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Conserved domains on  [gi|2111842748|gb|KAH0994263|]
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hypothetical protein GBA52_005746 [Prunus armeniaca]

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 ...
 72-168 9.38e-44

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: 144.80  E-value: 9.38e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2111842748  72 DCLIFDLDDTLYPSNTGLGEACKTNIDDFLVEKCGFPESKASSLRVELFKSYGSTLAGLRALgYDIDADDYHSVVHGRLP 151
Cdd:TIGR01993   1 DVWFFDLDNTLYPHSAGIFLQIDRNITEFVAARLKLSPEEARVLRKDYYKEYGTTLAGLMIL-HEIDADEYLRYVHGRLP 79

                          90
                  ....*....|....*..
gi 2111842748 152 YDRIKPDPQLRNLLRSI 168
Cdd:TIGR01993  80 YDKLKPDPELRNLLLRL 96
 
Name Accession Description Interval E-value
Pyr-5-nucltdase TIGR01993
pyrimidine 5'-nucleotidase; This family of proteins includes the SDT1/SSM1 gene from yeast ...
 72-168 9.38e-44

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: 144.80  E-value: 9.38e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2111842748  72 DCLIFDLDDTLYPSNTGLGEACKTNIDDFLVEKCGFPESKASSLRVELFKSYGSTLAGLRALgYDIDADDYHSVVHGRLP 151
Cdd:TIGR01993   1 DVWFFDLDNTLYPHSAGIFLQIDRNITEFVAARLKLSPEEARVLRKDYYKEYGTTLAGLMIL-HEIDADEYLRYVHGRLP 79

                          90
                  ....*....|....*..
gi 2111842748 152 YDRIKPDPQLRNLLRSI 168
Cdd:TIGR01993  80 YDKLKPDPELRNLLLRL 96
HAD_5NT cd02604
haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to Saccharomyces cerevisiae Phm8p ...
 73-168 2.93e-35

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: 122.74  E-value: 2.93e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2111842748  73 CLIFDLDDTLYPSNTGLGEACKTNIDDFLVEKCGFPESKASSLRVELFKSYGSTLAGLrALGYDIDADDYHSVVHGRLPY 152
Cdd:cd02604     1 VWFFDLDNTLYPLSTGLFDQIQARITEFVATKLGLSPEEARRLRKSYYKEYGTTLRGL-MAEHGIDPDEFLDRVVHLILY 79

                          90
                  ....*....|....*.
gi 2111842748 153 DRIKPDPQLRNLLRSI 168
Cdd:cd02604    80 DHLKPDPKLRNLLLAL 95
 
Name Accession Description Interval E-value
Pyr-5-nucltdase TIGR01993
pyrimidine 5'-nucleotidase; This family of proteins includes the SDT1/SSM1 gene from yeast ...
 72-168 9.38e-44

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: 144.80  E-value: 9.38e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2111842748  72 DCLIFDLDDTLYPSNTGLGEACKTNIDDFLVEKCGFPESKASSLRVELFKSYGSTLAGLRALgYDIDADDYHSVVHGRLP 151
Cdd:TIGR01993   1 DVWFFDLDNTLYPHSAGIFLQIDRNITEFVAARLKLSPEEARVLRKDYYKEYGTTLAGLMIL-HEIDADEYLRYVHGRLP 79

                          90
                  ....*....|....*..
gi 2111842748 152 YDRIKPDPQLRNLLRSI 168
Cdd:TIGR01993  80 YDKLKPDPELRNLLLRL 96
HAD_5NT cd02604
haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to Saccharomyces cerevisiae Phm8p ...
 73-168 2.93e-35

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: 122.74  E-value: 2.93e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2111842748  73 CLIFDLDDTLYPSNTGLGEACKTNIDDFLVEKCGFPESKASSLRVELFKSYGSTLAGLrALGYDIDADDYHSVVHGRLPY 152
Cdd:cd02604     1 VWFFDLDNTLYPLSTGLFDQIQARITEFVATKLGLSPEEARRLRKSYYKEYGTTLRGL-MAEHGIDPDEFLDRVVHLILY 79

                          90
                  ....*....|....*.
gi 2111842748 153 DRIKPDPQLRNLLRSI 168
Cdd:cd02604    80 DHLKPDPKLRNLLLAL 95
HAD-SF-IA-v3 TIGR01509
haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; ...
 73-167 5.38e-04

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: 39.33  E-value: 5.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2111842748  73 CLIFDLDDTLYPSNTGLGEACKTNIDDFLVEKCGFPESKASSLRVELFKS-YGSTLAGLRALGYdidadDYHSVVHGRLP 151
Cdd:TIGR01509   1 AILFDLDGVLVDTEFAIAKLINREELGLVPDELGVSAVGRLELALRRFKAqYGRTISPEDAQLL-----YKQLFYEQIEE 75

                          90
                  ....*....|....*.
gi 2111842748 152 YDRIKPDPQLRNLLRS 167
Cdd:TIGR01509  76 EAKLKPLPGVRALLEA 91
 
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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