MULTISPECIES: phosphoglycolate phosphatase [Klebsiella]
Protein Classification
HAD family hydrolase( domain architecture ID 11486482)
HAD (haloacid dehalogenase) family hydrolase such as phosphoglycolate phosphatase that catalyzes the dephosphorylation of 2-phosphoglycolate
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| PRK13222 | PRK13222 | N-acetylmuramic acid 6-phosphate phosphatase MupP; |
3-245 | 2.36e-124 | |||||
N-acetylmuramic acid 6-phosphate phosphatase MupP; : Pssm-ID: 237310 [Multi-domain] Cd Length: 226 Bit Score: 352.19 E-value: 2.36e-124
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| Name | Accession | Description | Interval | E-value | |||||
| PRK13222 | PRK13222 | N-acetylmuramic acid 6-phosphate phosphatase MupP; |
3-245 | 2.36e-124 | |||||
N-acetylmuramic acid 6-phosphate phosphatase MupP; Pssm-ID: 237310 [Multi-domain] Cd Length: 226 Bit Score: 352.19 E-value: 2.36e-124
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| HAD_PGPase | cd16417 | Escherichia coli Gph phosphoglycolate phosphatase and related proteins; belongs to the ... |
9-237 | 1.98e-110 | |||||
Escherichia coli Gph phosphoglycolate phosphatase and related proteins; belongs to the haloacid dehalogenase-like superfamily; Phosphoglycolate phosphatase (PGP; 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: 319854 [Multi-domain] Cd Length: 212 Bit Score: 316.48 E-value: 1.98e-110
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| PGP_bact | TIGR01449 | 2-phosphoglycolate phosphatase, prokaryotic; PGP is an essential enzyme in the glycolate ... |
10-240 | 1.53e-94 | |||||
2-phosphoglycolate phosphatase, prokaryotic; PGP is an essential enzyme in the glycolate salvage pathway in higher organisms (photorespiration in plants). Phosphoglycolate results from the oxidase activity of RubisCO in the Calvin cycle when concentrations of carbon dioxide are low relative to oxygen. In Ralstonia (Alcaligenes) eutropha and Rhodobacter sphaeroides, the PGP gene (CbbZ) is located on an operon along with other Calvin cycle enzymes including RubisCO. The only other pertinent experimental evidence concerns the gene from E. coli. The in vitro activity of the Ralstonia and Escherichia enzymes was determined with crude cell extracts of strains containing PGP on expression plasmids and compared to controls. In E. coli, however, there does not appear to be a functional Calvin cycle (RubisCO is absent), although the E. coli PGP gene (gph) is on the same operon (dam) with ribulose-5-phosphate-3-epimerase (rpe), a gene in the pentose-phosphate pathway (along with other, unrelated genes). The E. coli enzyme is not expressed under normal laboratory conditions; the pathway to which it belongs has not been determined. In fact, the possibility exists, although unlikely, that the E. coli enzyme and others within this equivalog have as their physiological substrate another, closely related molecule. The other seed chosen for this model, from Xylella fastidiosa has no experimental evidence, but is a plant pathogen and thus may obtain phosphoglycolate from its host. This model has been restricted to encompass only proteobacteria as no related PGP has been verified outside of this clade. Sequences from Aquifex aeolicus and Treponema pallidum fall between the trusted and noise cutoffs. Just below the noise cutoff is a gene which is part of the operon for the biosynthesis of the blue pigment, indigoidine, from Erwinia (Pectobacterium) chrysanthemi, a plant pathogen. It does not seem likely, considering the proposed biosynthetic mechanism, that the dephosphorylation of phosphoglycolate or a closely related compound is required. Possibly, this gene is fortuitously located in this operon, or has an indirect relationship to the necessity for the biosynthesis of this compound. Sequences from 11 species have been annotated as PGP or putative PGP but fall below the noise cutoff. None of these have experimental validation. This enzyme is a member of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolase enzymes (pfam00702). [Energy metabolism, Sugars] Pssm-ID: 130516 [Multi-domain] Cd Length: 213 Bit Score: 276.32 E-value: 1.53e-94
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| Gph | COG0546 | Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion]; |
7-241 | 4.23e-71 | |||||
Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion]; Pssm-ID: 440312 [Multi-domain] Cd Length: 214 Bit Score: 217.10 E-value: 4.23e-71
