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Conserved domains on  [gi|564328074|ref|XP_006229120|]
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bifunctional polynucleotide phosphatase/kinase isoform X2 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PNK-3'Pase super family cl31131
polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5 ...
3-476 0e+00

polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is believed to be involved in repair of oxidative DNA damage. Removal of 3' phosphates is essential for the further processing of the break by DNA polymerases. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is replaced by a conserved arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Very close relatives of this domain are also found separate from the N- and C-terminal domains seen here, as in the 3'-phosphatase found in plants. The larger family of these domains is described by TIGR01664. Outside of the phosphatase domain is a P-loop ATP-binding motif associated with the kinase activity. The entry for the mouse homolog appears to be missing a large piece of sequence corresponding to the first conserved catalytic motif of the phosphatase domain as well as the conserved threonine of the second motif. Either this is a sequencing artifact or this may represent a pseudo- or non-functional gene. Note that the EC number for the kinase function is: 2.7.1.78


The actual alignment was detected with superfamily member TIGR01663:

Pssm-ID: 130724 [Multi-domain]  Cd Length: 526  Bit Score: 718.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074    3 ELGSRGRLWLQS----PTGGPPPIFLPSDGQALVLGRGPLTQVMDRKCSRNQVELIADPETRTVAVKQLGVNPSTVGVQE 78
Cdd:TIGR01663   2 EVEAAGKDVAARictlKPGEAEHHFIHLDAGALFLGRGPETGIRDRKCSKRQIELQADLEKATVALKQLGVNPCGTGGLE 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074   79 LKPGVSGSLSVGDVLYLVNGLYPLTLRWEEISTPGSPPDTPPGNP-VDPEEGKDTEPQKKRMRKSSPGWESFKQLLVFTA 157
Cdd:TIGR01663  82 LKPGGEGELGHGDLLEIVNGLHPLTLQFEETFNPEPEPDKEKAEPlSSQDEKRDAEKPEKRDRKGNPGWENLEKLLIFTA 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  158 SGVKPRGK----------------------------------------------LVILTNQMGIGRGKLPAEVFKAKVEA 191
Cdd:TIGR01663 162 AGVKGQEKiagfdldgtiiktksgkvfpkgpddwqiifpeipeklkeleadgfkICIFTNQGGIARGKINADDFKAKIEA 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  192 VLEKLGVPFQVLVATHAGLNRKPVSGMWDHLQEKGNEGIPISIGDSVFVGDAAGRPAN-WAPGKKKKDFSCADRLFALNV 270
Cdd:TIGR01663 242 IVAKLGVPFQVFIAIGAGFYRKPLTGMWDHLKEEANDGTEIQEDDCFFVGDAAGRPANgKAAGKKKKDFSCADRLFAANL 321
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  271 GLPFATPEEFFLKWPAARFELPAFDPRTISSAGPLYLPESSFLLSPNPEVVVAVGFPGAGKSTFIQKHLVSAGYVHVNRD 350
Cdd:TIGR01663 322 GIPFATPEEFFLGKPAAGFEKPAFDPRSVQDQGPLCDPDDLALDDAPCEMVIAVGFPGAGKSHFCKKFFQPAGYKHVNAD 401
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  351 TLGSWQRCVNSCQAALRQGKQVVIDNTNPDIQSRARYIQCAKDAGVPCRCFSFCATIEQARHNNRFREMTDPSHAPVSDM 430
Cdd:TIGR01663 402 TLGSTQNCLTACERALDQGKRCAIDNTNPDAASRAKFLQCARAAGIPCRCFLFNAPLAQAKHNIAFRELSDSAHIKIKDM 481
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*.
gi 564328074  431 VMFSYRKQFEPPTLAEGFLEILQVPFRlQEHLDPALQRLYCQFSEG 476
Cdd:TIGR01663 482 VFNGMKKKFEAPALAEGFIAIHEINFK-PLFADEKLEKLYCMFLEE 526
 
