D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801   6 SKKLVVLDRDGVINVDSDAFIKSPDEWIPLPGSLEAIARLNHAGYRVVVATNQSGIGRGLFDMATLNAMHLKMHRAAAAV 85
Cdd:PRK08942   2 SMKAIFLDRDGVINVDSDGYVKSPDEWIPIPGSIEAIARLKQAGYRVVVATNQSGIARGLFTEAQLNALHEKMDWSLADR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801  86 GGRIDAVFFCPHTADDHCDCRKPKPGMMKLIAERFEIDPADTPVVGDSLRDLQAGEALGFRPHLVLTGKGKKALAAGGLP 165
Cdd:PRK08942  82 GGRLDGIYYCPHHPEDGCDCRKPKPGMLLSIAERLNIDLAGSPMVGDSLRDLQAAAAAGVTPVLVRTGKGVTTLAEGAAP 161

                        170       180
                 ....*....|....*....|.
gi 490657801 166 eGTRVHDDLRAFALDFLSEEH 186
Cdd:PRK08942 162 -GTWVLDSLADLPQALKKQQK 181

D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801   6 SKKLVVLDRDGVINVDSDAFIKSPDEWIPLPGSLEAIARLNHAGYRVVVATNQSGIGRGLFDMATLNAMHLKMHRAAAAV 85
Cdd:PRK08942   2 SMKAIFLDRDGVINVDSDGYVKSPDEWIPIPGSIEAIARLKQAGYRVVVATNQSGIARGLFTEAQLNALHEKMDWSLADR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801  86 GGRIDAVFFCPHTADDHCDCRKPKPGMMKLIAERFEIDPADTPVVGDSLRDLQAGEALGFRPHLVLTGKGKKALAAGGLP 165
Cdd:PRK08942  82 GGRLDGIYYCPHHPEDGCDCRKPKPGMLLSIAERLNIDLAGSPMVGDSLRDLQAAAAAGVTPVLVRTGKGVTTLAEGAAP 161

                        170       180
                 ....*....|....*....|.
gi 490657801 166 eGTRVHDDLRAFALDFLSEEH 186
Cdd:PRK08942 162 -GTWVLDSLADLPQALKKQQK 181

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801   8 KLVVLDRDGVINVDSDAFiKSPDEWIPLPGSLEAIARLNHAGYRVVVATNQSGIGRGLFDMATLNAMHLKMHRAAAAVGG 87
Cdd:cd07503    1 KALFLDRDGVINVDVPYV-HKPEDLEFLPGVIEALKKLKDAGYLVVVVTNQSGIARGYFSEADFEALHDKMRELLASQGV 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490657801  88 RIDAVFFCPHTADDHCDCRKPKPGMMKLIAERFEIDPADTPVVGDSLRDLQAGEALGFRPHLV 150
Cdd:cd07503   80 EIDDIYYCPHHPDDGCPCRKPKPGMLLDAAKELGIDLARSFVIGDRLSDIQAARNAGCKGILV 142

HAD-hyrolase-like;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490657801  105 CRKPKPGMMKLIAERFEIDPADTPVVGDSLR-DLQAGEALGFRPHLVLTGKGKKALAAGGLPEGTRVHDDLR 175
Cdd:pfam13242   2 CGKPNPGMLERALARLGLDPERTVMIGDRLDtDILGAREAGARTILVLTGVTRPADLEKAPIRPDYVVDDLA 73

D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801   6 SKKLVVLDRDGVINVDSDAFIKSPDEWIPLPGSLEAIARLNHAGYRVVVATNQSGIGRGLFDMATLNAMHLKMHRAAAAV 85
Cdd:PRK08942   2 SMKAIFLDRDGVINVDSDGYVKSPDEWIPIPGSIEAIARLKQAGYRVVVATNQSGIARGLFTEAQLNALHEKMDWSLADR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801  86 GGRIDAVFFCPHTADDHCDCRKPKPGMMKLIAERFEIDPADTPVVGDSLRDLQAGEALGFRPHLVLTGKGKKALAAGGLP 165
Cdd:PRK08942  82 GGRLDGIYYCPHHPEDGCDCRKPKPGMLLSIAERLNIDLAGSPMVGDSLRDLQAAAAAGVTPVLVRTGKGVTTLAEGAAP 161

                        170       180
                 ....*....|....*....|.
gi 490657801 166 eGTRVHDDLRAFALDFLSEEH 186
Cdd:PRK08942 162 -GTWVLDSLADLPQALKKQQK 181