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| HAD_2 | pfam13419 | Haloacid dehalogenase-like hydrolase; |
10-210 | 1.23e-42 | |||||
Haloacid dehalogenase-like hydrolase; Pssm-ID: 404323 [Multi-domain] Cd Length: 178 Bit Score: 143.11 E-value: 1.23e-42
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| Name | Accession | Description | Interval | E-value | |||||
| PRK13222 | PRK13222 | N-acetylmuramic acid 6-phosphate phosphatase MupP; |
3-245 | 2.36e-124 | |||||
N-acetylmuramic acid 6-phosphate phosphatase MupP; Pssm-ID: 237310 [Multi-domain] Cd Length: 226 Bit Score: 352.19 E-value: 2.36e-124
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| HAD_PGPase | cd16417 | Escherichia coli Gph phosphoglycolate phosphatase and related proteins; belongs to the ... |
9-237 | 1.98e-110 | |||||
Escherichia coli Gph phosphoglycolate phosphatase and related proteins; belongs to the haloacid dehalogenase-like superfamily; Phosphoglycolate phosphatase (PGP; 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: 319854 [Multi-domain] Cd Length: 212 Bit Score: 316.48 E-value: 1.98e-110
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| PGP_bact | TIGR01449 | 2-phosphoglycolate phosphatase, prokaryotic; PGP is an essential enzyme in the glycolate ... |
10-240 | 1.53e-94 | |||||
2-phosphoglycolate phosphatase, prokaryotic; PGP is an essential enzyme in the glycolate salvage pathway in higher organisms (photorespiration in plants). Phosphoglycolate results from the oxidase activity of RubisCO in the Calvin cycle when concentrations of carbon dioxide are low relative to oxygen. In Ralstonia (Alcaligenes) eutropha and Rhodobacter sphaeroides, the PGP gene (CbbZ) is located on an operon along with other Calvin cycle enzymes including RubisCO. The only other pertinent experimental evidence concerns the gene from E. coli. The in vitro activity of the Ralstonia and Escherichia enzymes was determined with crude cell extracts of strains containing PGP on expression plasmids and compared to controls. In E. coli, however, there does not appear to be a functional Calvin cycle (RubisCO is absent), although the E. coli PGP gene (gph) is on the same operon (dam) with ribulose-5-phosphate-3-epimerase (rpe), a gene in the pentose-phosphate pathway (along with other, unrelated genes). The E. coli enzyme is not expressed under normal laboratory conditions; the pathway to which it belongs has not been determined. In fact, the possibility exists, although unlikely, that the E. coli enzyme and others within this equivalog have as their physiological substrate another, closely related molecule. The other seed chosen for this model, from Xylella fastidiosa has no experimental evidence, but is a plant pathogen and thus may obtain phosphoglycolate from its host. This model has been restricted to encompass only proteobacteria as no related PGP has been verified outside of this clade. Sequences from Aquifex aeolicus and Treponema pallidum fall between the trusted and noise cutoffs. Just below the noise cutoff is a gene which is part of the operon for the biosynthesis of the blue pigment, indigoidine, from Erwinia (Pectobacterium) chrysanthemi, a plant pathogen. It does not seem likely, considering the proposed biosynthetic mechanism, that the dephosphorylation of phosphoglycolate or a closely related compound is required. Possibly, this gene is fortuitously located in this operon, or has an indirect relationship to the necessity for the biosynthesis of this compound. Sequences from 11 species have been annotated as PGP or putative PGP but fall below the noise cutoff. None of these have experimental validation. This enzyme is a member of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolase enzymes (pfam00702). [Energy metabolism, Sugars] Pssm-ID: 130516 [Multi-domain] Cd Length: 213 Bit Score: 276.32 E-value: 1.53e-94
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| Gph | COG0546 | Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion]; |
7-241 | 4.23e-71 | |||||
Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion]; Pssm-ID: 440312 [Multi-domain] Cd Length: 214 Bit Score: 217.10 E-value: 4.23e-71
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| PRK13223 | PRK13223 | phosphoglycolate phosphatase; Provisional |
8-246 | 2.08e-61 | |||||
