human N-acetylneuraminate-9-phosphate phosphatase, Escherichia coli house-cleaning phosphatase YjjG, and related phosphatases; N-acetylneuraminate-9- phosphatase (Neu5Ac-9-Pase; E.C. 3.1.3.29) catalyzes the dephosphorylation of N-acylneuraminate 9-phosphate during the synthesis of N-acetylneuraminate; Escherichia coli nucleotide phosphatase YjjG has a broad pyrimidine nucleotide activity spectrum and functions as an in vivo house-cleaning phosphatase for noncanonical pyrimidine nucleotides. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541751   3 QAGYALALITNGPSNAQWEKVAELNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGDKLETDIKGGHLA 82
Cdd:cd04305   22 KKGYKLGIITNGPTEVQWEKLEQLGIHKYFDHIVISEEVGVQKPNPEIFDYALNQLGVKPEETLMVGDSLESDILGAKNA 101

                 ....*..
gi 320541751  83 QLgLTFW 89
Cdd:cd04305  102 GI-KTVW 107

Haloacid dehalogenase-like hydrolase;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 320541751    2 RQAGYALALITNGPSNAQWEKVAELNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGDKLeTDIKGGH 80
Cdd:pfam13419  92 KEQGYKLGIVTSKSRENVEEFLKQLGLEDYFDVIVGGDDVEGKKPDPDPILKALEQLGLKPEEVIYVGDSP-RDIEAAK 169

human N-acetylneuraminate-9-phosphate phosphatase, Escherichia coli house-cleaning phosphatase YjjG, and related phosphatases; N-acetylneuraminate-9- phosphatase (Neu5Ac-9-Pase; E.C. 3.1.3.29) catalyzes the dephosphorylation of N-acylneuraminate 9-phosphate during the synthesis of N-acetylneuraminate; Escherichia coli nucleotide phosphatase YjjG has a broad pyrimidine nucleotide activity spectrum and functions as an in vivo house-cleaning phosphatase for noncanonical pyrimidine nucleotides. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541751   3 QAGYALALITNGPSNAQWEKVAELNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGDKLETDIKGGHLA 82
Cdd:cd04305   22 KKGYKLGIITNGPTEVQWEKLEQLGIHKYFDHIVISEEVGVQKPNPEIFDYALNQLGVKPEETLMVGDSLESDILGAKNA 101

                 ....*..
gi 320541751  83 QLgLTFW 89
Cdd:cd04305  102 GI-KTVW 107

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541751   2 RQAGYALALITNGPSNAQWEKVAELNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGDkLETDIKGGHL 81
Cdd:COG0546   97 KARGIKLAVVTNKPREFAERLLEALGLDDYFDAIVGGDDVPPAKPKPEPLLEALERLGLDPEEVLMVGD-SPHDIEAARA 175

                 .
gi 320541751  82 A 82
Cdd:COG0546  176 A 176

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 320541751    2 RQAGYALALITNGPSNAQWEKVAELNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGDKLeTDIKGGHL 81
Cdd:pfam00702 111 KERGIKVAILTGDNPEAAEALLRLLGLDDYFDVVISGDDVGVGKPKPEIYLAALERLGVKPEEVLMVGDGV-NDIPAAKA 189

                  .
gi 320541751   82 A 82
Cdd:pfam00702 190 A 190

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 320541751   1 MRQAGYALALITNGPSNAQWEKVAELNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGDKlETDIKGGH 80
Cdd:cd01427   19 LRAAGIKLAIVTNRSREALRALLEKLGLGDLFDGIIGSDGGGTPKPKPKPLLLLLLKLGVDPEEVLFVGDS-ENDIEAAR 97

                 ..
gi 320541751  81 LA 82
Cdd:cd01427   98 AA 99

N-acetylmuramic acid 6-phosphate phosphatase MupP;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541751   1 MRQAGYALALITNGPsnaqwEKVAE-----LNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGDKlETD 75
Cdd:PRK13222 105 LKAAGYPLAVVTNKP-----TPFVAplleaLGIADYFSVVIGGDSLPNKKPDPAPLLLACEKLGLDPEEMLFVGDS-RND 178