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801   8 KLVVLDRDGVINVDSDAFiKSPDEWIPLPGSLEAIARLNHAGYRVVVATNQSGIGRGLFDMATLNAMHLKMHRAAAAVGG 87
Cdd:cd07503    1 KALFLDRDGVINVDVPYV-HKPEDLEFLPGVIEALKKLKDAGYLVVVVTNQSGIARGYFSEADFEALHDKMRELLASQGV 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490657801  88 RIDAVFFCPHTADDHCDCRKPKPGMMKLIAERFEIDPADTPVVGDSLRDLQAGEALGFRPHLV 150
Cdd:cd07503   80 EIDDIYYCPHHPDDGCPCRKPKPGMLLDAAKELGIDLARSFVIGDRLSDIQAARNAGCKGILV 142

HAD-superfamily hydrolase, subfamily IIIA; This subfamily falls within the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The Class III subfamilies are characterized by the lack of any domains located between either between the first and second conserved catalytic motifs (as in the Class I subfamilies, TIGR01493, TIGR01509, TIGR01488 and TIGR01494) or between the second and third conserved catalytic motifs (as in the Class II subfamilies, TIGR01460 and TIGR01484) of the superfamily domain. The IIIA subfamily contains five major clades: histidinol-phosphatase (TIGR01261) and histidinol-phosphatase-related protein (TIGR00213) which together form a subfamily (TIGR01656), DNA 3'-phosphatase (TIGR01663, TIGR01664), YqeG (TIGR01668) and YrbI (TIGR01670). In the case of histidinol phosphatase and PNK-3'-phosphatase, this model represents a domain of a bifunctional system. In the histidinol phosphatase HisB, a C-terminal domain is an imidazoleglycerol-phosphate dehydratase which catalyzes a related step in histidine biosynthesis. In PNK-3'-phosphatase, N- and C-terminal domains constitute the polynucleotide kinase and DNA-binding components of the enzyme. [Unknown function, Enzymes of unknown specificity]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801    8 KLVVLDRDGVINVDSDaFIKSPDEWIPLPGSLEAIARLNHAGYRVVVATNQSGIGRGLFDMatlnAMHLKMHRAAAAVGG 87
Cdd:TIGR01662   1 KAVVLDLDGTLTDDVP-YVSDEDERILYPEVPDALAELKEAGYKVVIVTNQSGIGRGYFSR----SFSGRVARRLEELGV 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490657801   88 RIDAVFFCPHtaddhcdCRKPKPGMMKLIAERF-EIDPADTPVVGD-SLRDLQAGEALGFRPHLVLT 152
Cdd:TIGR01662  76 PIDILYACPG-------CRKPKPGMFLEALKRFnEIDPEESVYVGDqDLTDLQAAKRVGLATILVAP 135

bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801   6 SKKLVVLDRDGVINVD--SDAFIKSPDEWIPLPGSLEAIARLNHAGYRVVVATNQSGIGRGLFDMATLNAMHLKMHRAAA 83
Cdd:PRK05446   1 MQKILFIDRDGTLIEEppTDFQVDSLDKLAFEPGVIPALLKLQKAGYKLVMVTNQDGLGTDSFPQEDFDPPHNLMMQIFE 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490657801  84 AVGGRIDAVFFCPHTADDHCDCRKPKPGMMK-LIAERfEIDPADTPVVGDSLRDLQAGEALGFR 146
Cdd:PRK05446  81 SQGIKFDEVLICPHFPEDNCSCRKPKTGLVEeYLAEG-AIDLANSYVIGDRETDVQLAENMGIK 143

HAD-IIIA family hydrolase;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801  10 VVLDRDGVINVDSDafIKSPDEWIPLPGSLEAIARLNHAGYRVVVATNQSGIGRGLFDMATLNAmHLKmhraaaAVGgrI 89
Cdd:PRK06769   7 IFIDRDGTIGGDTT--IHYPGSFTLFPFTKASLQKLKANHIKIFSFTNQPGIADGIATIADFVQ-ELK------GFG--F 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801  90 DAVFFCPHTADDHCDCRKPKPGMMKLIAERFEIDPADTPVVGDSLRDLQAGEALGFRPHLVLTGKGKKAL 159
Cdd:PRK06769  76 DDIYLCPHKHGDGCECRKPSTGMLLQAAEKHGLDLTQCAVIGDRWTDIVAAAKVNATTILVRTGAGYDAL 145

