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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   5 GFLFDLDGTLVDSLPVVERSWINWAKRQGINPQQVLEFIHGKQAITSLRHFMPDAD--EARLQEEFDwleaLESRDTDGI 82
Cdd:cd07527    1 ALLFDMDGTLVDSTPAVERAWHKWAKEHGVDPEEVLKVSHGRRAIDVIRKLAPDDAdiELVLALETE----EPESYPEGV 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245  83 AAMPGAAALIARLDALAIPWGIVTSGSVPVAYARCKAAGLPKPAVFITAEQVQRGKPEPDAYLLGAQRLGLAPGACAVVE 162
Cdd:cd07527   77 IAIPGAVDLLASLPAAGDRWAIVTSGTRALAEARLEAAGLPHPEVLVTADDVKNGKPDPEPYLLGAKLLGLDPSDCVVFE 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 502612245 163 DAPAGILAGLTAGCQVIAVNAPAETPKL--DKVTLCLHSLAQIALT 206
Cdd:cd07527  157 DAPAGIKAGKAAGARVVAVNTSHDLEQLeaAGADLVVEDLSDISVD 202

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 502612245    6 FLFDLDGTLVDSLPVVErsWINWAKRQGINPQqvlEFIHG--KQAITSLRHFMPDADEARLQEEFDWLEA----LESRDT 79
Cdd:TIGR01509   2 ILFDLDGVLVDTEFAIA--KLINREELGLVPD---ELGVSavGRLELALRRFKAQYGRTISPEDAQLLYKqlfyEQIEEE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   80 DGIAAMPGAAALIARLDALAIPWGIVTSgSVPVAYARCKAAGLP-KPAVFITAEQVQRGKPEPDAYLLGAQRLGLAPGAC 158
Cdd:TIGR01509  77 AKLKPLPGVRALLEALRARGKKLALLTN-SPRAHKLVLALLGLRdLFDVVIDSSDVGLGKPDPDIYLQALKALGLEPSEC 155

                         170       180
                  ....*....|....*....|...
gi 502612245  159 AVVEDAPAGILAGLTAGCQVIAV 181
Cdd:TIGR01509 156 VFVDDSPAGIEAAKAAGMHTVGV 178

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   5 GFLFDLDGTLVDSLPVVERSWINWAKRQGINPQQVLEFIHGKQAITSLRHFMPDAD--EARLQEEFDwleaLESRDTDGI 82
Cdd:cd07527    1 ALLFDMDGTLVDSTPAVERAWHKWAKEHGVDPEEVLKVSHGRRAIDVIRKLAPDDAdiELVLALETE----EPESYPEGV 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245  83 AAMPGAAALIARLDALAIPWGIVTSGSVPVAYARCKAAGLPKPAVFITAEQVQRGKPEPDAYLLGAQRLGLAPGACAVVE 162
Cdd:cd07527   77 IAIPGAVDLLASLPAAGDRWAIVTSGTRALAEARLEAAGLPHPEVLVTADDVKNGKPDPEPYLLGAKLLGLDPSDCVVFE 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 502612245 163 DAPAGILAGLTAGCQVIAVNAPAETPKL--DKVTLCLHSLAQIALT 206
Cdd:cd07527  157 DAPAGIKAGKAAGARVVAVNTSHDLEQLeaAGADLVVEDLSDISVD 202

Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   4 KGFLFDLDGTLVDSLPVVERSWINWAKRQGINP---QQVLEFIhGKQAITSLRHFMPDADEARLQEEFD-WLEALESRDT 79
Cdd:COG0546    2 KLVLFDLDGTLVDSAPDIAAALNEALAELGLPPldlEELRALI-GLGLRELLRRLLGEDPDEELEELLArFRELYEEELL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245  80 DGIAAMPGAAALIARLDALAIPWGIVTSGSVPVAYARCKAAGLPKPAVFI-TAEQVQRGKPEPDAYLLGAQRLGLAPGAC 158
Cdd:COG0546   81 DETRLFPGVRELLEALKARGIKLAVVTNKPREFAERLLEALGLDDYFDAIvGGDDVPPAKPKPEPLLEALERLGLDPEEV 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 502612245 159 AVVEDAPAGILAGLTAGCQVIAVN---APAETPKLDKVTLCLHSLAQIA 204
Cdd:COG0546  161 LMVGDSPHDIEAARAAGVPFIGVTwgyGSAEELEAAGADYVIDSLAELL 209