phosphoglycolate phosphatase; Provisional Pssm-ID: 171912 [Multi-domain] Cd Length: 272 Bit Score: 194.31 E-value: 2.08e-61
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| HAD_PGPase | cd07512 | haloacid dehalogenase-like superfamily phosphoglycolate phosphatase, similar to Rhodobacter ... |
9-241 | 1.28e-49 | |||||
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: 162.10 E-value: 1.28e-49
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| HAD_PPase | cd02616 | pyrophosphatase similar to Bacillus subtilis PpaX; This family includes Bacillus subtilis PpaX ... |
7-238 | 6.85e-46 | |||||
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: 152.43 E-value: 6.85e-46
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| HAD_2 | pfam13419 | Haloacid dehalogenase-like hydrolase; |
10-210 | 1.23e-42 | |||||
Haloacid dehalogenase-like hydrolase; Pssm-ID: 404323 [Multi-domain] Cd Length: 178 Bit Score: 143.11 E-value: 1.23e-42
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| YcjU | COG0637 | Beta-phosphoglucomutase, HAD superfamily [Carbohydrate transport and metabolism]; |
7-236 | 8.51e-42 | |||||
Beta-phosphoglucomutase, HAD superfamily [Carbohydrate transport and metabolism]; Pssm-ID: 440402 [Multi-domain] Cd Length: 208 Bit Score: 141.89 E-value: 8.51e-42
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| Hydrolase | pfam00702 | haloacid dehalogenase-like hydrolase; This family is structurally different from the alpha ... |
7-205 | 2.13e-33 | |||||
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: 119.61 E-value: 2.13e-33
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| YigB | COG1011 | FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily ... |
7-240 | 1.40e-31 | |||||
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: 115.90 E-value: 1.40e-31
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| HAD_5NT | cd04302 | haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to the Pseudomonas aeruginosa PA0065; ... |
10-240 | 9.15e-30 | |||||
haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to the Pseudomonas aeruginosa PA0065; 5'-nucleotidases dephosphorylate nucleoside 5'-monophosphates to nucleosides and inorganic phosphate. Purified Pseudomonas aeruginosa PA0065 displayed high activity toward 5'-UMP and 5'-IMP, significant activity against 5'-XMP and 5'-TMP, and low activity against 5'-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: 319798 [Multi-domain] Cd Length: 209 Bit Score: 110.76 E-value: 9.15e-30
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| PRK13288 | PRK13288 | pyrophosphatase PpaX; Provisional |
7-241 | 6.44e-29 | |||||
pyrophosphatase PpaX; Provisional Pssm-ID: 237336 [Multi-domain] Cd Length: 214 Bit Score: 108.58 E-value: 6.44e-29
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| HAD_like | cd07533 | uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily, similar ... |
10-236 | 1.35e-25 | |||||
uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily, similar to Parvibaculum lavamentivorans HAD-superfamily hydrolase, subfamily IA, variant 1; 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: 319835 [Multi-domain] Cd Length: 207 Bit Score: 99.78 E-value: 1.35e-25
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| HAD_BPGM-like | cd07505 | beta-phosphoglucomutase-like family of the haloacid dehalogenase-like (HAD) hydrolase ... |
89-212 | 2.89e-24 | |||||
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: 94.22 E-value: 2.89e-24
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| HAD_like | cd01427 | Haloacid dehalogenase-like hydrolases; The haloacid dehalogenase-like (HAD) superfamily ... |
116-211 | 3.27e-24 | |||||
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: 93.23 E-value: 3.27e-24
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| HAD_BPGM-like | cd16423 | uncharacterized subfamily of beta-phosphoglucomutase-like family, similar to uncharacterized ... |
93-210 | 8.34e-24 | |||||
uncharacterized subfamily of beta-phosphoglucomutase-like family, similar to uncharacterized Bacillus subtilis YhcW; This subfamily includes the uncharacterized Bacillus subtilis YhcW. 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: 319859 [Multi-domain] Cd Length: 169 Bit Score: 93.86 E-value: 8.34e-24
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| PRK13226 | PRK13226 | phosphoglycolate phosphatase; Provisional |
8-222 | 1.49e-23 | |||||