HAD-hyrolase-like;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490657801  105 CRKPKPGMMKLIAERFEIDPADTPVVGDSLR-DLQAGEALGFRPHLVLTGKGKKALAAGGLPEGTRVHDDLR 175
Cdd:pfam13242   2 CGKPNPGMLERALARLGLDPERTVMIGDRLDtDILGAREAGARTILVLTGVTRPADLEKAPIRPDYVVDDLA 73

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 490657801   13 DRDGVINVDSDAFIKSPDEWIPLPGSLEAIARLNHAGYRVVVATNQSgigrglfdmatlnamHLKMHRAAAAVGgrIDAV 92
Cdd:pfam00702  78 EGLTVVLVELLGVIALADELKLYPGAAEALKALKERGIKVAILTGDN---------------PEAAEALLRLLG--LDDY 140

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 490657801   93 FFCPHTADDHcDCRKPKPGMMKLIAERFEIDPADTPVVGDSLRDLQAGEALG 144
Cdd:pfam00702 141 FDVVISGDDV-GVGKPKPEIYLAALERLGVKPEEVLMVGDGVNDIPAAKAAG 191

DNA 3'-phosphatase; This model represents a family of proteins and protein domains which catalyze the dephosphorylation of DNA 3'-phosphates. It is believed that this activity is important for the repair of single-strand breaks in DNA caused by radiation or oxidative damage. This domain is often (TIGR01663), but not always linked to a DNA 5'-kinase domain. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is usually replaced by an arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Alternatively, there is an additional conserved aspartate downstream of the ususal site which may indicate slightly different fold in this region.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801    6 SKKLVVLDRDG-VINVDSD-AFIKSPDEW-IPLPGSLEAIARLNHAGYRVVVATNQSGIGRGlfdmatlnamhlkmHRAA 82
Cdd:TIGR01664  12 QSKVAAFDLDGtLITTRSGkVFPTSASDWrFLYPEIPAKLQELDDEGYKIVIFTNQSGIGRG--------------KLSA 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490657801   83 AAVGGRIDAV---------FFCPHTADDHcdcRKPKPGMMKLIAERF--EIDPADTPVVGDS 133
Cdd:TIGR01664  78 ESFKNKIEAFleklkvpiqVLAATHAGLY---RKPMTGMWEYLQSQYnsPIKMTRSFYVGDA 136

haloacid dehalogenase-like superfamily phosphatases, UmpH/NagD family; Phosphatases in this UmpH/NagD family include Escherichia coli UmpH UMP phosphatase/NagD nucleotide phosphatase , Mycobacterium tuberculosis Rv1692 glycerol 3-phosphate phosphatase, human PGP phosphoglycolate phosphatase, Schizosaccharomyces pombe PHO2 p-nitrophenylphosphatase, Bacillus AraL a putative sugar phosphatase, and Plasmodium falciparum para nitrophenyl phosphate phosphatase PNPase. 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
                 ....*....|....*....|....*....|....*....|....*...
gi 490657801 107 KPKPGMMKLIAERFEIDPADTPVVGDSLR-DLQAGEALGFRPHLVLTG 153
Cdd:cd07508  197 KPSPWLGELALEKFGIDPERVLFVGDRLAtDVLFGKACGFQTLLVLTG 244

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 490657801  40 EAIARLNHAGYRVVVATNQSgigrglfdmatLNAMHLKMHRAAaaVGGRIDAVFFCphtadDHCDCRKPKPGMMKLIAER 119
Cdd:cd01427   14 ELLKRLRAAGIKLAIVTNRS-----------REALRALLEKLG--LGDLFDGIIGS-----DGGGTPKPKPKPLLLLLLK 75

                         90       100       110
                 ....*....|....*....|....*....|.
gi 490657801 120 FEIDPADTPVVGDSLRDLQAGEALGFRPHLV 150
Cdd:cd01427   76 LGVDPEEVLFVGDSENDIEAARAAGGRTVAV 106

Polynucleotide kinase 3 phosphatase; Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801   25 FIKSPDEWIPL-PGSLEAIARLNHAGYRVVVATNQSGIGR-GLFDMATLNAmhlKMHRAAAAVGGRIdaVFFCPhTADDH 102
Cdd:pfam08645  20 FPRNPDDWKWLyPSVPEKLKKLHEDGYKIVIFTNQGGIGRkGKKSLEKFKN---KIEAILKKLGVPL--QVYAA-TKKDI 93

