'-5' exoribonuclease YhaM; Provisional; Region: PRK13480 439292007588 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 439292007589 generic binding surface I; other site 439292007590 generic binding surface II; other site 439292007591 HD domain; Region: HD; pfam01966 439292007592 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 439292007593 YceG-like family; Region: YceG; pfam02618 439292007594 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 439292007595 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 439292007596 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 439292007597 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 439292007598 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 439292007599 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 439292007600 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 439292007601 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4918 439292007602 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 439292007603 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 439292007604 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 439292007605 PhoU domain; Region: PhoU; pfam01895 439292007606 PhoU domain; Region: PhoU; pfam01895 439292007607 Protein of unknown function (DUF1189); Region: DUF1189; pfam06691 439292007608 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 439292007609 Predicted secreted protein [Function unknown]; Region: COG4086 439292007610 Protein of unknown function (DUF1002); Region: DUF1002; pfam06207 439292007611 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 439292007612 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 439292007613 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 439292007614 Uncharacterized conserved protein [Function unknown]; Region: COG5663 439292007615 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 439292007616 metal binding site 2 [ion binding]; metal-binding site 439292007617 putative DNA binding helix; other site 439292007618 metal binding site 1 [ion binding]; metal-binding site 439292007619 dimer interface [polypeptide binding]; other site 439292007620 structural Zn2+ binding site [ion binding]; other site 439292007621 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 439292007622 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 439292007623 ABC-ATPase subunit interface; other site 439292007624 dimer interface [polypeptide binding]; other site 439292007625 putative PBP binding regions; other site 439292007626 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 439292007627 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 439292007628 ABC-ATPase subunit interface; other site 439292007629 dimer interface [polypeptide binding]; other site 439292007630 putative PBP binding regions; other site 439292007631 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 439292007632 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 439292007633 exopolyphosphatase; Region: exo_poly_only; TIGR03706 439292007634 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 439292007635 polyphosphate kinase; Provisional; Region: PRK05443 439292007636 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 439292007637 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 439292007638 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 439292007639 putative domain interface [polypeptide binding]; other site 439292007640 putative active site [active] 439292007641 catalytic site [active] 439292007642 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 439292007643 putative domain interface [polypeptide binding]; other site 439292007644 putative active site [active] 439292007645 catalytic site [active] 439292007646 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 439292007647 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 439292007648 N-acetyl-D-glucosamine binding site [chemical binding]; other site 439292007649 catalytic residue [active] 439292007650 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 439292007651 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 439292007652 ABC-ATPase subunit interface; other site 439292007653 dimer interface [polypeptide binding]; other site 439292007654 putative PBP binding regions; other site 439292007655 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 439292007656 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 439292007657 endonuclease IV; Provisional; Region: PRK01060 439292007658 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 439292007659 AP (apurinic/apyrimidinic) site pocket; other site 439292007660 DNA interaction; other site 439292007661 Metal-binding active site; metal-binding site 439292007662 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 439292007663 DEAD-like helicases superfamily; Region: DEXDc; smart00487 439292007664 ATP binding site [chemical binding]; other site 439292007665 Mg++ binding site [ion binding]; other site 439292007666 motif III; other site 439292007667 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 439292007668 nucleotide binding region [chemical binding]; other site 439292007669 ATP-binding site [chemical binding]; other site 439292007670 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 439292007671 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 439292007672 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 439292007673 Uncharacterized conserved protein [Function unknown]; Region: COG0327 439292007674 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 439292007675 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3323 439292007676 Uncharacterized conserved protein [Function unknown]; Region: COG0327 439292007677 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 439292007678 Predicted SAM-dependent methyltransferase [General function prediction only]; Region: COG2384 439292007679 Family of unknown function (DUF633); Region: DUF633; pfam04816 439292007680 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 439292007681 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 439292007682 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 439292007683 active site 439292007684 catalytic site [active] 439292007685 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 439292007686 RNA polymerase sigma factor RpoD; Validated; Region: PRK09210 439292007687 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 439292007688 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 439292007689 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 439292007690 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 439292007691 DNA binding residues [nucleotide binding] 439292007692 DNA primase; Validated; Region: dnaG; PRK05667 439292007693 CHC2 zinc finger; Region: zf-CHC2; pfam01807 439292007694 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 439292007695 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 439292007696 active site 439292007697 metal binding site [ion binding]; metal-binding site 439292007698 interdomain interaction site; other site 439292007699 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 439292007700 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 439292007701 PEP synthetase regulatory protein; Provisional; Region: PRK05339 439292007702 HTH domain; Region: HTH_11; pfam08279 439292007703 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_4; cd04617 439292007704 FOG: CBS domain [General function prediction only]; Region: COG0517 439292007705 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 439292007706 DALR anticodon binding domain; Region: DALR_1; pfam05746 439292007707 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 439292007708 dimer interface [polypeptide binding]; other site 439292007709 motif 1; other site 439292007710 active site 439292007711 motif 2; other site 439292007712 motif 3; other site 439292007713 Recombination protein O N terminal; Region: RecO_N; pfam11967 439292007714 DNA repair protein RecO; Region: reco; TIGR00613 439292007715 Recombination protein O C terminal; Region: RecO_C; pfam02565 439292007716 GTPase Era; Reviewed; Region: era; PRK00089 439292007717 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 439292007718 G1 box; other site 439292007719 GTP/Mg2+ binding site [chemical binding]; other site 439292007720 Switch I region; other site 439292007721 G2 box; other site 439292007722 Switch II region; other site 439292007723 G3 box; other site 439292007724 G4 box; other site 439292007725 G5 box; other site 439292007726 KH domain; Region: KH_2; pfam07650 439292007727 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; pfam01219 439292007728 metal-binding heat shock protein; Provisional; Region: PRK00016 439292007729 Predicted membrane-associated HD superfamily hydrolase [General function prediction only]; Region: COG1480 439292007730 7TM receptor with intracellular HD hydrolase; Region: 7TM-7TMR_HD; pfam07698 439292007731 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292007732 Zn2+ binding site [ion binding]; other site 439292007733 Mg2+ binding site [ion binding]; other site 439292007734 hypothetical protein; Provisional; Region: PRK13665 439292007735 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 439292007736 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_like; cd07021 439292007737 dimer interface [polypeptide binding]; other site 439292007738 active site residues [active] 439292007739 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 439292007740 Yqey-like protein; Region: YqeY; pfam09424 439292007741 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 439292007742 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 439292007743 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 439292007744 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 439292007745 FeS/SAM binding site; other site 439292007746 TRAM domain; Region: TRAM; cl01282 439292007747 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 439292007748 RNA methyltransferase, RsmE family; Region: TIGR00046 439292007749 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 439292007750 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 439292007751 S-adenosylmethionine binding site [chemical binding]; other site 439292007752 chaperone protein DnaJ; Provisional; Region: PRK14280 439292007753 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 439292007754 HSP70 interaction site [polypeptide binding]; other site 439292007755 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 439292007756 substrate binding site [polypeptide binding]; other site 439292007757 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 439292007758 Zn binding sites [ion binding]; other site 439292007759 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 439292007760 dimer interface [polypeptide binding]; other site 439292007761 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 439292007762 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 439292007763 nucleotide binding site [chemical binding]; other site 439292007764 NEF interaction site [polypeptide binding]; other site 439292007765 SBD interface [polypeptide binding]; other site 439292007766 heat shock protein GrpE; Provisional; Region: PRK14140 439292007767 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 439292007768 dimer interface [polypeptide binding]; other site 439292007769 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 439292007770 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 439292007771 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 439292007772 coproporphyrinogen III oxidase; Provisional; Region: PRK08599 439292007773 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 439292007774 FeS/SAM binding site; other site 439292007775 HemN C-terminal domain; Region: HemN_C; pfam06969 439292007776 GTP-binding protein LepA; Provisional; Region: PRK05433 439292007777 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 439292007778 G1 box; other site 439292007779 putative GEF interaction site [polypeptide binding]; other site 439292007780 GTP/Mg2+ binding site [chemical binding]; other site 439292007781 Switch I region; other site 439292007782 G2 box; other site 439292007783 G3 box; other site 439292007784 Switch II region; other site 439292007785 G4 box; other site 439292007786 G5 box; other site 439292007787 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 439292007788 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 439292007789 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 439292007790 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 439292007791 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 439292007792 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 439292007793 YqzM-like protein; Region: YqzM; pfam14141 439292007794 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 439292007795 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 439292007796 Competence protein; Region: Competence; pfam03772 439292007797 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 439292007798 SLBB domain; Region: SLBB; pfam10531 439292007799 comEA protein; Region: comE; TIGR01259 439292007800 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 439292007801 S-adenosylmethionine binding site [chemical binding]; other site 439292007802 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 439292007803 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292007804 Zn2+ binding site [ion binding]; other site 439292007805 Mg2+ binding site [ion binding]; other site 439292007806 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 439292007807 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 439292007808 active site 439292007809 (T/H)XGH motif; other site 439292007810 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]; Region: COG1534 439292007811 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 439292007812 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 439292007813 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 439292007814 shikimate binding site; other site 439292007815 NAD(P) binding site [chemical binding]; other site 439292007816 GTPase YqeH; Provisional; Region: PRK13796 439292007817 Circularly permuted YqeH GTPase; Region: YqeH; cd01855 439292007818 GTP/Mg2+ binding site [chemical binding]; other site 439292007819 G4 box; other site 439292007820 G5 box; other site 439292007821 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 439292007822 G1 box; other site 439292007823 G1 box; other site 439292007824 GTP/Mg2+ binding site [chemical binding]; other site 439292007825 Switch I region; other site 439292007826 G2 box; other site 439292007827 G2 box; other site 439292007828 Switch I region; other site 439292007829 G3 box; other site 439292007830 G3 box; other site 439292007831 Switch II region; other site 439292007832 Switch II region; other site 439292007833 G4 box; other site 439292007834 Predicted hydrolase of the HAD superfamily [General function prediction only]; Region: COG2179 439292007835 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 439292007836 active site 439292007837 motif I; other site 439292007838 motif II; other site 439292007839 monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12645 439292007840 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 439292007841 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 439292007842 Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism]; Region: MnhB; COG2111 439292007843 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12573 439292007844 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK08600 439292007845 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK07691 439292007846 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 439292007847 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK12651 439292007848 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12600 439292007849 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12586 439292007850 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 439292007851 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 439292007852 Cysteine-rich domain; Region: CCG; pfam02754 439292007853 Cysteine-rich domain; Region: CCG; pfam02754 439292007854 FAD binding domain; Region: FAD_binding_4; pfam01565 439292007855 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 439292007856 Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]; Region: CdaR; COG3835 439292007857 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 439292007858 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 439292007859 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 439292007860 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 439292007861 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 439292007862 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 439292007863 DHH family; Region: DHH; pfam01368 439292007864 FOG: CBS domain [General function prediction only]; Region: COG0517 439292007865 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with an upstream DHH domain which performs a phosphoesterase function and a downstream polyA polymerase domain. CBS is a small domain originally...; Region: CBS_pair_DHH_polyA_Pol_assoc; cd04595 439292007866 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 439292007867 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 439292007868 active site 439292007869 NTP binding site [chemical binding]; other site 439292007870 metal binding triad [ion binding]; metal-binding site 439292007871 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 439292007872 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 439292007873 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 439292007874 dimer interface [polypeptide binding]; other site 439292007875 decamer (pentamer of dimers) interface [polypeptide binding]; other site 439292007876 catalytic triad [active] 439292007877 peroxidatic and resolving cysteines [active] 439292007878 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 439292007879 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 439292007880 purine nucleoside phosphorylase; Reviewed; Region: deoD; PRK05819 439292007881 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 439292007882 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 439292007883 lipoyltransferase and lipoate-protein ligase; Region: lipoyltrans; TIGR00545 439292007884 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 439292007885 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 439292007886 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 439292007887 active site 439292007888 catalytic tetrad [active] 439292007889 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 439292007890 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 439292007891 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 439292007892 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 439292007893 dimer interface [polypeptide binding]; other site 439292007894 [2Fe-2S] cluster binding site [ion binding]; other site 439292007895 PAS fold; Region: PAS_4; pfam08448 439292007896 PAS domain S-box; Region: sensory_box; TIGR00229 439292007897 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 439292007898 putative active site [active] 439292007899 heme pocket [chemical binding]; other site 439292007900 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292007901 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292007902 metal binding site [ion binding]; metal-binding site 439292007903 active site 439292007904 I-site; other site 439292007905 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292007906 hybrid cluster protein; Provisional; Region: PRK05290 439292007907 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 439292007908 ACS interaction site; other site 439292007909 CODH interaction site; other site 439292007910 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 439292007911 hybrid metal cluster; other site 439292007912 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 439292007913 HSP70 interaction site [polypeptide binding]; other site 439292007914 PAS domain; Region: PAS_9; pfam13426 439292007915 PAS fold; Region: PAS_4; pfam08448 439292007916 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 439292007917 PAS fold; Region: PAS_3; pfam08447 439292007918 putative active site [active] 439292007919 heme pocket [chemical binding]; other site 439292007920 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 439292007921 PAS domain; Region: PAS_9; pfam13426 439292007922 putative active site [active] 439292007923 heme pocket [chemical binding]; other site 439292007924 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292007925 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292007926 metal binding site [ion binding]; metal-binding site 439292007927 active site 439292007928 I-site; other site 439292007929 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292007930 Zn2+ binding site [ion binding]; other site 439292007931 Mg2+ binding site [ion binding]; other site 439292007932 YceG-like family; Region: YceG; pfam02618 439292007933 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 439292007934 EDD domain protein, DegV family; Region: DegV; TIGR00762 439292007935 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 439292007936 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 439292007937 HAMP domain; Region: HAMP; pfam00672 439292007938 dimerization interface [polypeptide binding]; other site 439292007939 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292007940 dimer interface [polypeptide binding]; other site 439292007941 putative CheW interface [polypeptide binding]; other site 439292007942 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 439292007943 probable oxidoreductase, LLM family; Region: LLM_2I7G; TIGR03858 439292007944 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 439292007945 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 439292007946 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 439292007947 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; cd02883 439292007948 nudix motif; other site 439292007949 Integral membrane protein (intg_mem_TP0381); Region: Intg_mem_TP0381; pfam09529 439292007950 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 439292007951 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 439292007952 Protein of unknown function (DUF3006); Region: DUF3006; pfam11213 439292007953 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 439292007954 methionine sulfoxide reductase B; Provisional; Region: PRK00222 439292007955 SelR domain; Region: SelR; pfam01641 439292007956 EamA-like transporter family; Region: EamA; pfam00892 439292007957 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 439292007958 EamA-like transporter family; Region: EamA; pfam00892 439292007959 Predicted amidohydrolase [General function prediction only]; Region: COG0388 439292007960 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases); Region: nitrilase_5; cd07583 439292007961 putative active site [active] 439292007962 catalytic triad [active] 439292007963 putative dimer interface [polypeptide binding]; other site 439292007964 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 439292007965 DNA-binding site [nucleotide binding]; DNA binding site 439292007966 RNA-binding motif; other site 439292007967 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 439292007968 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 439292007969 Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that...; Region: PsaA; cd01137 439292007970 metal binding site [ion binding]; metal-binding site 439292007971 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 439292007972 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 439292007973 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 439292007974 regulatory protein interface [polypeptide binding]; other site 439292007975 regulatory phosphorylation site [posttranslational modification]; other site 439292007976 Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative...; Region: CoAse; cd03426 439292007977 putative active site [active] 439292007978 putative CoA binding site [chemical binding]; other site 439292007979 nudix motif; other site 439292007980 metal binding site [ion binding]; metal-binding site 439292007981 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 439292007982 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 