Name Accession Description Interval E-value
PNK-3'Pase TIGR01663
polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5 ...
3-476 0e+00

polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is believed to be involved in repair of oxidative DNA damage. Removal of 3' phosphates is essential for the further processing of the break by DNA polymerases. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is replaced by a conserved arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Very close relatives of this domain are also found separate from the N- and C-terminal domains seen here, as in the 3'-phosphatase found in plants. The larger family of these domains is described by TIGR01664. Outside of the phosphatase domain is a P-loop ATP-binding motif associated with the kinase activity. The entry for the mouse homolog appears to be missing a large piece of sequence corresponding to the first conserved catalytic motif of the phosphatase domain as well as the conserved threonine of the second motif. Either this is a sequencing artifact or this may represent a pseudo- or non-functional gene. Note that the EC number for the kinase function is: 2.7.1.78


Pssm-ID: 130724 [Multi-domain]  Cd Length: 526  Bit Score: 718.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074    3 ELGSRGRLWLQS----PTGGPPPIFLPSDGQALVLGRGPLTQVMDRKCSRNQVELIADPETRTVAVKQLGVNPSTVGVQE 78
Cdd:TIGR01663   2 EVEAAGKDVAARictlKPGEAEHHFIHLDAGALFLGRGPETGIRDRKCSKRQIELQADLEKATVALKQLGVNPCGTGGLE 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074   79 LKPGVSGSLSVGDVLYLVNGLYPLTLRWEEISTPGSPPDTPPGNP-VDPEEGKDTEPQKKRMRKSSPGWESFKQLLVFTA 157
Cdd:TIGR01663  82 LKPGGEGELGHGDLLEIVNGLHPLTLQFEETFNPEPEPDKEKAEPlSSQDEKRDAEKPEKRDRKGNPGWENLEKLLIFTA 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  158 SGVKPRGK----------------------------------------------LVILTNQMGIGRGKLPAEVFKAKVEA 191
Cdd:TIGR01663 162 AGVKGQEKiagfdldgtiiktksgkvfpkgpddwqiifpeipeklkeleadgfkICIFTNQGGIARGKINADDFKAKIEA 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  192 VLEKLGVPFQVLVATHAGLNRKPVSGMWDHLQEKGNEGIPISIGDSVFVGDAAGRPAN-WAPGKKKKDFSCADRLFALNV 270
Cdd:TIGR01663 242 IVAKLGVPFQVFIAIGAGFYRKPLTGMWDHLKEEANDGTEIQEDDCFFVGDAAGRPANgKAAGKKKKDFSCADRLFAANL 321
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  271 GLPFATPEEFFLKWPAARFELPAFDPRTISSAGPLYLPESSFLLSPNPEVVVAVGFPGAGKSTFIQKHLVSAGYVHVNRD 350
Cdd:TIGR01663 322 GIPFATPEEFFLGKPAAGFEKPAFDPRSVQDQGPLCDPDDLALDDAPCEMVIAVGFPGAGKSHFCKKFFQPAGYKHVNAD 401
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  351 TLGSWQRCVNSCQAALRQGKQVVIDNTNPDIQSRARYIQCAKDAGVPCRCFSFCATIEQARHNNRFREMTDPSHAPVSDM 430
Cdd:TIGR01663 402 TLGSTQNCLTACERALDQGKRCAIDNTNPDAASRAKFLQCARAAGIPCRCFLFNAPLAQAKHNIAFRELSDSAHIKIKDM 481
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*.
gi 564328074  431 VMFSYRKQFEPPTLAEGFLEILQVPFRlQEHLDPALQRLYCQFSEG 476
Cdd:TIGR01663 482 VFNGMKKKFEAPALAEGFIAIHEINFK-PLFADEKLEKLYCMFLEE 526
HAD_PNP cd01625
polynucleotide 3'-phosphatase domain similar to the phosphatase domain of the bifunctional ...
165-281 5.19e-57