phosphoglycolate phosphatase; Provisional Pssm-ID: 237311 [Multi-domain] Cd Length: 229 Bit Score: 94.92 E-value: 1.49e-23
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| HAD-SF-IA-v3 | TIGR01509 | haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; ... |
10-211 | 3.89e-22 | |||||
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: 89.79 E-value: 3.89e-22
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| HAD_CbbY-like | cd07528 | subfamily of beta-phosphoglucomutase-like family, similar to Rhodobacter sphaeroides ... |
12-205 | 1.17e-20 | |||||
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: 86.28 E-value: 1.17e-20
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| HAD_PGPase | cd04303 | phosphoglycolate phosphatase, similar to Synechococcus elongates phosphoglycolate phosphatase ... |
10-237 | 1.31e-19 | |||||
phosphoglycolate phosphatase, similar to Synechococcus elongates phosphoglycolate phosphatase PGP/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: 319799 [Multi-domain] Cd Length: 201 Bit Score: 83.56 E-value: 1.31e-19
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| HAD_ScGPP-like | cd07527 | subfamily of beta-phosphoglucomutase-like family, similar to Saccharomyces cerevisiae ... |
9-222 | 3.05e-19 | |||||
subfamily of beta-phosphoglucomutase-like family, similar to Saccharomyces cerevisiae DL-glycerol-3-phosphate phosphatase (GPP1p/ Rhr2p and GPP2p/HOR2p) and 2-deoxyglucose-6-phosphate phosphatase (DOG1p and DOG2p); This subfamily includes Saccharomyces cerevisiae DL-glycerol-3-phosphate phosphatase (GPP1p/ Rhr2p and GPP2p/HOR2p) and 2-deoxyglucose-6-phosphate phosphatase (DOG1p and DOG2p). GPP1p and GPP2p are involved in glycerol biosynthesis, GPP1 is induced in response to both anaerobic and hyperosmotic stress, GPP2 is induced in response to hyperosmotic or oxidative stress, and during diauxic shift; overexpression of DOG1 or DOG2 confers 2-deoxyglucose resistance. These belong 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), 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: 319829 [Multi-domain] Cd Length: 205 Bit Score: 82.78 E-value: 3.05e-19
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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 ... |
9-205 | 7.78e-19 | |||||
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: 80.52 E-value: 7.78e-19
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| HAD_L2-DEX | cd02588 | L-2-haloacid dehalogenase; L-2-Haloacid dehalogenase catalyzes the hydrolytic dehalogenation ... |
8-236 | 2.69e-18 | |||||
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: 80.39 E-value: 2.69e-18
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| CTE7 | TIGR02253 | HAD superfamily (subfamily IA) hydrolase, TIGR02253; This family of sequences from archaea and ... |
7-237 | 2.06e-17 | |||||
HAD superfamily (subfamily IA) hydrolase, TIGR02253; This family of sequences from archaea and metazoans includes the human uncharacterized protein CTE7. Pyrococcus species appear to have three different forms of this enzyme, so it is unclear whether all members of this family have the same function. 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: 274057 [Multi-domain] Cd Length: 221 Bit Score: 78.21 E-value: 2.06e-17
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| PRK13225 | PRK13225 | phosphoglycolate phosphatase; Provisional |
5-240 | 6.58e-17 | |||||
phosphoglycolate phosphatase; Provisional Pssm-ID: 106187 [Multi-domain] Cd Length: 273 Bit Score: 77.83 E-value: 6.58e-17
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| HAD_PGPase | cd16421 | Rhodobacter capsulatus Cbbz phosphoglycolate phosphatase and related proteins; ; belongs to ... |
117-210 | 4.71e-16 | |||||
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: 71.72 E-value: 4.71e-16
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| HAD_sEH-N_like | cd02603 | N-terminal lipase phosphatase domain of human soluble epoxide hydrolase, Escherichia coli YihX ... |
7-205 | 1.21e-14 | |||||
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: 70.07 E-value: 1.21e-14
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| HAD_type_II | TIGR01428 | 2-haloalkanoic acid dehalogenase, type II; Catalyzes the hydrolytic dehalogenation of small ... |
7-206 | 1.92e-13 | |||||
