acyl-CoA dehydrogenase family member 10 isoform X2 [Bos taurus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||||||
| PLN02876 super family | cl33587 | acyl-CoA dehydrogenase |
257-999 | 0e+00 | ||||||||||||
acyl-CoA dehydrogenase The actual alignment was detected with superfamily member PLN02876: Pssm-ID: 215473 [Multi-domain] Cd Length: 822 Bit Score: 830.59 E-value: 0e+00
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| HAD-1A3-hyp super family | cl26186 | epoxide hydrolase N-terminal domain-like phosphatase; This model represents a small clade of ... |
42-247 | 8.32e-88 | ||||||||||||
epoxide hydrolase N-terminal domain-like phosphatase; This model represents a small clade of sequences including C. elegans and mammalian sequences as well as a small number of bacteria. In eukaryotes, this domain exists as an N-terminal fusion to the soluble epoxide hydrolase enzyme and has recently been shown to be an active phosphatase, although the nature of the biological substrate is unclear. These appear to be members of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases by general homology and the conservation of all of the recognized catalytic motifs (although the first motif is unusual in the replacement of the more common aspartate with glycine...). The variable domain is found in between motifs 1 and 2, indicating membership in subfamily I and phylogeny and prediction of the alpha helical nature of the variable domain (by PSI-PRED) indicate membership in subfamily IA. The actual alignment was detected with superfamily member TIGR02247: Pssm-ID: 274054 [Multi-domain] Cd Length: 211 Bit Score: 280.17 E-value: 8.32e-88
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| Name | Accession | Description | Interval | E-value | ||||||||||||
| PLN02876 | PLN02876 | acyl-CoA dehydrogenase |
257-999 | 0e+00 | ||||||||||||
acyl-CoA dehydrogenase Pssm-ID: 215473 [Multi-domain] Cd Length: 822 Bit Score: 830.59 E-value: 0e+00
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| ACAD_FadE2 | cd01155 | Acyl-CoA dehydrogenases similar to fadE2; FadE2-like Acyl-CoA dehydrogenase (ACAD). Acyl-CoA ... |
658-999 | 0e+00 | ||||||||||||
Acyl-CoA dehydrogenases similar to fadE2; FadE2-like Acyl-CoA dehydrogenase (ACAD). Acyl-CoA dehydrogenases (ACAD) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACAD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. ACAD's are generally homotetramers and have an active site glutamate at a conserved position. Pssm-ID: 173844 [Multi-domain] Cd Length: 394 Bit Score: 550.46 E-value: 0e+00
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| CaiA | COG1960 | Acyl-CoA dehydrogenase related to the alkylation response protein AidB [Lipid transport and ... |
655-999 | 1.39e-88 | ||||||||||||
Acyl-CoA dehydrogenase related to the alkylation response protein AidB [Lipid transport and metabolism]; Acyl-CoA dehydrogenase related to the alkylation response protein AidB is part of the Pathway/BioSystem: Fatty acid biosynthesis Pssm-ID: 441563 [Multi-domain] Cd Length: 381 Bit Score: 288.66 E-value: 1.39e-88
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| HAD-1A3-hyp | TIGR02247 | epoxide hydrolase N-terminal domain-like phosphatase; This model represents a small clade of ... |
42-247 | 8.32e-88 | ||||||||||||
epoxide hydrolase N-terminal domain-like phosphatase; This model represents a small clade of sequences including C. elegans and mammalian sequences as well as a small number of bacteria. In eukaryotes, this domain exists as an N-terminal fusion to the soluble epoxide hydrolase enzyme and has recently been shown to be an active phosphatase, although the nature of the biological substrate is unclear. These appear to be members of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases by general homology and the conservation of all of the recognized catalytic motifs (although the first motif is unusual in the replacement of the more common aspartate with glycine...). The variable domain is found in between motifs 1 and 2, indicating membership in subfamily I and phylogeny and prediction of the alpha helical nature of the variable domain (by PSI-PRED) indicate membership in subfamily IA. Pssm-ID: 274054 [Multi-domain] Cd Length: 211 Bit Score: 280.17 E-value: 8.32e-88
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| HAD_sEH-N_like | cd02603 | N-terminal lipase phosphatase domain of human soluble epoxide hydrolase, Escherichia coli YihX ... |
43-242 | 5.19e-56 | ||||||||||||
N-terminal lipase phosphatase domain of human soluble epoxide hydrolase, Escherichia coli YihX/HAD4 alpha-D-glucose 1-phosphate phosphatase, and related domains, may be inactive; This family includes the N-terminal phosphatase domain of human soluble epoxide hydrolase (sEH). sEH is a bifunctional enzyme with two distinct enzyme activities, the C-terminal domain has epoxide hydrolysis activity and the N-terminal domain (Ntermphos), which belongs to this family, has lipid phosphatase activity. The latter prefers mono-phosphate esters, and lysophosphatidic acids (LPAs) are the best natural substrates found to date. In addition this family includes Gallus gallus sEH and Xenopus sEH which appears to lack phosphatase activity, and Escherichia coli YihX/HAD4 which selectively hydrolyzes alpha-Glucose-1-P, phosphatase, has significant phosphatase activity against pyridoxal phosphate, and has low beta phosphoglucomutase activity. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319790 [Multi-domain] Cd Length: 195 Bit Score: 192.17 E-value: 5.19e-56
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| APH | pfam01636 | Phosphotransferase enzyme family; This family consists of bacterial antibiotic resistance ... |
287-504 | 2.51e-51 | ||||||||||||
Phosphotransferase enzyme family; This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides they include: aminoglycoside 3'-phosphotransferase or kanamycin kinase / neomycin-kanamycin phosphotransferase and streptomycin 3''-kinase or streptomycin 3''-phosphotransferase. The aminoglycoside phosphotransferases inactivate aminoglycoside antibiotics via phosphorylation. This family also includes homoserine kinase. This family is related to fructosamine kinase pfam03881. Pssm-ID: 426359 [Multi-domain] Cd Length: 239 Bit Score: 180.77 E-value: 2.51e-51
