pyrimidine 5'-nucleotidase; This family of proteins includes the SDT1/SSM1 gene from yeast which has been shown to code for a pyrimidine (UMP/CMP) 5'nucleotidase. The family spans plants, fungi and a small number of bacteria. These enzymes are members of the haloacid dehalogenase (HAD) superfamily of hydrolases, specifically the IA subfamily (variant 3, TIGR01509).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656309   12 WVFDLDNTLYPPSARLFDQIERRMTDWVMTELRVVREEADRLRRHYWSTYGTTLAGLMAEHGVDPAPYLSHVHD-ISLDH 90
Cdd:TIGR01993   3 WFFDLDNTLYPHSAGIFLQIDRNITEFVAARLKLSPEEARVLRKDYYKEYGTTLAGLMILHEIDADEYLRYVHGrLPYDK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656309   91 LERDMILAARIRALPGRKIVYTNGCAPYAERVLEARGLANLFDAVYGVEHAGF--RPKPDRAAFETVFAADRLAPGTAAM 168
Cdd:TIGR01993  83 LKPDPELRNLLLRLPGRKIIFTNGDRAHARRALRRLGIEDCFDGIFCFDTANPdlLPKPSPQAYEKALREAGVDPERAIF 162

                         170       180
                  ....*....|....*....|.
gi 499656309  169 FEDDSRNLLAPHEMGMRTVHV 189
Cdd:TIGR01993 163 FDDSARNIAAGKALGMKTVLV 183

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 499656309   13 VFDLDNTLYPPSARLFDQIERRMTDWVMTE-LRVVREEADRLRRHYWSTYGTTLAGLMAEHG---VDPAPYLSHVHDISL 88
Cdd:pfam00702   5 VFDLDGTLTDGEPVVTEAIAELASEHPLAKaIVAAAEDLPIPVEDFTARLLLGKRDWLEELDilrGLVETLEAEGLTVVL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656309   89 DHLERDMILAARIRALPG-------------RKIVYTNGCAPYAERVLEARGLANLFDAVYGVEHAGFrPKPDRAAFEtv 155
Cdd:pfam00702  85 VELLGVIALADELKLYPGaaealkalkergiKVAILTGDNPEAAEALLRLLGLDDYFDVVISGDDVGV-GKPKPEIYL-- 161

                         170       180       190
                  ....*....|....*....|....*....|
gi 499656309  156 FAADRL--APGTAAMFEDDSRNLLAPHEMG 183
Cdd:pfam00702 162 AALERLgvKPEEVLMVGDGVNDIPAAKAAG 191

pyrimidine 5'-nucleotidase; This family of proteins includes the SDT1/SSM1 gene from yeast which has been shown to code for a pyrimidine (UMP/CMP) 5'nucleotidase. The family spans plants, fungi and a small number of bacteria. These enzymes are members of the haloacid dehalogenase (HAD) superfamily of hydrolases, specifically the IA subfamily (variant 3, TIGR01509).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656309   12 WVFDLDNTLYPPSARLFDQIERRMTDWVMTELRVVREEADRLRRHYWSTYGTTLAGLMAEHGVDPAPYLSHVHD-ISLDH 90
Cdd:TIGR01993   3 WFFDLDNTLYPHSAGIFLQIDRNITEFVAARLKLSPEEARVLRKDYYKEYGTTLAGLMILHEIDADEYLRYVHGrLPYDK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656309   91 LERDMILAARIRALPGRKIVYTNGCAPYAERVLEARGLANLFDAVYGVEHAGF--RPKPDRAAFETVFAADRLAPGTAAM 168
Cdd:TIGR01993  83 LKPDPELRNLLLRLPGRKIIFTNGDRAHARRALRRLGIEDCFDGIFCFDTANPdlLPKPSPQAYEKALREAGVDPERAIF 162

                         170       180
                  ....*....|....*....|.
gi 499656309  169 FEDDSRNLLAPHEMGMRTVHV 189
Cdd:TIGR01993 163 FDDSARNIAAGKALGMKTVLV 183

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 499656309   12 WVFDLDNTLYPPSARLFDQIERRMTDWVMTELRVVREEADRLRRHYWST-YGTTLAGlMAEHGVDPAPYLSHVHDISLDH 90
Cdd:TIGR01509   2 ILFDLDGVLVDTEFAIAKLINREELGLVPDELGVSAVGRLELALRRFKAqYGRTISP-EDAQLLYKQLFYEQIEEEAKLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656309   91 LERDMI-LAARIRALPGRKIVYTNGcAPYAERVLEARGLANLFDAVYGVEHAGfRPKPDRAAFETVFAADRLAPGTAAMF 169
Cdd:TIGR01509  81 PLPGVRaLLEALRARGKKLALLTNS-PRAHKLVLALLGLRDLFDVVIDSSDVG-LGKPDPDIYLQALKALGLEPSECVFV 158

                         170       180
                  ....*....|....*....|
gi 499656309  170 EDDSRNLLAPHEMGMRTVHV 189
Cdd:TIGR01509 159 DDSPAGIEAAKAAGMHTVGV 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 499656309   13 VFDLDNTLYPPSARLFDQIERRMTDWVMTE-LRVVREEADRLRRHYWSTYGTTLAGLMAEHG---VDPAPYLSHVHDISL 88
Cdd:pfam00702   5 VFDLDGTLTDGEPVVTEAIAELASEHPLAKaIVAAAEDLPIPVEDFTARLLLGKRDWLEELDilrGLVETLEAEGLTVVL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656309   89 DHLERDMILAARIRALPG-------------RKIVYTNGCAPYAERVLEARGLANLFDAVYGVEHAGFrPKPDRAAFEtv 155
Cdd:pfam00702  85 VELLGVIALADELKLYPGaaealkalkergiKVAILTGDNPEAAEALLRLLGLDDYFDVVISGDDVGV-GKPKPEIYL-- 161