2-haloalkanoic acid dehalogenase, type II; Catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. Belongs to the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases (pfam00702), class (subfamily) I. Note that the Type I HAD enzymes have not yet been fully characterized, but clearly utilize a substantially different catalytic mechanism and are thus unlikely to be related. Pssm-ID: 130495 [Multi-domain] Cd Length: 198 Bit Score: 66.98 E-value: 1.92e-13
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| PRK10826 | PRK10826 | hexitol phosphatase HxpB; |
7-204 | 9.12e-13 | |||||
hexitol phosphatase HxpB; Pssm-ID: 236770 [Multi-domain] Cd Length: 222 Bit Score: 65.35 E-value: 9.12e-13
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| HAD_BPGM | cd02598 | beta-phosphoglucomutase, similar to Lactococcus lactis beta-phosphoglucomutase (beta-PGM); ... |
101-236 | 1.85e-12 | |||||
beta-phosphoglucomutase, similar to Lactococcus lactis beta-phosphoglucomutase (beta-PGM); Lactococcus lactis beta-PGM catalyzes the interconversion of beta-D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), forming beta-D-glucose 1,6-(bis)phosphate as an intermediate. In the forward G6P-forming direction, this reaction links polysaccharide phosphorolysis to glycolysis, in the reverse direction, the reaction provides G1P for the biosynthesis of exo-polysaccharides. This subfamily belongs to the beta-phosphoglucomutase-like family whose other members include 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: 319788 [Multi-domain] Cd Length: 174 Bit Score: 63.85 E-value: 1.85e-12
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| HAD_Neu5Ac-Pase_like | cd04305 | human N-acetylneuraminate-9-phosphate phosphatase, Escherichia coli house-cleaning phosphatase ... |
113-205 | 3.58e-12 | |||||
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: 61.40 E-value: 3.58e-12
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| HAD_YsbA-like | cd07523 | uncharacterized family of the haloacid dehalogenase-like superfamily, similar to the ... |
13-205 | 9.39e-12 | |||||
uncharacterized family of the haloacid dehalogenase-like superfamily, similar to the uncharacterized Lactococcus lactis YsbA; The specific function of Lactococcus lactis YsbA is unknown. 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, 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: 319825 [Multi-domain] Cd Length: 173 Bit Score: 61.62 E-value: 9.39e-12
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| HAD | pfam12710 | haloacid dehalogenase-like hydrolase; |
10-202 | 2.21e-11 | |||||
haloacid dehalogenase-like hydrolase; Pssm-ID: 432733 [Multi-domain] Cd Length: 188 Bit Score: 61.01 E-value: 2.21e-11
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| HAD_dREG-2_like | cd16415 | uncharacterized family of the haloacid dehalogenase-like superfamily, similar to ... |
119-206 | 2.62e-11 | |||||
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: 59.61 E-value: 2.62e-11
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| PLN02940 | PLN02940 | riboflavin kinase |
5-205 | 1.05e-10 | |||||
riboflavin kinase Pssm-ID: 178528 [Multi-domain] Cd Length: 382 Bit Score: 61.00 E-value: 1.05e-10
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| PLN02779 | PLN02779 | haloacid dehalogenase-like hydrolase family protein |
77-207 | 1.42e-10 | |||||
haloacid dehalogenase-like hydrolase family protein Pssm-ID: 215416 [Multi-domain] Cd Length: 286 Bit Score: 60.11 E-value: 1.42e-10
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| PLN02770 | PLN02770 | haloacid dehalogenase-like hydrolase family protein |
127-235 | 2.10e-10 | |||||
haloacid dehalogenase-like hydrolase family protein Pssm-ID: 215413 [Multi-domain] Cd Length: 248 Bit Score: 59.08 E-value: 2.10e-10
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| PRK11587 | PRK11587 | putative phosphatase; Provisional |
8-206 | 2.91e-10 | |||||
putative phosphatase; Provisional Pssm-ID: 183215 [Multi-domain] Cd Length: 218 Bit Score: 58.47 E-value: 2.91e-10
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| PRK10725 | PRK10725 | fructose-1-phosphate/6-phosphogluconate phosphatase; |
130-205 | 8.62e-10 | |||||
fructose-1-phosphate/6-phosphogluconate phosphatase; Pssm-ID: 182679 [Multi-domain] Cd Length: 188 Bit Score: 56.62 E-value: 8.62e-10
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| PLN03243 | PLN03243 | haloacid dehalogenase-like hydrolase; Provisional |
85-213 | 2.06e-09 | |||||