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| YigB | COG1011 | FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily ... |
42-234 | 2.53e-25 | ||||||||||||
FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily (riboflavin biosynthesis) [Coenzyme transport and metabolism]; Pssm-ID: 440635 [Multi-domain] Cd Length: 220 Bit Score: 105.11 E-value: 2.53e-25
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| Hydrolase | pfam00702 | haloacid dehalogenase-like hydrolase; This family is structurally different from the alpha ... |
42-225 | 9.98e-17 | ||||||||||||
haloacid dehalogenase-like hydrolase; This family is structurally different from the alpha/beta hydrolase family (pfam00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain. Those members with the characteriztic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria. Pssm-ID: 459910 [Multi-domain] Cd Length: 191 Bit Score: 79.55 E-value: 9.98e-17
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| PRK09456 | PRK09456 | ?-D-glucose-1-phosphatase; Provisional |
46-236 | 1.23e-10 | ||||||||||||
?-D-glucose-1-phosphatase; Provisional Pssm-ID: 181872 [Multi-domain] Cd Length: 199 Bit Score: 61.98 E-value: 1.23e-10
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| arch_bud32 | TIGR03724 | Kae1-associated kinase Bud32; Members of this protein family are the Bud32 protein associated ... |
328-400 | 4.64e-03 | ||||||||||||
Kae1-associated kinase Bud32; Members of this protein family are the Bud32 protein associated with Kae1 (kinase-associated endopeptidase 1) in the Archaea. In many Archaeal genomes, Kae1 and Bud32 are fused. The complex is homologous to the Kae1 and Bud32 subunits of the eukaryotic KEOPS complex, an apparently ancient protein kinase-containing molecular machine. [Unknown function, General] Pssm-ID: 274749 [Multi-domain] Cd Length: 199 Bit Score: 39.50 E-value: 4.64e-03
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| Name | Accession | Description | Interval | E-value | ||||||||||||
| PLN02876 | PLN02876 | acyl-CoA dehydrogenase |
257-999 | 0e+00 | ||||||||||||
acyl-CoA dehydrogenase Pssm-ID: 215473 [Multi-domain] Cd Length: 822 Bit Score: 830.59 E-value: 0e+00
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| ACAD_FadE2 | cd01155 | Acyl-CoA dehydrogenases similar to fadE2; FadE2-like Acyl-CoA dehydrogenase (ACAD). Acyl-CoA ... |
658-999 | 0e+00 | ||||||||||||
Acyl-CoA dehydrogenases similar to fadE2; FadE2-like Acyl-CoA dehydrogenase (ACAD). Acyl-CoA dehydrogenases (ACAD) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACAD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. ACAD's are generally homotetramers and have an active site glutamate at a conserved position. Pssm-ID: 173844 [Multi-domain] Cd Length: 394 Bit Score: 550.46 E-value: 0e+00
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| ACAD10_11_N-like | cd05154 | N-terminal domain of Acyl-CoA dehydrogenase (ACAD) 10 and 11, and similar proteins; This ... |
286-536 | 5.86e-108 | ||||||||||||
N-terminal domain of Acyl-CoA dehydrogenase (ACAD) 10 and 11, and similar proteins; This subfamily is composed of the N-terminal domains of vertebrate ACAD10 and ACAD11, and similar uncharacterized bacterial and eukaryotic proteins. ACADs are a family of flavoproteins that are involved in the beta-oxidation of fatty acyl-CoA derivatives. ACAD deficiency can cause metabolic disorders including muscle fatigue, hypoglycemia, and hepatic lipidosis. There are at least 11 distinct ACADs, some of which show distinct substrate specificities to either straight-chain or branched-chain fatty acids. ACAD10 is widely expressed in human tissues and highly expressed in liver, kidney, pancreas, and spleen. ACAD10 and ACAD11 are both significantly expressed in human brain tissues. They contain a long N-terminal domain with similarity to phosphotransferases with a Protein Kinase fold, which is absent in other ACADs. They may exhibit multiple functions in acyl-CoA oxidation pathways. ACAD11 utilizes substrates with carbon chain lengths of 20 to 26, with optimal activity towards C22CoA. ACAD10 may be associated with an increased risk in type II diabetes. The ACAD10/11-like subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). Pssm-ID: 270703 [Multi-domain] Cd Length: 254 Bit Score: 335.35 E-value: 5.86e-108
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| CaiA | COG1960 | Acyl-CoA dehydrogenase related to the alkylation response protein AidB [Lipid transport and ... |
655-999 | 1.39e-88 | ||||||||||||
Acyl-CoA dehydrogenase related to the alkylation response protein AidB [Lipid transport and metabolism]; Acyl-CoA dehydrogenase related to the alkylation response protein AidB is part of the Pathway/BioSystem: Fatty acid biosynthesis Pssm-ID: 441563 [Multi-domain] Cd Length: 381 Bit Score: 288.66 E-value: 1.39e-88
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| HAD-1A3-hyp | TIGR02247 | epoxide hydrolase N-terminal domain-like phosphatase; This model represents a small clade of ... |
42-247 | 8.32e-88 | ||||||||||||
epoxide hydrolase N-terminal domain-like phosphatase; This model represents a small clade of sequences including C. elegans and mammalian sequences as well as a small number of bacteria. In eukaryotes, this domain exists as an N-terminal fusion to the soluble epoxide hydrolase enzyme and has recently been shown to be an active phosphatase, although the nature of the biological substrate is unclear. These appear to be members of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases by general homology and the conservation of all of the recognized catalytic motifs (although the first motif is unusual in the replacement of the more common aspartate with glycine...). The variable domain is found in between motifs 1 and 2, indicating membership in subfamily I and phylogeny and prediction of the alpha helical nature of the variable domain (by PSI-PRED) indicate membership in subfamily IA. Pssm-ID: 274054 [Multi-domain] Cd Length: 211 Bit Score: 280.17 E-value: 8.32e-88
