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Conserved domains on  [gi|517055723|ref|WP_018244541|]
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pyrimidine 5'-nucleotidase [Rhizobium leguminosarum]

Protein Classification

HAD family hydrolase( domain architecture ID 229399)

HAD (haloacid dehalogenase) family hydrolase; the HAD family includes phosphoesterases, ATPases, phosphonatases, dehalogenases, and sugar phosphomutases acting on a remarkably diverse set of substrates

EC:  3.6.3.-
Gene Ontology:  GO:0005524|GO:0016887|GO:0005215

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HAD_like super family cl21460
Haloacid Dehalogenase-like Hydrolases; The haloacid dehalogenase (HAD) superfamily includes ...
 17-196 4.90e-89

Haloacid Dehalogenase-like Hydrolases; The haloacid dehalogenase (HAD) superfamily includes carbon and phosphorus hydrolases such as 2-haloalkonoate dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, among others. These proteins catalyze nucleophilic substitution reactions at phosphorus or carbon centers, using a conserved Asp carboxylate in covalent catalysis. All members possess a conserve alpha/beta core domain, and many also possess a small cap domain, with varying folds and functions.


The actual alignment was detected with superfamily member TIGR01993:

Pssm-ID: 473868 [Multi-domain]  Cd Length: 183  Bit Score: 260.75  E-value: 4.90e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   17 TDWVFDLDNTLYPHHVNLFAQIDKNMTAYVAALLQMEREEARKLQKQYYLDHGTTLQGLMIHHGIDPNDFLEKAHA-IDY 95
Cdd:TIGR01993   1 DVWFFDLDNTLYPHSAGIFLQIDRNITEFVAARLKLSPEEARVLRKDYYKEYGTTLAGLMILHEIDADEYLRYVHGrLPY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   96 TALTPQPELGEAIKALPGRKFIFTNGSVKHAEMTAEALGILDHFDDIFDIVAA--DYVPKPAQATYDKFTALKRVETTKA 173
Cdd:TIGR01993  81 DKLKPDPELRNLLLRLPGRKIIFTNGDRAHARRALRRLGIEDCFDGIFCFDTAnpDLLPKPSPQAYEKALREAGVDPERA 160

                         170       180
                  ....*....|....*....|...
gi 517055723  174 AMFEDLPRNLTVPKALGMQTVLL 196
Cdd:TIGR01993 161 IFFDDSARNIAAGKALGMKTVLV 183
 
Name Accession Description Interval E-value
Pyr-5-nucltdase TIGR01993
pyrimidine 5'-nucleotidase; This family of proteins includes the SDT1/SSM1 gene from yeast ...
 17-196 4.90e-89

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).


Pssm-ID: 273917 [Multi-domain]  Cd Length: 183  Bit Score: 260.75  E-value: 4.90e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   17 TDWVFDLDNTLYPHHVNLFAQIDKNMTAYVAALLQMEREEARKLQKQYYLDHGTTLQGLMIHHGIDPNDFLEKAHA-IDY 95
Cdd:TIGR01993   1 DVWFFDLDNTLYPHSAGIFLQIDRNITEFVAARLKLSPEEARVLRKDYYKEYGTTLAGLMILHEIDADEYLRYVHGrLPY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   96 TALTPQPELGEAIKALPGRKFIFTNGSVKHAEMTAEALGILDHFDDIFDIVAA--DYVPKPAQATYDKFTALKRVETTKA 173
Cdd:TIGR01993  81 DKLKPDPELRNLLLRLPGRKIIFTNGDRAHARRALRRLGIEDCFDGIFCFDTAnpDLLPKPSPQAYEKALREAGVDPERA 160

                         170       180
                  ....*....|....*....|...
gi 517055723  174 AMFEDLPRNLTVPKALGMQTVLL 196
Cdd:TIGR01993 161 IFFDDSARNIAAGKALGMKTVLV 183
HAD_5NT cd02604
haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to Saccharomyces cerevisiae Phm8p ...
 19-198 1.36e-81

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.


