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Conserved domains on  [gi|1998586302|ref|YP_010002464|]
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polynucleotide kinase [Gordonia phage MelBins]

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 ...
 20-159 8.68e-13

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 cd07502:

Pssm-ID: 473868  Cd Length: 145  Bit Score: 62.55  E-value: 8.68e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998586302  20 PTAVIVDMDGTLCDVRDALVHLYGTRKDMRRFHEATRRCPPTPKVVRWCEQAIADGHRLLLVTARKYELEQLTREWLAEH 99
Cdd:cd07502     1 PKAVIFDLDGTLADTNGRQPYLERRPRDWDAFFEAADHDPPNAPVIELVKESALTGYEIVYLSGRPERYRRDTLRWLAKH 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1998586302 100 vpHLEFDHMLMRGDHDDRHDDDVKRDIL-RIIRDdhGYDVVEAFDDRPRVIRLWRSLGIPV 159
Cdd:cd07502    81 --GIPDDALHMRGNADRRKDRRVKLEILrRLIRT--RFEVRLLVDDREQVVDMWRRAGFPC 137
 
Name Accession Description Interval E-value
HAD_PNKP-C cd07502
C-terminal phosphatase domain of T4 polynucleotide kinase/phosphatase (PNKP) and related ...
 20-159 8.68e-13

C-terminal phosphatase domain of T4 polynucleotide kinase/phosphatase (PNKP) and related phosphatases; This family includes the C-terminal domain of the bifunctional enzyme T4 polynucleotide kinase/phosphatase, PNKP. The PNKP phosphatase domain can catalyze the hydrolytic removal of the 3'-phosphoryl of DNA, RNA and deoxynucleoside 3'-monophosphates. 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: 319805  Cd Length: 145  Bit Score: 62.55  E-value: 8.68e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998586302  20 PTAVIVDMDGTLCDVRDALVHLYGTRKDMRRFHEATRRCPPTPKVVRWCEQAIADGHRLLLVTARKYELEQLTREWLAEH 99
Cdd:cd07502     1 PKAVIFDLDGTLADTNGRQPYLERRPRDWDAFFEAADHDPPNAPVIELVKESALTGYEIVYLSGRPERYRRDTLRWLAKH 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1998586302 100 vpHLEFDHMLMRGDHDDRHDDDVKRDIL-RIIRDdhGYDVVEAFDDRPRVIRLWRSLGIPV 159
Cdd:cd07502    81 --GIPDDALHMRGNADRRKDRRVKLEILrRLIRT--RFEVRLLVDDREQVVDMWRRAGFPC 137
pseT PHA02530
polynucleotide kinase; Provisional
 20-159 9.45e-09

polynucleotide kinase; Provisional


Pssm-ID: 222856 [Multi-domain]  Cd Length: 300  Bit Score: 53.49  E-value: 9.45e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998586302  20 PTAVIVDMDGTLCDVrdalvhlyGTRK--DMRRFHEAtrrcPPTPKVVRWCEQAIADGHRLLLVTARKYELEQLTREWLA 97
Cdd:PHA02530  158 PKAVIFDIDGTLAKM--------GGRSpyDWTKVKED----KPNPMVVELVKMYKAAGYEIIVVSGRDGVCEEDTVEWLR 225

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1998586302  98 EHVPHLEFDHML------MRGDHDDRHDDDVKRDIL-RIIRDdhGYDVVEAFDDRPRVIRLWRSLGIPV 159
Cdd:PHA02530  226 QTDIWFDDLIGRppdmhfQREQGDKRPDDVVKEEIFwEKIAP--KYDVLLAVDDRDQVVDMWRRIGLEC 292
YqfW COG5663
Uncharacterized conserved protein YqfW, HAD superfamily [General function prediction only];
25-165 6.06e-08

Uncharacterized conserved protein YqfW, HAD superfamily [General function prediction only];


Pssm-ID: 444382 [Multi-domain]  Cd Length: 187  Bit Score: 50.23  E-value: 6.06e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998586302  25 VDMDGTLCDVRDALVHL----------------------YG-TRKDMRRFHEAT-----RRCPPTPKVVRwCEQAIADGH 76
Cdd:COG5663     5 IDIDGTITDPYPYFIPLlnkyfgknitledittydlhevLGlTEEEFDKFFEENeeeiyTEAPPVPGAKE-VLNKLKDQH 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998586302  77 RLLLVTARKYELEQLTREWLAEHVPHLEFDHMLmrGDHDDrhdddvkrdiLRIIRdDHGYDVveAFDDRPRVIRLWRSLG 156
Cdd:COG5663    84 ELYYITARPKHLEEVTENWLEKHGIPYDELILL--GSHDK----------VEAAK-ELGIDL--FIEDKPDNALQLAEEG 148


                  ....*....
gi 1998586302 157 IPVRVVYRP 165
Cdd:COG5663   149 IPVLLFDTP 157
Hydrolase pfam00702
haloacid dehalogenase-like hydrolase; This family is structurally different from the alpha ...
 22-162 6.30e-03

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: 36.02  E-value: 6.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998586302  22 AVIVDMDGTLCDVRDALVHLygtrkdmrrFHEATRRCPPTPKVVRWCEQAIADGHRLllvtARKYELEQltREWLAEHVP 101
Cdd:pfam00702   3 AVVFDLDGTLTDGEPVVTEA---------IAELASEHPLAKAIVAAAEDLPIPVEDF----TARLLLGK--RDWLEELDI 67

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1998586302 102 hlefdhmlMRGDHDDRHDDDVKRDILRIIRDDHGYDVVEAFDDRPRVIRLWRSLGIPVRVV 162
Cdd:pfam00702  68 --------LRGLVETLEAEGLTVVLVELLGVIALADELKLYPGAAEALKALKERGIKVAIL 120
 