                         90
                 ....*....|....*.
gi 320541751  76 IKGGHLAQ---LGLTF 88
Cdd:PRK13222 179 IQAARAAGcpsVGVTY 194

noncanonical pyrimidine nucleotidase, YjjG family; This HAD superfamily includes including YjjG from E. coli and YfnB from B. subtilis. YjjG has been shown to act as a house-cleaning enzyme, cleaving nucleotides with non-canonical nucleotide bases. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541751    3 QAGYALALITNGPSNAQWEKVAELNVRGYFDCVLVSSDLPWEKPHPEIF-YAACNFLNVKPQECVMIGDKLETDIKGGHL 81
Cdd:TIGR02254 110 QQKFRLYIVTNGVRETQYKRLRKSGLFPFFDDIFVSEDAGIQKPDKEIFnYALERMPKFSKEEVLMIGDSLTADIKGGQN 189

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 320541751   82 AQLGLTFWTPLSNSSAAaqsledvEYKPHVKLGSLLEMYKYF 123
Cdd:TIGR02254 190 AGLDTCWMNPDMHPNPD-------DIIPTYEIRSLEELYEIL 224

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 320541751    2 RQAGYALALITNGPSNAQWEKVAELNVRGYFDCVLVSSDLPwEKPHPEIFYAACNFLNVKPqECVMIGDKLEtDIKGGHL 81
Cdd:TIGR01549  86 KSAGIKLGIISNGSLRAQKLLLRLFGLGDYFELILVSDEPG-SKPEPEIFLAALESLGVPP-EVLHVGDNLN-DIEGARN 162

                  ..
gi 320541751   82 AQ 83
Cdd:TIGR01549 163 AG 164

Ribonucleotide monophosphatase NagD, HAD superfamily [Nucleotide transport and metabolism];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 320541751  45 KPHPEIFYAACNFLNVKPQECVMIGDKLETDIKGGHlaQLGLTFWTPLSNSSAAAQsLEDVEYKPHVKLGSLLEMY 120
Cdd:COG0647  186 KPSPPIYELALERLGVDPERVLMVGDRLDTDILGAN--AAGLDTLLVLTGVTTAED-LEAAPIRPDYVLDSLAELL 258

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 320541751   2 RQAGYALALITNGPSNAQWEKVAELNV-RGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGDKL 72
Cdd:cd07505   54 KAAGIPVAVATSSSRRNVELLLLELGLlRGYFDVIVSGDDVERGKPAPDIYLLAAERLGVDPERCLVFEDSL 125

hexitol phosphatase HxpB;

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541751   2 RQAGYALALITNGPSNAQwEKVAE-LNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGD 70
Cdd:PRK10826 105 KAQGLKIGLASASPLHML-EAVLTmFDLRDYFDALASAEKLPYSKPHPEVYLNCAAKLGVDPLTCVALED 173

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 320541751   1 MRQAGYALALITNgpsnaqweKVAELNVRG--------YFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGDKl 72
Cdd:cd02616   92 LKSQGIKLGVVTT--------KLRETALKGlkllgldkYFDVIVGGDDVTHHKPDPEPVLKALELLGAEPEEALMVGDS- 162

                         90
                 ....*....|
gi 320541751  73 ETDIKGGHLA 82
Cdd:cd02616  163 PHDILAGKNA 172