                          90       100       110
                  ....*....|....*....|....*....|....
gi 490657801  103 cdCRKPKPGMMKLIAERFE----IDPADTPVVGD 132
Cdd:pfam08645  94 --YRKPNTGMWDEMKKDYNdgveIDLEKSFYVGD 125

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801  36 PGSLEAIARLNHAGYRVVVATNQSGIGrglfdmatLNAMhLKMHraaaAVGGRIDAVffcpHTADDHCDcrKPKPGMMKL 115
Cdd:cd07533   87 PGVREALDALAAQGVLLAVATGKSRRG--------LDRV-LEQH----GLGGYFDAT----RTADDTPS--KPHPEMLRE 147

                         90       100
                 ....*....|....*....|....*....
gi 490657801 116 IAERFEIDPADTPVVGDSLRDLQAGEALG 144
Cdd:cd07533  148 ILAELGVDPSRAVMVGDTAYDMQMAANAG 176

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 490657801   34 PLPGSLEAIARLNHAGYRVVVATNQ-SGIGRGLFDMATLnamhlkMHRAAAAVGGridavffcphtadDHCDCRKPKPGM 112
Cdd:TIGR01449  86 VFPGVEATLGALRAKGLRLGLVTNKpTPLARPLLELLGL------AKYFSVLIGG-------------DSLAQRKPHPDP 146

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 490657801  113 MKLIAERFEIDPADTPVVGDSLRDLQAGEALGFRPHLVLTG 153
Cdd:TIGR01449 147 LLLAAERLGVAPQQMVYVGDSRVDIQAARAAGCPSVLLTYG 187

polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is believed to be involved in repair of oxidative DNA damage. Removal of 3' phosphates is essential for the further processing of the break by DNA polymerases. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is replaced by a conserved arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Very close relatives of this domain are also found separate from the N- and C-terminal domains seen here, as in the 3'-phosphatase found in plants. The larger family of these domains is described by TIGR01664. Outside of the phosphatase domain is a P-loop ATP-binding motif associated with the kinase activity. The entry for the mouse homolog appears to be missing a large piece of sequence corresponding to the first conserved catalytic motif of the phosphatase domain as well as the conserved threonine of the second motif. Either this is a sequencing artifact or this may represent a pseudo- or non-functional gene. Note that the EC number for the kinase function is: 2.7.1.78

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801    6 SKKLVVLDRDG-VINVDSD-AFIKSPDEW-IPLPGSLEAIARLNHAGYRVVVATNQSGIGRGLFDMATLNAmhlKMHRAA 82
Cdd:TIGR01663 167 QEKIAGFDLDGtIIKTKSGkVFPKGPDDWqIIFPEIPEKLKELEADGFKICIFTNQGGIARGKINADDFKA---KIEAIV 243

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 490657801   83 AAVGGRIDaVFFCPHTAddhcDCRKPKPGMMKLIAERF----EIDPADTPVVGDS 133
Cdd:TIGR01663 244 AKLGVPFQ-VFIAIGAG----FYRKPLTGMWDHLKEEAndgtEIQEDDCFFVGDA 293

UmpH/NagD family phosphatase, similar to Escherichia coli UmpH UMP phosphatase/NagD nucleotide phosphatase and Mycobacterium tuberculosis Rv1692 glycerol 3-phosphate phosphatase; Escherichia coli UmpH/NagD is a ribonucleoside tri-, di-, and monophosphatase with a preference for purines, it shows peak activity with UMP and functions in UMP-degradation. It is also an effective phosphatase with AMP, GMP and CMP. Mycobacterium tuberculosis phosphatase, Rv1692 is a glycerol 3-phosphate phosphatase. Rv1692 is the final enzyme involved in glycerophospholipid recycling/catabolism. This subfamily belongs to the UmpH/NagD phosphatase family, and 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657801 107 KPKPGMMKLIAERFEIDPADTPVVGDSLR-DLQAGEALGFRPHLVLTGKGKKALAAGGLPEGTRVHDDLR 175
Cdd:cd07530  177 KPEPIMMRAALEKLGLKSEETLMVGDRLDtDIAAGIAAGIDTLLVLTGVTTREDLAKPPYRPTYIVPSLR 246

