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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645  16 AEVARLFDSELEAIAGANTLLKSIKTPMCVVSNGPVSKMQHSLGKLGMLHHFPDLLFSGYDIQRWKPDPALMFHAANAMN 95
Cdd:cd07526    31 ARVLAAFEAELQPIPGAAAALSALTLPFCVASNSSRERLTHSLGLAGLLAYFEGRIFSASDVGRGKPAPDLFLHAAAQMG 110

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1438323645  96 VNVEQCILVDDSSAGAQSGIAAGMEVFYFCA 126
Cdd:cd07526   111 VAPERCLVIEDSPTGVRAALAAGMTVFGFTG 141

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645   2 ALRWQRAELELVYRAEVARLFDSELEAIAGANTL-----------LKSIKTPMCVVSNGPVSKMQHSLGKLGMLHHFpDL 70
Cdd:TIGR01449  52 VLAWAGQEPDAQRVAELRKLFDRHYEEVAGELTSvfpgveatlgaLRAKGLRLGLVTNKPTPLARPLLELLGLAKYF-SV 130

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1438323645  71 LFSGYDIQRWKPDPALMFHAANAMNVNVEQCILVDDSSAGAQSGIAAGMEV 121
Cdd:TIGR01449 131 LIGGDSLAQRKPHPDPLLLAAERLGVAPQQMVYVGDSRVDIQAARAAGCPS 181

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645  16 AEVARLFDSELEAIAGANTLLKSIKTPMCVVSNGPVSKMQHSLGKLGMLHHFPDLLFSGYDIQRWKPDPALMFHAANAMN 95
Cdd:cd07526    31 ARVLAAFEAELQPIPGAAAALSALTLPFCVASNSSRERLTHSLGLAGLLAYFEGRIFSASDVGRGKPAPDLFLHAAAQMG 110

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1438323645  96 VNVEQCILVDDSSAGAQSGIAAGMEVFYFCA 126
Cdd:cd07526   111 VAPERCLVIEDSPTGVRAALAAGMTVFGFTG 141

FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily (riboflavin biosynthesis) [Coenzyme transport and metabolism];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645  15 RAEVARLFDSELEAIAGANTLLKSIKT---PMCVVSNGPVSKMQHSLGKLGMLHHFpDLLFSGYDIQRWKPDPAlMF-HA 90
Cdd:COG1011    81 AEAFLAALPELVEPYPDALELLEALKArgyRLALLTNGSAELQEAKLRRLGLDDLF-DAVVSSEEVGVRKPDPE-IFeLA 158

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1438323645  91 ANAMNVNVEQCILVDDSS----AGAQsgiAAGMEVFYFCADPHNKPIVHPKVTTFTDLAQLQGL 150
Cdd:COG1011   159 LERLGVPPEEALFVGDSPetdvAGAR---AAGMRTVWVNRSGEPAPAEPRPDYVISDLAELLEL 219

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645   5 WQRAELELVYRAE--VARLFDSELEAIAGANTLLKSIKT---PMCVVSNGPVSKMQHSLGKLGMLHHFPDLLFSGYDIQR 79
Cdd:cd07505    17 HRQAWQLLERKNAllLELIASEGLKLKPGVVELLDALKAagiPVAVATSSSRRNVELLLLELGLLRGYFDVIVSGDDVER 96

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1438323645  80 WKPDPALMFHAANAMNVNVEQCILVDDSSAGAQSGIAAGMEVF 122
Cdd:cd07505    97 GKPAPDIYLLAAERLGVDPERCLVFEDSLAGIEAAKAAGMTVV 139

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645   2 ALRWQRAELELVYRAEVARLFDSELEAIAGANTL-----------LKSIKTPMCVVSNGPVSKMQHSLGKLGMLHHFpDL 70
Cdd:TIGR01449  52 VLAWAGQEPDAQRVAELRKLFDRHYEEVAGELTSvfpgveatlgaLRAKGLRLGLVTNKPTPLARPLLELLGLAKYF-SV 130

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1438323645  71 LFSGYDIQRWKPDPALMFHAANAMNVNVEQCILVDDSSAGAQSGIAAGMEV 121
Cdd:TIGR01449 131 LIGGDSLAQRKPHPDPLLLAAERLGVAPQQMVYVGDSRVDIQAARAAGCPS 181

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645   2 ALRWQRAELELVYRAEVARLFDsELEAIAGANTLLKSIKT---PMCVVSNGPVSKMQHSLGKLGMLHHFpDLLFSGYDIQ 78
Cdd:pfam00702  74 TLEAEGLTVVLVELLGVIALAD-ELKLYPGAAEALKALKErgiKVAILTGDNPEAAEALLRLLGLDDYF-DVVISGDDVG 151