439292007983 Protein of unknown function (DUF1510); Region: DUF1510; pfam07423 439292007984 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 439292007985 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 439292007986 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 439292007987 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 439292007988 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 439292007989 Sugar specificity; other site 439292007990 Pyrimidine base specificity; other site 439292007991 ATP-binding site [chemical binding]; other site 439292007992 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 439292007993 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 439292007994 Peptidase family U32; Region: Peptidase_U32; pfam01136 439292007995 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 439292007996 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 439292007997 Peptidase family U32; Region: Peptidase_U32; pfam01136 439292007998 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 439292007999 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 439292008000 YceG-like family; Region: YceG; pfam02618 439292008001 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 439292008002 dimerization interface [polypeptide binding]; other site 439292008003 hypothetical protein; Provisional; Region: PRK13678 439292008004 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 439292008005 hypothetical protein; Provisional; Region: PRK05473 439292008006 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 439292008007 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 439292008008 motif 1; other site 439292008009 active site 439292008010 motif 2; other site 439292008011 motif 3; other site 439292008012 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 439292008013 helicase, putative, RecD/TraA family; Region: recD_rel; TIGR01448 439292008014 AAA domain; Region: AAA_30; pfam13604 439292008015 Family description; Region: UvrD_C_2; pfam13538 439292008016 TPR repeat; Region: TPR_11; pfam13414 439292008017 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 439292008018 binding surface 439292008019 TPR motif; other site 439292008020 Tetratricopeptide repeat; Region: TPR_16; pfam13432 439292008021 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 439292008022 binding surface 439292008023 TPR motif; other site 439292008024 TPR repeat; Region: TPR_11; pfam13414 439292008025 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 439292008026 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 439292008027 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 439292008028 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 439292008029 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 439292008030 catalytic residue [active] 439292008031 Predicted transcriptional regulator [Transcription]; Region: COG1959 439292008032 Transcriptional regulator; Region: Rrf2; pfam02082 439292008033 Predicted membrane protein [Function unknown]; Region: COG2364 439292008034 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 439292008035 recombination factor protein RarA; Reviewed; Region: PRK13342 439292008036 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 439292008037 Walker A motif; other site 439292008038 ATP binding site [chemical binding]; other site 439292008039 Walker B motif; other site 439292008040 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 439292008041 Uncharacterized conserved protein [Function unknown]; Region: COG1556 439292008042 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 439292008043 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 439292008044 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 439292008045 CoB--CoM heterodisulfide reductase, subunit B; Region: CoB_CoM_SS_B; TIGR03288 439292008046 Cysteine-rich domain; Region: CCG; pfam02754 439292008047 Cysteine-rich domain; Region: CCG; pfam02754 439292008048 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 439292008049 L-lactate permease; Region: Lactate_perm; cl00701 439292008050 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 439292008051 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 439292008052 putative ATP binding site [chemical binding]; other site 439292008053 putative substrate interface [chemical binding]; other site 439292008054 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 439292008055 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 439292008056 dimer interface [polypeptide binding]; other site 439292008057 anticodon binding site; other site 439292008058 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 439292008059 homodimer interface [polypeptide binding]; other site 439292008060 motif 1; other site 439292008061 active site 439292008062 motif 2; other site 439292008063 GAD domain; Region: GAD; pfam02938 439292008064 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 439292008065 active site 439292008066 motif 3; other site 439292008067 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 439292008068 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 439292008069 dimer interface [polypeptide binding]; other site 439292008070 motif 1; other site 439292008071 active site 439292008072 motif 2; other site 439292008073 motif 3; other site 439292008074 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 439292008075 anticodon binding site; other site 439292008076 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 439292008077 putative active site [active] 439292008078 dimerization interface [polypeptide binding]; other site 439292008079 putative tRNAtyr binding site [nucleotide binding]; other site 439292008080 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 439292008081 active site 439292008082 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 439292008083 DHH family; Region: DHH; pfam01368 439292008084 DHHA1 domain; Region: DHHA1; pfam02272 439292008085 Single-strand DNA-specific exonuclease, C terminal domain; Region: ssDNA-exonuc_C; cl11538 439292008086 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 439292008087 Protein export membrane protein; Region: SecD_SecF; pfam02355 439292008088 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 439292008089 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 439292008090 Post-transcriptional regulator; Region: Post_transc_reg; pfam13797 439292008091 Domain of unknown function (DUF368); Region: DUF368; pfam04018 439292008092 Preprotein translocase subunit; Region: YajC; pfam02699 439292008093 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 439292008094 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 439292008095 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 439292008096 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 439292008097 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 439292008098 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 439292008099 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 439292008100 Walker A motif; other site 439292008101 ATP binding site [chemical binding]; other site 439292008102 Walker B motif; other site 439292008103 arginine finger; other site 439292008104 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 439292008105 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 439292008106 RuvA N terminal domain; Region: RuvA_N; pfam01330 439292008107 prephenate dehydratase; Provisional; Region: PRK11898 439292008108 Prephenate dehydratase; Region: PDT; pfam00800 439292008109 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 439292008110 putative L-Phe binding site [chemical binding]; other site 439292008111 hypothetical protein; Provisional; Region: PRK04435 439292008112 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 439292008113 C-terminal ACT domain of a small (; 147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains; Region: ACT_PheB-BS; cd04888 439292008114 GTPase CgtA; Reviewed; Region: obgE; PRK12297 439292008115 GTP1/OBG; Region: GTP1_OBG; pfam01018 439292008116 Obg GTPase; Region: Obg; cd01898 439292008117 G1 box; other site 439292008118 GTP/Mg2+ binding site [chemical binding]; other site 439292008119 Switch I region; other site 439292008120 G2 box; other site 439292008121 G3 box; other site 439292008122 Switch II region; other site 439292008123 G4 box; other site 439292008124 G5 box; other site 439292008125 Domain of unknown function (DUF1967); Region: DUF1967; pfam09269 439292008126 agmatinase; Region: agmatinase; TIGR01230 439292008127 Agmatinase-like family; Region: Agmatinase-like; cd09990 439292008128 active site 439292008129 oligomer interface [polypeptide binding]; other site 439292008130 Mn binding site [ion binding]; other site 439292008131 protoporphyrinogen oxidase; Reviewed; Region: PRK11883 439292008132 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 439292008133 ferrochelatase; Provisional; Region: PRK12435 439292008134 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 439292008135 C-terminal domain interface [polypeptide binding]; other site 439292008136 active site 439292008137 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 439292008138 active site 439292008139 N-terminal domain interface [polypeptide binding]; other site 439292008140 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 439292008141 substrate binding site [chemical binding]; other site 439292008142 active site 439292008143 Transglycosylase; Region: Transgly; pfam00912 439292008144 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 439292008145 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 439292008146 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 439292008147 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 439292008148 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 439292008149 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 439292008150 metal binding site [ion binding]; metal-binding site 439292008151 dimer interface [polypeptide binding]; other site 439292008152 Bacterial ABC transporter protein EcsB; Region: EcsB; pfam05975 439292008153 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 439292008154 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 439292008155 Walker A/P-loop; other site 439292008156 ATP binding site [chemical binding]; other site 439292008157 Q-loop/lid; other site 439292008158 ABC transporter signature motif; other site 439292008159 Walker B; other site 439292008160 D-loop; other site 439292008161 H-loop/switch region; other site 439292008162 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 439292008163 HIT family signature motif; other site 439292008164 catalytic residue [active] 439292008165 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 439292008166 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 439292008167 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 439292008168 catalytic residue [active] 439292008169 transcriptional regulator Hpr; Provisional; Region: PRK13777 439292008170 MarR family; Region: MarR; pfam01047 439292008171 Protein of unknown function (DUF3267); Region: DUF3267; pfam11667 439292008172 Uncharacterized protein conserved in bacteria (DUF2140); Region: DUF2140; cl11548 439292008173 3'-5' exoribonuclease YhaM; Provisional; Region: PRK13480 439292008174 YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is...; Region: YhaM_OBF_like; cd04492 439292008175 generic binding surface II; other site 439292008176 generic binding surface I; other site 439292008177 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292008178 Zn2+ binding site [ion binding]; other site 439292008179 Mg2+ binding site [ion binding]; other site 439292008180 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 439292008181 HAMP domain; Region: HAMP; pfam00672 439292008182 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 439292008183 dimer interface [polypeptide binding]; other site 439292008184 phosphorylation site [posttranslational modification] 439292008185 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 439292008186 ATP binding site [chemical binding]; other site 439292008187 Mg2+ binding site [ion binding]; other site 439292008188 G-X-G motif; other site 439292008189 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 439292008190 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 439292008191 active site 439292008192 phosphorylation site [posttranslational modification] 439292008193 intermolecular recognition site; other site 439292008194 dimerization interface [polypeptide binding]; other site 439292008195 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 439292008196 DNA binding site [nucleotide binding] 439292008197 Uncharacterized conserved protein [Function unknown]; Region: COG4717 439292008198 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292008199 Walker A/P-loop; other site 439292008200 ATP binding site [chemical binding]; other site 439292008201 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 439292008202 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 439292008203 active site 439292008204 metal binding site [ion binding]; metal-binding site 439292008205 DNA binding site [nucleotide binding] 439292008206 YhzD-like protein; Region: YhzD; pfam14120 439292008207 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 439292008208 CoenzymeA binding site [chemical binding]; other site 439292008209 subunit interaction site [polypeptide binding]; other site 439292008210 PHB binding site; other site 439292008211 hypothetical protein; Provisional; Region: PRK13676 439292008212 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4399 439292008213 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 439292008214 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 439292008215 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 439292008216 Walker A/P-loop; other site 439292008217 ATP binding site [chemical binding]; other site 439292008218 Q-loop/lid; other site 439292008219 ABC transporter signature motif; other site 439292008220 Walker B; other site 439292008221 D-loop; other site 439292008222 H-loop/switch region; other site 439292008223 TOBE domain; Region: TOBE; pfam03459 439292008224 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 439292008225 Family description; Region: DsbD_2; pfam13386 439292008226 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 439292008227 NADH(P)-binding; Region: NAD_binding_10; pfam13460 439292008228 NAD(P) binding site [chemical binding]; other site 439292008229 active site 439292008230 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 439292008231 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 439292008232 DNA binding residues [nucleotide binding] 439292008233 dimerization interface [polypeptide binding]; other site 439292008234 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 439292008235 Cytochrome bd-type quinol oxidase, subunit 2 [Energy production and conversion]; Region: AppB; COG1294 439292008236 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 439292008237 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292008238 Walker A/P-loop; other site 439292008239 ATP binding site [chemical binding]; other site 439292008240 Q-loop/lid; other site 439292008241 ABC transporter signature motif; other site 439292008242 Walker B; other site 439292008243 D-loop; other site 439292008244 H-loop/switch region; other site 439292008245 PTS system, trehalose-specific IIBC component; Region: PTS-IIBC-Tre; TIGR01992 439292008246 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cd00212 439292008247 active site turn [active] 439292008248 phosphorylation site [posttranslational modification] 439292008249 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 439292008250 Indigoidine synthase A like protein; Region: Indigoidine_A; pfam04227 439292008251 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 439292008252 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 439292008253 YeiC-like sugar kinase. Found in eukaryotes and bacteria, YeiC-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time; Region: YeiC_kinase_like; cd01941 439292008254 substrate binding site [chemical binding]; other site 439292008255 ATP binding site [chemical binding]; other site 439292008256 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 439292008257 ABC1 family; Region: ABC1; cl17513 439292008258 Uncharacterized conserved protein [Function unknown]; Region: COG3937 439292008259 conjugal transfer protein TraV; Provisional; Region: PRK13733 439292008260 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 439292008261 Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation; Region: STAS_RsbR_RsbS_like; cd07041 439292008262 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 439292008263 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 439292008264 Eukaryotic protein of unknown function (DUF829); Region: DUF829; pfam05705 439292008265 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 439292008266 active site 439292008267 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 439292008268 Major Facilitator Superfamily; Region: MFS_1; pfam07690 439292008269 putative substrate translocation pore; other site 439292008270 oligoendopeptidase, M3 family; Region: M3_not_pepF; TIGR02289 439292008271 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_1; cd09606 439292008272 active site 439292008273 Zn binding site [ion binding]; other site 439292008274 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 439292008275 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 439292008276 active site 439292008277 catalytic tetrad [active] 439292008278 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 439292008279 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 439292008280 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 439292008281 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 439292008282 homodimer interface [polypeptide binding]; other site 439292008283 substrate-cofactor binding pocket; other site 439292008284 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292008285 catalytic residue [active] 439292008286 acetolactate synthase catalytic subunit; Reviewed; Region: PRK07710 439292008287 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 439292008288 PYR/PP interface [polypeptide binding]; other site 439292008289 dimer interface [polypeptide binding]; other site 439292008290 TPP binding site [chemical binding]; other site 439292008291 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 439292008292 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 439292008293 TPP-binding site [chemical binding]; other site 439292008294 dimer interface [polypeptide binding]; other site 439292008295 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 439292008296 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 439292008297 putative valine binding site [chemical binding]; other site 439292008298 dimer interface [polypeptide binding]; other site 439292008299 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 439292008300 ketol-acid reductoisomerase; Provisional; Region: PRK05479 439292008301 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 439292008302 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 439292008303 2-isopropylmalate synthase; Validated; Region: PRK00915 439292008304 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 439292008305 active site 439292008306 catalytic residues [active] 439292008307 metal binding site [ion binding]; metal-binding site 439292008308 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; pfam08502 439292008309 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 439292008310 tartrate dehydrogenase; Region: TTC; TIGR02089 439292008311 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 439292008312 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 439292008313 substrate binding site [chemical binding]; other site 439292008314 ligand binding site [chemical binding]; other site 439292008315 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 439292008316 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 439292008317 substrate binding site [chemical binding]; other site 439292008318 Nitrogen regulatory protein P-II; Region: P-II; smart00938 439292008319 Protein of unknown function (DUF1538); Region: DUF1538; pfam07556 439292008320 Protein of unknown function (DUF1538); Region: DUF1538; pfam07556 439292008321 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 439292008322 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 439292008323 G1 box; other site 439292008324 putative GEF interaction site [polypeptide binding]; other site 439292008325 GTP/Mg2+ binding site [chemical binding]; other site 439292008326 Switch I region; other site 439292008327 G2 box; other site 439292008328 G3 box; other site 439292008329 Switch II region; other site 439292008330 G4 box; other site 439292008331 G5 box; other site 439292008332 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 439292008333 Spo0E like sporulation regulatory protein; Region: SpoOE-like; pfam09388 439292008334 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 439292008335 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 439292008336 active site 439292008337 substrate binding site [chemical binding]; other site 439292008338 metal binding site [ion binding]; metal-binding site 439292008339 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 439292008340 glycerol kinase; Provisional; Region: glpK; PRK00047 439292008341 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 439292008342 N- and C-terminal domain interface [polypeptide binding]; other site 439292008343 active site 439292008344 MgATP binding site [chemical binding]; other site 439292008345 catalytic site [active] 439292008346 metal binding site [ion binding]; metal-binding site 439292008347 glycerol binding site [chemical binding]; other site 439292008348 homotetramer interface [polypeptide binding]; other site 439292008349 homodimer interface [polypeptide binding]; other site 439292008350 FBP binding site [chemical binding]; other site 439292008351 protein IIAGlc interface [polypeptide binding]; other site 439292008352 Glycerol uptake facilitator and related permeases (Major Intrinsic Protein Family) [Carbohydrate transport and metabolism]; Region: GlpF; COG0580 439292008353 amphipathic channel; other site 439292008354 Asn-Pro-Ala signature motifs; other site 439292008355 Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription]; Region: GlpP; COG1954 439292008356 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 439292008357 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292008358 Coenzyme A binding pocket [chemical binding]; other site 439292008359 Predicted amidohydrolase [General function prediction only]; Region: COG0388 439292008360 Uncharacterized subgroup of the nitrilase superfamily; some members of this subgroup have an N-terminal RimI domain (class 12 nitrilases); Region: nitrilase_Rim1_like; cd07574 439292008361 putative active site [active] 439292008362 catalytic triad [active] 439292008363 putative dimer interface [polypeptide binding]; other site 439292008364 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 439292008365 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 439292008366 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1655 439292008367 Uncharacterized protein conserved in bacteria (DUF2225); Region: DUF2225; pfam09986 439292008368 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 439292008369 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 439292008370 TM-ABC transporter signature motif; other site 439292008371 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 439292008372 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 439292008373 TM-ABC transporter signature motif; other site 439292008374 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 439292008375 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292008376 Walker A/P-loop; other site 439292008377 ATP binding site [chemical binding]; other site 439292008378 Q-loop/lid; other site 439292008379 ABC transporter signature motif; other site 439292008380 Walker B; other site 439292008381 D-loop; other site 439292008382 H-loop/switch region; other site 439292008383 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 439292008384 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 439292008385 Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea; Region: PBP1_BmpA_PnrA_like; cd06354 439292008386 ligand binding site [chemical binding]; other site 439292008387 ethanolamine utilization protein EutH; Provisional; Region: PRK15086 439292008388 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 439292008389 Uncharacterized conserved protein [Function unknown]; Region: COG3342 439292008390 Family of unknown function (DUF1028); Region: DUF1028; pfam06267 439292008391 Putative peptidoglycan binding domain; Region: PG_binding_2; pfam08823 439292008392 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 439292008393 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 439292008394 Catalytic site [active] 439292008395 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 439292008396 Transglycosylase; Region: Transgly; pfam00912 439292008397 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 439292008398 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 439292008399 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 439292008400 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 439292008401 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 439292008402 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 439292008403 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 439292008404 DNA binding site [nucleotide binding] 439292008405 active site 439292008406 epoxyqueuosine reductase; Region: TIGR00276 439292008407 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 439292008408 Domain of unknown function DUF302; Region: DUF302; cl01364 439292008409 hypothetical protein; Provisional; Region: PRK12378 439292008410 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 439292008411 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 439292008412 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 439292008413 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 439292008414 DNA-binding site [nucleotide binding]; DNA binding site 439292008415 UTRA domain; Region: UTRA; pfam07702 439292008416 Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: CelF; COG1486 439292008417 Glycoside Hydrolases Family 4; GlvA- and pagL-like glycosidases; Region: GH4_GlvA_pagL_like; cd05298 439292008418 NAD binding site [chemical binding]; other site 439292008419 sugar binding site [chemical binding]; other site 439292008420 divalent metal binding site [ion binding]; other site 439292008421 putative tetramer (dimer of dimers) interface [polypeptide binding]; other site 439292008422 dimer interface [polypeptide binding]; other site 439292008423 PTS system, glucose-specific IIBC component; Region: PTS-II-BC-glcB; TIGR02002 439292008424 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 439292008425 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cd00212 439292008426 active site turn [active] 439292008427 phosphorylation site [posttranslational modification] 439292008428 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 439292008429 Predicted permease; Region: DUF318; cl17795 439292008430 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 439292008431 dimerization interface [polypeptide binding]; other site 439292008432 putative DNA binding site [nucleotide binding]; other site 439292008433 putative Zn2+ binding site [ion binding]; other site 439292008434 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292008435 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292008436 dimer interface [polypeptide binding]; other site 439292008437 putative CheW interface [polypeptide binding]; other site 439292008438 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 439292008439 N-acetyl-D-glucosamine binding site [chemical binding]; other site 439292008440 catalytic residue [active] 439292008441 Vitamin K epoxide reductase (VKOR) family; Region: VKOR; cd10546 439292008442 putative active site [active] 439292008443 redox center [active] 439292008444 glutamine ABC transporter periplasmic protein; Reviewed; Region: glnH; PRK09495 439292008445 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 439292008446 substrate binding pocket [chemical binding]; other site 439292008447 membrane-bound complex binding site; other site 439292008448 hinge residues; other site 439292008449 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 439292008450 dimer interface [polypeptide binding]; other site 439292008451 conserved gate region; other site 439292008452 putative PBP binding loops; other site 439292008453 ABC-ATPase subunit interface; other site 439292008454 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 439292008455 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 439292008456 Walker A/P-loop; other site 439292008457 ATP binding site [chemical binding]; other site 439292008458 Q-loop/lid; other site 439292008459 ABC transporter signature motif; other site 439292008460 Walker B; other site 439292008461 D-loop; other site 439292008462 H-loop/switch region; other site 439292008463 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 439292008464 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 439292008465 HAMP domain; Region: HAMP; pfam00672 439292008466 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292008467 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292008468 dimer interface [polypeptide binding]; other site 439292008469 putative CheW interface [polypeptide binding]; other site 439292008470 Cache domain; Region: Cache_1; pfam02743 439292008471 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292008472 dimerization interface [polypeptide binding]; other site 439292008473 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292008474 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292008475 dimer interface [polypeptide binding]; other site 439292008476 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 439292008477 putative CheW interface [polypeptide binding]; other site 439292008478 Probable transposase; Region: OrfB_IS605; pfam01385 439292008479 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 439292008480 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 439292008481 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 439292008482 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 439292008483 synthetase active site [active] 439292008484 NTP binding site [chemical binding]; other site 439292008485 metal binding site [ion binding]; metal-binding site 439292008486 Domain of unknown function (DUF202); Region: DUF202; pfam02656 439292008487 Domain of unknown function (DUF897); Region: DUF897; cl01312 439292008488 Uncharacterized conserved protein (DUF2294); Region: DUF2294; pfam10057 439292008489 hydroxyglutarate oxidase; Provisional; Region: PRK11728 439292008490 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 439292008491 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 439292008492 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 439292008493 dimer interface [polypeptide binding]; other site 439292008494 conserved gate region; other site 439292008495 putative PBP binding loops; other site 439292008496 ABC-ATPase subunit interface; other site 439292008497 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 439292008498 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 439292008499 ABC-ATPase subunit interface; other site 439292008500 putative PBP binding loops; other site 439292008501 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 439292008502 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 439292008503 Walker A/P-loop; other site 439292008504 ATP binding site [chemical binding]; other site 439292008505 Q-loop/lid; other site 439292008506 ABC transporter signature motif; other site 439292008507 Walker B; other site 439292008508 D-loop; other site 439292008509 H-loop/switch region; other site 439292008510 ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: PhnD; COG3221 439292008511 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 439292008512 Putative transcription activator [Transcription]; Region: TenA; COG0819 439292008513 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 439292008514 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 439292008515 Walker A/P-loop; other site 439292008516 ATP binding site [chemical binding]; other site 439292008517 Q-loop/lid; other site 439292008518 ABC transporter signature motif; other site 439292008519 Walker B; other site 439292008520 D-loop; other site 439292008521 H-loop/switch region; other site 439292008522 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 439292008523 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 439292008524 dimer interface [polypeptide binding]; other site 439292008525 conserved gate region; other site 439292008526 putative PBP binding loops; other site 439292008527 ABC-ATPase subunit interface; other site 439292008528 NMT1/THI5 like; Region: NMT1; pfam09084 439292008529 topology modulation protein; Reviewed; Region: PRK08118 439292008530 AAA domain; Region: AAA_17; pfam13207 439292008531 Predicted kinase related to dihydroxyacetone kinase [General function prediction only]; Region: COG1461 439292008532 DAK2 domain; Region: Dak2; pfam02734 439292008533 EDD domain protein, DegV family; Region: DegV; TIGR00762 439292008534 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 439292008535 Protein of unknown function (DUF1295); Region: DUF1295; cl17837 439292008536 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 439292008537 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 439292008538 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 439292008539 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 439292008540 4Fe-4S binding domain; Region: Fer4; pfam00037 439292008541 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 439292008542 This CD includes the respiratory arsenate reductase, As(V), catalytic subunit (ArrA) and other related proteins. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_Arsenate-R; cd02757 439292008543 putative [Fe4-S4] binding site [ion binding]; other site 439292008544 putative molybdopterin cofactor binding site [chemical binding]; other site 439292008545 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 439292008546 This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins; Region: MopB_CT_Tetrathionate_Arsenate-R; cd02780 439292008547 putative molybdopterin cofactor binding site; other site 439292008548 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 439292008549 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 439292008550 substrate binding pocket [chemical binding]; other site 439292008551 membrane-bound complex binding site; other site 439292008552 hinge residues; other site 439292008553 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292008554 dimerization interface [polypeptide binding]; other site 439292008555 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 439292008556 Histidine kinase; Region: HisKA_3; pfam07730 439292008557 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 439292008558 ATP binding site [chemical binding]; other site 439292008559 Mg2+ binding site [ion binding]; other site 439292008560 G-X-G motif; other site 439292008561 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 439292008562 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 439292008563 active site 439292008564 phosphorylation site [posttranslational modification] 439292008565 intermolecular recognition site; other site 439292008566 dimerization interface [polypeptide binding]; other site 439292008567 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 439292008568 DNA binding residues [nucleotide binding] 439292008569 dimerization interface [polypeptide binding]; other site 439292008570 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 439292008571 Sodium Bile acid symporter family; Region: SBF; cl17470 439292008572 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 439292008573 classical (c) SDRs; Region: SDR_c; cd05233 439292008574 NAD(P) binding site [chemical binding]; other site 439292008575 active site 439292008576 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292008577 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292008578 dimer interface [polypeptide binding]; other site 439292008579 putative CheW interface [polypeptide binding]; other site 439292008580 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 439292008581 putative substrate translocation pore; other site 439292008582 Major Facilitator Superfamily; Region: MFS_1; pfam07690 439292008583 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 439292008584 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08642 439292008585 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 439292008586 NAD(P) binding site [chemical binding]; other site 439292008587 active site 439292008588 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 439292008589 Protein export membrane protein; Region: SecD_SecF; cl14618 439292008590 amidase; Provisional; Region: PRK08137 439292008591 Amidase; Region: Amidase; cl11426 439292008592 Transcriptional regulator [Transcription]; Region: LysR; COG0583 439292008593 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 439292008594 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 439292008595 dimerization interface [polypeptide binding]; other site 439292008596 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 439292008597 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 439292008598 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 439292008599 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 439292008600 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292008601 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292008602 dimer interface [polypeptide binding]; other site 439292008603 putative CheW interface [polypeptide binding]; other site 439292008604 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 439292008605 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 439292008606 putative active site [active] 439292008607 PhoH-like protein; Region: PhoH; cl17668 439292008608 phosphoenolpyruvate synthase; Validated; Region: PRK06241 439292008609 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 439292008610 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 439292008611 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 439292008612 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292008613 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 439292008614 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 439292008615 Probable transposase; Region: OrfB_IS605; pfam01385 439292008616 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 439292008617 Growth regulator [Signal transduction mechanisms]; Region: MazE; COG2336 439292008618 PemK-like protein; Region: PemK; cl00995 439292008619 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: Bsubt_queE; TIGR03365 439292008620 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 439292008621 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 439292008622 active site 439292008623 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 439292008624 Ligand Binding Site [chemical binding]; other site 439292008625 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 439292008626 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 439292008627 Probable transposase; Region: OrfB_IS605; pfam01385 439292008628 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 439292008629 2-aminoethylphosphonate ABC transporter substrate-binding protein; Provisional; Region: PRK15046 439292008630 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 439292008631 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 439292008632 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 439292008633 putative PBP binding loops; other site 439292008634 dimer interface [polypeptide binding]; other site 439292008635 ABC-ATPase subunit interface; other site 439292008636 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 439292008637 dimer interface [polypeptide binding]; other site 439292008638 conserved gate region; other site 439292008639 putative PBP binding loops; other site 439292008640 ABC-ATPase subunit interface; other site 439292008641 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 439292008642 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292008643 Walker A/P-loop; other site 439292008644 ATP binding site [chemical binding]; other site 439292008645 Q-loop/lid; other site 439292008646 ABC transporter signature motif; other site 439292008647 Walker B; other site 439292008648 D-loop; other site 439292008649 H-loop/switch region; other site 439292008650 TOBE domain; Region: TOBE_2; pfam08402 439292008651 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 439292008652 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 439292008653 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 439292008654 A new structural DNA glycosylase containing HEAT-like repeats; Region: AlkD_like_1; cd07064 439292008655 active site 439292008656 HAMP domain; Region: HAMP; pfam00672 439292008657 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292008658 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292008659 dimer interface [polypeptide binding]; other site 439292008660 putative CheW interface [polypeptide binding]; other site 439292008661 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292008662 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292008663 dimer interface [polypeptide binding]; other site 439292008664 putative CheW interface [polypeptide binding]; other site 439292008665 Cache domain; Region: Cache_1; pfam02743 439292008666 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292008667 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292008668 metal binding site [ion binding]; metal-binding site 439292008669 active site 439292008670 I-site; other site 439292008671 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292008672 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 439292008673 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 439292008674 dimer interface [polypeptide binding]; other site 439292008675 phosphorylation site [posttranslational modification] 439292008676 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 439292008677 ATP binding site [chemical binding]; other site 439292008678 Mg2+ binding site [ion binding]; other site 439292008679 G-X-G motif; other site 439292008680 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 439292008681 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 439292008682 active site 439292008683 phosphorylation site [posttranslational modification] 439292008684 intermolecular recognition site; other site 439292008685 dimerization interface [polypeptide binding]; other site 439292008686 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 439292008687 DNA binding site [nucleotide binding] 439292008688 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 439292008689 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 439292008690 Walker A/P-loop; other site 439292008691 ATP binding site [chemical binding]; other site 439292008692 Q-loop/lid; other site 439292008693 ABC transporter signature motif; other site 439292008694 Walker B; other site 439292008695 D-loop; other site 439292008696 H-loop/switch region; other site 439292008697 Protein of unknown function (DUF1093); Region: DUF1093; cl02185 439292008698 YcxB-like protein; Region: YcxB; pfam14317 439292008699 putative transposase OrfB; Reviewed; Region: PHA02517 439292008700 HTH-like domain; Region: HTH_21; pfam13276 439292008701 Integrase core domain; Region: rve; pfam00665 439292008702 Integrase core domain; Region: rve_2; pfam13333 439292008703 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 439292008704 Transposase; Region: HTH_Tnp_1; pfam01527 439292008705 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 439292008706 active site 439292008707 FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into...; Region: FHIT; cd01275 439292008708 nucleotide binding site/active site [active] 439292008709 HIT family signature motif; other site 439292008710 catalytic residue [active] 439292008711 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 439292008712 Uncharacterized conserved protein (DUF2075); Region: DUF2075; pfam09848 439292008713 Walker A motif; other site 439292008714 ATP binding site [chemical binding]; other site 439292008715 Walker B motif; other site 439292008716 Uncharacterized conserved protein [Function unknown]; Region: COG3410 439292008717 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 439292008718 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 439292008719 putative active site [active] 439292008720 putative NTP binding site [chemical binding]; other site 439292008721 putative nucleic acid binding site [nucleotide binding]; other site 439292008722 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 439292008723 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 439292008724 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 439292008725 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 439292008726 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 439292008727 NodB motif; other site 439292008728 active site 439292008729 catalytic site [active] 439292008730 metal binding site [ion binding]; metal-binding site 439292008731 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292008732 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292008733 metal binding site [ion binding]; metal-binding site 439292008734 active site 439292008735 I-site; other site 439292008736 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292008737 metal binding site [ion binding]; metal-binding site 439292008738 active site 439292008739 I-site; other site 439292008740 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292008741 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 439292008742 classical (c) SDRs; Region: SDR_c; cd05233 439292008743 NAD(P) binding site [chemical binding]; other site 439292008744 active site 439292008745 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 439292008746 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292008747 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 439292008748 triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs; Region: TMR_SDR_a; cd05269 439292008749 NADP binding site [chemical binding]; other site 439292008750 Haemolysin XhlA; Region: XhlA; pfam10779 439292008751 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 439292008752 Ferritin-like domain; Region: Ferritin; pfam00210 439292008753 ferroxidase diiron center [ion binding]; other site 439292008754 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 439292008755 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 439292008756 Probable transposase; Region: OrfB_IS605; pfam01385 439292008757 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 439292008758 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 439292008759 TPR repeat; Region: TPR_11; pfam13414 439292008760 TPR motif; other site 439292008761 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 439292008762 Peptidase family M28; Region: Peptidase_M28; pfam04389 439292008763 metal binding site [ion binding]; metal-binding site 439292008764 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 439292008765 metal binding site [ion binding]; metal-binding site 439292008766 Uncharacterized protein conserved in bacteria (DUF2128); Region: DUF2128; pfam09901 439292008767 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 439292008768 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 439292008769 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 439292008770 Walker A/P-loop; other site 439292008771 ATP binding site [chemical binding]; other site 439292008772 Q-loop/lid; other site 439292008773 ABC transporter signature motif; other site 439292008774 Walker B; other site 439292008775 D-loop; other site 439292008776 H-loop/switch region; other site 439292008777 Domain of unknown function (DUF4162); Region: DUF4162; pfam13732 439292008778 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 439292008779 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated; Region: PRK07688 439292008780 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 439292008781 ATP binding site [chemical binding]; other site 439292008782 substrate interface [chemical binding]; other site 439292008783 