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| YcbJ | COG3173 | Predicted kinase, aminoglycoside phosphotransferase (APT) family [General function prediction ... |
263-552 | 9.39e-80 | ||||||||||||
Predicted kinase, aminoglycoside phosphotransferase (APT) family [General function prediction only]; Pssm-ID: 442406 [Multi-domain] Cd Length: 284 Bit Score: 261.20 E-value: 9.39e-80
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| ACAD | cd00567 | Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal ... |
756-995 | 2.99e-65 | ||||||||||||
Acyl-CoA dehydrogenase; Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast, AXO catalyzes a different oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities. The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH), glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase. The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC) Pssm-ID: 173838 [Multi-domain] Cd Length: 327 Bit Score: 222.93 E-value: 2.99e-65
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| HAD_sEH-N_like | cd02603 | N-terminal lipase phosphatase domain of human soluble epoxide hydrolase, Escherichia coli YihX ... |
43-242 | 5.19e-56 | ||||||||||||
N-terminal lipase phosphatase domain of human soluble epoxide hydrolase, Escherichia coli YihX/HAD4 alpha-D-glucose 1-phosphate phosphatase, and related domains, may be inactive; This family includes the N-terminal phosphatase domain of human soluble epoxide hydrolase (sEH). sEH is a bifunctional enzyme with two distinct enzyme activities, the C-terminal domain has epoxide hydrolysis activity and the N-terminal domain (Ntermphos), which belongs to this family, has lipid phosphatase activity. The latter prefers mono-phosphate esters, and lysophosphatidic acids (LPAs) are the best natural substrates found to date. In addition this family includes Gallus gallus sEH and Xenopus sEH which appears to lack phosphatase activity, and Escherichia coli YihX/HAD4 which selectively hydrolyzes alpha-Glucose-1-P, phosphatase, has significant phosphatase activity against pyridoxal phosphate, and has low beta phosphoglucomutase activity. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319790 [Multi-domain] Cd Length: 195 Bit Score: 192.17 E-value: 5.19e-56
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| APH | pfam01636 | Phosphotransferase enzyme family; This family consists of bacterial antibiotic resistance ... |
287-504 | 2.51e-51 | ||||||||||||
Phosphotransferase enzyme family; This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides they include: aminoglycoside 3'-phosphotransferase or kanamycin kinase / neomycin-kanamycin phosphotransferase and streptomycin 3''-kinase or streptomycin 3''-phosphotransferase. The aminoglycoside phosphotransferases inactivate aminoglycoside antibiotics via phosphorylation. This family also includes homoserine kinase. This family is related to fructosamine kinase pfam03881. Pssm-ID: 426359 [Multi-domain] Cd Length: 239 Bit Score: 180.77 E-value: 2.51e-51
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| SCAD_SBCAD | cd01158 | Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA ... |
761-999 | 1.37e-41 | ||||||||||||
Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Short chain acyl-CoA dehydrogenase (SCAD). SCAD is a mitochondrial beta-oxidation enzyme. It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of SCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. This subgroup also contains the eukaryotic short/branched chain acyl-CoA dehydrogenase(SBCAD), the bacterial butyryl-CoA dehydorgenase(BCAD) and 2-methylbutyryl-CoA dehydrogenase, which is involved in isoleucine catabolism. These enzymes are homotetramers. Pssm-ID: 173847 [Multi-domain] Cd Length: 373 Bit Score: 157.04 E-value: 1.37e-41
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| Acyl-CoA_dh_1 | pfam00441 | Acyl-CoA dehydrogenase, C-terminal domain; C-terminal domain of Acyl-CoA dehydrogenase is an ... |
847-995 | 3.27e-37 | ||||||||||||
Acyl-CoA dehydrogenase, C-terminal domain; C-terminal domain of Acyl-CoA dehydrogenase is an all-alpha, four helical up-and-down bundle. Pssm-ID: 395354 [Multi-domain] Cd Length: 149 Bit Score: 136.62 E-value: 3.27e-37
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| VLCAD | cd01161 | Very long chain acyl-CoA dehydrogenase; VLCAD is an acyl-CoA dehydrogenase (ACAD), which is ... |
702-1000 | 3.39e-31 | ||||||||||||
Very long chain acyl-CoA dehydrogenase; VLCAD is an acyl-CoA dehydrogenase (ACAD), which is found in the mitochondria of eukaryotes and in some bacteria. It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. VLCAD acts as a homodimer. Pssm-ID: 173850 [Multi-domain] Cd Length: 409 Bit Score: 127.20 E-value: 3.39e-31
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| IBD | cd01162 | Isobutyryl-CoA dehydrogenase; Isobutyryl-CoA dehydrogenase (IBD) catalyzes the alpha, beta- ... |
762-998 | 1.88e-28 | ||||||||||||
Isobutyryl-CoA dehydrogenase; Isobutyryl-CoA dehydrogenase (IBD) catalyzes the alpha, beta- dehydrogenation of short branched chain acyl-CoA intermediates in valine catabolism. It is predicted to be a homotetramer. Pssm-ID: 173851 [Multi-domain] Cd Length: 375 Bit Score: 118.31 E-value: 1.88e-28
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| LCAD | cd01160 | Long chain acyl-CoA dehydrogenase; LCAD is an acyl-CoA dehydrogenases (ACAD), which is found ... |
664-995 | 1.58e-27 | ||||||||||||
Long chain acyl-CoA dehydrogenase; LCAD is an acyl-CoA dehydrogenases (ACAD), which is found in the mitochondria of eukaryotes and in some prokaryotes. It catalyzes the alpha, beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of LCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. LCAD acts as a homodimer. Pssm-ID: 173849 [Multi-domain] Cd Length: 372 Bit Score: 115.68 E-value: 1.58e-27