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1438323645  79 RWKPDPALMFHAANAMNVNVEQCILVDDSSAGAQSGIAAG 118
Cdd:pfam00702 152 VGKPKPEIYLAALERLGVKPEEVLMVGDGVNDIPAAKAAG 191

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645   2 ALRWQRAELELVYRAEVARL---FDSELEAIAGAntlLKSIKTPMCVVSNGPVSkMQHSLGKLGMLHHFPDLLFSGyDIQ 78
Cdd:TIGR01509  58 PEDAQLLYKQLFYEQIEEEAklkPLPGVRALLEA---LRARGKKLALLTNSPRA-HKLVLALLGLRDLFDVVIDSS-DVG 132

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1438323645  79 RWKPDPALMFHAANAMNVNVEQCILVDDSSAGAQSGIAAGMEV 121
Cdd:TIGR01509 133 LGKPDPDIYLQALKALGLEPSECVFVDDSPAGIEAAKAAGMHT 175

riboflavin kinase

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645  26 LEAIAGANTLLKSIKT---PMCVVSNGPVSKMQHSLG-KLGMLHHFPdLLFSGYDIQRWKPDPALMFHAANAMNVNVEQC 101
Cdd:PLN02940   92 IKALPGANRLIKHLKShgvPMALASNSPRANIEAKIScHQGWKESFS-VIVGGDEVEKGKPSPDIFLEAAKRLNVEPSNC 170

                          90       100
                  ....*....|....*....|
gi 1438323645 102 ILVDDSSAGAQSGIAAGMEV 121
Cdd:PLN02940  171 LVIEDSLPGVMAGKAAGMEV 190

beta-phosphoglucomutase family hydrolase; This subfamily model groups together three clades: the characterized beta-phosphoglucomutases (including those from E.coli, B.subtilus and L.lactis, TIGR01990), a clade of putative bPGM's from mycobacteria and a clade including the uncharacterized E.coli and H.influenzae yqaB genes which may prove to be beta-mutases of a related 1-phosphosugar. All of these are members of the larger Haloacid dehalogenase (HAD) subfamily IA and include the "variant 3" glu-asp version of the third conserved HAD domain (TIGR01509).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1438323645  58 LGKLGMLHHFpDLLFSGYDIQRWKPDPALMFHAANAMNVNVEQCILVDDSSAGAQSGIAAGMEVF 122
Cdd:TIGR02009 120 LAKLGLRDYF-DAIVDASEVKNGKPHPETFLLAAELLGVPPNECIVFEDALAGVQAARAAGMFAV 183

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1438323645  55 QHSLGKLGMLHHFpDLLFSGYDIQRWKPDPALMFHAANAMNVNVEQCILVDDSSAGAQSGIAAGM 119
Cdd:cd02598    78 PKILEKLGLAEYF-DAIVDGAVLAKGKPDPDIFLAAAEGLGLNPKDCIGVEDAQAGIRAIKAAGF 141

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645  14 YRAEVA---RLFDSELEAIAGantlLKSIKTPMCVVSNGPVSKMQHSLGKLGMLHHFpDLLFSGYDIQRWKPDPALMFHA 90
Cdd:cd07512    77 YEADPPgltRPYPGVIEALER----LRAAGWRLAICTNKPEAPARALLSALGLADLF-AAVVGGDTLPQRKPDPAPLRAA 151

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1438323645  91 ANAMNVNVEQCILVDDSSAGAQSGIAAGMEVFYFCADPHNKPIV----HPKVTTFTDLAQL 147
Cdd:cd07512   152 IRRLGGDVSRALMVGDSETDAATARAAGVPFVLVTFGYRHAPVAelphDAVFSDFDALPDL 212

haloacid dehalogenase-like hydrolase

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645   1 MALRwqRAELELVYRAEVARLFDSELEAIagaNTLLKSiKTPMCVVSNGPVSKMQHSLGKLGMLHHFpDLLFSGYDIQRW 80
Cdd:PLN02575  199 MATR--KEEIYQALQGGIYRLRTGSQEFV---NVLMNY-KIPMALVSTRPRKTLENAIGSIGIRGFF-SVIVAAEDVYRG 271