L-2-haloacid dehalogenase; L-2-Haloacid dehalogenase catalyzes the hydrolytic dehalogenation of L-2-haloacids to produce the corresponding D-2-hydroxyacids with an inversion of the C2-configuration. 2-haloacid dehalogenases are of interest for their potential to degrade recalcitrant halogenated environmental pollutants and their use in the synthesis of industrial chemicals. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 320541751   2 RQAGYALALITNGpSNAQWEKVAE-LNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMI 68
Cdd:cd02588  104 REAGYRLAILSNG-SPDLIEDVVAnAGLRDLFDAVLSAEDVRAYKPAPAVYELAAERLGVPPDEILHV 170

beta-phosphoglucomutase; This model represents the beta-phosphoglucomutase enzyme which catalyzes the interconverison of beta-D-glucose-1-phosphate and beta-D-glucose-6-phosphate. The 6-phosphate is capable of non-enzymatic anomerization (alpha <-> beta) while the 1-phosphate is not. A separate enzyme is responsible for the isomerization of the alpha anomers. Beta-D-glucose-1-phosphate results from the phosphorylysis of maltose (2.4.1.8), trehalose (2.4.1.64) or trehalose-6-phosphate (2.4.1.216). Alternatively, these reactions can be run in the synthetic direction to create the disaccharides. All sequenced genomes which contain a member of this family also appear to contain at least one putative maltose or trehalose phosphorylase. Three species, Lactococcus, Enterococcus and Neisseria appear to contain a pair of paralogous beta-PGM's. Beta-phosphoglucomutase is a member of the haloacid dehalogenase superfamily of hydrolase enzymes. These enzymes are characterized by a series of three catalytic motifs positioned within an alpha-beta (Rossman) fold. beta-PGM contains an inserted alpha helical domain in between the first and second conserved motifs and thus is a member of subfamily IA of the superfamily. The third catalytic motif comes in three variants, the third of which, containing a conserved DD or ED, is the only one found here as well as in several other related enzymes (TIGR01509). The enzyme from L. lactis has been extensively characterized including a remarkable crystal structure which traps the pentacoordinate transition state. [Energy metabolism, Biosynthesis and degradation of polysaccharides]

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 320541751    1 MRQAGYALALI---TNGPSnaqweKVAELNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGD 70
Cdd:TIGR01990  99 LKKNNIKIALAsasKNAPT-----ILEKLELIDYFDAIVDPAELKKGKPDPEIFLAAAEGLGVSPSECIGIED 166

dUMP phosphatase; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541751   8 LALITNGPSNAQWEKVAELNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECV-MIGDKLETDIKGGHLAqlGL 86
Cdd:PRK09449 113 MGIITNGFTELQQVRLERTGLRDYFDLLVISEQVGVAKPDVAIFDYALEQMGNPDRSRVlMVGDNLHSDILGGINA--GI 190

                         90       100       110
                 ....*....|....*....|....*....|....
gi 320541751  87 -TFWTplsNSSAAAQSlEDVeyKPHVKLGSLLEM 119
Cdd:PRK09449 191 dTCWL---NAHGREQP-EGI--APTYQVSSLSEL 218

haloacid dehalogenase-like hydrolase

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 320541751   8 LALITNGPSNAQWEKVAELNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGDKLETdIKGGHLAQL 84
Cdd:PLN02575 235 MALVSTRPRKTLENAIGSIGIRGFFSVIVAAEDVYRGKPDPEMFIYAAQLLNFIPERCIVFGNSNQT-VEAAHDARM 310

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
                 ....*....|....*....|....*....|....
gi 320541751  45 KPHPEIFYAACNFLNVKPQECVMIGDKLETDIKG 78
Cdd:cd07509  172 KPSPEFFLSALRSLGVDPEEAVMIGDDLRDDVGG 205

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 320541751   1 MRQAGYALALITnGPSNAQWEKVAELN-VRGYFDCVLVSSDLPwEKPHPEIFYAACNFLNVKPQECVMIGD 70
Cdd:cd07533   96 LAAQGVLLAVAT-GKSRRGLDRVLEQHgLGGYFDATRTADDTP-SKPHPEMLREILAELGVDPSRAVMVGD 164

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
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320541751  17 NAqwEKVAE-LNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGD 70
Cdd:cd02598   76 NA--PKILEkLGLAEYFDAIVDGAVLAKGKPDPDIFLAAAEGLGLNPKDCIGVED 128