Pssm-ID: 319791 [Multi-domain]  Cd Length: 182  Bit Score: 241.77  E-value: 1.36e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  19 WVFDLDNTLYPHHVNLFAQIDKNMTAYVAALLQMEREEARKLQKQYYLDHGTTLQGLMIHHGIDPNDFLEK-AHAIDYTA 97
Cdd:cd02604    2 WFFDLDNTLYPLSTGLFDQIQARITEFVATKLGLSPEEARRLRKSYYKEYGTTLRGLMAEHGIDPDEFLDRvVHLILYDH 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  98 LTPQPELGEAIKALPGRKFIFTNGSVKHAEMTAEALGILDHFDDIFDIVAADYVPKPAQATYDKFTALKRVETTKAAMFE 177
Cdd:cd02604   82 LKPDPKLRNLLLALPGRKIIFTNASKNHAIRVLKRLGLADLFDGIFDIEYAGPDPKPHPAAFEKAIREAGLDPKRAAFFD 161

                        170       180
                 ....*....|....*....|.
gi 517055723 178 DLPRNLTVPKALGMQTVLLVP 198
Cdd:cd02604  162 DSIRNLLAAKALGMKTVLVGP 182
YigB COG1011
FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily ...
 19-231 8.06e-27

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


Pssm-ID: 440635 [Multi-domain]  Cd Length: 220  Bit Score: 102.80  E-value: 8.06e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  19 WVFDLDNTLYPHHVNLFAQIDKnMTAYVAALLQME------REEARKLQKQY---YLDHGTTLQGLMIHHGIDPNDFLEK 89
Cdd:COG1011    4 VLFDLDGTLLDFDPVIAEALRA-LAERLGLLDEAEelaeayRAIEYALWRRYergEITFAELLRRLLEELGLDLAEELAE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  90 AHAIDY-TALTPQPELGEAIKALPG---RKFIFTNGSVKHAEMTAEALGILDHFDDIFDIVAADYvPKPAQATYDKFTAL 165
Cdd:COG1011   83 AFLAALpELVEPYPDALELLEALKArgyRLALLTNGSAELQEAKLRRLGLDDLFDAVVSSEEVGV-RKPDPEIFELALER 161

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 517055723 166 KRVETTKAAMFEDLPR-NLTVPKALGMQTVLLVPRNleetvvewweKTSGEEDHIDFVTDDLAAFLR 231
Cdd:COG1011  162 LGVPPEEALFVGDSPEtDVAGARAAGMRTVWVNRSG----------EPAPAEPRPDYVISDLAELLE 218
Hydrolase pfam00702
haloacid dehalogenase-like hydrolase; This family is structurally different from the alpha ...
 20-190 3.35e-08

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.


Pssm-ID: 459910 [Multi-domain]  Cd Length: 191  Bit Score: 51.82  E-value: 3.35e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   20 VFDLDNTLYPHHVNLFAQIDKNMTAYVAALLQMEREEARKLQKQYY------------LDHGTTLQGLMIHHGIDPNDFL 87
Cdd:pfam00702   5 VFDLDGTLTDGEPVVTEAIAELASEHPLAKAIVAAAEDLPIPVEDFtarlllgkrdwlEELDILRGLVETLEAEGLTVVL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   88 EKAHAI--DYTALTPQPELGEAIKALPGRK---FIFTNGSVKHAEMTAEALGILDHFDDIFDiVAADYVPKPAQATYDKF 162
Cdd:pfam00702  85 VELLGViaLADELKLYPGAAEALKALKERGikvAILTGDNPEAAEALLRLLGLDDYFDVVIS-GDDVGVGKPKPEIYLAA 163

                         170       180
                  ....*....|....*....|....*...
gi 517055723  163 TALKRVETTKAAMFEDLPRNLTVPKALG 190
Cdd:pfam00702 164 LERLGVKPEEVLMVGDGVNDIPAAKAAG 191
PRK10725 PRK10725
fructose-1-phosphate/6-phosphogluconate phosphatase;
100-194 5.10e-03

fructose-1-phosphate/6-phosphogluconate phosphatase;