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 439292008784 ThiS interaction site; other site 439292008785 putative active site [active] 439292008786 tetramer interface [polypeptide binding]; other site 439292008787 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 439292008788 thiS-thiF/thiG interaction site; other site 439292008789 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 439292008790 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 439292008791 thiamine phosphate binding site [chemical binding]; other site 439292008792 active site 439292008793 pyrophosphate binding site [ion binding]; other site 439292008794 Uncharacterized conserved protein [Function unknown]; Region: COG5646 439292008795 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 439292008796 Pseudomonas fluorescens MupV-like, extended (e) SDRs; Region: MupV_like_SDR_e; cd05263 439292008797 putative NAD(P) binding site [chemical binding]; other site 439292008798 active site 439292008799 putative substrate binding site [chemical binding]; other site 439292008800 C-terminal domain of fatty acyl CoA reductases; Region: FAR_C; cl03838 439292008801 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 439292008802 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 439292008803 Protein of unknown function (DUF4242); Region: DUF4242; pfam14026 439292008804 Predicted transcriptional regulators [Transcription]; Region: COG1733 439292008805 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 439292008806 dimerization interface [polypeptide binding]; other site 439292008807 putative DNA binding site [nucleotide binding]; other site 439292008808 putative Zn2+ binding site [ion binding]; other site 439292008809 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 439292008810 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 439292008811 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 439292008812 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 439292008813 substrate binding pocket [chemical binding]; other site 439292008814 membrane-bound complex binding site; other site 439292008815 hinge residues; other site 439292008816 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 439292008817 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 439292008818 Walker A/P-loop; other site 439292008819 ATP binding site [chemical binding]; other site 439292008820 Q-loop/lid; other site 439292008821 ABC transporter signature motif; other site 439292008822 Walker B; other site 439292008823 D-loop; other site 439292008824 H-loop/switch region; other site 439292008825 Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Region: HTH_TipAL-Mta; cd01106 439292008826 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 439292008827 DNA binding residues [nucleotide binding] 439292008828 dimer interface [polypeptide binding]; other site 439292008829 TipAS antibiotic-recognition domain; Region: TipAS; pfam07739 439292008830 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 439292008831 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 439292008832 NAD(P) binding site [chemical binding]; other site 439292008833 active site 439292008834 H+ Antiporter protein; Region: 2A0121; TIGR00900 439292008835 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 439292008836 putative DNA binding site [nucleotide binding]; other site 439292008837 dimerization interface [polypeptide binding]; other site 439292008838 putative Zn2+ binding site [ion binding]; other site 439292008839 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 439292008840 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 439292008841 RRXRR protein; Region: RRXRR; pfam14239 439292008842 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 439292008843 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 439292008844 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 439292008845 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 439292008846 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 439292008847 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 439292008848 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 439292008849 Protein of unknown function (DUF2614); Region: DUF2614; pfam11023 439292008850 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 439292008851 metal binding site 2 [ion binding]; metal-binding site 439292008852 putative DNA binding helix; other site 439292008853 metal binding site 1 [ion binding]; metal-binding site 439292008854 dimer interface [polypeptide binding]; other site 439292008855 structural Zn2+ binding site [ion binding]; other site 439292008856 Protein of unknown function (DUF970); Region: DUF970; cl17525 439292008857 Putative D-isomer specific 2-hydroxyacid dehydrogenase; Region: 2-Hacid_dh_1; cd05300 439292008858 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 439292008859 NAD binding site [chemical binding]; other site 439292008860 ligand binding site [chemical binding]; other site 439292008861 catalytic site [active] 439292008862 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 439292008863 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 439292008864 catalytic triad [active] 439292008865 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK12389 439292008866 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 439292008867 inhibitor-cofactor binding pocket; inhibition site 439292008868 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292008869 catalytic residue [active] 439292008870 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 439292008871 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 439292008872 active site 439292008873 dimer interface [polypeptide binding]; other site 439292008874 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 439292008875 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 439292008876 active site 439292008877 FMN binding site [chemical binding]; other site 439292008878 substrate binding site [chemical binding]; other site 439292008879 3Fe-4S cluster binding site [ion binding]; other site 439292008880 GXGXG domain. This domain of unknown function is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS), in subunit C of tungsten formylmethanofuran dehydrogenase (FwdC) and in subunit C of molybdenum formylmethanofuran...; Region: GXGXG; cd00504 439292008881 domain_subunit interface; other site 439292008882 Predicted membrane protein [Function unknown]; Region: COG4129 439292008883 Bacterial protein of unknown function (DUF939); Region: DUF939; pfam06081 439292008884 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 439292008885 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 439292008886 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 439292008887 Walker A/P-loop; other site 439292008888 ATP binding site [chemical binding]; other site 439292008889 Q-loop/lid; other site 439292008890 ABC transporter signature motif; other site 439292008891 Walker B; other site 439292008892 D-loop; other site 439292008893 H-loop/switch region; other site 439292008894 hypothetical protein; Provisional; Region: PRK13662 439292008895 Protein of unknown function (DUF3939); Region: DUF3939; pfam13075 439292008896 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 439292008897 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 439292008898 DXD motif; other site 439292008899 HEAT repeats; Region: HEAT_2; pfam13646 439292008900 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; cl17736 439292008901 active site 439292008902 phosphorylation site [posttranslational modification] 439292008903 intermolecular recognition site; other site 439292008904 dimerization interface [polypeptide binding]; other site 439292008905 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292008906 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292008907 metal binding site [ion binding]; metal-binding site 439292008908 active site 439292008909 I-site; other site 439292008910 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 439292008911 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 439292008912 active site 439292008913 phosphorylation site [posttranslational modification] 439292008914 intermolecular recognition site; other site 439292008915 dimerization interface [polypeptide binding]; other site 439292008916 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 439292008917 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 439292008918 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 439292008919 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 439292008920 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 439292008921 classical (c) SDRs; Region: SDR_c; cd05233 439292008922 NAD(P) binding site [chemical binding]; other site 439292008923 active site 439292008924 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 439292008925 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 439292008926 minor groove reading motif; other site 439292008927 helix-hairpin-helix signature motif; other site 439292008928 substrate binding pocket [chemical binding]; other site 439292008929 active site 439292008930 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 439292008931 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 439292008932 DNA binding and oxoG recognition site [nucleotide binding] 439292008933 Predicted membrane-bound metal-dependent hydrolases [General function prediction only]; Region: COG1988 439292008934 WVELL protein; Region: WVELL; pfam14043 439292008935 Protein of unknown function (DUF1811); Region: DUF1811; pfam08838 439292008936 RecX family; Region: RecX; cl00936 439292008937 atypical (a) SDRs, subgroup 8; Region: SDR_a8; cd05242 439292008938 TIGR01777 family protein; Region: yfcH 439292008939 putative NAD(P) binding site [chemical binding]; other site 439292008940 putative active site [active] 439292008941 trehalose operon repressor, B. subtilis-type; Region: trehalos_R_Bsub; TIGR02404 439292008942 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 439292008943 DNA-binding site [nucleotide binding]; DNA binding site 439292008944 UTRA domain; Region: UTRA; pfam07702 439292008945 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 439292008946 Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins; Region: AmyAc_SI_OligoGlu_DGase; cd11333 439292008947 Ca binding site [ion binding]; other site 439292008948 active site 439292008949 catalytic site [active] 439292008950 Predicted permeases [General function prediction only]; Region: COG0679 439292008951 YtkA-like; Region: YtkA; pfam13115 439292008952 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 439292008953 putative mercuric reductase; Provisional; Region: PRK14727 439292008954 Domain of unknown function (DUF4372); Region: DUF4372; pfam14294 439292008955 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 439292008956 active site 439292008957 TRAM domain; Region: TRAM; pfam01938 439292008958 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 439292008959 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 439292008960 catalytic core [active] 439292008961 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG0535 439292008962 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 439292008963 FeS/SAM binding site; other site 439292008964 YfkB-like domain; Region: YfkB; pfam08756 439292008965 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 439292008966 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 439292008967 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 439292008968 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 439292008969 putative substrate translocation pore; other site 439292008970 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 439292008971 Protein of unknown function (DUF3901); Region: DUF3901; pfam13040 439292008972 SCP-2 sterol transfer family; Region: SCP2; pfam02036 439292008973 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 439292008974 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 439292008975 putative acyl-acceptor binding pocket; other site 439292008976 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 439292008977 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 439292008978 Acylphosphatase; Region: Acylphosphatase; pfam00708 439292008979 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 439292008980 DNA photolyase; Region: DNA_photolyase; pfam00875 439292008981 Acetyltransferase (GNAT) domain; Region: Acetyltransf_9; pfam13527 439292008982 Predicted acetyltransferase involved in intracellular survival and related acetyltransferases [General function prediction only]; Region: Eis; COG4552 439292008983 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 439292008984 Bacillus subtilis aldehyde dehydrogenase ywdH-like; Region: ALDH_YwdH-P39616; cd07136 439292008985 NAD(P) binding site [chemical binding]; other site 439292008986 catalytic residues [active] 439292008987 Methyltransferase domain; Region: Methyltransf_23; pfam13489 439292008988 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 439292008989 S-adenosylmethionine binding site [chemical binding]; other site 439292008990 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; cl00391 439292008991 active site clefts [active] 439292008992 zinc binding site [ion binding]; other site 439292008993 dimer interface [polypeptide binding]; other site 439292008994 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 439292008995 CPxP motif; other site 439292008996 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 439292008997 CPxP motif; other site 439292008998 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 439292008999 active site residue [active] 439292009000 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 439292009001 catalytic residues [active] 439292009002 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 439292009003 DXD motif; other site 439292009004 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 439292009005 Domain of unknown function DUF20; Region: UPF0118; pfam01594 439292009006 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 439292009007 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 439292009008 Predicted esterase [General function prediction only]; Region: COG0400 439292009009 putative hydrolase; Provisional; Region: PRK11460 439292009010 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 439292009011 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 439292009012 ATP binding site [chemical binding]; other site 439292009013 putative Mg++ binding site [ion binding]; other site 439292009014 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 439292009015 nucleotide binding region [chemical binding]; other site 439292009016 ATP-binding site [chemical binding]; other site 439292009017 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 439292009018 HRDC domain; Region: HRDC; pfam00570 439292009019 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 439292009020 dimer interface [polypeptide binding]; other site 439292009021 putative tRNA-binding site [nucleotide binding]; other site 439292009022 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 439292009023 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK09412 439292009024 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292009025 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292009026 dimer interface [polypeptide binding]; other site 439292009027 putative CheW interface [polypeptide binding]; other site 439292009028 Cache domain; Region: Cache_1; pfam02743 439292009029 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292009030 dimerization interface [polypeptide binding]; other site 439292009031 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292009032 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292009033 metal binding site [ion binding]; metal-binding site 439292009034 active site 439292009035 I-site; other site 439292009036 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292009037 Adenine deaminase [Nucleotide transport and metabolism]; Region: AdeC; COG1001 439292009038 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 439292009039 Adenine deaminase (AdeC) directly deaminates adenine to form hypoxanthine. This reaction is part of one of the adenine salvage pathways, as well as the degradation pathway. It is important for adenine utilization as a purine, as well as a nitrogen source...; Region: AdeC; cd01295 439292009040 active site 439292009041 Adenine deaminase C-terminal domain; Region: Adenine_deam_C; pfam13382 439292009042 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 439292009043 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 439292009044 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 439292009045 Walker A/P-loop; other site 439292009046 ATP binding site [chemical binding]; other site 439292009047 Q-loop/lid; other site 439292009048 ABC transporter signature motif; other site 439292009049 Walker B; other site 439292009050 D-loop; other site 439292009051 H-loop/switch region; other site 439292009052 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 439292009053 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 439292009054 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292009055 Walker A/P-loop; other site 439292009056 ATP binding site [chemical binding]; other site 439292009057 Q-loop/lid; other site 439292009058 ABC transporter signature motif; other site 439292009059 Walker B; other site 439292009060 D-loop; other site 439292009061 H-loop/switch region; other site 439292009062 Glycerate kinase [Carbohydrate transport and metabolism]; Region: COG1929 439292009063 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 439292009064 Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins; Region: AmyAc_SI_OligoGlu_DGase; cd11333 439292009065 Ca binding site [ion binding]; other site 439292009066 active site 439292009067 catalytic site [active] 439292009068 Predicted permeases [General function prediction only]; Region: RarD; COG2962 439292009069 Multidrug resistance efflux transporter; Region: EmrE; pfam13536 439292009070 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 439292009071 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 439292009072 putative NAD(P) binding site [chemical binding]; other site 439292009073 putative active site [active] 439292009074 LabA_like proteins; Region: LabA_like/DUF88; cl10034 439292009075 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292009076 Coenzyme A binding pocket [chemical binding]; other site 439292009077 Predicted permease [General function prediction only]; Region: COG2985 439292009078 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 439292009079 TrkA-C domain; Region: TrkA_C; pfam02080 439292009080 TrkA-C domain; Region: TrkA_C; pfam02080 439292009081 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 439292009082 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 439292009083 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292009084 Coenzyme A binding pocket [chemical binding]; other site 439292009085 conserved hypothetical protein; Region: TIGR03833 439292009086 PAS domain S-box; Region: sensory_box; TIGR00229 439292009087 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 439292009088 putative active site [active] 439292009089 heme pocket [chemical binding]; other site 439292009090 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 439292009091 PAS fold; Region: PAS_3; pfam08447 439292009092 putative active site [active] 439292009093 heme pocket [chemical binding]; other site 439292009094 PAS fold; Region: PAS; pfam00989 439292009095 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 439292009096 putative active site [active] 439292009097 heme pocket [chemical binding]; other site 439292009098 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292009099 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292009100 metal binding site [ion binding]; metal-binding site 439292009101 active site 439292009102 I-site; other site 439292009103 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292009104 Zn2+ binding site [ion binding]; other site 439292009105 Mg2+ binding site [ion binding]; other site 439292009106 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 439292009107 Major Facilitator Superfamily; Region: MFS_1; pfam07690 439292009108 putative substrate translocation pore; other site 439292009109 Transcriptional regulators [Transcription]; Region: PurR; COG1609 439292009110 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 439292009111 DNA binding site [nucleotide binding] 439292009112 domain linker motif; other site 439292009113 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 439292009114 dimerization interface [polypeptide binding]; other site 439292009115 ligand binding site [chemical binding]; other site 439292009116 Trehalose and maltose hydrolases (possible phosphorylases) [Carbohydrate transport and metabolism]; Region: ATH1; COG1554 439292009117 Glycosyl hydrolase family 65, N-terminal domain; Region: Glyco_hydro_65N; pfam03636 439292009118 Glycosyl hydrolase family 65 central catalytic domain; Region: Glyco_hydro_65m; pfam03632 439292009119 Glycosyl hydrolase family 65, C-terminal domain; Region: Glyco_hydro_65C; pfam03633 439292009120 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: PRK12748 439292009121 classical (c) SDRs; Region: SDR_c; cd05233 439292009122 NAD(P) binding site [chemical binding]; other site 439292009123 active site 439292009124 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 439292009125 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 439292009126 ABC-ATPase subunit interface; other site 439292009127 dimer interface [polypeptide binding]; other site 439292009128 putative PBP binding regions; other site 439292009129 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 439292009130 ABC-ATPase subunit interface; other site 439292009131 dimer interface [polypeptide binding]; other site 439292009132 putative PBP binding regions; other site 439292009133 ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CeuD; COG4604 439292009134 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 439292009135 Walker A/P-loop; other site 439292009136 ATP binding site [chemical binding]; other site 439292009137 Q-loop/lid; other site 439292009138 ABC transporter signature motif; other site 439292009139 Walker B; other site 439292009140 D-loop; other site 439292009141 H-loop/switch region; other site 439292009142 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 439292009143 Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins...; Region: FatB; cd01140 439292009144 putative ligand binding residues [chemical binding]; other site 439292009145 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 439292009146 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 439292009147 active site 439292009148 putative acetyltransferase YhhY; Provisional; Region: PRK10140 439292009149 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292009150 Coenzyme A binding pocket [chemical binding]; other site 439292009151 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 439292009152 active site 439292009153 catalytic residues [active] 439292009154 Escherichia coli xylulokinase-like D-xylulose kinases; a subgroup of the FGGY family of carbohydrate kinases; Region: FGGY_D-XK_EcXK-like; cd07808 439292009155 N- and C-terminal domain interface [polypeptide binding]; other site 439292009156 D-xylulose kinase; Region: XylB; TIGR01312 439292009157 active site 439292009158 MgATP binding site [chemical binding]; other site 439292009159 catalytic site [active] 439292009160 metal binding site [ion binding]; metal-binding site 439292009161 xylulose binding site [chemical binding]; other site 439292009162 homodimer interface [polypeptide binding]; other site 439292009163 xylose isomerase; Provisional; Region: PRK05474 439292009164 xylose isomerase; Region: xylose_isom_A; TIGR02630 439292009165 Transcriptional regulators [Transcription]; Region: MarR; COG1846 439292009166 MarR family; Region: MarR; pfam01047 439292009167 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 439292009168 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 439292009169 nucleotide binding site [chemical binding]; other site 439292009170 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 439292009171 RRXRR protein; Region: RRXRR; pfam14239 439292009172 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 439292009173 