                         170       180       190
                  ....*....|....*....|....*....|
gi 499656309  156 FAADRL--APGTAAMFEDDSRNLLAPHEMG 183
Cdd:pfam00702 162 AALERLgvKPEEVLMVGDGVNDIPAAKAAG 191

HAD superfamily (subfamily IA) hydrolase, TIGR02253; This family of sequences from archaea and metazoans includes the human uncharacterized protein CTE7. Pyrococcus species appear to have three different forms of this enzyme, so it is unclear whether all members of this family have the same function. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656309    9 VRGWVFDLDNTLYPPSArlFDQIERRMTDWVMTE--LRVVREEA-------------------DRLRRHYWSTYGTTL-- 65
Cdd:TIGR02253   2 IKAIFFDLDDTLIDTSG--LAEKARRNAIEVLIEagLNVDFEEAyeellklikeygsnypthfDYLIRRLWEEYNPKLva 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656309   66 AGLMAEHGVdPAPYLSHVHDIsldhleRDMILaaRIRALPGRKIVYTNGCAPYAERVLEARGLANLFDAVYGVEHAGFRp 145
Cdd:TIGR02253  80 AFVYAYHKL-KFAYLRVYPGV------RDTLM--ELRESGYRLGIITDGLPVKQWEKLERLGVRDFFDAVITSEEEGVE- 149

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 499656309  146 KPDRAAFEtvFAADRLA--PGTAAMFEDD-SRNLLAPHEMGMRTV 187
Cdd:TIGR02253 150 KPHPKIFY--AALKRLGvkPEEAVMVGDRlDKDIKGAKNAGMKTV 192

N-terminal lipase phosphatase domain of human soluble epoxide hydrolase, Escherichia coli YihX/HAD4 alpha-D-glucose 1-phosphate phosphatase, and related domains, may be inactive; This family includes the N-terminal phosphatase domain of human soluble epoxide hydrolase (sEH). sEH is a bifunctional enzyme with two distinct enzyme activities, the C-terminal domain has epoxide hydrolysis activity and the N-terminal domain (Ntermphos), which belongs to this family, has lipid phosphatase activity. The latter prefers mono-phosphate esters, and lysophosphatidic acids (LPAs) are the best natural substrates found to date. In addition this family includes Gallus gallus sEH and Xenopus sEH which appears to lack phosphatase activity, and Escherichia coli YihX/HAD4 which selectively hydrolyzes alpha-Glucose-1-P, phosphatase, has significant phosphatase activity against pyridoxal phosphate, and has low beta phosphoglucomutase activity. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656309  13 VFDLDNTL-YPPSARLFDQIERRMTDWVMTELRVVREEADRLRRH-YWSTYGTTLAGLMAEHGVDPAPYLshVHDISLD- 89
Cdd:cd02603    5 LFDFGGVLiDPDPAAAVARFEALTGEPSEFVLDTEGLAGAFLELErGRITEEEFWEELREELGRPLSAEL--FEELVLAa 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656309  90 -HLERDMI-LAARIRALPGRKIVYTNgcAPYAERVLEARGLAN---LFDAVYGVEHAGFRpKPDRAAFETVFAADRLAPG 164
Cdd:cd02603   83 vDPNPEMLdLLEALRAKGYKVYLLSN--TWPDHFKFQLELLPRrgdLFDGVVESCRLGVR-KPDPEIYQLALERLGVKPE 159

                        170       180
                 ....*....|....*....|....*
gi 499656309 165 TAAMFEDDSRNLLAPHEMGMRTVHV 189
Cdd:cd02603  160 EVLFIDDREENVEAARALGIHAILV 184

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 499656309   13 VFDLDNTLYPPSA---RLFDQIERRMTDW-----VMTELRVVREEA---------DRLRRHYWSTYGTTLAglmaeHGVD 75
Cdd:TIGR01549   3 LFDIDGTLVDIKFairRAFPQTFEEFGLDpasfkALKQAGGLAEEEwyriatsalEELQGRFWSEYDAEEA-----YIRG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656309   76 PAPYLshvhdisldhlerdmilaARIRALPGRKIVYTNGCAPYAERVLEARGLANLFDAVYGVEHAGfrPKPDRAAFETv 155
Cdd:TIGR01549  78 AADLL------------------ARLKSAGIKLGIISNGSLRAQKLLLRLFGLGDYFELILVSDEPG--SKPEPEIFLA- 136

                         170
                  ....*....|....
gi 499656309  156 fAADRLAPGTAAMF 169
Cdd:TIGR01549 137 -ALESLGVPPEVLH 149

uncharacterized family of the haloacid dehalogenase-like superfamily, similar to uncharacterized Drosophila melanogaster rhythmically expressed gene 2 protein and human haloacid dehalogenase-like hydrolase domain-containing protein 3; The haloacid dehalogenase-like (HAD) hydrolases are a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499656309 117 PYAERVLEARGLANLFDAVYGVEHAGFrPKPDRAAFETVFAADRLAPGTAAMFEDDSRN-LLAPHEMGMR 185
Cdd:cd16415   34 RRLRELLEALGLDDYFDFVVFSYEVGY-EKPDPRIFQKALERLGVSPEEALHVGDDLKNdYLGARAVGWH 102