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| MCAD | cd01157 | Medium chain acyl-CoA dehydrogenase; MCADs are mitochondrial beta-oxidation enzymes, which ... |
660-1000 | 3.36e-26 | ||||||||||||
Medium chain acyl-CoA dehydrogenase; MCADs are mitochondrial beta-oxidation enzymes, which catalyze the alpha,beta dehydrogenation of the corresponding medium chain acyl-CoA by FAD, which becomes reduced. The reduced form of MCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. MCAD is a homotetramer. Pssm-ID: 173846 [Multi-domain] Cd Length: 378 Bit Score: 111.91 E-value: 3.36e-26
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| HAD-SF-IA-v3 | TIGR01509 | haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; ... |
44-231 | 3.71e-26 | ||||||||||||
haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; This model represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The subfamilies are defined based on the location and the observed or predicted fold of a so-called "capping domain", or the absence of such a domain. Subfamily I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Subfamily II consists of sequences in which the capping domain is found between the second and third motifs. Subfamily III sequences have no capping domain in either of these positions. The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. Subfamily I encompasses such a wide region of sequence space (the sequences are highly divergent) that representing it with a single model is impossible, resulting in an overly broad description which allows in many unrelated sequences. Subfamily IA and IB are separated based on an aparrent phylogenetic bifurcation. Subfamily IA is still too broad to model, but cannot be further subdivided into large chunks based on phylogenetic trees. Of the three motifs defining the HAD superfamily, the third has three variant forms: (1) hhhhsDxxx(x)D, (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s where _s_ refers to a small amino acid and _h_ to a hydrophobic one. All three of these variants are found in subfamily IA. Individual models were made based on seeds exhibiting only one of the variants each. Variant 3 (this model) is found in the enzymes beta-phosphoglucomutase (TIGR01990) and deoxyglucose-6-phosphatase, while many other enzymes of subfamily IA exhibit this variant as well as variant 1 (TIGR01549). These three variant models were created with the knowledge that there will be overlap among them - this is by design and serves the purpose of eliminating the overlap with models of more distantly related HAD subfamilies caused by an overly broad single model. [Unknown function, Enzymes of unknown specificity] Pssm-ID: 273662 [Multi-domain] Cd Length: 178 Bit Score: 106.35 E-value: 3.71e-26
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| YigB | COG1011 | FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily ... |
42-234 | 2.53e-25 | ||||||||||||
FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily (riboflavin biosynthesis) [Coenzyme transport and metabolism]; Pssm-ID: 440635 [Multi-domain] Cd Length: 220 Bit Score: 105.11 E-value: 2.53e-25
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| ACAD_fadE6_17_26 | cd01152 | Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26; Putative acyl-CoA ... |
661-995 | 9.32e-23 | ||||||||||||
Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26; Putative acyl-CoA dehydrogenases (ACAD). Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze the alpha, beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. The mitochondrial ACD's are generally homotetramers and have an active site glutamate at a conserved position. Pssm-ID: 173841 [Multi-domain] Cd Length: 380 Bit Score: 101.66 E-value: 9.32e-23
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| PTZ00461 | PTZ00461 | isovaleryl-CoA dehydrogenase; Provisional |
768-999 | 1.21e-21 | ||||||||||||
isovaleryl-CoA dehydrogenase; Provisional Pssm-ID: 185640 [Multi-domain] Cd Length: 410 Bit Score: 98.86 E-value: 1.21e-21
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| IVD | cd01156 | Isovaleryl-CoA dehydrogenase; Isovaleryl-CoA dehydrogenase (IVD) is an is an acyl-CoA ... |
654-995 | 2.33e-19 | ||||||||||||
Isovaleryl-CoA dehydrogenase; Isovaleryl-CoA dehydrogenase (IVD) is an is an acyl-CoA dehydrogenase, which catalyzes the third step in leucine catabolism, the conversion of isovaleryl-CoA (3-methylbutyryl-CoA) into 3-methylcrotonyl-CoA. IVD is a homotetramer and has the greatest affinity for small branched chain substrates. Pssm-ID: 173845 [Multi-domain] Cd Length: 376 Bit Score: 91.32 E-value: 2.33e-19
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| GCD | cd01151 | Glutaryl-CoA dehydrogenase; Glutaryl-CoA dehydrogenase (GCD). GCD is an acyl-CoA dehydrogenase, ... |
660-989 | 9.09e-17 | ||||||||||||
Glutaryl-CoA dehydrogenase; Glutaryl-CoA dehydrogenase (GCD). GCD is an acyl-CoA dehydrogenase, which catalyzes the oxidative decarboxylation of glutaryl-CoA to crotonyl-CoA and carbon dioxide in the catabolism of lysine, hydroxylysine, and tryptophan. It uses electron transfer flavoprotein (ETF) as an electron acceptor. GCD is a homotetramer. GCD deficiency leads to a severe neurological disorder in humans. Pssm-ID: 173840 [Multi-domain] Cd Length: 386 Bit Score: 83.56 E-value: 9.09e-17
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| Hydrolase | pfam00702 | haloacid dehalogenase-like hydrolase; This family is structurally different from the alpha ... |
42-225 | 9.98e-17 | ||||||||||||
haloacid dehalogenase-like hydrolase; This family is structurally different from the alpha/beta hydrolase family (pfam00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain. Those members with the characteriztic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria. Pssm-ID: 459910 [Multi-domain] Cd Length: 191 Bit Score: 79.55 E-value: 9.98e-17
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| PRK12341 | PRK12341 | acyl-CoA dehydrogenase; |
737-994 | 1.09e-16 | ||||||||||||
acyl-CoA dehydrogenase; Pssm-ID: 183454 [Multi-domain] Cd Length: 381 Bit Score: 83.24 E-value: 1.09e-16