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 439292009174 active site 439292009175 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 439292009176 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 439292009177 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 439292009178 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292009179 dimerization interface [polypeptide binding]; other site 439292009180 Histidine kinase; Region: His_kinase; pfam06580 439292009181 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 439292009182 ATP binding site [chemical binding]; other site 439292009183 Mg2+ binding site [ion binding]; other site 439292009184 G-X-G motif; other site 439292009185 Response regulator receiver domain; Region: Response_reg; pfam00072 439292009186 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 439292009187 active site 439292009188 phosphorylation site [posttranslational modification] 439292009189 intermolecular recognition site; other site 439292009190 dimerization interface [polypeptide binding]; other site 439292009191 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 439292009192 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 439292009193 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 439292009194 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 439292009195 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 439292009196 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 439292009197 dimer interface [polypeptide binding]; other site 439292009198 putative PBP binding loops; other site 439292009199 ABC-ATPase subunit interface; other site 439292009200 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 439292009201 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 439292009202 dimer interface [polypeptide binding]; other site 439292009203 conserved gate region; other site 439292009204 putative PBP binding loops; other site 439292009205 ABC-ATPase subunit interface; other site 439292009206 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 439292009207 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_1; cd09000 439292009208 inhibitor binding site; inhibition site 439292009209 active site 439292009210 Protein of unknown function, DUF624; Region: DUF624; cl02369 439292009211 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 439292009212 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles; Region: ttLC_FACS_AlkK_like; cd12119 439292009213 dimer interface [polypeptide binding]; other site 439292009214 acyl-activating enzyme (AAE) consensus motif; other site 439292009215 putative active site [active] 439292009216 AMP binding site [chemical binding]; other site 439292009217 putative CoA binding site [chemical binding]; other site 439292009218 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 439292009219 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292009220 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]; Region: COG2231 439292009221 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 439292009222 minor groove reading motif; other site 439292009223 helix-hairpin-helix signature motif; other site 439292009224 substrate binding pocket [chemical binding]; other site 439292009225 active site 439292009226 putative rSAM target protein, CGCGG family; Region: target_X_rSAM; TIGR03995 439292009227 Tic20-like protein; Region: Tic20; pfam09685 439292009228 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 439292009229 transmembrane helices; other site 439292009230 TrkA-C domain; Region: TrkA_C; pfam02080 439292009231 TrkA-C domain; Region: TrkA_C; pfam02080 439292009232 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 439292009233 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 439292009234 NAD-dependent deacetylase; Provisional; Region: PRK00481 439292009235 SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2-fam; cd01407 439292009236 NAD+ binding site [chemical binding]; other site 439292009237 substrate binding site [chemical binding]; other site 439292009238 Zn binding site [ion binding]; other site 439292009239 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3584 439292009240 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 439292009241 putative active site pocket [active] 439292009242 dimerization interface [polypeptide binding]; other site 439292009243 putative catalytic residue [active] 439292009244 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 439292009245 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 439292009246 DNA binding residues [nucleotide binding] 439292009247 Uncharacterized protein conserved in bacteria (DUF2087); Region: DUF2087; pfam09860 439292009248 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 439292009249 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 439292009250 ligand binding site [chemical binding]; other site 439292009251 flexible hinge region; other site 439292009252 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 439292009253 non-specific DNA interactions [nucleotide binding]; other site 439292009254 DNA binding site [nucleotide binding] 439292009255 sequence specific DNA binding site [nucleotide binding]; other site 439292009256 putative cAMP binding site [chemical binding]; other site 439292009257 Domain of unknown function DUF302; Region: DUF302; cl01364 439292009258 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 439292009259 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 439292009260 TPP-binding site [chemical binding]; other site 439292009261 Pyruvate ferredoxin oxidoreductase beta subunit C terminal; Region: PFO_beta_C; pfam12367 439292009262 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 439292009263 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 439292009264 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 439292009265 dimer interface [polypeptide binding]; other site 439292009266 PYR/PP interface [polypeptide binding]; other site 439292009267 TPP binding site [chemical binding]; other site 439292009268 substrate binding site [chemical binding]; other site 439292009269 drug efflux system protein MdtG; Provisional; Region: PRK09874 439292009270 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 439292009271 putative substrate translocation pore; other site 439292009272 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292009273 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292009274 metal binding site [ion binding]; metal-binding site 439292009275 active site 439292009276 I-site; other site 439292009277 Predicted amidohydrolase [General function prediction only]; Region: COG0388 439292009278 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 439292009279 active site 439292009280 catalytic triad [active] 439292009281 dimer interface [polypeptide binding]; other site 439292009282 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 439292009283 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 439292009284 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 439292009285 PLD-like domain; Region: PLDc_2; pfam13091 439292009286 putative active site [active] 439292009287 catalytic site [active] 439292009288 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 439292009289 PLD-like domain; Region: PLDc_2; pfam13091 439292009290 putative active site [active] 439292009291 catalytic site [active] 439292009292 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 439292009293 PAS domain; Region: PAS_9; pfam13426 439292009294 putative active site [active] 439292009295 heme pocket [chemical binding]; other site 439292009296 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 439292009297 PAS domain; Region: PAS_9; pfam13426 439292009298 putative active site [active] 439292009299 heme pocket [chemical binding]; other site 439292009300 PAS domain S-box; Region: sensory_box; TIGR00229 439292009301 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 439292009302 putative active site [active] 439292009303 heme pocket [chemical binding]; other site 439292009304 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292009305 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292009306 metal binding site [ion binding]; metal-binding site 439292009307 active site 439292009308 I-site; other site 439292009309 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292009310 Globin domain present in Globin-Coupled-Sensors (GCS). These domains detect changes in intracellular concentrations of oxygen, carbon monoxyde, or nitrous oxide, which result in aerotaxis and/or gene regulation. One subgroup, the HemATs, are aerotactic...; Region: sensor_globin; cd01068 439292009311 heme-binding site [chemical binding]; other site 439292009312 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292009313 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292009314 dimer interface [polypeptide binding]; other site 439292009315 putative CheW interface [polypeptide binding]; other site 439292009316 YusW-like protein; Region: YusW; pfam14039 439292009317 putative selenium metabolism protein, YedE family; Region: seleno_YedE; TIGR04112 439292009318 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 439292009319 CPxP motif; other site 439292009320 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 439292009321 active site residue [active] 439292009322 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 439292009323 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 439292009324 active site residue [active] 439292009325 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 439292009326 active site residue [active] 439292009327 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 439292009328 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 439292009329 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 439292009330 EamA-like transporter family; Region: EamA; pfam00892 439292009331 Putative D-isomer specific 2-hydroxyacid dehydrogenase; Region: 2-Hacid_dh_1; cd05300 439292009332 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 439292009333 NAD binding site [chemical binding]; other site 439292009334 ligand binding site [chemical binding]; other site 439292009335 catalytic site [active] 439292009336 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 439292009337 ABC1 family; Region: ABC1; pfam03109 439292009338 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 439292009339 active site 439292009340 ATP binding site [chemical binding]; other site 439292009341 YvrJ protein family; Region: YvrJ; pfam12841 439292009342 Cupin superfamily (DUF985); Region: Cupin_5; pfam06172 439292009343 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 439292009344 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 439292009345 probable F420-dependent oxidoreductase, MSMEG_4141 family; Region: F420_MSMEG_4141; TIGR03620 439292009346 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 439292009347 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 439292009348 non-specific DNA binding site [nucleotide binding]; other site 439292009349 salt bridge; other site 439292009350 sequence-specific DNA binding site [nucleotide binding]; other site 439292009351 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 439292009352 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 439292009353 NAD(P) binding site [chemical binding]; other site 439292009354 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 439292009355 Superfamily I DNA and RNA helicases [General function prediction only]; Region: COG3973 439292009356 Part of AAA domain; Region: AAA_19; pfam13245 439292009357 Family description; Region: UvrD_C_2; pfam13538 439292009358 SurA N-terminal domain; Region: SurA_N_3; cl07813 439292009359 Cation efflux family; Region: Cation_efflux; cl00316 439292009360 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 439292009361 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 439292009362 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292009363 Possible lysine decarboxylase; Region: Lysine_decarbox; pfam03641 439292009364 Ion transport protein; Region: Ion_trans; pfam00520 439292009365 NF-kappa-B essential modulator NEMO; Region: NEMO; pfam11577 439292009366 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 439292009367 catalytic motif [active] 439292009368 Zn binding site [ion binding]; other site 439292009369 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 439292009370 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 439292009371 NAD(P) binding site [chemical binding]; other site 439292009372 active site 439292009373 glutamate dehydrogenase; Provisional; Region: PRK09414 439292009374 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 439292009375 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 439292009376 NAD(P) binding pocket [chemical binding]; other site 439292009377 Uncharacterized conserved protein [Function unknown]; Region: COG0397 439292009378 hypothetical protein; Validated; Region: PRK00029 439292009379 Protein of unknown function (DUF4003); Region: DUF4003; pfam13170 439292009380 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 439292009381 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292009382 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 439292009383 Periplasmic binding protein YvrC. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct...; Region: YvrC; cd01143 439292009384 putative binding site residues; other site 439292009385 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 439292009386 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 439292009387 ABC-ATPase subunit interface; other site 439292009388 dimer interface [polypeptide binding]; other site 439292009389 putative PBP binding regions; other site 439292009390 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 439292009391 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 439292009392 Walker A/P-loop; other site 439292009393 ATP binding site [chemical binding]; other site 439292009394 Q-loop/lid; other site 439292009395 ABC transporter signature motif; other site 439292009396 Walker B; other site 439292009397 D-loop; other site 439292009398 H-loop/switch region; other site 439292009399 Adenosylcobinamide amidohydrolase; Region: CbiZ; pfam01955 439292009400 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 439292009401 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 439292009402 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 439292009403 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 439292009404 dimer interface [polypeptide binding]; other site 439292009405 conserved gate region; other site 439292009406 putative PBP binding loops; other site 439292009407 ABC-ATPase subunit interface; other site 439292009408 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 439292009409 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 439292009410 dimer interface [polypeptide binding]; other site 439292009411 conserved gate region; other site 439292009412 putative PBP binding loops; other site 439292009413 ABC-ATPase subunit interface; other site 439292009414 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 439292009415 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 439292009416 Walker A/P-loop; other site 439292009417 ATP binding site [chemical binding]; other site 439292009418 Q-loop/lid; other site 439292009419 ABC transporter signature motif; other site 439292009420 Walker B; other site 439292009421 D-loop; other site 439292009422 H-loop/switch region; other site 439292009423 azoreductase; Reviewed; Region: PRK00170 439292009424 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 439292009425 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 439292009426 active site 439292009427 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 439292009428 catalytic core [active] 439292009429 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 439292009430 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292009431 dimerization interface [polypeptide binding]; other site 439292009432 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292009433 dimer interface [polypeptide binding]; other site 439292009434 putative CheW interface [polypeptide binding]; other site 439292009435 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 439292009436 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 439292009437 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 439292009438 motif II; other site 439292009439 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 439292009440 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 439292009441 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 439292009442 metal binding site [ion binding]; metal-binding site 439292009443 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 439292009444 PAS fold; Region: PAS_3; pfam08447 439292009445 putative active site [active] 439292009446 heme pocket [chemical binding]; other site 439292009447 PAS fold; Region: PAS_4; pfam08448 439292009448 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 439292009449 PAS domain; Region: PAS_9; pfam13426 439292009450 putative active site [active] 439292009451 heme pocket [chemical binding]; other site 439292009452 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292009453 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292009454 metal binding site [ion binding]; metal-binding site 439292009455 active site 439292009456 I-site; other site 439292009457 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 439292009458 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292009459 Zn2+ binding site [ion binding]; other site 439292009460 Mg2+ binding site [ion binding]; other site 439292009461 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 439292009462 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 439292009463 active site 439292009464 putative luciferase-like monooxygenase, FMN-dependent, CE1758 family; Region: LLM_CE1758_fam; TIGR04036 439292009465 probable oxidoreductase, LLM family; Region: LLM_2I7G; TIGR03858 439292009466 Heat induced stress protein YflT; Region: YflT; pfam11181 439292009467 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 439292009468 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 439292009469 Walker A/P-loop; other site 439292009470 ATP binding site [chemical binding]; other site 439292009471 Q-loop/lid; other site 439292009472 ABC transporter signature motif; other site 439292009473 Walker B; other site 439292009474 D-loop; other site 439292009475 H-loop/switch region; other site 439292009476 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 439292009477 dimer interface [polypeptide binding]; other site 439292009478 conserved gate region; other site 439292009479 putative PBP binding loops; other site 439292009480 ABC-ATPase subunit interface; other site 439292009481 PBP superfamily domain; Region: PBP_like_2; pfam12849 439292009482 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 439292009483 Helix-turn-helix domain; Region: HTH_17; pfam12728 439292009484 PBP superfamily domain; Region: PBP_like; pfam12727 439292009485 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 439292009486 apolar tunnel; other site 439292009487 heme binding site [chemical binding]; other site 439292009488 dimerization interface [polypeptide binding]; other site 439292009489 H+ Antiporter protein; Region: 2A0121; TIGR00900 439292009490 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 439292009491 putative substrate translocation pore; other site 439292009492 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 439292009493 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 439292009494 FMN binding site [chemical binding]; other site 439292009495 substrate binding site [chemical binding]; other site 439292009496 putative catalytic residue [active] 439292009497 glycosyl hydrolase family 16; Region: Glyco_hydrolase_16; cd00413 439292009498 active site 439292009499 catalytic residues [active] 439292009500 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 439292009501 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 439292009502 active site 439292009503 catalytic tetrad [active] 439292009504 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 439292009505 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 439292009506 active site 439292009507 motif I; other site 439292009508 motif II; other site 439292009509 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 439292009510 Predicted ring-cleavage extradiol dioxygenase [General function prediction only]; Region: COG2514 439292009511 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_12; cd07255 439292009512 putative metal binding site [ion binding]; other site 439292009513 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 439292009514 active site 439292009515 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 439292009516 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 439292009517 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 439292009518 catalytic residue [active] 439292009519 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 439292009520 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 439292009521 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 439292009522 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 439292009523 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cl12060 439292009524 DNA interaction; other site 439292009525 Metal-binding active site; metal-binding site 439292009526 AP endonuclease family 2 C terminus; Region: AP_endonuc_2_N; pfam07582 439292009527 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 439292009528 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 439292009529 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 439292009530 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 439292009531 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 439292009532 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 439292009533 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 439292009534 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 439292009535 maltose O-acetyltransferase; Provisional; Region: PRK10092 439292009536 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 439292009537 active site 439292009538 substrate binding site [chemical binding]; other site 439292009539 trimer interface [polypeptide binding]; other site 439292009540 CoA binding site [chemical binding]; other site 439292009541 glutaminase; Reviewed; Region: PRK12357 439292009542 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 439292009543 AAA domain; Region: AAA_21; pfam13304 439292009544 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292009545 Walker A/P-loop; other site 439292009546 ATP binding site [chemical binding]; other site 439292009547 Q-loop/lid; other site 439292009548 ABC transporter signature motif; other site 439292009549 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 439292009550 Walker B; other site 439292009551 Walker B; other site 439292009552 D-loop; other site 439292009553 D-loop; other site 439292009554 H-loop/switch region; other site 439292009555 H-loop/switch region; other site 439292009556 Predicted membrane protein (DUF2207); Region: DUF2207; pfam09972 439292009557 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 439292009558 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292009559 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292009560 metal binding site [ion binding]; metal-binding site 439292009561 active site 439292009562 I-site; other site 439292009563 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 439292009564 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292009565 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292009566 metal binding site [ion binding]; metal-binding site 439292009567 active site 439292009568 I-site; other site 439292009569 Nitric oxide synthase (NOS) prokaryotic oxygenase domain. NOS produces nitric oxide (NO) by catalyzing a five-electron heme-based oxidation of a guanidine nitrogen of L-arginine to L-citrulline via two successive monooxygenation reactions producing N...; Region: NOS_oxygenase_prok; cd00794 439292009570 active site 439292009571 dimer interface [polypeptide binding]; other site 439292009572 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Provisional; Region: PLN00412 439292009573 NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase and ALDH family 11; Region: ALDH_F11_NP-GAPDH; cd07082 