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1438323645  81 KPDPALMFHAANAMNVNVEQCILVDDSSagaqSGIAAGMEVFYFCADPHNKpivHP 136
Cdd:PLN02575  272 KPDPEMFIYAAQLLNFIPERCIVFGNSN----QTVEAAHDARMKCVAVASK---HP 320

haloacid dehalogenase-like hydrolase; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645  35 LLKSIKTPMCVVSNGPVSKMQHSLGKLGMlHHFPDLLFSGYDIQRWKPDPALMFHAANAMNVNVEQCILVDDSSAGAQSG 114
Cdd:PLN03243  120 ALKKHEIPIAVASTRPRRYLERAIEAVGM-EGFFSVVLAAEDVYRGKPDPEMFMYAAERLGFIPERCIVFGNSNSSVEAA 198

                  ....*.
gi 1438323645 115 IAAGME 120
Cdd:PLN03243  199 HDGCMK 204

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1438323645  69 DLLFSGYDIQRWKPDPALMFHAANAMNVNVEQCILVDDSSAGAQSGIAAGMEV 121
Cdd:cd07528   142 DAIAAGDDVAEKKPDPDIYLLALERLGVSPSDCLAIEDSAIGLQAAKAAGLPC 194

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645  14 YRAEVARLFDSELEAIAGANTLLKSIKT---PMCVVSNGPVSKMQHSLGKLGMLHHFPDLLFSGyDIQRwKPDPALMFHA 90
Cdd:TIGR01549  60 LQGRFWSEYDAEEAYIRGAADLLARLKSagiKLGIISNGSLRAQKLLLRLFGLGDYFELILVSD-EPGS-KPEPEIFLAA 137

                          90       100
                  ....*....|....*....|....*...
gi 1438323645  91 ANAMNVNvEQCILVDDSSAGAQSGIAAG 118
Cdd:TIGR01549 138 LESLGVP-PEVLHVGDNLNDIEGARNAG 164

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645  36 LKSIKTPMCVVSNGPVSKMQHSLGKLGMLHHFPDLLFSGYDIQRWKPDPALMFHAANAMNVNVEQCILVDDSSAGAQSGI 115
Cdd:cd02603    96 LRAKGYKVYLLSNTWPDHFKFQLELLPRRGDLFDGVVESCRLGVRKPDPEIYQLALERLGVKPEEVLFIDDREENVEAAR 175

                  ....*....
gi 1438323645 116 AAGMEVFYF 124
Cdd:cd02603   176 ALGIHAILV 184

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645   9 ELELVYRAEVARLFDSELEAIAGANTLLKSIKT---PMCV-VSNGPVS---KMQHSLGKLGMLHHfpdlLFSGYD---IQ 78
Cdd:cd07529    66 EEFDEQQEALAELFMGTAKLMPGAERLLRHLHAhniPIALaTSSCTRHfklKTSRHKELFSLFHH----VVTGDDpevKG 141

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1438323645  79 RWKPDPALMFHAANAMN---VNVEQCILVDDSSAGAQSGIAAGMEV 121
Cdd:cd07529   142 RGKPAPDIFLVAAKRFNeppKDPSKCLVFEDSPNGVKAAKAAGMQV 187

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645  42 PMCVVSNGP---VSKMQHSLGKLgmlhHFPDLLFSGYDIQRwKPDPALMFHAANAMNVNVEQCILVDDSSAGAQSGIAAG 118
Cdd:cd16421    25 KLAVLSNKPneaVQVLVEELFPG----SFDFVLGEKEGIRR-KPDPT*ALECAKVLGVPPDEVLYVGDSGVDMQTARNAG 99

                  ...
gi 1438323645 119 MEV 121
Cdd:cd16421   100 MDE 102

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1438323645  68 PDLLFSGYDIQRWKPDPALMFHAANAMNV-NVEQCILVDDSSAGAQSGIAAGM 119
Cdd:cd02586   142 PDSLVTPDDVPAGRPYPWMCYKNAIELGVyDVAAVVKVGDTVPDIKEGLNAGM 194

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323645  27 EAIAGANtLLKSIKTPMCVVSNGPVSKMQHSLGKLGMLHHFpDLLFSGYDIQRWKPDPALMFHAANAMNVNVEQCILV-- 104
Cdd:TIGR01428  96 DVPAGLR-ALKERGYRLAILSNGSPAMLKSLVKHAGLDDPF-DAVLSADAVRAYKPAPQVYQLALEALGVPPDEVLFVas 173

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1438323645 105 ---DDSSAGaqsgiAAGMEVFYFcADPHNKP 132
Cdd:TIGR01428 174 npwDLGGAK-----KFGFKTAWI-NRPGEPP 198