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 502612245    6 FLFDLDGTLVDSLPVVErsWINWAKRQGINPQqvlEFIHG--KQAITSLRHFMPDADEARLQEEFDWLEA----LESRDT 79
Cdd:TIGR01509   2 ILFDLDGVLVDTEFAIA--KLINREELGLVPD---ELGVSavGRLELALRRFKAQYGRTISPEDAQLLYKqlfyEQIEEE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   80 DGIAAMPGAAALIARLDALAIPWGIVTSgSVPVAYARCKAAGLP-KPAVFITAEQVQRGKPEPDAYLLGAQRLGLAPGAC 158
Cdd:TIGR01509  77 AKLKPLPGVRALLEALRARGKKLALLTN-SPRAHKLVLALLGLRdLFDVVIDSSDVGLGKPDPDIYLQALKALGLEPSEC 155

                         170       180
                  ....*....|....*....|...
gi 502612245  159 AVVEDAPAGILAGLTAGCQVIAV 181
Cdd:TIGR01509 156 VFVDDSPAGIEAAKAAGMHTVGV 178

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 502612245    4 KGFLFDLDGTLVDSLPVVERSWINWAKRQGINPQQVLEFIHGKQAITSLRHFMPDADEARLQEEFDWLEALESRDTDGIA 83
Cdd:pfam00702   2 KAVVFDLDGTLTDGEPVVTEAIAELASEHPLAKAIVAAAEDLPIPVEDFTARLLLGKRDWLEELDILRGLVETLEAEGLT 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   84 A-----------------MPGAAALIARLDALAIPWGIVTSGSVPVAYARCKAAGLPKP-AVFITAEQVQRGKPEPDAYL 145
Cdd:pfam00702  82 VvlvellgvialadelklYPGAAEALKALKERGIKVAILTGDNPEAAEALLRLLGLDDYfDVVISGDDVGVGKPKPEIYL 161

                         170       180       190
                  ....*....|....*....|....*....|
gi 502612245  146 LGAQRLGLAPGACAVVEDAPAGILAGLTAG 175
Cdd:pfam00702 162 AALERLGVKPEEVLMVGDGVNDIPAAKAAG 191

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 502612245   7 LFDLDGTLVDSLPVVERSWINWAKRQGinpqqvlefihgkqaitslrhfmpdadeARLQEEFDwlealesrdtDGIAAMP 86
Cdd:cd07526    4 IFDCDGVLVDSEVIAARVLVEVLAELG----------------------------ARVLAAFE----------AELQPIP 45

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245  87 GAAALiarLDALAIPWGIVTSGSVPVAYARCKAAGLPK---PAVFiTAEQVQRGKPEPDAYLLGAQRLGLAPGACAVVED 163
Cdd:cd07526   46 GAAAA---LSALTLPFCVASNSSRERLTHSLGLAGLLAyfeGRIF-SASDVGRGKPAPDLFLHAAAQMGVAPERCLVIED 121

                        170
                 ....*....|....*.
gi 502612245 164 APAGILAGLTAGCQVI 179
Cdd:cd07526  122 SPTGVRAALAAGMTVF 137

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 502612245   4 KGFLFDLDGTLVDSLPVVERSWINWAKRQGInPQQVLEFIHGKQAITSLRHFMPDADEARLQEEFDWL------------ 71
Cdd:COG1011    2 KAVLFDLDGTLLDFDPVIAEALRALAERLGL-LDEAEELAEAYRAIEYALWRRYERGEITFAELLRRLleelgldlaeel 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245  72 -EALESRDTDGIAAMPGAAALIARLDALAIPWGIVTSGSVPVAYARCKAAGLPKP-AVFITAEQVQRGKPEPDAYLLGAQ 149
Cdd:COG1011   81 aEAFLAALPELVEPYPDALELLEALKARGYRLALLTNGSAELQEAKLRRLGLDDLfDAVVSSEEVGVRKPDPEIFELALE 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 502612245 150 RLGLAPGACAVVEDAPAG-ILAGLTAGCQVIAVNAPAETPKLD-KVTLCLHSLAQIA 204
Cdd:COG1011  161 RLGVPPEEALFVGDSPETdVAGARAAGMRTVWVNRSGEPAPAEpRPDYVISDLAELL 217