439292009574 tetrameric interface [polypeptide binding]; other site 439292009575 activator binding site; other site 439292009576 NADP binding site [chemical binding]; other site 439292009577 substrate binding site [chemical binding]; other site 439292009578 catalytic residues [active] 439292009579 Firmicute fructose-1,6-bisphosphatase; Region: FBPase_2; pfam06874 439292009580 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 439292009581 Transposase; Region: DDE_Tnp_ISL3; pfam01610 439292009582 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 439292009583 non-specific DNA binding site [nucleotide binding]; other site 439292009584 salt bridge; other site 439292009585 sequence-specific DNA binding site [nucleotide binding]; other site 439292009586 Protein of unknown function (DUF2281); Region: DUF2281; cl02355 439292009587 putative transposase OrfB; Reviewed; Region: PHA02517 439292009588 HTH-like domain; Region: HTH_21; pfam13276 439292009589 Integrase core domain; Region: rve; pfam00665 439292009590 Integrase core domain; Region: rve_2; pfam13333 439292009591 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 439292009592 Transposase; Region: HTH_Tnp_1; pfam01527 439292009593 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 439292009594 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 439292009595 catalytic residues [active] 439292009596 catalytic nucleophile [active] 439292009597 Recombinase; Region: Recombinase; pfam07508 439292009598 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 439292009599 Protein of unknown function (DUF2800); Region: DUF2800; pfam10926 439292009600 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 439292009601 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 439292009602 DNA binding residues [nucleotide binding] 439292009603 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 439292009604 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 439292009605 non-specific DNA binding site [nucleotide binding]; other site 439292009606 salt bridge; other site 439292009607 sequence-specific DNA binding site [nucleotide binding]; other site 439292009608 Helix-turn-helix domain; Region: HTH_17; pfam12728 439292009609 type II restriction m6 adenine DNA methyltransferase, Alw26I/Eco31I/Esp3I family; Region: met_A_Alw26; TIGR02987 439292009610 Methyltransferase domain; Region: Methyltransf_26; pfam13659 439292009611 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 439292009612 Transposase [DNA replication, recombination, and repair]; Region: COG5421 439292009613 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 439292009614 IstB-like ATP binding N-terminal; Region: IstB_IS21_ATP; pfam08483 439292009615 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 439292009616 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 439292009617 Transposase; Region: HTH_Tnp_1; pfam01527 439292009618 putative transposase OrfB; Reviewed; Region: PHA02517 439292009619 HTH-like domain; Region: HTH_21; pfam13276 439292009620 Integrase core domain; Region: rve; pfam00665 439292009621 Integrase core domain; Region: rve_2; pfam13333 439292009622 putative transposase OrfB; Reviewed; Region: PHA02517 439292009623 HTH-like domain; Region: HTH_21; pfam13276 439292009624 Integrase core domain; Region: rve; pfam00665 439292009625 Integrase core domain; Region: rve_2; pfam13333 439292009626 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 439292009627 Transposase; Region: HTH_Tnp_1; pfam01527 439292009628 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 439292009629 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 439292009630 catalytic residues [active] 439292009631 catalytic nucleophile [active] 439292009632 Recombinase; Region: Recombinase; pfam07508 439292009633 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 439292009634 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 439292009635 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 439292009636 catalytic residues [active] 439292009637 catalytic nucleophile [active] 439292009638 Recombinase; Region: Recombinase; pfam07508 439292009639 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 439292009640 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 439292009641 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 439292009642 non-specific DNA binding site [nucleotide binding]; other site 439292009643 salt bridge; other site 439292009644 sequence-specific DNA binding site [nucleotide binding]; other site 439292009645 TPR repeat; Region: TPR_11; pfam13414 439292009646 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 439292009647 binding surface 439292009648 TPR motif; other site 439292009649 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 439292009650 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 439292009651 catalytic residues [active] 439292009652 catalytic nucleophile [active] 439292009653 Recombinase; Region: Recombinase; pfam07508 439292009654 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 439292009655 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 439292009656 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 439292009657 catalytic residues [active] 439292009658 catalytic nucleophile [active] 439292009659 Recombinase; Region: Recombinase; pfam07508 439292009660 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 439292009661 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 439292009662 amidase catalytic site [active] 439292009663 Zn binding residues [ion binding]; other site 439292009664 substrate binding site [chemical binding]; other site 439292009665 Sporulation related domain; Region: SPOR; pfam05036 439292009666 Holin family; Region: Phage_holin_4; pfam05105 439292009667 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 439292009668 Prophage endopeptidase tail; Region: Prophage_tail; cl12123 439292009669 Phage-related protein [Function unknown]; Region: COG4722 439292009670 Phage tail protein; Region: Sipho_tail; cl17486 439292009671 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 439292009672 phage major tail protein, phi13 family; Region: maj_tail_phi13; TIGR01603 439292009673 phage protein, HK97 gp10 family; Region: phge_HK97_gp10; TIGR01725 439292009674 Phage head-tail joining protein; Region: Phage_H_T_join; pfam05521 439292009675 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 439292009676 oligomerization interface [polypeptide binding]; other site 439292009677 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 439292009678 Phage capsid family; Region: Phage_capsid; pfam05065 439292009679 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 439292009680 oligomer interface [polypeptide binding]; other site 439292009681 active site residues [active] 439292009682 Phage-related protein [Function unknown]; Region: COG4695 439292009683 Phage portal protein; Region: Phage_portal; pfam04860 439292009684 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 439292009685 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl17442 439292009686 Homing endonuclease; Region: Hom_end; pfam05204 439292009687 Phage Terminase; Region: Terminase_1; pfam03354 439292009688 Phage terminase, small subunit; Region: Terminase_4; pfam05119 439292009689 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 439292009690 ParB-like nuclease domain; Region: ParB; smart00470 439292009691 FMN-binding domain; Region: FMN_bind; cl01081 439292009692 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 439292009693 DNA methylase; Region: N6_N4_Mtase; pfam01555 439292009694 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 439292009695 active site 439292009696 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 439292009697 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; cl17257 439292009698 DNA binding residues [nucleotide binding] 439292009699 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 439292009700 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 439292009701 ATP binding site [chemical binding]; other site 439292009702 putative Mg++ binding site [ion binding]; other site 439292009703 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 439292009704 nucleotide binding region [chemical binding]; other site 439292009705 ATP-binding site [chemical binding]; other site 439292009706 VRR-NUC domain; Region: VRR_NUC; pfam08774 439292009707 Virulence-associated protein E; Region: VirE; pfam05272 439292009708 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_A; cd08642 439292009709 DNA binding site [nucleotide binding] 439292009710 active site 439292009711 catalytic site [active] 439292009712 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 439292009713 Protein of unknown function (DUF2815); Region: DUF2815; pfam10991 439292009714 Protein of unknown function (DUF2800); Region: DUF2800; pfam10926 439292009715 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 439292009716 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 439292009717 DNA binding residues [nucleotide binding] 439292009718 Restriction endonuclease; Region: Mrr_cat; pfam04471 439292009719 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 439292009720 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 439292009721 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 439292009722 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 439292009723 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 439292009724 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 439292009725 putative NAD(P) binding site [chemical binding]; other site 439292009726 active site 439292009727 putative substrate binding site [chemical binding]; other site 439292009728 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 439292009729 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 439292009730 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 439292009731 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 439292009732 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 439292009733 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 439292009734 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 439292009735 substrate binding site [chemical binding]; other site 439292009736 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 439292009737 active site 439292009738 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 439292009739 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 439292009740 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 439292009741 active site 439292009742 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 439292009743 putative ADP-binding pocket [chemical binding]; other site 439292009744 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 439292009745 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 439292009746 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 439292009747 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 439292009748 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 439292009749 putative ADP-binding pocket [chemical binding]; other site 439292009750 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 439292009751 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 439292009752 NAD(P) binding site [chemical binding]; other site 439292009753 active site 439292009754 Sugar transferases involved in lipopolysaccharide synthesis [Cell envelope biogenesis, outer membrane]; Region: WcaJ; COG2148 439292009755 RNA polymerase factor sigma-70; Validated; Region: PRK06759 439292009756 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 439292009757 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; cl17257 439292009758 ComK protein; Region: ComK; cl11560 439292009759 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 439292009760 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 439292009761 active site 439292009762 tetramer interface; other site 439292009763 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 439292009764 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 439292009765 NAD(P) binding site [chemical binding]; other site 439292009766 homodimer interface [polypeptide binding]; other site 439292009767 substrate binding site [chemical binding]; other site 439292009768 active site 439292009769 Capsular polysaccharide biosynthesis protein [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: CapC; COG4464 439292009770 capsular exopolysaccharide family; Region: eps_fam; TIGR01007 439292009771 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 439292009772 Capsular polysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3944 439292009773 Chain length determinant protein; Region: Wzz; cl15801 439292009774 S-layer homology domain; Region: SLH; pfam00395 439292009775 S-layer homology domain; Region: SLH; pfam00395 439292009776 S-layer homology domain; Region: SLH; pfam00395 439292009777 S-layer homology domain; Region: SLH; pfam00395 439292009778 S-layer homology domain; Region: SLH; pfam00395 439292009779 S-layer homology domain; Region: SLH; pfam00395 439292009780 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 439292009781 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 439292009782 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 439292009783 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292009784 Coenzyme A binding pocket [chemical binding]; other site 439292009785 Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]; Region: WecG; COG1922 439292009786 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 439292009787 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 439292009788 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 439292009789 Mg++ binding site [ion binding]; other site 439292009790 putative catalytic motif [active] 439292009791 substrate binding site [chemical binding]; other site 439292009792 UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: WecC; COG0677 439292009793 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 439292009794 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 439292009795 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 439292009796 Polysaccharide pyruvyl transferase family protein [Cell wall/membrane/envelope biogenesis]; Region: WcaK; COG2327 439292009797 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; cl09156 439292009798 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 439292009799 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 439292009800 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 439292009801 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 439292009802 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 439292009803 NlpC/P60 family; Region: NLPC_P60; pfam00877 439292009804 S-layer homology domain; Region: SLH; pfam00395 439292009805 S-layer homology domain; Region: SLH; pfam00395 439292009806 S-layer homology domain; Region: SLH; pfam00395 439292009807 Peptidase S8 family domain in Subtilisin proteins; Region: Peptidases_S8_Subtilisin_subset; cd07477 439292009808 active site 439292009809 catalytic residues [active] 439292009810 S-layer homology domain; Region: SLH; pfam00395 439292009811 S-layer homology domain; Region: SLH; pfam00395 439292009812 S-layer homology domain; Region: SLH; pfam00395 439292009813 S-layer homology domain; Region: SLH; pfam00395 439292009814 S-layer homology domain; Region: SLH; pfam00395 439292009815 S-layer homology domain; Region: SLH; pfam00395 439292009816 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 439292009817 S-layer homology domain; Region: SLH; pfam00395 439292009818 S-layer homology domain; Region: SLH; pfam00395 439292009819 S-layer homology domain; Region: SLH; pfam00395 439292009820 Bacterial SH3 domain; Region: SH3_3; pfam08239 439292009821 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 439292009822 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 439292009823 active site 439292009824 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 439292009825 N-acetyl-D-glucosamine binding site [chemical binding]; other site 439292009826 catalytic residue [active] 439292009827 Bacterial SH3 domain; Region: SH3_3; cl17532 439292009828 Bacterial Ig-like domain; Region: Big_5; pfam13205 439292009829 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 439292009830 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 439292009831 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 439292009832 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 439292009833 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 439292009834 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 439292009835 putative active site [active] 439292009836 putative metal binding site [ion binding]; other site 439292009837 Capsule biosynthesis CapC; Region: Caps_synth_CapC; pfam14102 439292009838 poly-gamma-glutamate synthase PgsB/CapB; Region: poly_gGlu_PgsB; TIGR04012 439292009839 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 439292009840 Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane]; Region: COG3409 439292009841 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 439292009842 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 439292009843 Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane]; Region: COG3409 439292009844 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 439292009845 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 439292009846 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 439292009847 NlpC/P60 family; Region: NLPC_P60; pfam00877 439292009848 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3883 439292009849 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 439292009850 NlpC/P60 family; Region: NLPC_P60; pfam00877 439292009851 Cell envelope-related transcriptional attenuator domain; Region: LytR_cpsA_psr; cl00581 439292009852 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 439292009853 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 439292009854 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292009855 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292009856 dimer interface [polypeptide binding]; other site 439292009857 putative CheW interface [polypeptide binding]; other site 439292009858 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 439292009859 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 439292009860 ATP binding site [chemical binding]; other site 439292009861 Mg2+ binding site [ion binding]; other site 439292009862 G-X-G motif; other site 439292009863 X-Pro dipeptidyl-peptidase (S15 family); Region: Peptidase_S15; pfam02129 439292009864 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; smart00939 439292009865 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 439292009866 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 439292009867 BCCT family transporter; Region: BCCT; pfam02028 439292009868 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 439292009869 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 439292009870 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 439292009871 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 439292009872 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292009873 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292009874 metal binding site [ion binding]; metal-binding site 439292009875 active site 439292009876 I-site; other site 439292009877 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292009878 Nitrate and nitrite sensing; Region: NIT; pfam08376 439292009879 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 439292009880 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292009881 dimerization interface [polypeptide binding]; other site 439292009882 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292009883 dimer interface [polypeptide binding]; other site 439292009884 putative CheW interface [polypeptide binding]; other site 439292009885 Lysine/ornithine N-monooxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: IucD; COG3486 439292009886 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 439292009887 Predicted integral membrane protein [Function unknown]; Region: COG5652 439292009888 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 439292009889 Stage V sporulation protein B, also known as Stage III sporulation protein F, and related proteins; Region: MATE_SpoVB_like; cd13124 439292009890 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 439292009891 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 439292009892 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 439292009893 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292009894 Coenzyme A binding pocket [chemical binding]; other site 439292009895 Membrane transport protein; Region: Mem_trans; cl09117 439292009896 Radical SAM superfamily; Region: Radical_SAM; pfam04055 439292009897 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 439292009898 FeS/SAM binding site; other site 439292009899 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl17519 439292009900 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 439292009901 anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family; Region: dmsA_ynfE; TIGR02166 439292009902 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 439292009903 molybdopterin cofactor binding site; other site 439292009904 Molybdopterin-Binding, C-terminal (MopB_CT) 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-...; Region: MopB_CT; cl09929 439292009905 molybdopterin cofactor binding site; other site 439292009906 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 439292009907 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 439292009908 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 439292009909 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 439292009910 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 439292009911 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 439292009912 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members...; Region: MopB_3; cd02766 439292009913 putative [4Fe-4S] binding site [ion binding]; other site 439292009914 putative molybdopterin cofactor binding site [chemical binding]; other site 439292009915 Molybdopterin-Binding, C-terminal (MopB_CT) 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-...; Region: MopB_CT; cl09929 439292009916 molybdopterin cofactor binding site; other site 439292009917 Coenzyme A transferase; Region: CoA_trans; cl17247 439292009918 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 439292009919 coenzyme A disulfide reductase; Reviewed; Region: PRK09564 439292009920 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 439292009921 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 439292009922 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 439292009923 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 439292009924 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 439292009925 Ethanolamine utilisation protein and carboxysome structural protein domain family; Region: EutN_CcmL; cd01614 439292009926 Hexamer/Pentamer interface [polypeptide binding]; other site 439292009927 central pore; other site 439292009928 propanediol utilization phosphotransacylase; Provisional; Region: PRK15070 439292009929 Propanediol utilisation protein PduL; Region: PduL; pfam06130 439292009930 Propanediol utilisation protein PduL; Region: PduL; pfam06130 439292009931 Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]; Region: CcmK; COG4577 439292009932 Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain; Region: BMC_CcmK_like; cd07045 439292009933 Hexamer interface [polypeptide binding]; other site 439292009934 Hexagonal pore residue; other site 439292009935 Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]; Region: CcmK; COG4577 439292009936 Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain; Region: BMC_CcmK_like; cd07045 439292009937 Hexamer interface [polypeptide binding]; other site 439292009938 Hexagonal pore residue; other site 439292009939 Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]; Region: CcmK; COG4577 439292009940 Bacterial Micro-Compartment (BMC) domain; Region: BMC; cd06169 439292009941 Hexamer interface [polypeptide binding]; other site 439292009942 Hexagonal pore residue; other site 439292009943 Bacterial Micro-Compartment (BMC) domain; Region: BMC; cd06169 439292009944 Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]; Region: CcmK; COG4577 439292009945 Hexamer interface [polypeptide binding]; other site 439292009946 