polynucleotide 3'-phosphatase domain similar to the phosphatase domain of the bifunctional enzyme polynucleotide 5'-kinase/3'-phosphatase; Polynucleotide 3'-phosphatase (PNP) domain. This domain dephosphorylates single-stranded as well as double-stranded 3'-phospho termini. It is found in bifunctional enzyme polynucleotide kinase/phosphatase (PNKP) which contain both kinase and phosphatase domains. PNKP plays a key role in both base excision repair and non-homologous end-joining DNA repair pathway. DNA strand breaks can result from DNA damage by ionizing radiation and chemical agents, such as alkylating agents or anticancer agents. Such DNA damage often results in DNA strands with 5'-hydroxyl and 3'-phosphate termini. However, the repair of DNA damage by DNA polymerases and ligases requires 5'-phosphate and 3'-hydroxyl termini. PNKP acts as a 5'-kinase/3'-phosphatase to create 5'-phosphate/3'-hydroxyl termini, which are a necessary prerequisite for ligation during repair. 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: 319766  Cd Length: 154  Bit Score: 186.02  E-value: 5.19e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074 165 KLVILTNQMGIGRGKLPAEVFKAKVEAVLEKLGVPFQVLVATHAGLNRKPVSGMWDHLQEKGNEGIPISIGDSVFVGDAA 244
Cdd:cd01625   47 KIVIFTNQGGIVRGKLTPEVFKGKIEAILEKLGVPIQVYAATKKGKYRKPVTGMWDHLKEDLNSGIPINLKDSFYVGDAA 126
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 564328074 245 GRPanwapgkkkKDFSCADRLFALNVGLPFATPEEFF 281
Cdd:cd01625  127 GRP---------KDFSDSDRLFAENVGLKFFTPEEFF 154
PNK3P pfam08645
Polynucleotide kinase 3 phosphatase; Polynucleotide kinase 3 phosphatases play a role in the ...
165-281 6.44e-52

Polynucleotide kinase 3 phosphatase; Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin.


Pssm-ID: 370030  Cd Length: 161  Bit Score: 172.83  E-value: 6.44e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  165 KLVILTNQMGIGR-GKLPAEVFKAKVEAVLEKLGVPFQVLVATHAGLNRKPVSGMWDHLQEKGNEGIPISIGDSVFVGDA 243
Cdd:pfam08645  47 KIVIFTNQGGIGRkGKKSLEKFKNKIEAILKKLGVPLQVYAATKKDIYRKPNTGMWDEMKKDYNDGVEIDLEKSFYVGDA 126
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 564328074  244 AGRPanwAPGKKKKDFSCADRLFALNVGLPFATPEEFF 281
Cdd:pfam08645 127 AGRP---YDTRRKKDFSDSDRKFALNVGIKFKTPEEFF 161
COG4639 COG4639
Predicted kinase [General function prediction only];
318-452 2.53e-18

Predicted kinase [General function prediction only];


Pssm-ID: 443677 [Multi-domain]  Cd Length: 145  Bit Score: 81.41  E-value: 2.53e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074 318 PEVVVAVGFPGAGKSTFIQKHL-----VSA----GYVHVNRDTLGSWQRCVN----SCQAALRQGKQVVIDNTNPDIQSR 384
Cdd:COG4639    2 LSLVVLIGLPGSGKSTFARRLFaptevVSSddirALLGGDENDQSAWGDVFQlaheIARARLRAGRLTVVDATNLQREAR 81
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564328074 385 ARYIQCAKDAGVPCRCFSFCATIEQARHNNRFREmtdpshAPVSDMVMFSYRKQFE-PPTLAEGFLEIL 452
Cdd:COG4639   82 RRLLALARAYGALVVAVVLDVPLEVCLARNAARD------RQVPEEVIRRMLRRLRrPPLPEEGFRVVY 144
pseT PHA02530
polynucleotide kinase; Provisional
318-439 5.13e-06

polynucleotide kinase; Provisional


Pssm-ID: 222856 [Multi-domain]  Cd Length: 300  Bit Score: 48.09  E-value: 5.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074 318 PEVVVAVGFPGAGKST----FIQKhlvSAGYVHVNRDTL-------GSW---------QRCVNSCQ-----AALRQGKQV 372
Cdd:PHA02530   2 MKIILTVGVPGSGKSTwareFAAK---NPKAVNVNRDDLrqslfghGEWgeykftkekEDLVTKAQeaaalAALKSGKSV 78
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564328074 373 VIDNTNPDIQSRARYIQCAKDAGVPCRCFSFCATIEQARHNNRFR-EMTDPSHAPVSdmvMFSYRKQF 439
Cdd:PHA02530  79 IISDTNLNPERRRKWKELAKELGAEFEEKVFDVPVEELVKRNRKRgERAVPEDVLRS---MFKQMKEY 143
 