Name Accession Description Interval E-value
HAD_PNKP-C cd07502
C-terminal phosphatase domain of T4 polynucleotide kinase/phosphatase (PNKP) and related ...
 20-159 8.68e-13

C-terminal phosphatase domain of T4 polynucleotide kinase/phosphatase (PNKP) and related phosphatases; This family includes the C-terminal domain of the bifunctional enzyme T4 polynucleotide kinase/phosphatase, PNKP. The PNKP phosphatase domain can catalyze the hydrolytic removal of the 3'-phosphoryl of DNA, RNA and deoxynucleoside 3'-monophosphates. 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: 319805  Cd Length: 145  Bit Score: 62.55  E-value: 8.68e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998586302  20 PTAVIVDMDGTLCDVRDALVHLYGTRKDMRRFHEATRRCPPTPKVVRWCEQAIADGHRLLLVTARKYELEQLTREWLAEH 99
Cdd:cd07502     1 PKAVIFDLDGTLADTNGRQPYLERRPRDWDAFFEAADHDPPNAPVIELVKESALTGYEIVYLSGRPERYRRDTLRWLAKH 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1998586302 100 vpHLEFDHMLMRGDHDDRHDDDVKRDIL-RIIRDdhGYDVVEAFDDRPRVIRLWRSLGIPV 159
Cdd:cd07502    81 --GIPDDALHMRGNADRRKDRRVKLEILrRLIRT--RFEVRLLVDDREQVVDMWRRAGFPC 137
pseT PHA02530
polynucleotide kinase; Provisional
 20-159 9.45e-09

polynucleotide kinase; Provisional


Pssm-ID: 222856 [Multi-domain]  Cd Length: 300  Bit Score: 53.49  E-value: 9.45e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998586302  20 PTAVIVDMDGTLCDVrdalvhlyGTRK--DMRRFHEAtrrcPPTPKVVRWCEQAIADGHRLLLVTARKYELEQLTREWLA 97
Cdd:PHA02530  158 PKAVIFDIDGTLAKM--------GGRSpyDWTKVKED----KPNPMVVELVKMYKAAGYEIIVVSGRDGVCEEDTVEWLR 225

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1998586302  98 EHVPHLEFDHML------MRGDHDDRHDDDVKRDIL-RIIRDdhGYDVVEAFDDRPRVIRLWRSLGIPV 159
Cdd:PHA02530  226 QTDIWFDDLIGRppdmhfQREQGDKRPDDVVKEEIFwEKIAP--KYDVLLAVDDRDQVVDMWRRIGLEC 292
YqfW COG5663
Uncharacterized conserved protein YqfW, HAD superfamily [General function prediction only];
25-165 6.06e-08

Uncharacterized conserved protein YqfW, HAD superfamily [General function prediction only];


Pssm-ID: 444382 [Multi-domain]  Cd Length: 187  Bit Score: 50.23  E-value: 6.06e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998586302  25 VDMDGTLCDVRDALVHL----------------------YG-TRKDMRRFHEAT-----RRCPPTPKVVRwCEQAIADGH 76
Cdd:COG5663     5 IDIDGTITDPYPYFIPLlnkyfgknitledittydlhevLGlTEEEFDKFFEENeeeiyTEAPPVPGAKE-VLNKLKDQH 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998586302  77 RLLLVTARKYELEQLTREWLAEHVPHLEFDHMLmrGDHDDrhdddvkrdiLRIIRdDHGYDVveAFDDRPRVIRLWRSLG 156
Cdd:COG5663    84 ELYYITARPKHLEEVTENWLEKHGIPYDELILL--GSHDK----------VEAAK-ELGIDL--FIEDKPDNALQLAEEG 148


                  ....*....
gi 1998586302 157 IPVRVVYRP 165
Cdd:COG5663   149 IPVLLFDTP 157
HAD_BPGM-like cd07505
beta-phosphoglucomutase-like family of the haloacid dehalogenase-like (HAD) hydrolase ...
 22-111 8.75e-04

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.


Pssm-ID: 319808 [Multi-domain]  Cd Length: 143  Bit Score: 37.98  E-value: 8.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998586302  22 AVIVDMDGTLCD----VRDALvHLYGTRKDMRRFHEATRRCPPTPKVVRWCEQAIADGHRLLLVTARKYELEqltREWLA 97
Cdd:cd07505     1 AVIFDMDGVLIDteplHRQAW-QLLERKNALLLELIASEGLKLKPGVVELLDALKAAGIPVAVATSSSRRNV---ELLLL 76

                          90
                  ....*....|....*
gi 1998586302  98 EHVPHLE-FDHMLMR 111
Cdd:cd07505    77 ELGLLRGyFDVIVSG 91
Hydrolase pfam00702
haloacid dehalogenase-like hydrolase; This family is structurally different from the alpha ...
 22-162 6.30e-03

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: 36.02  E-value: 6.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998586302  22 AVIVDMDGTLCDVRDALVHLygtrkdmrrFHEATRRCPPTPKVVRWCEQAIADGHRLllvtARKYELEQltREWLAEHVP 101
Cdd:pfam00702   3 AVVFDLDGTLTDGEPVVTEA---------IAELASEHPLAKAIVAAAEDLPIPVEDF----TARLLLGK--RDWLEELDI 67

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1998586302 102 hlefdhmlMRGDHDDRHDDDVKRDILRIIRDDHGYDVVEAFDDRPRVIRLWRSLGIPVRVV 162
Cdd:pfam00702  68 --------LRGLVETLEAEGLTVVLVELLGVIALADELKLYPGAAEALKALKERGIKVAIL 120
 
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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