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 502612245    5 GFLFDLDGTLVDSLPVVERSWINWAKRQGINPQQV--LEFIHGKQA--ITSLRHFMPDadeaRLQEEFdWLEALESRDTd 80
Cdd:TIGR01549   1 AILFDIDGTLVDIKFAIRRAFPQTFEEFGLDPASFkaLKQAGGLAEeeWYRIATSALE----ELQGRF-WSEYDAEEAY- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   81 giaaMPGAAALIARLDALAIPWGIVTSGSVPVAYARCKAAGLPKPAVFITAEQVQRGKPEPDAYLLGAQRLGLAPGaCAV 160
Cdd:TIGR01549  75 ----IRGAADLLARLKSAGIKLGIISNGSLRAQKLLLRLFGLGDYFELILVSDEPGSKPEPEIFLAALESLGVPPE-VLH 149

                         170
                  ....*....|....*
gi 502612245  161 VEDAPAGILAGLTAG 175
Cdd:TIGR01549 150 VGDNLNDIEGARNAG 164

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   4 KGFLFDLDGTLVDSLPVVERSWINWAKRQGIN---PQQVLEFIhGKQAITSLRHFMPDADEARLQEEFDwlEALESRDtD 80
Cdd:cd02616    2 TTILFDLDGTLIDTNELIIKSFNHTLKEYGLEgytREEVLPFI-GPPLRETFEKIDPDKLEDMVEEFRK--YYREHND-D 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245  81 GIAAMPGAAALIARLDALAIPWGIVTSGSVPVAYARCKAAGLPKP-AVFITAEQVQRGKPEPDAYLLGAQRLGLAPGACA 159
Cdd:cd02616   78 LTKEYPGVYETLARLKSQGIKLGVVTTKLRETALKGLKLLGLDKYfDVIVGGDDVTHHKPDPEPVLKALELLGAEPEEAL 157

                        170       180
                 ....*....|....*....|..
gi 502612245 160 VVEDAPAGILAGLTAGCQVIAV 181
Cdd:cd02616  158 MVGDSPHDILAGKNAGVKTVGV 179

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   7 LFDLDGTLVDSLPVVERSWIN-WAKRQGIN-------PQQVLEFIHGKQAITSLrHFMPDADEARLQEEFDWLEALESRD 78
Cdd:cd07528    3 IFDVDGTLAETEELHRRAFNNaFFAERGLDwywdrelYGELLRVGGGKERIAAY-FEKVGWPESAPKDLKELIADLHKAK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245  79 TDGIAAM---------PGAAALIARLDALAIPWGIVTSGSvPVAYARCKAAGLPKPA-----VFITAEQVQRGKPEPDAY 144
Cdd:cd07528   82 TERYAELiaagllplrPGVARLIDEAKAAGVRLAIATTTS-PANVDALLSALLGPERraifdAIAAGDDVAEKKPDPDIY 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 502612245 145 LLGAQRLGLAPGACAVVEDAPAGILAGLTAGCQVI 179
Cdd:cd07528  161 LLALERLGVSPSDCLAIEDSAIGLQAAKAAGLPCI 195

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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   5 GFLFDLDGTLVDSLPVVERSWINWAKrqginpqqvlefihgKQAITSLRHFMPdadearlQEEfdwLEALESRDTdgiaa 84
Cdd:cd02598    1 GVIFDLDGVITDTAEYHYRAWKKLAD---------------KEELAARKNRIY-------VEL---IEELTPVDV----- 50

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245  85 MPGAAALIARLDALAIPWGIVT-SGSVPVAYARCKAAGLPkpAVFITAEQVQRGKPEPDAYLLGAQRLGLAPGACAVVED 163
Cdd:cd02598   51 LPGIASLLVDLKAKGIKIALASaSKNAPKILEKLGLAEYF--DAIVDGAVLAKGKPDPDIFLAAAEGLGLNPKDCIGVED 128

                        170       180
                 ....*....|....*....|...
gi 502612245 164 APAGILAGLTAGCQVIAVNAPAE 186
Cdd:cd02598  129 AQAGIRAIKAAGFLVVGVGREED 151

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 502612245    7 LFDLDGTLVDSLP-VVERSWINWAKRQG--INPQQVLEFIHG-----KQAITSLRHFMPDADEAR-LQEEFD-WLEALES 76
Cdd:TIGR01449   2 LFDLDGTLVDSAPdIAAAVNMALAALGLppATLARVIGFIGNgvpvlMERVLAWAGQEPDAQRVAeLRKLFDrHYEEVAG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   77 RDTdgiAAMPGAAALIARLDALAIPWGIVTSGSVPVAYARCKAAGLPKP-AVFITAEQVQRGKPEPDAYLLGAQRLGLAP 155
Cdd:TIGR01449  82 ELT---SVFPGVEATLGALRAKGLRLGLVTNKPTPLARPLLELLGLAKYfSVLIGGDSLAQRKPHPDPLLLAAERLGVAP 158