Pssm-ID: 182679 [Multi-domain]  Cd Length: 188  Bit Score: 36.98  E-value: 5.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723 100 PQPeLGEAIKALPGRKFIFTNGSVKHAemTAEAL----GILDHFDDIfdiVAADYVP--KPAQATYDKFTALKRVETTKA 173
Cdd:PRK10725  89 PLP-LIEVVKAWHGRRPMAVGTGSESA--IAEALlahlGLRRYFDAV---VAADDVQhhKPAPDTFLRCAQLMGVQPTQC 162

                         90       100
                 ....*....|....*....|.
gi 517055723 174 AMFEDLPRNLTVPKALGMQTV 194
Cdd:PRK10725 163 VVFEDADFGIQAARAAGMDAV 183
 
Name Accession Description Interval E-value
Pyr-5-nucltdase TIGR01993
pyrimidine 5'-nucleotidase; This family of proteins includes the SDT1/SSM1 gene from yeast ...
 17-196 4.90e-89

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).


Pssm-ID: 273917 [Multi-domain]  Cd Length: 183  Bit Score: 260.75  E-value: 4.90e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   17 TDWVFDLDNTLYPHHVNLFAQIDKNMTAYVAALLQMEREEARKLQKQYYLDHGTTLQGLMIHHGIDPNDFLEKAHA-IDY 95
Cdd:TIGR01993   1 DVWFFDLDNTLYPHSAGIFLQIDRNITEFVAARLKLSPEEARVLRKDYYKEYGTTLAGLMILHEIDADEYLRYVHGrLPY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   96 TALTPQPELGEAIKALPGRKFIFTNGSVKHAEMTAEALGILDHFDDIFDIVAA--DYVPKPAQATYDKFTALKRVETTKA 173
Cdd:TIGR01993  81 DKLKPDPELRNLLLRLPGRKIIFTNGDRAHARRALRRLGIEDCFDGIFCFDTAnpDLLPKPSPQAYEKALREAGVDPERA 160

                         170       180
                  ....*....|....*....|...
gi 517055723  174 AMFEDLPRNLTVPKALGMQTVLL 196
Cdd:TIGR01993 161 IFFDDSARNIAAGKALGMKTVLV 183
HAD_5NT cd02604
haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to Saccharomyces cerevisiae Phm8p ...
 19-198 1.36e-81

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.


Pssm-ID: 319791 [Multi-domain]  Cd Length: 182  Bit Score: 241.77  E-value: 1.36e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  19 WVFDLDNTLYPHHVNLFAQIDKNMTAYVAALLQMEREEARKLQKQYYLDHGTTLQGLMIHHGIDPNDFLEK-AHAIDYTA 97
Cdd:cd02604    2 WFFDLDNTLYPLSTGLFDQIQARITEFVATKLGLSPEEARRLRKSYYKEYGTTLRGLMAEHGIDPDEFLDRvVHLILYDH 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  98 LTPQPELGEAIKALPGRKFIFTNGSVKHAEMTAEALGILDHFDDIFDIVAADYVPKPAQATYDKFTALKRVETTKAAMFE 177
Cdd:cd02604   82 LKPDPKLRNLLLALPGRKIIFTNASKNHAIRVLKRLGLADLFDGIFDIEYAGPDPKPHPAAFEKAIREAGLDPKRAAFFD 161

                        170       180
                 ....*....|....*....|.
gi 517055723 178 DLPRNLTVPKALGMQTVLLVP 198
Cdd:cd02604  162 DSIRNLLAAKALGMKTVLVGP 182
YigB COG1011
FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily ...
 19-231 8.06e-27

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


Pssm-ID: 440635 [Multi-domain]  Cd Length: 220  Bit Score: 102.80  E-value: 8.06e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  19 WVFDLDNTLYPHHVNLFAQIDKnMTAYVAALLQME------REEARKLQKQY---YLDHGTTLQGLMIHHGIDPNDFLEK 89
Cdd:COG1011    4 VLFDLDGTLLDFDPVIAEALRA-LAERLGLLDEAEelaeayRAIEYALWRRYergEITFAELLRRLLEELGLDLAEELAE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  90 AHAIDY-TALTPQPELGEAIKALPG---RKFIFTNGSVKHAEMTAEALGILDHFDDIFDIVAADYvPKPAQATYDKFTAL 165
Cdd:COG1011   83 AFLAALpELVEPYPDALELLEALKArgyRLALLTNGSAELQEAKLRRLGLDDLFDAVVSSEEVGV-RKPDPEIFELALER 161