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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 320541751  45 KPHPEIFYAACNFLNVKPQECVMIGDKLETDIKGGHLAqlGLTFWTPLSNSSAAAQsLEDVEYKPHVKLGSLLE 118
Cdd:cd16422  177 KPNPIILDPVLEKFDYSKEETVMVGDRLYTDIVLGINA--GVDSILVLSGETTRED-LEDLERKPTYVFDNVGE 247

uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily; The haloacid dehalogenase-like (HAD) hydrolases are a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 320541751   4 AGYALALITNGPSNAQWEKVAELNVRGYFDCVLVSSDlpwekPHPEIFYAACNFLNVKPQECVMIGDKLETDI 76
Cdd:cd07515   31 ADYRLVLITKGDLLDQEQKLARSGLSDYFDAVEVVSE-----KDPDTYRRVLSRYGIGPERFVMVGNSLRSDI 98

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 320541751   1 MRQAGYALALITNGPsNAQWEKVAELNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGDKlETDIK 77
Cdd:cd16421   19 LRQKGIKLAVLSNKP-NEAVQVLVEELFPGSFDFVLGEKEGIRRKPDPT*ALECAKVLGVPPDEVLYVGDS-GVDMQ 93

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 320541751    2 RQAGYALALITNGPSNAQWEKVAELNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVM 67
Cdd:TIGR01428 105 KERGYRLAILSNGSPAMLKSLVKHAGLDDPFDAVLSADAVRAYKPAPQVYQLALEALGVPPDEVLF 170

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 320541751    1 MRQAGYALALITNGPSNAQWEKVAELNVRGYFDC--VLVSSDLPW-----EKPHPEIF-YAACNFLNVKPQECVMIGDKL 72
Cdd:TIGR01662  37 LKEAGYKVVIVTNQSGIGRGYFSRSFSGRVARRLeeLGVPIDILYacpgcRKPKPGMFlEALKRFNEIDPEESVYVGDQD 116

                          90
                  ....*....|....*.
gi 320541751   73 ETDIKGGHLAqlGLTF 88
Cdd:TIGR01662 117 LTDLQAAKRV--GLAT 130

uncharacterized family of the haloacid dehalogenase-like superfamily, similar to the uncharacterized Lactococcus lactis YsbA; The specific function of Lactococcus lactis YsbA is unknown. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 320541751  10 LITNGPSNAqWEKVAELNVRGYF-DCVLVSSDLPwEKPHPEifyaACNFL----NVKPQECVMIGDKlETDIKGGHLA 82
Cdd:cd07523   96 LMTHRDHSA-LTILKKDGIASYFtEIVTSDNGFP-RKPNPE----AINYLlnkyQLNPEETVMIGDR-ELDIEAGHNA 166

haloacid dehalogenase-like hydrolase family protein

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 320541751   32 FDCVlVSSDLpWE--KPHPEIFYAACNFLNVKPQECVMIGDKL 72
Cdd:PLN02919  205 FDAI-VSADA-FEnlKPAPDIFLAAAKILGVPTSECVVIEDAL 245

D,D-heptose 1,7-bisphosphate phosphatase; This family of proteins formerly designated yaeD resembles the histidinol phosphatase domain of the bifunctional protein HisB. The member from E. coli has been characterized as D,D-heptose 1,7-bisphosphate phosphatase, GmhB, involved in inner core LPS assembly (). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541751    1 MRQAGYALALITNGP-------SNAQWEKVAE----------LNVRGYFDC-------VLVSSDLPWEKPHPEIFYAACN 56
Cdd:TIGR00213  38 LKKMGYALVLVTNQSgiargyfTEAQFEQLTEwmdwslaerdVDLDGIYYCphhpegvEEFRQVCDCRKPKPGMLLQARK 117