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| APH_ChoK_like | cd05120 | Aminoglycoside 3'-phosphotransferase and Choline Kinase family; This family is composed of APH, ... |
286-498 | 6.39e-16 | ||||||||||||
Aminoglycoside 3'-phosphotransferase and Choline Kinase family; This family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides and macrolides, leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine. 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), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). Pssm-ID: 270690 [Multi-domain] Cd Length: 158 Bit Score: 76.19 E-value: 6.39e-16
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| PLN02519 | PLN02519 | isovaleryl-CoA dehydrogenase |
763-995 | 1.54e-15 | ||||||||||||
isovaleryl-CoA dehydrogenase Pssm-ID: 215284 [Multi-domain] Cd Length: 404 Bit Score: 79.92 E-value: 1.54e-15
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| SrkA | COG2334 | Ser/Thr protein kinase RdoA involved in Cpx stress response, MazF antagonist [Signal ... |
267-497 | 6.84e-14 | ||||||||||||
Ser/Thr protein kinase RdoA involved in Cpx stress response, MazF antagonist [Signal transduction mechanisms]; Ser/Thr protein kinase RdoA involved in Cpx stress response, MazF antagonist is part of the Pathway/BioSystem: Threonine biosynthesis Pssm-ID: 441905 [Multi-domain] Cd Length: 297 Bit Score: 73.42 E-value: 6.84e-14
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| AidB | cd01154 | Proteins involved in DNA damage response, similar to the AidB gene product; AidB is one of ... |
664-988 | 1.70e-13 | ||||||||||||
Proteins involved in DNA damage response, similar to the AidB gene product; AidB is one of several genes involved in the SOS adaptive response to DNA alkylation damage, whose expression is activated by the Ada protein. Its function has not been entirely elucidated; however, it is similar in sequence and function to acyl-CoA dehydrogenases. It has been proposed that aidB directly destroys DNA alkylating agents such as nitrosoguanidines (nitrosated amides) or their reaction intermediates. Pssm-ID: 173843 [Multi-domain] Cd Length: 418 Bit Score: 73.56 E-value: 1.70e-13
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| ACAD_fadE5 | cd01153 | Putative acyl-CoA dehydrogenases similar to fadE5; Putative acyl-CoA dehydrogenase (ACAD). ... |
757-984 | 1.90e-13 | ||||||||||||
Putative acyl-CoA dehydrogenases similar to fadE5; Putative acyl-CoA dehydrogenase (ACAD). Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. The mitochondrial ACD's are generally homotetramers and have an active site glutamate at a conserved position. Pssm-ID: 173842 [Multi-domain] Cd Length: 407 Bit Score: 73.58 E-value: 1.90e-13
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| HomoserineK_II | cd05153 | Type II Homoserine Kinase; This subfamily is composed of unusual homoserine kinases, from a ... |
267-497 | 6.03e-12 | ||||||||||||
Type II Homoserine Kinase; This subfamily is composed of unusual homoserine kinases, from a subset of bacteria, which have a Protein Kinase fold. These proteins do not bear any similarity to the GHMP family homoserine kinases present in most bacteria and eukaryotes. Homoserine kinase catalyzes the transfer of the gamma-phosphoryl group from ATP to L-homoserine producing L-homoserine phosphate, an intermediate in the production of the amino acids threonine, methionine, and isoleucine. The Type II homoserine kinase subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). Pssm-ID: 270702 [Multi-domain] Cd Length: 300 Bit Score: 67.67 E-value: 6.03e-12
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| Acyl-CoA_dh_M | pfam02770 | Acyl-CoA dehydrogenase, middle domain; Central domain of Acyl-CoA dehydrogenase has a ... |
787-827 | 5.31e-11 | ||||||||||||
Acyl-CoA dehydrogenase, middle domain; Central domain of Acyl-CoA dehydrogenase has a beta-barrel fold. Pssm-ID: 460685 [Multi-domain] Cd Length: 95 Bit Score: 59.99 E-value: 5.31e-11
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| PRK09456 | PRK09456 | ?-D-glucose-1-phosphatase; Provisional |
46-236 | 1.23e-10 | ||||||||||||
?-D-glucose-1-phosphatase; Provisional Pssm-ID: 181872 [Multi-domain] Cd Length: 199 Bit Score: 61.98 E-value: 1.23e-10
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| PRK03354 | PRK03354 | crotonobetainyl-CoA dehydrogenase; Validated |
666-1001 | 1.84e-10 | ||||||||||||
crotonobetainyl-CoA dehydrogenase; Validated Pssm-ID: 179566 [Multi-domain] Cd Length: 380 Bit Score: 64.08 E-value: 1.84e-10
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| HAD_dREG-2_like | cd16415 | uncharacterized family of the haloacid dehalogenase-like superfamily, similar to ... |
140-250 | 2.56e-10 | ||||||||||||
uncharacterized family of the haloacid dehalogenase-like superfamily, similar to uncharacterized Drosophila melanogaster rhythmically expressed gene 2 protein and human haloacid dehalogenase-like hydrolase domain-containing protein 3; The haloacid dehalogenase-like (HAD) hydrolases are a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319852 [Multi-domain] Cd Length: 128 Bit Score: 59.23 E-value: 2.56e-10
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| Acyl-CoA_dh_N | pfam02771 | Acyl-CoA dehydrogenase, N-terminal domain; The N-terminal domain of Acyl-CoA dehydrogenase is ... |
660-783 | 3.06e-10 | ||||||||||||
Acyl-CoA dehydrogenase, N-terminal domain; The N-terminal domain of Acyl-CoA dehydrogenase is an all-alpha domain. Pssm-ID: 460686 [Multi-domain] Cd Length: 113 Bit Score: 58.24 E-value: 3.06e-10
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| PRK13026 | PRK13026 | acyl-CoA dehydrogenase; Reviewed |
699-824 | 1.48e-09 | ||||||||||||
acyl-CoA dehydrogenase; Reviewed Pssm-ID: 237277 [Multi-domain] Cd Length: 774 Bit Score: 61.90 E-value: 1.48e-09
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| Gph | COG0546 | Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion]; |
42-244 | 2.06e-09 | ||||||||||||
Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion]; Pssm-ID: 440312 [Multi-domain] Cd Length: 214 Bit Score: 58.79 E-value: 2.06e-09