Name Accession Description Interval E-value
PNK-3'Pase TIGR01663
polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5 ...
3-476 0e+00

polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is believed to be involved in repair of oxidative DNA damage. Removal of 3' phosphates is essential for the further processing of the break by DNA polymerases. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is replaced by a conserved arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Very close relatives of this domain are also found separate from the N- and C-terminal domains seen here, as in the 3'-phosphatase found in plants. The larger family of these domains is described by TIGR01664. Outside of the phosphatase domain is a P-loop ATP-binding motif associated with the kinase activity. The entry for the mouse homolog appears to be missing a large piece of sequence corresponding to the first conserved catalytic motif of the phosphatase domain as well as the conserved threonine of the second motif. Either this is a sequencing artifact or this may represent a pseudo- or non-functional gene. Note that the EC number for the kinase function is: 2.7.1.78


Pssm-ID: 130724 [Multi-domain]  Cd Length: 526  Bit Score: 718.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074    3 ELGSRGRLWLQS----PTGGPPPIFLPSDGQALVLGRGPLTQVMDRKCSRNQVELIADPETRTVAVKQLGVNPSTVGVQE 78
Cdd:TIGR01663   2 EVEAAGKDVAARictlKPGEAEHHFIHLDAGALFLGRGPETGIRDRKCSKRQIELQADLEKATVALKQLGVNPCGTGGLE 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074   79 LKPGVSGSLSVGDVLYLVNGLYPLTLRWEEISTPGSPPDTPPGNP-VDPEEGKDTEPQKKRMRKSSPGWESFKQLLVFTA 157
Cdd:TIGR01663  82 LKPGGEGELGHGDLLEIVNGLHPLTLQFEETFNPEPEPDKEKAEPlSSQDEKRDAEKPEKRDRKGNPGWENLEKLLIFTA 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  158 SGVKPRGK----------------------------------------------LVILTNQMGIGRGKLPAEVFKAKVEA 191
Cdd:TIGR01663 162 AGVKGQEKiagfdldgtiiktksgkvfpkgpddwqiifpeipeklkeleadgfkICIFTNQGGIARGKINADDFKAKIEA 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  192 VLEKLGVPFQVLVATHAGLNRKPVSGMWDHLQEKGNEGIPISIGDSVFVGDAAGRPAN-WAPGKKKKDFSCADRLFALNV 270
Cdd:TIGR01663 242 IVAKLGVPFQVFIAIGAGFYRKPLTGMWDHLKEEANDGTEIQEDDCFFVGDAAGRPANgKAAGKKKKDFSCADRLFAANL 321
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  271 GLPFATPEEFFLKWPAARFELPAFDPRTISSAGPLYLPESSFLLSPNPEVVVAVGFPGAGKSTFIQKHLVSAGYVHVNRD 350
Cdd:TIGR01663 322 GIPFATPEEFFLGKPAAGFEKPAFDPRSVQDQGPLCDPDDLALDDAPCEMVIAVGFPGAGKSHFCKKFFQPAGYKHVNAD 401
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  351 TLGSWQRCVNSCQAALRQGKQVVIDNTNPDIQSRARYIQCAKDAGVPCRCFSFCATIEQARHNNRFREMTDPSHAPVSDM 430
Cdd:TIGR01663 402 TLGSTQNCLTACERALDQGKRCAIDNTNPDAASRAKFLQCARAAGIPCRCFLFNAPLAQAKHNIAFRELSDSAHIKIKDM 481
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*.
gi 564328074  431 VMFSYRKQFEPPTLAEGFLEILQVPFRlQEHLDPALQRLYCQFSEG 476
Cdd:TIGR01663 482 VFNGMKKKFEAPALAEGFIAIHEINFK-PLFADEKLEKLYCMFLEE 526
HAD_PNP cd01625
polynucleotide 3'-phosphatase domain similar to the phosphatase domain of the bifunctional ...
165-281 5.19e-57