UmpH/NagD family phosphatase, similar to human PGP phosphoglycolate phosphatase and Schizosaccharomyces pombe PHO2 p-nitrophenylphosphatase; This subfamily includes the phosphoglycolate phosphatases (human PGP and Arabidopsis thaliana PGLP2) and p-nitrophenylphosphatases (Schizosaccharomyces pombe PHO2 and Saccharomyces PHO13p). It belongs to the UmpH/NagD phosphatase family, and 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 490657801 105 CRKPKPGMMKLIAERFEIDPADTPVVGDSLR-DLQAGEALGFRPHLVLTG 153
Cdd:cd07510  202 VGKPSRFMFDCISSKFSIDPARTCMVGDRLDtDILFGQNCGLKTLLVLTG 251

Haloacid dehalogenase-like hydrolase; This family is part of the HAD superfamily.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 490657801   10 VVLDRDGVINVDSDafikspdewiPLPGSLEAIARLNHAGYRVVVATNQSGIGR 63
Cdd:pfam13344   1 FLFDIDGVLWRGGE----------PIPGAAEALRALRAAGKPVVFVTNNSSRSR 44

uncharacterized subfamily of the UmpH/NagD phosphatase family, belongs to the haloacid dehalogenase-like superfamily; This uncharacterized subfamily belongs to the UmpH/NagD phosphatase family and 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 490657801 107 KPKPGMMKLIAERFEIDPADTPVVGDSL-RDLQAGEALGFRPHLVLTGKGKKALAAGGLPEGTRVHDDL 174
Cdd:cd16422  177 KPNPIILDPVLEKFDYSKEETVMVGDRLyTDIVLGINAGVDSILVLSGETTREDLEDLERKPTYVFDNV 245

haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to Saccharomyces cerevisiae Phm8p and Sdt1p; This family includes Saccharomyces cerevisiae Phm8p (phosphate metabolism protein 8) and Sdt1p (Suppressor of disruption of TFIIS). Phm8p participates in the ribose salvage pathway, it catalyzes the dephosphorylation of nucleotide monophosphates to nucleosides, its preferred substrates are nucleotide monophosphates AMP, GMP, CMP, and UMP. Phm8p is also a lysophosphatidic acid phosphatase, dephosphorylating lysophosphatidic acids (LPAs) to monoacylglycerol in response to phosphate starvation. Sdt1p is a pyrimidine and pyridine-specific 5'-nucleotidase; it is an NMN/NaMN 5'-nucleotidases involved in the production of nicotinamide riboside and nicotinic acid riboside, and is a pyrimidine 5'-nucleotidase with high specificity for UMP and CMP. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490657801  90 DAVFFCpHTADDHCdcrKPKPGMMKLIAERFEIDPADTPVVGDSLRDLQAGEALGFRPHLVLT 152
Cdd:cd02604  124 DGIFDI-EYAGPDP---KPHPAAFEKAIREAGLDPKRAAFFDDSIRNLLAAKALGMKTVLVGP 182

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 490657801  33 IPL-PGSLEAIARLNHAGYRVVVATNQSgigrglfdMATLNAMhlkmhrAAAAVGGRIDAVFFCPHTADDhCDCRKPKPG 111
Cdd:cd07528   94 LPLrPGVARLIDEAKAAGVRLAIATTTS--------PANVDAL------LSALLGPERRAIFDAIAAGDD-VAEKKPDPD 158

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 490657801 112 MMKLIAERFEIDPADTPVVGDSLRDLQAGEALGFR 146
Cdd:cd07528  159 IYLLALERLGVSPSDCLAIEDSAIGLQAAKAAGLP 193

inorganic pyrophosphatase similar to a human phospholysine phosphohistidine inorganic pyrophosphate phosphatase (LHPP); LHPP hydrolyzes nitrogen-phosphorus bonds in phospholysine, phosphohistidine and imidodiphosphate as well as oxygen-phosphorus bonds in inorganic pyrophosphate in vitro. This family also includes human haloacid dehalogenase like hydrolase domain containing 2 protine (HDHD2) a phosphatase which may be involved in polygenic hypertension. 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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 490657801   8 KLVVLDRDGVINvdsdafikspDEWIPLPGSLEAIARLNHAGYRVVVATNQSG 60
Cdd:cd07509    1 KAVLLDLSGTLY----------ISGAAIPGAAEALKRLRHAGLKVRFLTNTTK 43