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| YcjU | COG0637 | Beta-phosphoglucomutase, HAD superfamily [Carbohydrate transport and metabolism]; |
41-242 | 3.13e-09 | ||||||||||||
Beta-phosphoglucomutase, HAD superfamily [Carbohydrate transport and metabolism]; Pssm-ID: 440402 [Multi-domain] Cd Length: 208 Bit Score: 57.91 E-value: 3.13e-09
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| HAD_BPGM-like | cd07505 | beta-phosphoglucomutase-like family of the haloacid dehalogenase-like (HAD) hydrolase ... |
126-233 | 6.39e-08 | ||||||||||||
beta-phosphoglucomutase-like family of the haloacid dehalogenase-like (HAD) hydrolase superfamily; This family represents the beta-phosphoglucomutase-like family of the haloacid dehalogenase-like (HAD) hydrolase superfamily. Family members include Lactococcus lactis beta-PGM, a mutase which catalyzes the interconversion of beta-D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), Saccharomyces cerevisiae phosphatases GPP1 and GPP2 that dephosphorylate DL-glycerol-3-phosphate and DOG1 and DOG2 that dephosphorylate 2-deoxyglucose-6-phosphate, and Escherichia coli 6-phosphogluconate phosphatase YieH. It belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319808 [Multi-domain] Cd Length: 143 Bit Score: 52.62 E-value: 6.39e-08
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| fadE | PRK09463 | acyl-CoA dehydrogenase; Reviewed |
761-803 | 9.32e-08 | ||||||||||||
acyl-CoA dehydrogenase; Reviewed Pssm-ID: 236528 [Multi-domain] Cd Length: 777 Bit Score: 56.36 E-value: 9.32e-08
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| Bud32 | COG3642 | tRNA A-37 threonylcarbamoyl transferase component Bud32 [Translation, ribosomal structure and ... |
326-499 | 1.14e-07 | ||||||||||||
tRNA A-37 threonylcarbamoyl transferase component Bud32 [Translation, ribosomal structure and biogenesis]; tRNA A-37 threonylcarbamoyl transferase component Bud32 is part of the Pathway/BioSystem: tRNA modification Pssm-ID: 442859 [Multi-domain] Cd Length: 159 Bit Score: 52.27 E-value: 1.14e-07
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| HAD_like | cd01427 | Haloacid dehalogenase-like hydrolases; The haloacid dehalogenase-like (HAD) superfamily ... |
137-231 | 1.93e-07 | ||||||||||||
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. This superfamily includes a variety of enzymes that catalyze the cleavage of substrate C-Cl, P-C, and P-OP bonds via nucleophilic substitution pathways. All of which use a nucleophilic aspartate in their phosphoryl transfer reaction. They catalyze nucleophilic substitution reactions at phosphorus or carbon centers, using a conserved Asp carboxylate in covalent catalysis. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319763 [Multi-domain] Cd Length: 106 Bit Score: 50.09 E-value: 1.93e-07
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| CotS | COG0510 | Thiamine kinase or a related kinase [Coenzyme transport and metabolism]; |
425-504 | 3.11e-07 | ||||||||||||
Thiamine kinase or a related kinase [Coenzyme transport and metabolism]; Pssm-ID: 440276 [Multi-domain] Cd Length: 156 Bit Score: 50.94 E-value: 3.11e-07
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| HAD_2 | pfam13419 | Haloacid dehalogenase-like hydrolase; |
133-231 | 3.85e-07 | ||||||||||||
Haloacid dehalogenase-like hydrolase; Pssm-ID: 404323 [Multi-domain] Cd Length: 178 Bit Score: 51.05 E-value: 3.85e-07
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| HAD_Neu5Ac-Pase_like | cd04305 | human N-acetylneuraminate-9-phosphate phosphatase, Escherichia coli house-cleaning phosphatase ... |
172-229 | 2.98e-05 | ||||||||||||
human N-acetylneuraminate-9-phosphate phosphatase, Escherichia coli house-cleaning phosphatase YjjG, and related phosphatases; N-acetylneuraminate-9- phosphatase (Neu5Ac-9-Pase; E.C. 3.1.3.29) catalyzes the dephosphorylation of N-acylneuraminate 9-phosphate during the synthesis of N-acetylneuraminate; Escherichia coli nucleotide phosphatase YjjG has a broad pyrimidine nucleotide activity spectrum and functions as an in vivo house-cleaning phosphatase for noncanonical pyrimidine nucleotides. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319800 [Multi-domain] Cd Length: 109 Bit Score: 44.07 E-value: 2.98e-05
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| RIO1 | pfam01163 | RIO1 family; This is a family of atypical serine kinases which are found in archaea, bacteria ... |
291-416 | 3.56e-05 | ||||||||||||
RIO1 family; This is a family of atypical serine kinases which are found in archaea, bacteria and eukaryotes. Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance. The structure of RIO1 has been determined. Pssm-ID: 460091 [Multi-domain] Cd Length: 184 Bit Score: 45.69 E-value: 3.56e-05
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| PLN02526 | PLN02526 | acyl-coenzyme A oxidase |
767-823 | 4.01e-05 | ||||||||||||
acyl-coenzyme A oxidase Pssm-ID: 178141 [Multi-domain] Cd Length: 412 Bit Score: 47.15 E-value: 4.01e-05
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| HAD_5NT | cd02604 | haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to Saccharomyces cerevisiae Phm8p ... |
183-232 | 4.25e-05 | ||||||||||||
haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to Saccharomyces cerevisiae Phm8p and Sdt1p; This family includes Saccharomyces cerevisiae Phm8p (phosphate metabolism protein 8) and Sdt1p (Suppressor of disruption of TFIIS). Phm8p participates in the ribose salvage pathway, it catalyzes the dephosphorylation of nucleotide monophosphates to nucleosides, its preferred substrates are nucleotide monophosphates AMP, GMP, CMP, and UMP. Phm8p is also a lysophosphatidic acid phosphatase, dephosphorylating lysophosphatidic acids (LPAs) to monoacylglycerol in response to phosphate starvation. Sdt1p is a pyrimidine and pyridine-specific 5'-nucleotidase; it is an NMN/NaMN 5'-nucleotidases involved in the production of nicotinamide riboside and nicotinic acid riboside, and is a pyrimidine 5'-nucleotidase with high specificity for UMP and CMP. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319791 [Multi-domain] Cd Length: 182 Bit Score: 45.32 E-value: 4.25e-05