polynucleotide 3'-phosphatase domain similar to the phosphatase domain of the bifunctional enzyme polynucleotide 5'-kinase/3'-phosphatase; Polynucleotide 3'-phosphatase (PNP) domain. This domain dephosphorylates single-stranded as well as double-stranded 3'-phospho termini. It is found in bifunctional enzyme polynucleotide kinase/phosphatase (PNKP) which contain both kinase and phosphatase domains. PNKP plays a key role in both base excision repair and non-homologous end-joining DNA repair pathway. DNA strand breaks can result from DNA damage by ionizing radiation and chemical agents, such as alkylating agents or anticancer agents. Such DNA damage often results in DNA strands with 5'-hydroxyl and 3'-phosphate termini. However, the repair of DNA damage by DNA polymerases and ligases requires 5'-phosphate and 3'-hydroxyl termini. PNKP acts as a 5'-kinase/3'-phosphatase to create 5'-phosphate/3'-hydroxyl termini, which are a necessary prerequisite for ligation during repair. 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: 319766  Cd Length: 154  Bit Score: 186.02  E-value: 5.19e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074 165 KLVILTNQMGIGRGKLPAEVFKAKVEAVLEKLGVPFQVLVATHAGLNRKPVSGMWDHLQEKGNEGIPISIGDSVFVGDAA 244
Cdd:cd01625   47 KIVIFTNQGGIVRGKLTPEVFKGKIEAILEKLGVPIQVYAATKKGKYRKPVTGMWDHLKEDLNSGIPINLKDSFYVGDAA 126
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 564328074 245 GRPanwapgkkkKDFSCADRLFALNVGLPFATPEEFF 281
Cdd:cd01625  127 GRP---------KDFSDSDRLFAENVGLKFFTPEEFF 154
FHA_PNKP cd22736
forkhead associated (FHA) domain found in bifunctional polynucleotide phosphatase/kinase (PNKP) ...
9-108 5.09e-55

forkhead associated (FHA) domain found in bifunctional polynucleotide phosphatase/kinase (PNKP) and similar proteins; PNKP (EC 3.1.3.32/EC 2.7.1.78), also called DNA 5'-kinase/3'-phosphatase, or polynucleotide kinase-3'-phosphatase, plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNKP ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone. PNKP contains an FHA domain at its N-terminus. The FHA domain is a small phosphopeptide recognition module.


Pssm-ID: 438788  Cd Length: 99  Bit Score: 178.82  E-value: 5.09e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074   9 RLWLQSPTGGPPPIFLPsDGQALVLGRGPLTQVMDRKCSRNQVELIADPETRTVAVKQLGVNPSTVGVQELKPGVSGSLS 88
Cdd:cd22736    1 RCWLVSVDGGHPPIFLP-DGQALVLGRGPETRVTDRKCSRTQVELVADYESRTVAVTQLGVNPSSVGEQELKPGLSGSLK 79
                         90       100
                 ....*....|....*....|
gi 564328074  89 VGDVLYLVNGLYPLTLRWEE 108
Cdd:cd22736   80 EGQTLYLVNGLYPLTLRFEE 99
DNA-3'-Pase TIGR01664
DNA 3'-phosphatase; This model represents a family of proteins and protein domains which ...
136-282 9.29e-54

DNA 3'-phosphatase; This model represents a family of proteins and protein domains which catalyze the dephosphorylation of DNA 3'-phosphates. It is believed that this activity is important for the repair of single-strand breaks in DNA caused by radiation or oxidative damage. This domain is often (TIGR01663), but not always linked to a DNA 5'-kinase domain. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is usually replaced by an arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Alternatively, there is an additional conserved aspartate downstream of the ususal site which may indicate slightly different fold in this region.


Pssm-ID: 211680  Cd Length: 166  Bit Score: 178.03  E-value: 9.29e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  136 KKRMRKSSPGWESFKQLLVFTA-----SGVKPRGKLVILTNQMGIGRGKLPAEVFKAKVEAVLEKLGVPFQVLVATHAGL 210
Cdd:TIGR01664  26 TTRSGKVFPTSASDWRFLYPEIpaklqELDDEGYKIVIFTNQSGIGRGKLSAESFKNKIEAFLEKLKVPIQVLAATHAGL 105
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564328074  211 NRKPVSGMWDHLQEKGNEgiPISIGDSVFVGDAAGRpanwapgkkKKDFSCADRLFALNVGLPFATPEEFFL 282
Cdd:TIGR01664 106 YRKPMTGMWEYLQSQYNS--PIKMTRSFYVGDAAGR---------KLDFSDADIKFAKNLGLEFKYPEEFFL 166
PNK3P pfam08645
Polynucleotide kinase 3 phosphatase; Polynucleotide kinase 3 phosphatases play a role in the ...
165-281 6.44e-52

Polynucleotide kinase 3 phosphatase; Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin.