haloacid dehalogenase-like hydrolase; Provisional Pssm-ID: 215644 [Multi-domain] Cd Length: 260 Bit Score: 56.58 E-value: 2.06e-09
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| HAD_BPGM_like | cd07526 | subfamily of beta-phosphoglucomutase-like family, similar to Escherichia coli ... |
102-212 | 9.47e-09 | |||||
subfamily of beta-phosphoglucomutase-like family, similar to Escherichia coli 6-phosphogluconate phosphatase YieH; This subfamily includes Escherichia coli YieH/HAD3 an 6-phosphogluconate phosphatase, which can hydrolyzed purines and pyrimidines as secondary substrates. 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. 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: 319828 [Multi-domain] Cd Length: 141 Bit Score: 52.71 E-value: 9.47e-09
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| PLN02575 | PLN02575 | haloacid dehalogenase-like hydrolase |
129-204 | 1.28e-08 | |||||
haloacid dehalogenase-like hydrolase Pssm-ID: 215313 [Multi-domain] Cd Length: 381 Bit Score: 54.87 E-value: 1.28e-08
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| HAD_AtGPP-like | cd07529 | subfamily of beta-phosphoglucomutase-like family, similar to Arabidopsis thaliana Gpp1 and ... |
12-205 | 1.08e-07 | |||||
subfamily of beta-phosphoglucomutase-like family, similar to Arabidopsis thaliana Gpp1 and Gpp2; This subfamily includes Arabidopsis thaliana AtGpp1 and AtGpp2, and Drosophila GS1-like protein (Dmel\Gs1l) of unknown function. AtGpp1 and AtGpp2 are constitutively expressed in all the Arabidopsis tissues and unaffected under abiotic stress. Overexpression of AtGpp2 in transgenic Arabidopsis plants increases the specific DL-glycerol-3-phosphatase activity and improves the plants tolerance to salt, osmotic and oxidative stress. 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: 319831 [Multi-domain] Cd Length: 192 Bit Score: 50.81 E-value: 1.08e-07
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| PRK06769 | PRK06769 | HAD-IIIA family hydrolase; |
110-235 | 1.14e-07 | |||||
HAD-IIIA family hydrolase; Pssm-ID: 180686 [Multi-domain] Cd Length: 173 Bit Score: 50.11 E-value: 1.14e-07
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| HAD_PHN | cd02586 | Phosphonoacetaldehyde hydrolase (phosphonatase); similar to Bacillus cereus phosphonatase; ... |
7-228 | 1.14e-07 | |||||
Phosphonoacetaldehyde hydrolase (phosphonatase); similar to Bacillus cereus phosphonatase; Degradation of the ubiquitous natural phosphonate 2-aminoethylphosphonate (AEP) into useable forms of nitrogen, carbon, and phosphorus is a two-step metabolic pathway. The first step, catalyzed by AEP transaminase, involves the transfer of NH3 from AEP to pyruvate, yielding phosphonoacetaldehyde (P-Ald) and alanine. In the second step, phosphonatase catalyzes the hydrolytic P-C bond cleavage of P-Ald to form orthophosphate and acetaldehyde. 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: 319785 [Multi-domain] Cd Length: 242 Bit Score: 51.15 E-value: 1.14e-07
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| PLN02919 | PLN02919 | haloacid dehalogenase-like hydrolase family protein |
7-212 | 2.64e-07 | |||||
haloacid dehalogenase-like hydrolase family protein Pssm-ID: 215497 [Multi-domain] Cd Length: 1057 Bit Score: 51.39 E-value: 2.64e-07
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| PRK08942 | PRK08942 | D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase; |
168-206 | 4.24e-07 | |||||
D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase; Pssm-ID: 236354 [Multi-domain] Cd Length: 181 Bit Score: 48.66 E-value: 4.24e-07
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| HisB1/GmhB | COG0241 | Histidinol phosphatase/D-glycero-mannoheptose bisphosphatephosphatase, HAD superfamily [Amino ... |
168-235 | 6.94e-07 | |||||
Histidinol phosphatase/D-glycero-mannoheptose bisphosphatephosphatase, HAD superfamily [Amino acid transport and metabolism]; Histidinol phosphatase/D-glycero-mannoheptose bisphosphatephosphatase, HAD superfamily is part of the Pathway/BioSystem: Histidine biosynthesis Pssm-ID: 440011 [Multi-domain] Cd Length: 176 Bit Score: 48.17 E-value: 6.94e-07
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| PRK13478 | PRK13478 | phosphonoacetaldehyde hydrolase; Provisional |
73-228 | 2.44e-06 | |||||
phosphonoacetaldehyde hydrolase; Provisional Pssm-ID: 184075 [Multi-domain] Cd Length: 267 Bit Score: 47.55 E-value: 2.44e-06