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| APH | cd05150 | Aminoglycoside 3'-phosphotransferase; APH catalyzes the transfer of the gamma-phosphoryl group ... |
297-534 | 1.48e-04 | ||||||||||||
Aminoglycoside 3'-phosphotransferase; APH catalyzes the transfer of the gamma-phosphoryl group from ATP to aminoglycoside antibiotics such as kanamycin, streptomycin, neomycin, and gentamicin, among others. The aminoglycoside antibiotics target the 30S ribosome and promote miscoding, leading to the production of defective proteins which insert into the bacterial membrane, resulting in membrane damage and the ultimate demise of the bacterium. Phosphorylation of the aminoglycoside antibiotics results in their inactivation, leading to bacterial antibiotic resistance. The APH gene is found on transposons and plasmids and is thought to have originated as a self-defense mechanism used by microorganisms that produce the antibiotics. The APH subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). Pssm-ID: 270699 [Multi-domain] Cd Length: 244 Bit Score: 44.49 E-value: 1.48e-04
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| PTZ00456 | PTZ00456 | acyl-CoA dehydrogenase; Provisional |
720-826 | 2.77e-04 | ||||||||||||
acyl-CoA dehydrogenase; Provisional Pssm-ID: 185635 [Multi-domain] Cd Length: 622 Bit Score: 44.86 E-value: 2.77e-04
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| AXO | cd01150 | Peroxisomal acyl-CoA oxidase; Peroxisomal acyl-CoA oxidases (AXO) catalyze the first set in ... |
653-841 | 3.07e-04 | ||||||||||||
Peroxisomal acyl-CoA oxidase; Peroxisomal acyl-CoA oxidases (AXO) catalyze the first set in the peroxisomal fatty acid beta-oxidation, the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. In a second oxidative half-reaction, the reduced FAD is reoxidized by molecular oxygen. AXO is generally a homodimer, but it has been reported to form a different type of oligomer in yeast. There are several subtypes of AXO's, based on substrate specificity. Palmitoyl-CoA oxidase acts on straight-chain fatty acids and prostanoids; whereas, the closely related Trihydroxycoprostanoly-CoA oxidase has the greatest activity for 2-methyl branched side chains of bile precursors. Pristanoyl-CoA oxidase, acts on 2-methyl branched fatty acids. AXO has an additional domain, C-terminal to the region with similarity to acyl-CoA dehydrogenases, which is included in this alignment. Pssm-ID: 173839 [Multi-domain] Cd Length: 610 Bit Score: 44.63 E-value: 3.07e-04
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| RIO2_C | cd05144 | C-terminal catalytic domain of the atypical protein serine kinase, RIO2 kinase; RIO2 is ... |
322-368 | 3.09e-04 | ||||||||||||
C-terminal catalytic domain of the atypical protein serine kinase, RIO2 kinase; RIO2 is present in archaea and eukaryotes. It contains an N-terminal winged helix (wHTH) domain and a C-terminal RIO kinase catalytic domain. The wHTH domain is primarily seen in DNA-binding proteins, although some wHTH domains may be involved in RNA recognition. RIO2 is essential for survival and is necessary for rRNA cleavage during 40S ribosomal subunit maturation. RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. The RIO2 kinase catalytic domain 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), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). Pssm-ID: 270695 [Multi-domain] Cd Length: 183 Bit Score: 42.88 E-value: 3.09e-04
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| PKc_like | cd13968 | Catalytic domain of the Protein Kinase superfamily; The PK superfamily contains the large ... |
325-403 | 9.92e-04 | ||||||||||||
Catalytic domain of the Protein Kinase superfamily; The PK superfamily contains the large family of typical PKs that includes serine/threonine kinases (STKs), protein tyrosine kinases (PTKs), and dual-specificity PKs that phosphorylate both serine/threonine and tyrosine residues of target proteins, as well as pseudokinases that lack crucial residues for catalytic activity and/or ATP binding. It also includes phosphoinositide 3-kinases (PI3Ks), aminoglycoside 3'-phosphotransferases (APHs), choline kinase (ChoK), Actin-Fragmin Kinase (AFK), and the atypical RIO and Abc1p-like protein kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to their target substrates; these include serine/threonine/tyrosine residues in proteins for typical or atypical PKs, the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives for PI3Ks, the 4-hydroxyl of PtdIns for PI4Ks, and other small molecule substrates for APH/ChoK and similar proteins such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Pssm-ID: 270870 [Multi-domain] Cd Length: 136 Bit Score: 40.50 E-value: 9.92e-04
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| HAD_L2-DEX | cd02588 | L-2-haloacid dehalogenase; L-2-Haloacid dehalogenase catalyzes the hydrolytic dehalogenation ... |
43-207 | 1.07e-03 | ||||||||||||
L-2-haloacid dehalogenase; L-2-Haloacid dehalogenase catalyzes the hydrolytic dehalogenation of L-2-haloacids to produce the corresponding D-2-hydroxyacids with an inversion of the C2-configuration. 2-haloacid dehalogenases are of interest for their potential to degrade recalcitrant halogenated environmental pollutants and their use in the synthesis of industrial chemicals. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319787 [Multi-domain] Cd Length: 216 Bit Score: 41.48 E-value: 1.07e-03
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| HAD_CbbY-like | cd07528 | subfamily of beta-phosphoglucomutase-like family, similar to Rhodobacter sphaeroides ... |
136-229 | 1.40e-03 | ||||||||||||