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 517055723 166 KRVETTKAAMFEDLPR-NLTVPKALGMQTVLLVPRNleetvvewweKTSGEEDHIDFVTDDLAAFLR 231
Cdd:COG1011  162 LGVPPEEALFVGDSPEtDVAGARAAGMRTVWVNRSG----------EPAPAEPRPDYVISDLAELLE 218
HAD-SF-IA-v3 TIGR01509
haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; ...
 19-196 1.37e-15

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]


Pssm-ID: 273662 [Multi-domain]  Cd Length: 178  Bit Score: 72.07  E-value: 1.37e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   19 WVFDLDNTLYPHHVNLFAQIDKNMTAYVAALLQMEREEARKLQKQYY-LDHGTTLQGlMIHHGIDPNDFLEkaHAIDYTA 97
Cdd:TIGR01509   2 ILFDLDGVLVDTEFAIAKLINREELGLVPDELGVSAVGRLELALRRFkAQYGRTISP-EDAQLLYKQLFYE--QIEEEAK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   98 LTPQPELGEAIKALPGRKF---IFTNgSVKHAEMTAEALGILDHFDDIfdIVAADYV-PKPAQATYDKFTALKRVETTKA 173
Cdd:TIGR01509  79 LKPLPGVRALLEALRARGKklaLLTN-SPRAHKLVLALLGLRDLFDVV--IDSSDVGlGKPDPDIYLQALKALGLEPSEC 155

                         170       180
                  ....*....|....*....|...
gi 517055723  174 AMFEDLPRNLTVPKALGMQTVLL 196
Cdd:TIGR01509 156 VFVDDSPAGIEAAKAAGMHTVGV 178
Hydrolase pfam00702
haloacid dehalogenase-like hydrolase; This family is structurally different from the alpha ...
 20-190 3.35e-08

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.


Pssm-ID: 459910 [Multi-domain]  Cd Length: 191  Bit Score: 51.82  E-value: 3.35e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   20 VFDLDNTLYPHHVNLFAQIDKNMTAYVAALLQMEREEARKLQKQYY------------LDHGTTLQGLMIHHGIDPNDFL 87
Cdd:pfam00702   5 VFDLDGTLTDGEPVVTEAIAELASEHPLAKAIVAAAEDLPIPVEDFtarlllgkrdwlEELDILRGLVETLEAEGLTVVL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   88 EKAHAI--DYTALTPQPELGEAIKALPGRK---FIFTNGSVKHAEMTAEALGILDHFDDIFDiVAADYVPKPAQATYDKF 162
Cdd:pfam00702  85 VELLGViaLADELKLYPGAAEALKALKERGikvAILTGDNPEAAEALLRLLGLDDYFDVVIS-GDDVGVGKPKPEIYLAA 163

                         170       180
                  ....*....|....*....|....*...
gi 517055723  163 TALKRVETTKAAMFEDLPRNLTVPKALG 190
Cdd:pfam00702 164 LERLGVKPEEVLMVGDGVNDIPAAKAAG 191
YcjU COG0637
Beta-phosphoglucomutase, HAD superfamily [Carbohydrate transport and metabolism];
20-194 2.61e-05

Beta-phosphoglucomutase, HAD superfamily [Carbohydrate transport and metabolism];


Pssm-ID: 440402 [Multi-domain]  Cd Length: 208  Bit Score: 43.66  E-value: 2.61e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  20 VFDLDNTLyphhvnlfaqIDkNMTAYVAALLQMEREEARKLQKQYYLD-HG----TTLQGLMIHHGID--PNDFLEKAHA 92
Cdd:COG0637    6 IFDMDGTL----------VD-SEPLHARAWREAFAELGIDLTEEEYRRlMGrsreDILRYLLEEYGLDlpEEELAARKEE 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  93 -----IDYTALTPQPELGEAIKALPGRKF---IFTNGSVKHAEMTAEALGILDHFDdifDIVAADYVP--KPAQATYdkF 162
Cdd:COG0637   75 lyrelLAEEGLPLIPGVVELLEALKEAGIkiaVATSSPRENAEAVLEAAGLLDYFD---VIVTGDDVArgKPDPDIY--L 149

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 517055723 163 TALKR--VETTKAAMFEDlprnlTVP-----KALGMQTV 194
Cdd:COG0637  150 LAAERlgVDPEECVVFED-----SPAgiraaKAAGMRVV 183
CTE7 TIGR02253
HAD superfamily (subfamily IA) hydrolase, TIGR02253; This family of sequences from archaea and ...
 21-196 7.84e-05

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).