                          90       100
                  ....*....|....*....|....*....
gi 320541751   57 FLNVKPQECVMIGDKLEtDIKGGHLAQLG 85
Cdd:TIGR00213 118 ELHIDMAQSYMVGDKLE-DMQAGVAAKVK 145

phosphoglycolate/pyridoxal phosphate phosphatase family; 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 mammals, PGP is found in many tissues, notably in red blood cells where P-glycolate is and important activator of the hydrolysis of 2,3-bisphosphoglycerate, a major modifier of the oxygen affinity of hemoglobin. Pyridoxal phosphate (PLP, Vitamin B6) phosphatase is involved in the degradation of PLP in mammals and is widely distributed in human tissues including erythrocyes. The enzymes described here are members of the Haloacid dehalogenase superfamily of hydrolase enzymes (pfam00702). Unlike the bacterial PGP equivalog (TIGR01449), which is a member of class (subfamily) I, these enzymes are members of class (subfamily) II. These two families have almost certainly arisen from convergent evolution (although these two ancestors may themselves have diverged from a more distant HAD superfamily progenitor). The primary seed sequence for this model comes from Chlamydomonas reinhardtii, a photosynthetic alga. The enzyme has been purified and characterized and these data are fully consistent with the assignment of function as a PGPase involved in photorespiration. The second seed, from Homo sapiens chromosome 22 has been characterized as a pyridoxal phosphatase. Biochemical characterization of partially purified PGP's from various tissues including red blood cells have been performed while one gene for PGP has been localized to chromosome 16p13.3. The sequence used here maps to chromosome 22. There is indeed a related gene on chromosome 16 (and it is expressed, since EST's are found) which shows 46% identity. The chromosome 16 gene is not in evidence in nraa but translated from the genomic sequence. The third seed, from C. elegans, is only supported by sequence similarity. This model is limited to eukaryotic species including S. pombe and S. cerevisiae, although several archaea score between the trusted and noise cutoffs. This model is closely related to a family of bacterial sequences including the E. coli NagD and B. subtilus AraL genes which are characterized by the ability to hydrolyze para-nitrophenylphosphate (pNPPases or NPPases). The chlamydomonas PGPase d

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 320541751   45 KPHPEIFYAACNFLNVKPQECVMIGDKLETDIKGGH 80
Cdd:TIGR01452 202 KPSPYMFNCITEKFSIDPARTLMVGDRLETDILFGH 237

haloacid dehalogenase-like hydrolase; Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 320541751   8 LALITNGPSNAQWEKVAELNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGD 70
Cdd:PLN03243 128 IAVASTRPRRYLERAIEAVGMEGFFSVVLAAEDVYRGKPDPEMFMYAAERLGFIPERCIVFGN 190

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
                 ....*....|....*....|....*....|....*....
gi 320541751  32 FDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGD 70
Cdd:cd07528  141 FDAIAAGDDVAEKKPDPDIYLLALERLGVSPSDCLAIED 179

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 320541751   1 MRQAGYALALITNGPSNAQWEKVAELNVRGYFDCVLVS-SDLPWEKPHPEIFYAACNFLNVKPQECVMIGDKLeTDIKGG 79
Cdd:cd07526   51 LSALTLPFCVASNSSRERLTHSLGLAGLLAYFEGRIFSaSDVGRGKPAPDLFLHAAAQMGVAPERCLVIEDSP-TGVRAA 129

                         90
                 ....*....|
gi 320541751  80 HLAqlGLTFW 89
Cdd:cd07526  130 LAA--GMTVF 137

phosphoglycolate phosphatase; Provisional

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541751   1 MRQAGYALALITNGPSNAQWEKVAELNVRGYFDCVLVSSDLPWEKPHPEIFYAACNFLNVKPQECVMIGD 70
Cdd:PRK13223 113 LKKQGVEMALITNKPERFVAPLLDQMKIGRYFRWIIGGDTLPQKKPDPAALLFVMKMAGVPPSQSLFVGD 182

fructose-1-phosphate/6-phosphogluconate phosphatase;