Hexagonal pore residue; other site 439292009947 Bacterial Micro-Compartment (BMC) domain; Region: BMC; cd06169 439292009948 Hexamer interface [polypeptide binding]; other site 439292009949 Hexagonal pore residue; other site 439292009950 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 439292009951 Ethanolamine utilization protein EutE-like; Region: ALDH_EutE; cd07121 439292009952 putative catalytic cysteine [active] 439292009953 Class II Aldolase and Adducin N-terminal domain; Region: Aldolase_II; pfam00596 439292009954 intersubunit interface [polypeptide binding]; other site 439292009955 active site 439292009956 Zn2+ binding site [ion binding]; other site 439292009957 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 439292009958 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 439292009959 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 439292009960 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 439292009961 S-methyl-5-thioribose-1-phosphate isomerase; Region: salvage_mtnA; TIGR00512 439292009962 5-methylribose kinase; Reviewed; Region: PRK12396 439292009963 Phosphotransferase enzyme family; Region: APH; pfam01636 439292009964 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 439292009965 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 439292009966 TM-ABC transporter signature motif; other site 439292009967 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 439292009968 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 439292009969 Walker A/P-loop; other site 439292009970 ATP binding site [chemical binding]; other site 439292009971 Q-loop/lid; other site 439292009972 ABC transporter signature motif; other site 439292009973 Walker B; other site 439292009974 D-loop; other site 439292009975 H-loop/switch region; other site 439292009976 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 439292009977 Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_methylthioribose_binding_like; cd06305 439292009978 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 439292009979 putative ligand binding site [chemical binding]; other site 439292009980 Inosine-uridine preferring nucleoside hydrolase; Region: IU_nuc_hydro; pfam01156 439292009981 active site 439292009982 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 439292009983 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 439292009984 active site 439292009985 phosphorylation site [posttranslational modification] 439292009986 intermolecular recognition site; other site 439292009987 dimerization interface [polypeptide binding]; other site 439292009988 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 439292009989 DNA binding site [nucleotide binding] 439292009990 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 439292009991 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 439292009992 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 439292009993 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 439292009994 dimer interface [polypeptide binding]; other site 439292009995 phosphorylation site [posttranslational modification] 439292009996 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 439292009997 ATP binding site [chemical binding]; other site 439292009998 Mg2+ binding site [ion binding]; other site 439292009999 G-X-G motif; other site 439292010000 Response regulator receiver domain; Region: Response_reg; pfam00072 439292010001 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 439292010002 active site 439292010003 phosphorylation site [posttranslational modification] 439292010004 intermolecular recognition site; other site 439292010005 dimerization interface [polypeptide binding]; other site 439292010006 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 439292010007 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 439292010008 dimer interface [polypeptide binding]; other site 439292010009 phosphorylation site [posttranslational modification] 439292010010 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 439292010011 ATP binding site [chemical binding]; other site 439292010012 Mg2+ binding site [ion binding]; other site 439292010013 G-X-G motif; other site 439292010014 Predicted membrane protein [Function unknown]; Region: COG4818 439292010015 Transcriptional activator of glycolytic enzymes; Region: GCR1_C; pfam12550 439292010016 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 439292010017 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 439292010018 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 439292010019 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 439292010020 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 439292010021 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 439292010022 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 439292010023 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 439292010024 rod shape-determining protein Mbl; Provisional; Region: PRK13928 439292010025 MreB and similar proteins; Region: MreB_like; cd10225 439292010026 nucleotide binding site [chemical binding]; other site 439292010027 Mg binding site [ion binding]; other site 439292010028 putative protofilament interaction site [polypeptide binding]; other site 439292010029 RodZ interaction site [polypeptide binding]; other site 439292010030 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 439292010031 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 439292010032 hinge; other site 439292010033 active site 439292010034 Protein of unknown function (DUF1146); Region: DUF1146; cl11486 439292010035 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 439292010036 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 439292010037 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 439292010038 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 439292010039 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 439292010040 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 439292010041 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 439292010042 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 439292010043 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 439292010044 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 439292010045 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 439292010046 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 439292010047 4Fe-4S binding domain; Region: Fer4; pfam00037 439292010048 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 439292010049 NADH dehydrogenase subunit D; Validated; Region: PRK06075; cl17338 439292010050 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 439292010051 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; pfam00329 439292010052 NADH dehydrogenase subunit B; Validated; Region: PRK06411 439292010053 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 439292010054 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 439292010055 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 439292010056 gamma subunit interface [polypeptide binding]; other site 439292010057 epsilon subunit interface [polypeptide binding]; other site 439292010058 LBP interface [polypeptide binding]; other site 439292010059 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 439292010060 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 439292010061 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 439292010062 alpha subunit interaction interface [polypeptide binding]; other site 439292010063 Walker A motif; other site 439292010064 ATP binding site [chemical binding]; other site 439292010065 Walker B motif; other site 439292010066 inhibitor binding site; inhibition site 439292010067 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 439292010068 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 439292010069 core domain interface [polypeptide binding]; other site 439292010070 delta subunit interface [polypeptide binding]; other site 439292010071 epsilon subunit interface [polypeptide binding]; other site 439292010072 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 439292010073 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 439292010074 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 439292010075 beta subunit interaction interface [polypeptide binding]; other site 439292010076 Walker A motif; other site 439292010077 ATP binding site [chemical binding]; other site 439292010078 Walker B motif; other site 439292010079 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 439292010080 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 439292010081 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 439292010082 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 439292010083 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 439292010084 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 439292010085 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 439292010086 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 439292010087 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 439292010088 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 439292010089 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 439292010090 active site 439292010091 homodimer interface [polypeptide binding]; other site 439292010092 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 439292010093 active site 439292010094 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 439292010095 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 439292010096 dimer interface [polypeptide binding]; other site 439292010097 active site 439292010098 glycine-pyridoxal phosphate binding site [chemical binding]; other site 439292010099 folate binding site [chemical binding]; other site 439292010100 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 439292010101 PAS domain; Region: PAS_9; pfam13426 439292010102 putative active site [active] 439292010103 heme pocket [chemical binding]; other site 439292010104 PAS fold; Region: PAS_4; pfam08448 439292010105 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292010106 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292010107 metal binding site [ion binding]; metal-binding site 439292010108 active site 439292010109 I-site; other site 439292010110 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292010111 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 439292010112 PAS fold; Region: PAS_4; pfam08448 439292010113 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 439292010114 putative active site [active] 439292010115 heme pocket [chemical binding]; other site 439292010116 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 439292010117 PAS domain; Region: PAS_9; pfam13426 439292010118 putative active site [active] 439292010119 heme pocket [chemical binding]; other site 439292010120 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292010121 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292010122 metal binding site [ion binding]; metal-binding site 439292010123 active site 439292010124 I-site; other site 439292010125 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 439292010126 hypothetical protein; Provisional; Region: PRK13690 439292010127 ribose-5-phosphate isomerase B; Provisional; Region: PRK05571 439292010128 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292010129 dimerization interface [polypeptide binding]; other site 439292010130 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 439292010131 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292010132 dimer interface [polypeptide binding]; other site 439292010133 putative CheW interface [polypeptide binding]; other site 439292010134 Low molecular weight phosphatase family; Region: LMWPc; cd00115 439292010135 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 439292010136 active site 439292010137 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 439292010138 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 439292010139 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 439292010140 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 439292010141 S-adenosylmethionine binding site [chemical binding]; other site 439292010142 peptide chain release factor 1; Validated; Region: prfA; PRK00591 439292010143 This domain is found in peptide chain release factors; Region: PCRF; smart00937 439292010144 RF-1 domain; Region: RF-1; pfam00472 439292010145 coenzyme A disulfide reductase; Reviewed; Region: PRK09564 439292010146 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 439292010147 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 439292010148 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 439292010149 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 439292010150 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292010151 dimerization interface [polypeptide binding]; other site 439292010152 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292010153 dimer interface [polypeptide binding]; other site 439292010154 putative CheW interface [polypeptide binding]; other site 439292010155 thymidine kinase; Provisional; Region: PRK04296 439292010156 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 439292010157 transcription termination factor Rho; Provisional; Region: rho; PRK09376 439292010158 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 439292010159 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 439292010160 RNA binding site [nucleotide binding]; other site 439292010161 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 439292010162 multimer interface [polypeptide binding]; other site 439292010163 Walker A motif; other site 439292010164 ATP binding site [chemical binding]; other site 439292010165 Walker B motif; other site 439292010166 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 439292010167 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 439292010168 hinge; other site 439292010169 active site 439292010170 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 439292010171 active site 439292010172 intersubunit interactions; other site 439292010173 catalytic residue [active] 439292010174 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 439292010175 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 439292010176 intersubunit interface [polypeptide binding]; other site 439292010177 active site 439292010178 zinc binding site [ion binding]; other site 439292010179 Na+ binding site [ion binding]; other site 439292010180 Response regulator receiver domain; Region: Response_reg; pfam00072 439292010181 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 439292010182 active site 439292010183 phosphorylation site [posttranslational modification] 439292010184 intermolecular recognition site; other site 439292010185 dimerization interface [polypeptide binding]; other site 439292010186 Protein of unknown function (DUF2529); Region: DUF2529; pfam10740 439292010187 CTP synthetase; Validated; Region: pyrG; PRK05380 439292010188 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 439292010189 Catalytic site [active] 439292010190 active site 439292010191 UTP binding site [chemical binding]; other site 439292010192 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 439292010193 active site 439292010194 putative oxyanion hole; other site 439292010195 catalytic triad [active] 439292010196 DNA-directed RNA polymerase delta subunit; Region: RNA_pol_delta; pfam05066 439292010197 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 439292010198 B12 binding site [chemical binding]; other site 439292010199 cobalt ligand [ion binding]; other site 439292010200 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 439292010201 Walker A; other site 439292010202 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 439292010203 Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]; Region: ArgK; COG1703 439292010204 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 439292010205 Walker A; other site 439292010206 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 439292010207 G4 box; other site 439292010208 G5 box; other site 439292010209 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 439292010210 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 439292010211 FAD binding site [chemical binding]; other site 439292010212 homotetramer interface [polypeptide binding]; other site 439292010213 substrate binding pocket [chemical binding]; other site 439292010214 catalytic base [active] 439292010215 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 439292010216 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 439292010217 FAD binding site [chemical binding]; other site 439292010218 homotetramer interface [polypeptide binding]; other site 439292010219 substrate binding pocket [chemical binding]; other site 439292010220 catalytic base [active] 439292010221 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 439292010222 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 439292010223 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 439292010224 acetyl-CoA acetyltransferase; Provisional; Region: PRK08235 439292010225 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 439292010226 dimer interface [polypeptide binding]; other site 439292010227 active site 439292010228 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 439292010229 Cysteine-rich domain; Region: CCG; pfam02754 439292010230 Cysteine-rich domain; Region: CCG; pfam02754 439292010231 spermidine synthase; Provisional; Region: PRK00811 439292010232 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 439292010233 S-adenosylmethionine binding site [chemical binding]; other site 439292010234 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 439292010235 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 439292010236 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292010237 Walker A/P-loop; other site 439292010238 ATP binding site [chemical binding]; other site 439292010239 Q-loop/lid; other site 439292010240 ABC transporter signature motif; other site 439292010241 Walker B; other site 439292010242 D-loop; other site 439292010243 H-loop/switch region; other site 439292010244 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 439292010245 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 439292010246 ligand binding site [chemical binding]; other site 439292010247 flexible hinge region; other site 439292010248 Protease prsW family; Region: PrsW-protease; cl15823 439292010249 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 439292010250 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 439292010251 Walker A/P-loop; other site 439292010252 ATP binding site [chemical binding]; other site 439292010253 Q-loop/lid; other site 439292010254 ABC transporter signature motif; other site 439292010255 Walker B; other site 439292010256 D-loop; other site 439292010257 H-loop/switch region; other site 439292010258 Predicted transcriptional regulators [Transcription]; Region: COG1725 439292010259 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 439292010260 DNA-binding site [nucleotide binding]; DNA binding site 439292010261 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 439292010262 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 439292010263 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292010264 dimerization interface [polypeptide binding]; other site 439292010265 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292010266 dimer interface [polypeptide binding]; other site 439292010267 putative CheW interface [polypeptide binding]; other site 439292010268 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 439292010269 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 439292010270 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 439292010271 active site 439292010272 HIGH motif; other site 439292010273 KMSK motif region; other site 439292010274 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 439292010275 tRNA binding surface [nucleotide binding]; other site 439292010276 anticodon binding site; other site 439292010277 Domain of unknown function (DUF1934); Region: DUF1934; pfam09148 439292010278 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 439292010279 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 439292010280 non-specific DNA binding site [nucleotide binding]; other site 439292010281 salt bridge; other site 439292010282 sequence-specific DNA binding site [nucleotide binding]; other site 439292010283 Cupin domain; Region: Cupin_2; pfam07883 439292010284 oligopeptide ABC transporter ATP-binding protein OppF; Provisional; Region: PRK15079 439292010285 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 439292010286 Walker A/P-loop; other site 439292010287 ATP binding site [chemical binding]; other site 439292010288 Q-loop/lid; other site 439292010289 ABC transporter signature motif; other site 439292010290 Walker B; other site 439292010291 D-loop; other site 439292010292 H-loop/switch region; other site 439292010293 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 439292010294 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 439292010295 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 439292010296 Walker A/P-loop; other site 439292010297 ATP binding site [chemical binding]; other site 439292010298 Q-loop/lid; other site 439292010299 ABC transporter signature motif; other site 439292010300 Walker B; other site 439292010301 D-loop; other site 439292010302 H-loop/switch region; other site 439292010303 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 439292010304 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 439292010305 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 439292010306 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 439292010307 dimer interface [polypeptide binding]; other site 439292010308 conserved gate region; other site 439292010309 putative PBP binding loops; other site 439292010310 ABC-ATPase subunit interface; other site 439292010311 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 439292010312 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 439292010313 dimer interface [polypeptide binding]; other site 439292010314 conserved gate region; other site 439292010315 putative PBP binding loops; other site 439292010316 ABC-ATPase subunit interface; other site 439292010317 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 439292010318 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 439292010319 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 439292010320 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 439292010321 metal binding site [ion binding]; metal-binding site 439292010322 dimer interface [polypeptide binding]; other site 439292010323 agmatinase; Region: agmatinase; TIGR01230 439292010324 Agmatinase and related proteins; Region: Agmatinase-like_2; cd11593 439292010325 putative active site [active] 439292010326 Mn binding site [ion binding]; other site 439292010327 spermidine synthase; Provisional; Region: PRK00811 439292010328 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 439292010329 YwhD family; Region: YwhD; pfam08741 439292010330 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cd00491 439292010331 active site 1 [active] 439292010332 dimer interface [polypeptide binding]; other site 439292010333 hexamer interface [polypeptide binding]; other site 439292010334 active site 2 [active] 439292010335 HD superfamily phosphohydrolases [General function prediction only]; Region: COG1078 439292010336 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 439292010337 Zn2+ binding site [ion binding]; other site 439292010338 Mg2+ binding site [ion binding]; other site 439292010339 Protein of unknown function (DUF1450); Region: DUF1450; cl11488 439292010340 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 439292010341 conserved hypothetical integral membrane protein; Region: TIGR00697 439292010342 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 439292010343 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 439292010344 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 439292010345 active site 439292010346 FMN binding site [chemical binding]; other site 439292010347 2,4-decadienoyl-CoA binding site; other site 439292010348 catalytic residue [active] 439292010349 4Fe-4S cluster binding site [ion binding]; other site 439292010350 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 439292010351 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 439292010352 