Pssm-ID: 274057 [Multi-domain]  Cd Length: 221  Bit Score: 42.39  E-value: 7.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   21 FDLDNTLYPHH-VNLFA--QIDKNMTAYVaalLQMEREEAR----KLQKQYYLDHGTTLQGLMIHHGIDPN-----DFLE 88
Cdd:TIGR02253   7 FDLDDTLIDTSgLAEKArrNAIEVLIEAG---LNVDFEEAYeellKLIKEYGSNYPTHFDYLIRRLWEEYNpklvaAFVY 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   89 KAHAIDYTALTPQPELGEAIKALPGRKF---IFTNGSVKHAEMTAEALGILDHFDDIfdIVAADY-VPKPAQATYDKftA 164
Cdd:TIGR02253  84 AYHKLKFAYLRVYPGVRDTLMELRESGYrlgIITDGLPVKQWEKLERLGVRDFFDAV--ITSEEEgVEKPHPKIFYA--A 159

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 517055723  165 LKR--VETTKAAMFED-LPRNLTVPKALGMQTVLL 196
Cdd:TIGR02253 160 LKRlgVKPEEAVMVGDrLDKDIKGAKNAGMKTVWI 194
Gph COG0546
Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion];
19-195 1.43e-04

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


Pssm-ID: 440312 [Multi-domain]  Cd Length: 214  Bit Score: 41.45  E-value: 1.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  19 WVFDLDNTLyphhVNLFAQIDKnmtAYVAALLQM-----EREEARKLqkqyyldHGTTLQGLMIHH-GIDPND------- 85
Cdd:COG0546    4 VLFDLDGTL----VDSAPDIAA---ALNEALAELglpplDLEELRAL-------IGLGLRELLRRLlGEDPDEeleella 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  86 -FLEKAHAIDYTALTPQPELGEAIKALPGRKF---IFTNGSVKHAEMTAEALGILDHFDdifDIVAADYVP--KPAQATY 159
Cdd:COG0546   70 rFRELYEEELLDETRLFPGVRELLEALKARGIklaVVTNKPREFAERLLEALGLDDYFD---AIVGGDDVPpaKPKPEPL 146

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 517055723 160 DKFTALKRVETTKAAMFEDLPRNLTVPKALGMQTVL 195
Cdd:COG0546  147 LEALERLGLDPEEVLMVGDSPHDIEAARAAGVPFIG 182
HAD_BPGM_like cd07526
subfamily of beta-phosphoglucomutase-like family, similar to Escherichia coli ...
 96-198 1.01e-03

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.


Pssm-ID: 319828 [Multi-domain]  Cd Length: 141  Bit Score: 38.45  E-value: 1.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  96 TALTPQPELGEAIKALPGRKFIFTNGSVKHAEMTAEALGILDHFDD-IFDivaADYV--PKPAQATYDKFTALKRVETTK 172
Cdd:cd07526   39 AELQPIPGAAAALSALTLPFCVASNSSRERLTHSLGLAGLLAYFEGrIFS---ASDVgrGKPAPDLFLHAAAQMGVAPER 115

                         90       100
                 ....*....|....*....|....*.
gi 517055723 173 AAMFEDLPRNLTVPKALGMQTVLLVP 198
Cdd:cd07526  116 CLVIEDSPTGVRAALAAGMTVFGFTG 141
HAD_L2-DEX cd02588
L-2-haloacid dehalogenase; L-2-Haloacid dehalogenase catalyzes the hydrolytic dehalogenation ...
 20-164 1.61e-03

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.