Pssm-ID: 370030  Cd Length: 161  Bit Score: 172.83  E-value: 6.44e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  165 KLVILTNQMGIGR-GKLPAEVFKAKVEAVLEKLGVPFQVLVATHAGLNRKPVSGMWDHLQEKGNEGIPISIGDSVFVGDA 243
Cdd:pfam08645  47 KIVIFTNQGGIGRkGKKSLEKFKNKIEAILKKLGVPLQVYAATKKDIYRKPNTGMWDEMKKDYNDGVEIDLEKSFYVGDA 126
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 564328074  244 AGRPanwAPGKKKKDFSCADRLFALNVGLPFATPEEFF 281
Cdd:pfam08645 127 AGRP---YDTRRKKDFSDSDRKFALNVGIKFKTPEEFF 161
FHA_2 pfam17913
FHA domain; This entry represents a divergent FHA domain which in PNK binds to phosphorylated ...
11-107 2.06e-40

FHA domain; This entry represents a divergent FHA domain which in PNK binds to phosphorylated segment of XRCC1.


Pssm-ID: 436135 [Multi-domain]  Cd Length: 97  Bit Score: 140.12  E-value: 2.06e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074   11 WLQSPTGGPPPIFLPsDGQALVLGRGPLTQVMDRKCSRNQVELIADPETRTVAVKQLGVNPSTVGVQELKPGVSGSLSVG 90
Cdd:pfam17913   2 YLVSLEGTHPPIPLP-HGQPVVIGRGPETGITDKKCSRNQVELKADCEKRYVKVKQLGANPSGLNGFKLKKGESYELKHG 80
                          90
                  ....*....|....*..
gi 564328074   91 DVLYLVNGLYPLTLRWE 107
Cdd:pfam17913  81 DVLELLNGKHPHRVEFN 97
FHA_APTX_PNKP cd22716
forkhead associated (FHA) domain found in aprataxin, bifunctional polynucleotide phosphatase ...
11-108 9.32e-40

forkhead associated (FHA) domain found in aprataxin, bifunctional polynucleotide phosphatase/kinase (PNKP), and similar proteins; The subfamily includes aprataxin and PNKP. Aprataxin (EC 3.6.1.71/EC 3.6.1.72), also called forkhead-associated domain histidine triad-like protein (FHA-HIT), is a DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair, and base excision repair. It catalyzes the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined. It can also hydrolyze adenosine 5'-monophosphoramidate (AMP-NH(2)) and diadenosine tetraphosphate (AppppA), but with lower catalytic activity. Likewise, it catalyzes the release of 3'-linked guanosine (DNAppG) and inosine (DNAppI) from DNA but has higher specific activity with 5'-linked adenosine (AppDNA). PNKP (EC 3.1.3.32/EC 2.7.1.78), also called DNA 5'-kinase/3'-phosphatase, or polynucleotide kinase-3'-phosphatase, plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNKP ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone. Both aprataxin and PNKP contain an FHA domain at their N-terminus. The FHA domain is a small phosphopeptide recognition module.


Pssm-ID: 438768 [Multi-domain]  Cd Length: 97  Bit Score: 138.57  E-value: 9.32e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  11 WLQSPTGGPPPIFLPsDGQALVLGRGPLTQVMDRKCSRNQVELIADPETRTVAVKQLGVNPSTVGVQELKPGVSGSLSVG 90
Cdd:cd22716    1 ILVCCSSSHPPIPLP-DGVPVILGRGPQTQITDKRCSRQQVELTANYEKRYVLVKQLGPNPSSVGGKLLEKGDEAELSPG 79
                         90
                 ....*....|....*...
gi 564328074  91 DVLYLVNGLYPLTLRWEE 108
Cdd:cd22716   80 ETLHLLNGKYPHTVYFEG 97
FHA_APTX-like cd22671
forkhead associated (FHA) domain found in aprataxin, bifunctional polynucleotide phosphatase ...
11-105 2.65e-26