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 439292010353 substrate binding site [chemical binding]; other site 439292010354 oxyanion hole (OAH) forming residues; other site 439292010355 trimer interface [polypeptide binding]; other site 439292010356 putative heme peroxidase; Provisional; Region: PRK12276 439292010357 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 439292010358 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 439292010359 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 439292010360 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 439292010361 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 439292010362 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 439292010363 dimer interface [polypeptide binding]; other site 439292010364 conserved gate region; other site 439292010365 putative PBP binding loops; other site 439292010366 ABC-ATPase subunit interface; other site 439292010367 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 439292010368 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 439292010369 dimer interface [polypeptide binding]; other site 439292010370 conserved gate region; other site 439292010371 putative PBP binding loops; other site 439292010372 ABC-ATPase subunit interface; other site 439292010373 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 439292010374 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 439292010375 Predicted transcriptional regulator [Transcription]; Region: COG4189 439292010376 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 439292010377 putative DNA binding site [nucleotide binding]; other site 439292010378 dimerization interface [polypeptide binding]; other site 439292010379 putative Zn2+ binding site [ion binding]; other site 439292010380 Uncharacterized small membrane protein [Function unknown]; Region: COG2363 439292010381 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 439292010382 Coenzyme A binding pocket [chemical binding]; other site 439292010383 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 439292010384 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_2; cd09607 439292010385 active site 439292010386 Zn binding site [ion binding]; other site 439292010387 CC3(TIP30)-like, atypical (a) SDRs; Region: CC3_like_SDR_a; cd05250 439292010388 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 439292010389 NAD binding site [chemical binding]; other site 439292010390 active site 439292010391 Cache domain; Region: Cache_1; pfam02743 439292010392 sensory histidine kinase AtoS; Provisional; Region: PRK11360 439292010393 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 439292010394 dimer interface [polypeptide binding]; other site 439292010395 phosphorylation site [posttranslational modification] 439292010396 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 439292010397 ATP binding site [chemical binding]; other site 439292010398 Mg2+ binding site [ion binding]; other site 439292010399 G-X-G motif; other site 439292010400 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 439292010401 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 439292010402 Response regulator receiver domain; Region: Response_reg; pfam00072 439292010403 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 439292010404 active site 439292010405 phosphorylation site [posttranslational modification] 439292010406 intermolecular recognition site; other site 439292010407 dimerization interface [polypeptide binding]; other site 439292010408 sucrose-6-phosphate hydrolase; Region: scrB_fam; TIGR01322 439292010409 Glycosyl hydrolase family 32, beta-fructosidases; Region: GH32_B_Fructosidase; cd08996 439292010410 substrate binding [chemical binding]; other site 439292010411 active site 439292010412 Glycosyl hydrolases family 32 C terminal; Region: Glyco_hydro_32C; pfam08244 439292010413 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 439292010414 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 439292010415 putative substrate binding site [chemical binding]; other site 439292010416 putative ATP binding site [chemical binding]; other site 439292010417 Cache domain; Region: Cache_1; pfam02743 439292010418 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 439292010419 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292010420 dimerization interface [polypeptide binding]; other site 439292010421 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292010422 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 439292010423 dimer interface [polypeptide binding]; other site 439292010424 putative CheW interface [polypeptide binding]; other site 439292010425 Protein of unknown function (DUF1806); Region: DUF1806; pfam08830 439292010426 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 439292010427 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 439292010428 Sulfatase; Region: Sulfatase; cl17466 439292010429 Thermophilic metalloprotease (M29); Region: Peptidase_M29; pfam02073 439292010430 Leucyl aminopeptidase (aminopeptidase T) [Amino acid transport and metabolism]; Region: AmpS; COG2309 439292010431 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 439292010432 Nucleoside recognition; Region: Gate; pfam07670 439292010433 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 439292010434 homotrimer interaction site [polypeptide binding]; other site 439292010435 putative active site [active] 439292010436 pantothenate kinase; Provisional; Region: PRK05439 439292010437 Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point...; Region: PanK; cd02025 439292010438 ATP-binding site [chemical binding]; other site 439292010439 CoA-binding site [chemical binding]; other site 439292010440 Mg2+-binding site [ion binding]; other site 439292010441 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 439292010442 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 439292010443 NAD(P) binding site [chemical binding]; other site 439292010444 active site 439292010445 M20 Peptidase Aminoacylase 1-like protein 2-like, amidohydrolase subfamily; Region: M20_ACY1L2_like; cd05672 439292010446 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 439292010447 metal binding site [ion binding]; metal-binding site 439292010448 PilZ domain; Region: PilZ; pfam07238 439292010449 Aspartate racemase [Cell envelope biogenesis, outer membrane]; Region: RacX; COG1794 439292010450 aspartate racemase; Region: asp_race; TIGR00035 439292010451 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 439292010452 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 439292010453 active site 439292010454 HIGH motif; other site 439292010455 nucleotide binding site [chemical binding]; other site 439292010456 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 439292010457 active site 439292010458 KMSKS motif; other site 439292010459 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 439292010460 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 439292010461 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 439292010462 putative RNA binding site [nucleotide binding]; other site 439292010463 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 439292010464 Preprotein translocase subunit YidC [Intracellular trafficking and secretion]; Region: YidC; COG0706 439292010465 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 439292010466 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 439292010467 DXD motif; other site 439292010468 HEAT repeats; Region: HEAT_2; pfam13646 439292010469 homoserine dehydrogenase; Provisional; Region: PRK06349 439292010470 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 439292010471 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 439292010472 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 439292010473 threonine synthase; Reviewed; Region: PRK06721 439292010474 Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants; Region: Thr-synth_1; cd01563 439292010475 homodimer interface [polypeptide binding]; other site 439292010476 pyridoxal 5'-phosphate binding site [chemical binding]; other site 439292010477 catalytic residue [active] 439292010478 homoserine kinase; Provisional; Region: PRK01212 439292010479 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 439292010480 Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily; Region: Cof-subfamily; TIGR00099 439292010481 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 439292010482 active site 439292010483 motif I; other site 439292010484 motif II; other site 439292010485 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 439292010486 homoserine O-succinyltransferase; Provisional; Region: PRK05368 439292010487 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 439292010488 proposed active site lysine [active] 439292010489 conserved cys residue [active] 439292010490 cytoplasmic alpha-amylase; Reviewed; Region: PRK09441 439292010491 Alpha amylase catalytic domain found in bacterial and fungal Alpha amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_bac_fung_AmyA; cd11318 439292010492 active site 439292010493 Na/Ca binding site [ion binding]; other site 439292010494 catalytic site [active] 439292010495 Domain of unknown function (DUF1939); Region: DUF1939; pfam09154 439292010496 aspartate kinase; Reviewed; Region: PRK09034 439292010497 AAK_AKiii-YclM-BS: Amino Acid Kinase Superfamily (AAK), AKiii-YclM-BS; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in...; Region: AAK_AKiii-YclM-BS; cd04245 439292010498 putative catalytic residues [active] 439292010499 putative nucleotide binding site [chemical binding]; other site 439292010500 putative aspartate binding site [chemical binding]; other site 439292010501 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-YclM-BS_1; cd04911 439292010502 allosteric regulatory residue; other site 439292010503 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-YclM-BS_2; cd04916 439292010504 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 439292010505 The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold; Region: PBP2_Ylib_like; cd08499 439292010506 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 439292010507 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 439292010508 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 439292010509 dimer interface [polypeptide binding]; other site 439292010510 conserved gate region; other site 439292010511 putative PBP binding loops; other site 439292010512 ABC-ATPase subunit interface; other site 439292010513 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 439292010514 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 439292010515 dimer interface [polypeptide binding]; other site 439292010516 conserved gate region; other site 439292010517 putative PBP binding loops; other site 439292010518 ABC-ATPase subunit interface; other site 439292010519 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 439292010520 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 439292010521 Walker A/P-loop; other site 439292010522 ATP binding site [chemical binding]; other site 439292010523 Q-loop/lid; other site 439292010524 ABC transporter signature motif; other site 439292010525 Walker B; other site 439292010526 D-loop; other site 439292010527 H-loop/switch region; other site 439292010528 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 439292010529 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 439292010530 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 439292010531 Walker A/P-loop; other site 439292010532 ATP binding site [chemical binding]; other site 439292010533 Q-loop/lid; other site 439292010534 ABC transporter signature motif; other site 439292010535 Walker B; other site 439292010536 D-loop; other site 439292010537 H-loop/switch region; other site 439292010538 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 439292010539 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 439292010540 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 439292010541 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 439292010542 Walker A/P-loop; other site 439292010543 ATP binding site [chemical binding]; other site 439292010544 Q-loop/lid; other site 439292010545 ABC transporter signature motif; other site 439292010546 Walker B; other site 439292010547 D-loop; other site 439292010548 H-loop/switch region; other site 439292010549 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 439292010550 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 439292010551 dimer interface [polypeptide binding]; other site 439292010552 conserved gate region; other site 439292010553 putative PBP binding loops; other site 439292010554 ABC-ATPase subunit interface; other site 439292010555 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 439292010556 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 439292010557 dimer interface [polypeptide binding]; other site 439292010558 conserved gate region; other site 439292010559 putative PBP binding loops; other site 439292010560 ABC-ATPase subunit interface; other site 439292010561 hypothetical protein; Provisional; Region: PRK11622 439292010562 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 439292010563 Uncharacterized conserved protein [Function unknown]; Region: COG0398 439292010564 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 439292010565 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 439292010566 active site residue [active] 439292010567 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 439292010568 active site residue [active] 439292010569 Cysteine-rich domain; Region: CCG; pfam02754 439292010570 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 439292010571 Cysteine-rich domain; Region: CCG; pfam02754 439292010572 putative glutamate synthase (NADPH) small subunit; Provisional; Region: PRK12771 439292010573 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 439292010574 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 439292010575 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 439292010576 PAS domain; Region: PAS_9; pfam13426 439292010577 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292010578 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292010579 metal binding site [ion binding]; metal-binding site 439292010580 active site 439292010581 I-site; other site 439292010582 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 439292010583 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 439292010584 active site 439292010585 phosphorylation site [posttranslational modification] 439292010586 intermolecular recognition site; other site 439292010587 dimerization interface [polypeptide binding]; other site 439292010588 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 439292010589 DNA binding residues [nucleotide binding] 439292010590 dimerization interface [polypeptide binding]; other site 439292010591 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 439292010592 Histidine kinase; Region: HisKA_3; pfam07730 439292010593 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 439292010594 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 439292010595 ATP binding site [chemical binding]; other site 439292010596 Mg2+ binding site [ion binding]; other site 439292010597 G-X-G motif; other site 439292010598 The Delta12 Fatty Acid Desaturase (Delta12-FADS)-like CD includes the integral-membrane enzymes, delta-12 acyl-lipid desaturases, oleate 12-hydroxylases, omega3 and omega6 fatty acid desaturases, and other related proteins, found in a wide range of...; Region: Delta12-FADS-like; cd03507 439292010599 Fatty acid desaturase; Region: FA_desaturase; pfam00487 439292010600 putative di-iron ligands [ion binding]; other site 439292010601 ABC-2 type transporter; Region: ABC2_membrane; cl17235 439292010602 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 439292010603 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 439292010604 daunorubicin resistance ABC transporter ATP-binding subunit; Region: drrA; TIGR01188 439292010605 Walker A/P-loop; other site 439292010606 ATP binding site [chemical binding]; other site 439292010607 Q-loop/lid; other site 439292010608 ABC transporter signature motif; other site 439292010609 Walker B; other site 439292010610 D-loop; other site 439292010611 H-loop/switch region; other site 439292010612 Domain of unknown function (DUF4162); Region: DUF4162; pfam13732 439292010613 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 439292010614 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 439292010615 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 439292010616 metal binding site [ion binding]; metal-binding site 439292010617 active site 439292010618 I-site; other site 439292010619 malate:quinone oxidoreductase; Validated; Region: PRK05257 439292010620 malate:quinone-oxidoreductase; Region: mal_quin_oxido; TIGR01320 439292010621 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 439292010622 EamA-like transporter family; Region: EamA; pfam00892 439292010623 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 439292010624 extended (e) SDRs; Region: SDR_e; cd08946 439292010625 NAD(P) binding site [chemical binding]; other site 439292010626 active site 439292010627 substrate binding site [chemical binding]; other site 439292010628 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 439292010629 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 439292010630 RNA binding surface [nucleotide binding]; other site 439292010631 Pseudouridine synthase, Escherichia coli RluF like; Region: PseudoU_synth_RluF; cd02554 439292010632 probable active site [active] 439292010633 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 439292010634 CxxH/CxxC protein, BA_5709 family; Region: CxxH_BA5709; TIGR04129 439292010635 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 439292010636 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 439292010637 protein binding site [polypeptide binding]; other site 439292010638 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 439292010639 YycH protein; Region: YycI; cl02015 439292010640 YycH protein; Region: YycH; pfam07435 439292010641 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4863 439292010642 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 439292010643 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 439292010644 dimerization interface [polypeptide binding]; other site 439292010645 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 439292010646 putative active site [active] 439292010647 heme pocket [chemical binding]; other site 439292010648 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 439292010649 dimer interface [polypeptide binding]; other site 439292010650 phosphorylation site [posttranslational modification] 439292010651 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 439292010652 ATP binding site [chemical binding]; other site 439292010653 Mg2+ binding site [ion binding]; other site 439292010654 G-X-G motif; other site 439292010655 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 439292010656 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 439292010657 active site 439292010658 phosphorylation site [posttranslational modification] 439292010659 intermolecular recognition site; other site 439292010660 dimerization interface [polypeptide binding]; other site 439292010661 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 439292010662 DNA binding site [nucleotide binding] 439292010663 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 439292010664 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 439292010665 G5 domain; Region: G5; pfam07501 439292010666 Peptidase family M23; Region: Peptidase_M23; pfam01551 439292010667 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 439292010668 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 439292010669 GDP-binding site [chemical binding]; other site 439292010670 ACT binding site; other site 439292010671 IMP binding site; other site 439292010672 replicative DNA helicase; Provisional; Region: PRK05748 439292010673 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 439292010674 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 439292010675 Walker A motif; other site 439292010676 ATP binding site [chemical binding]; other site 439292010677 Walker B motif; other site 439292010678 DNA binding loops [nucleotide binding] 439292010679 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 439292010680 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 439292010681 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 439292010682 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]; Region: COG3887 439292010683 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 439292010684 DHH family; Region: DHH; pfam01368 439292010685 DHHA1 domain; Region: DHHA1; pfam02272 439292010686 Predicted membrane protein (DUF2232); Region: DUF2232; pfam09991 439292010687 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 439292010688 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 439292010689 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 439292010690 dimer interface [polypeptide binding]; other site 439292010691 ssDNA binding site [nucleotide binding]; other site 439292010692 tetramer (dimer of dimers) interface [polypeptide binding]; other site 439292010693 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 439292010694 GTP-binding protein YchF; Reviewed; Region: PRK09601 439292010695 YchF GTPase; Region: YchF; cd01900 439292010696 G1 box; other site 439292010697 GTP/Mg2+ binding site [chemical binding]; other site 439292010698 Switch I region; other site 439292010699 G2 box; other site 439292010700 Switch II region; other site 439292010701 G3 box; other site 439292010702 G4 box; other site 439292010703 G5 box; other site 439292010704 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 439292010705 Bacterial protein of unknown function (DUF951); Region: DUF951; pfam06107 439292010706 Protein of unknown function (DUF554); Region: DUF554; pfam04474 439292010707 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 439292010708 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 439292010709 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 439292010710 catalytic residue [active] 439292010711 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 439292010712 ParB-like nuclease domain; Region: ParB; smart00470 439292010713 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 439292010714 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 439292010715 P-loop; other site 439292010716 Magnesium ion binding site [ion binding]; other site 439292010717 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 439292010718 Magnesium ion binding site [ion binding]; other site 439292010719 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 439292010720 ParB-like nuclease domain; Region: ParB; smart00470 439292010721 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 439292010722 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 439292010723 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 439292010724 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 439292010725 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 439292010726 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 439292010727 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 439292010728 trmE is a tRNA modification GTPase; Region: trmE; cd04164 439292010729 G1 box; other site 439292010730 GTP/Mg2+ binding site [chemical binding]; other site 439292010731 Switch I region; other site 439292010732 G2 box; other site 439292010733 Switch II region; other site 439292010734 G3 box; other site 439292010735 G4 box; other site 439292010736 G5 box; other site 439292010737 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 439292010738 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 439292010739 jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta...; Region: jag_KH; cd02414 439292010740 G-X-X-G motif; other site 439292010741 R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine...; Region: R3H_jag; cd02644 439292010742 RxxxH motif; other site 439292010743 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 439292010744 Preprotein translocase subunit YidC [Intracellular trafficking and secretion]; Region: YidC; COG0706 439292010745 Haemolytic domain; Region: Haemolytic; pfam01809 439292010746 ribonuclease P; Reviewed; Region: rnpA; PRK00499 439292010747 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399