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| HAD_HisB-N | cd07503 | histidinol phosphate phosphatase and related phosphatases; This family includes the N-terminal ... |
113-206 | 2.66e-06 | |||||
histidinol phosphate phosphatase and related phosphatases; This family includes the N-terminal domain of the Escherichia coli bifunctional enzyme histidinol-phosphate phosphatase/imidazole-glycerol-phosphate dehydratase, HisB. The N-terminal histidinol-phosphate phosphatase domain catalyzes the dephosphorylation of histidinol phosphate, the eight step of L-histidine biosynthesis. This family also includes Escherichia coli GmhB phosphatase which is highly specific for D-glycero-D-manno-heptose-1,7-bisphosphate, it removes the C(7)phosphate and not the C(1)phosphate, and this is the third essential step of lipopolysaccharide heptose biosynthesis. 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: 319806 [Multi-domain] Cd Length: 142 Bit Score: 45.60 E-value: 2.66e-06
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| Hydrolase_like | pfam13242 | HAD-hyrolase-like; |
168-236 | 3.93e-06 | |||||
HAD-hyrolase-like; Pssm-ID: 433056 [Multi-domain] Cd Length: 75 Bit Score: 43.76 E-value: 3.93e-06
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| SerB | COG0560 | Phosphoserine phosphatase [Amino acid transport and metabolism]; Phosphoserine phosphatase is ... |
6-205 | 4.30e-06 | |||||
Phosphoserine phosphatase [Amino acid transport and metabolism]; Phosphoserine phosphatase is part of the Pathway/BioSystem: Serine biosynthesis Pssm-ID: 440326 [Multi-domain] Cd Length: 221 Bit Score: 46.37 E-value: 4.30e-06
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| NagD | COG0647 | Ribonucleotide monophosphatase NagD, HAD superfamily [Nucleotide transport and metabolism]; |
126-237 | 7.05e-06 | |||||
Ribonucleotide monophosphatase NagD, HAD superfamily [Nucleotide transport and metabolism]; Pssm-ID: 440412 [Multi-domain] Cd Length: 259 Bit Score: 45.87 E-value: 7.05e-06
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| Histidinol-ppas | TIGR01656 | histidinol-phosphate phosphatase family domain; This domain is found in authentic ... |
100-206 | 1.78e-05 | |||||
histidinol-phosphate phosphatase family domain; This domain is found in authentic histidinol-phosphate phosphatases which are sometimes found as stand-alone entities and sometimes as fusions with imidazoleglycerol-phosphate dehydratase (TIGR01261). Additionally, a family of proteins including YaeD from E. coli (TIGR00213) and various other proteins are closely related but may not have the same substrate specificity. This domain is a member of the haloacid-dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. This superfamily is distinguished by the presence of three motifs: an N-terminal motif containing the nucleophilic aspartate, a central motif containing an conserved serine or threonine, and a C-terminal motif containing a conserved lysine (or arginine) and conserved aspartates. More specifically, the domian modelled here is a member of subfamily III of the HAD-superfamily by virtue of lacking a "capping" domain in either of the two common positions, between motifs 1 and 2, or between motifs 2 and 3. Pssm-ID: 273737 Cd Length: 147 Bit Score: 43.54 E-value: 1.78e-05
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| HAD_Pase | cd07514 | phosphatase, similar to Thermoplasma acidophilum TA0175 phosphoglycolate phosphatase (PCPase), ... |
115-205 | 3.20e-05 | |||||
phosphatase, similar to Thermoplasma acidophilum TA0175 phosphoglycolate phosphatase (PCPase), and Pyrococcus horikoshii PH1421, a magnesium-dependent phosphatase; belongs to the haloacid dehalogenase-like superfamily; Thermoplasma acidophilum TA0175 phosphoglycolate phosphatase (PGPase) catalyzes the magnesium-dependent dephosphorylation of phosphoglycolate. This family also includes Pyrococcus horikoshii OT3 PH1421, a magnesium-dependent phosphatase. 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: 319816 [Multi-domain] Cd Length: 139 Bit Score: 42.58 E-value: 3.20e-05
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| HAD-SF-IB | TIGR01488 | Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like; This model ... |
10-204 | 6.78e-05 | |||||
Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like; This model represents a subfamily of the Haloacid Dehalogenase superfamily of aspartate-nucleophile hydrolases. Subfamily IA, B, C and D are distinguished from the rest of the superfamily by the presence of a variable domain between the first and second conserved catalytic motifs. In subfamilies IA and IB, this domain consists of an alpha-helical bundle. It was necessary to model these two subfamilies separately, breaking them at a an apparent phylogenetic bifurcation, so that the resulting model(s) are not so broadly defined that members of subfamily III (which lack the variable domain) are included. Subfamily IA includes the enzyme phosphoserine phosphatase (TIGR00338) as well as three hypothetical equivalogs. Many members of these hypothetical equivalogs have been annotated as PSPase-like or PSPase-family proteins. In particular, the hypothetical equivalog which appears to be most closely related to PSPase contains only Archaea (while TIGR00338 contains only eukaryotes and bacteria) of which some are annotated as PSPases. Although this is a reasonable conjecture, none of these sequences has sufficient evidence for this assignment. If such should be found, this model should be retired while the PSPase model should be broadened to include these sequences. [Unknown function, Enzymes of unknown specificity] Pssm-ID: 273653 [Multi-domain] Cd Length: 177 Bit Score: 42.34 E-value: 6.78e-05
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| HAD_like | cd07506 | uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily; The ... |
113-214 | 2.43e-04 | |||||
uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily; 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: 319809 Cd Length: 115 Bit Score: 39.66 E-value: 2.43e-04
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| PRK10748 | PRK10748 | 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB; |
4-193 | 3.43e-04 | |||||
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB; Pssm-ID: 182696 [Multi-domain] Cd Length: 238 Bit Score: 40.87 E-value: 3.43e-04
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| HAD-SF-IA-v2 | TIGR01493 | Haloacid dehalogenase superfamily, subfamily IA, variant 2 with 3rd motif like haloacid ... |
9-203 | 1.89e-03 | |||||
Haloacid dehalogenase superfamily, subfamily IA, variant 2 with 3rd motif like haloacid dehalogenase; 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 2 (this model) is distinctive of the type II haloacid dehalogenases, and nearly all of the sequences are also part of the HAD, type II equivalog model (TIGR01428). 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. Pssm-ID: 130557 [Multi-domain] Cd Length: 175 Bit Score: 38.27 E-value: 1.89e-03
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| HAD_KDO-like | cd01630 | haloacid dehalogenase-like (HAD) hydrolase, similar to Escherichia coli ... |
117-205 | 2.58e-03 | |||||
haloacid dehalogenase-like (HAD) hydrolase, similar to Escherichia coli 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) phosphatase KdsC, and rainbow trout N-acylneuraminate cytidylyltransferase; KDO 8-P phosphatase catalyzes the hydrolysis of KDO 8-P to KDO (3-deoxy-D-manno-octulosonate) and inorganic phosphate and is the last enzyme in the KDO biosynthetic pathway. KDO is an 8-carbon sugar that links the lipid A and polysaccharide moieties of the lipopolysaccharide region in Gram-negative bacteria. An interruption in KDO biosynthesis leads to the accumulation of lipid A precursors and subsequent arrest in cell growth. The KDO biosynthesis pathway involves five sequential enzymatic reactions. This family also includes rainbow trout CMP-sialic acid synthetase which effectively converts both deaminoneuraminic acid (KDN, 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid) and N-acetylneuraminic acid (Neu5Ac) to CMP-KDN and CMP-Neu5Ac, respectively. 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: 319769 [Multi-domain] Cd Length: 146 Bit Score: 37.12 E-value: 2.58e-03
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| PRK01158 | PRK01158 | phosphoglycolate phosphatase; Provisional |
174-205 | 7.89e-03 | |||||
phosphoglycolate phosphatase; Provisional Pssm-ID: 234910 [Multi-domain] Cd Length: 230 Bit Score: 36.49 E-value: 7.89e-03
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| PLN02811 | PLN02811 | hydrolase |
111-205 | 9.26e-03 | |||||
hydrolase Pssm-ID: 178407 [Multi-domain] Cd Length: 220 Bit Score: 36.27 E-value: 9.26e-03
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