forkhead associated (FHA) domain found in aprataxin, bifunctional polynucleotide phosphatase/kinase (PNKP), aprataxin and PNK-like factor (APLF), and similar proteins; The family includes aprataxin, PNKP, and APLF. Aprataxin (EC 3.6.1.71/EC 3.6.1.72), also called forkhead-associated domain histidine triad-like protein (FHA-HIT), is a DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair, and base excision repair. It catalyzes the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined. It can also hydrolyze adenosine 5'-monophosphoramidate (AMP-NH(2)) and diadenosine tetraphosphate (AppppA), but with lower catalytic activity. Likewise, it catalyzes the release of 3'-linked guanosine (DNAppG) and inosine (DNAppI) from DNA but has higher specific activity with 5'-linked adenosine (AppDNA). PNKP (EC 3.1.3.32/EC 2.7.1.78), also called DNA 5'-kinase/3'-phosphatase, or polynucleotide kinase-3'-phosphatase, plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNKP ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone. APLF, also called apurinic-apyrimidinic endonuclease APLF, PNK and APTX-like FHA domain-containing protein, or XRCC1-interacting protein 1 (XIP1), is a novel apurinic-apyrimidinic (AP) endonuclease and 3'-5' exonuclease with conserved zinc-finger-like motifs involved in single-strand and double-strand DNA break repair. It is recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. It can introduce nicks at hydroxyuracil and other types of pyrimidine base damage. Together with PARP3, APLF promotes the retention of the LIG4-XRCC4 complex on chromatin and accelerate DNA ligation during non-homologous end-joining (NHEJ). Members of this family contain an FHA domain at their N-terminus. The FHA domain is a small phosphopeptide recognition module.


Pssm-ID: 438723 [Multi-domain]  Cd Length: 101  Bit Score: 102.39  E-value: 2.65e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  11 WLQSPTGGP-PPIFLPsDGQALVLGRGPLTQVMDRKCSRNQVELIADPETRTVAVKQLGVNPSTVGV-----QELKPGVS 84
Cdd:cd22671    1 FLRPVDGGGgPPIELK-EGGPTVLGRGPLLGIRDKRVSRKQAEITVDDDTGSVTVTQLGTNPSFVNRadgegKVLKKGES 79
                         90       100
                 ....*....|....*....|.
gi 564328074  85 GSLSVGDVLYLVNGLYPLTLR 105
Cdd:cd22671   80 VELKDGDVISLLPGKYPFRVE 100
HAD-SF-IIIA TIGR01662
HAD-superfamily hydrolase, subfamily IIIA; This subfamily falls within the Haloacid ...
165-263 9.16e-26

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]


Pssm-ID: 273742 [Multi-domain]  Cd Length: 135  Bit Score: 102.10  E-value: 9.16e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  165 KLVILTNQMGIGRGKLPaEVFKAKVEAVLEKLGVPFQVLVAthAGLNRKPVSGMWDHLQEKGNEgipISIGDSVFVGDAA 244
Cdd:TIGR01662  43 KVVIVTNQSGIGRGYFS-RSFSGRVARRLEELGVPIDILYA--CPGCRKPKPGMFLEALKRFNE---IDPEESVYVGDQD 116
                          90
                  ....*....|....*....
gi 564328074  245 GRPANWAPGKKKKDFSCAD 263
Cdd:TIGR01662 117 LTDLQAAKRVGLATILVAP 135
FHA_APTX cd22735
forkhead associated (FHA) domain found in aprataxin and similar proteins; Aprataxin (EC 3.6.1. ...
11-108 7.69e-23

forkhead associated (FHA) domain found in aprataxin and similar proteins; Aprataxin (EC 3.6.1.71/EC 3.6.1.72), also called forkhead-associated domain histidine triad-like protein (FHA-HIT), is a DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair, and base excision repair. It catalyzes the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined. It can also hydrolyze adenosine 5'-monophosphoramidate (AMP-NH(2)) and diadenosine tetraphosphate (AppppA), but with lower catalytic activity. Likewise, it catalyzes the release of 3'-linked guanosine (DNAppG) and inosine (DNAppI) from DNA but has higher specific activity with 5'-linked adenosine (AppDNA). Mutations in the gene APTX have been associated with ataxia-ocular apraxia. Aprataxin contains an FHA domain at its N-terminus. The FHA domain is a small phosphopeptide recognition module.


Pssm-ID: 438787  Cd Length: 100  Bit Score: 92.55  E-value: 7.69e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  11 WLQSPTGGPPPIFLPSDgQALVLGRGPLTQVMDRKCSRNQVELIADPETRTVAVKQLGVNPSTVGVQELKPGVSGSLSVG 90
Cdd:cd22735    4 WLVSKDGRHLRIRLPHL-EAVVIGRGPETKITDKKCSRHQVQLKADCNKGYVKVKQLGVNPTSIDLVDIGKDEEVKLKPG 82
                         90
                 ....*....|....*...
gi 564328074  91 DVLYLVNGLYPLTLRWEE 108
Cdd:cd22735   83 QVLHIVNQLYPYIVEFEE 100
AAA_33 pfam13671
AAA domain; This family of domains contain only a P-loop motif, that is characteriztic of the ...
320-442 1.06e-22

AAA domain; This family of domains contain only a P-loop motif, that is characteriztic of the AAA superfamily. Many of the proteins in this family are just short fragments so there is no Walker B motif.