                         170       180
                  ....*....|....*....|....*.
gi 502612245  156 GACAVVEDAPAGILAGLTAGCQVIAV 181
Cdd:TIGR01449 159 QQMVYVGDSRVDIQAARAAGCPSVLL 184

N-acetylmuramic acid 6-phosphate phosphatase MupP;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   1 MKCKGFLFDLDGTLVDSLPVVERSwINWAKRQ-GINP---QQVLEFI-HG-----KQAITSLRHFMPDADEARLQEEFD- 69
Cdd:PRK13222   4 MDIRAVAFDLDGTLVDSAPDLAAA-VNAALAAlGLPPageERVRTWVgNGadvlvERALTWAGREPDEELLEKLRELFDr 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245  70 -WLEALESRDTdgiaAMPGAAALIARLDALAIPWGIVTSGSVPVAYARCKAAGLPKP-AVFITAEQVQRGKPEPDAYLLG 147
Cdd:PRK13222  83 hYAENVAGGSR----LYPGVKETLAALKAAGYPLAVVTNKPTPFVAPLLEALGIADYfSVVIGGDSLPNKKPDPAPLLLA 158

                        170       180       190
                 ....*....|....*....|....*....|....
gi 502612245 148 AQRLGLAPGACAVVEDAPAGILAGLTAGCQVIAV 181
Cdd:PRK13222 159 CEKLGLDPEEMLFVGDSRNDIQAARAAGCPSVGV 192

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245  88 AAALIARLDALAIPWGIVTSGSVPVAYARCKAAGLP-KPAVFITAEQVQRGKPEPDAYLLGAQRLGLAPGACAVVEDAPA 166
Cdd:cd01427   12 AVELLKRLRAAGIKLAIVTNRSREALRALLEKLGLGdLFDGIIGSDGGGTPKPKPKPLLLLLLKLGVDPEEVLFVGDSEN 91

                         90
                 ....*....|....*
gi 502612245 167 GILAGLTAGCQVIAV 181
Cdd:cd01427   92 DIEAARAAGGRTVAV 106

phosphoglycolate phosphatase; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   7 LFDLDGTLVDSLP---VVERSWINWAKRQGINPQQVLEFIH-GKQAITSLR--HFMPDADEARLQEEFDWLEAL---ESR 77
Cdd:PRK13226  16 LFDLDGTLLDSAPdmlATVNAMLAARGRAPITLAQLRPVVSkGARAMLAVAfpELDAAARDALIPEFLQRYEALigtQSQ 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245  78 DTDGIAAMpgaaalIARLDALAIPWGIVTSGsvPVAYARCKAAGL---PKPAVFITAEQVQRGKPEPDAYLLGAQRLGLA 154
Cdd:PRK13226  96 LFDGVEGM------LQRLECAGCVWGIVTNK--PEYLARLILPQLgweQRCAVLIGGDTLAERKPHPLPLLVAAERIGVA 167

                        170       180
                 ....*....|....*....|....*..
gi 502612245 155 PGACAVVEDAPAGILAGLTAGCQVIAV 181
Cdd:PRK13226 168 PTDCVYVGDDERDILAARAAGMPSVAA 194

haloacid dehalogenase-like hydrolase; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245   5 GFLFDLDGTLV-DSLPVVERSWINWAKRQGINPQQVL-----EFIHGKQAITSL----RHFMPDADEARLQEE-FDWLEA 73
Cdd:PLN03243  26 GVVLEWEGVIVeDDSELERKAWRALAEEEGKRPPPAFllkraEGMKNEQAISEVlcwsRDFLQMKRLAIRKEDlYEYMQG 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502612245  74 LESRdtdgiaAMPGAAALIARLDALAIPWGIVTSGSVPVAYARCKAAGLPKP-AVFITAEQVQRGKPEPDAYLLGAQRLG 152
Cdd:PLN03243 106 GLYR------LRPGSREFVQALKKHEIPIAVASTRPRRYLERAIEAVGMEGFfSVVLAAEDVYRGKPDPEMFMYAAERLG 179

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 502612245 153 LAPGACAVVEDAPAGILAGLTAGCQVIAVNAPAETPKLDKVTLCLHSLAQIAL 205
Cdd:PLN03243 180 FIPERCIVFGNSNSSVEAAHDGCMKCVAVAGKHPVYELSAGDLVVRRLDDLSV 232