subfamily of beta-phosphoglucomutase-like family, similar to Rhodobacter sphaeroides xylulose-1,5-bisphosphate phosphatase CbbY; This family includes Rhodobacter sphaeroides and Arabidopsis thaliana xylulose-1,5-bisphosphate phosphatase CbbY which convert xylulose-1,5-bisphosphate (a potent inhibitor of Ribulose-1,5-bisphosphate carboxylase/oxygenase, Rubisco), to the non-inhibitory compound xylulose-5-phosphate. It belongs to the beta-phosphoglucomutase-like family whose other members include Lactococcus lactis beta-PGM, a mutase which catalyzes the interconversion of beta-D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), Saccharomyces cerevisiae phosphatases GPP1 and GPP2 that dephosphorylate DL-glycerol-3-phosphate and DOG1 and DOG2 that dephosphorylate 2-deoxyglucose-6-phosphate, and Escherichia coli 6-phosphogluconate phosphatase YieH. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319830 [Multi-domain] Cd Length: 199 Bit Score: 41.21 E-value: 1.40e-03
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| HAD_PGPase | cd16421 | Rhodobacter capsulatus Cbbz phosphoglycolate phosphatase and related proteins; ; belongs to ... |
140-231 | 1.99e-03 | ||||||||||||
Rhodobacter capsulatus Cbbz phosphoglycolate phosphatase and related proteins; ; belongs to the haloacid dehalogenase-like superfamily; Phosphoglycolate phosphatase (PGPase; EC 3.1.3.18) catalyzes the conversion of 2-phosphoglycolate into glycolate and phosphate. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319857 [Multi-domain] Cd Length: 105 Bit Score: 38.59 E-value: 1.99e-03
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| HAD_PGPase | cd07512 | haloacid dehalogenase-like superfamily phosphoglycolate phosphatase, similar to Rhodobacter ... |
135-226 | 3.20e-03 | ||||||||||||
haloacid dehalogenase-like superfamily phosphoglycolate phosphatase, similar to Rhodobacter sphaeroides CbbZ; Phosphoglycolate phosphatase catalyzes the dephosphorylation of phosphoglycolate; its activity requires divalent cations, especially Mg++. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319815 [Multi-domain] Cd Length: 214 Bit Score: 39.99 E-value: 3.20e-03
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| YjjG/YfnB | TIGR02254 | noncanonical pyrimidine nucleotidase, YjjG family; This HAD superfamily includes including ... |
175-244 | 4.44e-03 | ||||||||||||
noncanonical pyrimidine nucleotidase, YjjG family; This HAD superfamily includes including YjjG from E. coli and YfnB from B. subtilis. YjjG has been shown to act as a house-cleaning enzyme, cleaving nucleotides with non-canonical nucleotide bases. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549). Pssm-ID: 162788 [Multi-domain] Cd Length: 224 Bit Score: 39.78 E-value: 4.44e-03
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| arch_bud32 | TIGR03724 | Kae1-associated kinase Bud32; Members of this protein family are the Bud32 protein associated ... |
328-400 | 4.64e-03 | ||||||||||||
Kae1-associated kinase Bud32; Members of this protein family are the Bud32 protein associated with Kae1 (kinase-associated endopeptidase 1) in the Archaea. In many Archaeal genomes, Kae1 and Bud32 are fused. The complex is homologous to the Kae1 and Bud32 subunits of the eukaryotic KEOPS complex, an apparently ancient protein kinase-containing molecular machine. [Unknown function, General] Pssm-ID: 274749 [Multi-domain] Cd Length: 199 Bit Score: 39.50 E-value: 4.64e-03
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| HAD-SF-IA-v1 | TIGR01549 | haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or ... |
44-225 | 7.01e-03 | ||||||||||||
haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E; This model represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The subfamilies are defined based on the location and the observed or predicted fold of a so-called "capping domain", or the absence of such a domain. Subfamily I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Subfamily II consists of sequences in which the capping domain is found between the second and third motifs. Subfamily III sequences have no capping domain in either of these positions.The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. Subfamily I encompasses such a wide region of sequence space (the sequences are highly divergent) that representing it with a single model is impossible, resulting in an overly broad description which allows in many unrelated sequences. Subfamily IA and IB are separated based on an aparrent phylogenetic bifurcation. Subfamily IA is still too broad to model, but cannot be further subdivided into large chunks based on phylogenetic trees. Of the three motifs defining the HAD superfamily, the third has three variant forms: (1) hhhhsDxxx(x)(D/E), (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s where _s_ refers to a small amino acid and _h_ to a hydrophobic one. All three of these variants are found in subfamily IA. Individual models were made based on seeds exhibiting only one of the variants each. Variant 1 (this model) is found in the enzymes phosphoglycolate phosphatase (TIGR01449) and enolase-phosphatase. These three variant models (see also TIGR01493 and TIGR01509) were created withthe knowledge that there will be overlap among them - this is by design and serves the purpose of eliminating the overlap with models of more distantly relatedHAD subfamilies caused by an overly broad single model. [Unknown function, Enzymes of unknown specificity] Pssm-ID: 273686 [Multi-domain] Cd Length: 164 Bit Score: 38.53 E-value: 7.01e-03
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| HAD_PPase | cd02616 | pyrophosphatase similar to Bacillus subtilis PpaX; This family includes Bacillus subtilis PpaX ... |
42-231 | 7.64e-03 | ||||||||||||
pyrophosphatase similar to Bacillus subtilis PpaX; This family includes Bacillus subtilis PpaX which hydrolyzes pyrophosphate formed during serine-46-phosphorylated HPr (P-Ser-HPr) dephosphorylation by the bifunctional enzyme HPr kinase/phosphorylase. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319797 [Multi-domain] Cd Length: 207 Bit Score: 38.80 E-value: 7.64e-03
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| PRK14879 | PRK14879 | Kae1-associated kinase Bud32; |
328-417 | 7.89e-03 | ||||||||||||
Kae1-associated kinase Bud32; Pssm-ID: 237847 [Multi-domain] Cd Length: 211 Bit Score: 38.73 E-value: 7.89e-03
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