Pssm-ID: 319787 [Multi-domain]  Cd Length: 216  Bit Score: 38.40  E-value: 1.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  20 VFDLDNTLYPHHvNLFAQIDKNMTAYVAALLQMEREEA-----RKLQKQYYLD----HGTTLQGLMIHHGIDPnDFLEKA 90
Cdd:cd02588    4 VFDVYGTLIDWH-SGLAAAERAFPGRGEELSRLWRQKQleytwLVTLMGPYVDfdelTRDALRATAAELGLEL-DESDLD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  91 HAID-YTALTPQPELGEAIKALPGRKF---IFTNGSVKHAEMTAEALGILDHFDDIF--DIVAAdYvpKPAQATYDKFTA 164
Cdd:cd02588   82 ELGDaYLRLPPFPDVVAGLRRLREAGYrlaILSNGSPDLIEDVVANAGLRDLFDAVLsaEDVRA-Y--KPAPAVYELAAE 158
HAD_2 pfam13419
Haloacid dehalogenase-like hydrolase;
20-194 3.83e-03

Haloacid dehalogenase-like hydrolase;


Pssm-ID: 404323 [Multi-domain]  Cd Length: 178  Bit Score: 37.18  E-value: 3.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   20 VFDLDNTLY---PHHVNLFAQIDKNMTAYvaallQMEREEARKLQkqyyldhGTTLQGLMIHHGI------DPNDFLEKA 90
Cdd:pfam13419   2 IFDFDGTLLdteELIIKSFNYLLEEFGYG-----ELSEEEILKFI-------GLPLREIFRYLGVsedeeeKIEFYLRKY 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723   91 HAIDYTA-LTPQPELGEAIKALPGRKF---IFTNGSVKHAEMTAEALGILDHFDdifDIVAADYV--PKPAQATYDKftA 164
Cdd:pfam13419  70 NEELHDKlVKPYPGIKELLEELKEQGYklgIVTSKSRENVEEFLKQLGLEDYFD---VIVGGDDVegKKPDPDPILK--A 144

                         170       180       190
                  ....*....|....*....|....*....|..
gi 517055723  165 LKRVETTK--AAMFEDLPRNLTVPKALGMQTV 194
Cdd:pfam13419 145 LEQLGLKPeeVIYVGDSPRDIEAAKNAGIKVI 176
PRK10725 PRK10725
fructose-1-phosphate/6-phosphogluconate phosphatase;
100-194 5.10e-03

fructose-1-phosphate/6-phosphogluconate phosphatase;


Pssm-ID: 182679 [Multi-domain]  Cd Length: 188  Bit Score: 36.98  E-value: 5.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723 100 PQPeLGEAIKALPGRKFIFTNGSVKHAemTAEAL----GILDHFDDIfdiVAADYVP--KPAQATYDKFTALKRVETTKA 173
Cdd:PRK10725  89 PLP-LIEVVKAWHGRRPMAVGTGSESA--IAEALlahlGLRRYFDAV---VAADDVQhhKPAPDTFLRCAQLMGVQPTQC 162

                         90       100
                 ....*....|....*....|.
gi 517055723 174 AMFEDLPRNLTVPKALGMQTV 194
Cdd:PRK10725 163 VVFEDADFGIQAARAAGMDAV 183
HAD_like cd01427
Haloacid dehalogenase-like hydrolases; The haloacid dehalogenase-like (HAD) superfamily ...
 93-196 5.18e-03

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.


Pssm-ID: 319763 [Multi-domain]  Cd Length: 106  Bit Score: 35.45  E-value: 5.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517055723  93 IDYTALTPqpelgEAIKALPGRKF---IFTNGSVKHAEMTAEALGILDHFDDIFdIVAADYVPKPAQATYDKFTALKRVE 169
Cdd:cd01427    6 LDGTLLAV-----ELLKRLRAAGIklaIVTNRSREALRALLEKLGLGDLFDGII-GSDGGGTPKPKPKPLLLLLLKLGVD 79

                         90       100
                 ....*....|....*....|....*..
gi 517055723 170 TTKAAMFEDLPRNLTVPKALGMQTVLL 196
Cdd:cd01427   80 PEEVLFVGDSENDIEAARAAGGRTVAV 106
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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