Pssm-ID: 463952 [Multi-domain]  Cd Length: 143  Bit Score: 93.91  E-value: 1.06e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  320 VVVAVGFPGAGKSTFIQKHLVSAGYVHVNRDTL-----------GSWQ-----RCVNS----CQAALRQGKQVVIDNTNP 379
Cdd:pfam13671   1 LILLVGLPGSGKSTLARRLLEELGAVRLSSDDErkrlfgegrpsISYYtdatdRTYERlhelARIALRAGRPVILDATNL 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564328074  380 DIQSRARYIQCAKDAGVPCRCFSFCATIEQARHNNRFREMTDPSHAPVSDMVMFSYRKQFEPP 442
Cdd:pfam13671  81 RRDERARLLALAREYGVPVRIVVFEAPEEVLRERLAARARAGGDPSDVPEEVLDRQKARFEPP 143
COG4639 COG4639
Predicted kinase [General function prediction only];
318-452 2.53e-18

Predicted kinase [General function prediction only];


Pssm-ID: 443677 [Multi-domain]  Cd Length: 145  Bit Score: 81.41  E-value: 2.53e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074 318 PEVVVAVGFPGAGKSTFIQKHL-----VSA----GYVHVNRDTLGSWQRCVN----SCQAALRQGKQVVIDNTNPDIQSR 384
Cdd:COG4639    2 LSLVVLIGLPGSGKSTFARRLFaptevVSSddirALLGGDENDQSAWGDVFQlaheIARARLRAGRLTVVDATNLQREAR 81
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564328074 385 ARYIQCAKDAGVPCRCFSFCATIEQARHNNRFREmtdpshAPVSDMVMFSYRKQFE-PPTLAEGFLEIL 452
Cdd:COG4639   82 RRLLALARAYGALVVAVVLDVPLEVCLARNAARD------RQVPEEVIRRMLRRLRrPPLPEEGFRVVY 144
COG0645 COG0645
Predicted kinase, contains AAA domain [General function prediction only];
320-452 1.48e-10

Predicted kinase, contains AAA domain [General function prediction only];


Pssm-ID: 440410 [Multi-domain]  Cd Length: 164  Bit Score: 59.54  E-value: 1.48e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074 320 VVVAVGFPGAGKSTF-----------------IQKHLVSAGYVHVNRD---TLGSWQRCVNSCQAALRQGKQVVIDNTNP 379
Cdd:COG0645    1 LILVCGLPGSGKSTLaralaerlgavrlrsdvVRKRLFGAGLAPLERSpeaTARTYARLLALARELLAAGRSVILDATFL 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564328074 380 DIQSRARYIQCAKDAGVPCRCFSFCATIEQARHNNRFR-EMTDPSHApvSDMVMFSYRKQFEPPTLAEGFLEIL 452
Cdd:COG0645   81 RRAQREAFRALAEEAGAPFVLIWLDAPEEVLRERLEARnAEGGDSDA--TWEVLERQLAFEEPLTEDEGFLLVV 152
HisB1/GmhB COG0241
Histidinol phosphatase/D-glycero-mannoheptose bisphosphatephosphatase, HAD superfamily [Amino ...
165-242 7.18e-09

Histidinol phosphatase/D-glycero-mannoheptose bisphosphatephosphatase, HAD superfamily [Amino acid transport and metabolism]; Histidinol phosphatase/D-glycero-mannoheptose bisphosphatephosphatase, HAD superfamily is part of the Pathway/BioSystem: Histidine biosynthesis


Pssm-ID: 440011 [Multi-domain]  Cd Length: 176  Bit Score: 55.10  E-value: 7.18e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074 165 KLVILTNQMGIGRGKLPAEVFKA---KVEAVLEKLGVPF-QVLVATHAG----LNRKPVSGMWDHLQEKGNegipISIGD 236
Cdd:COG0241   46 RLVVVTNQSGIGRGLFTEEDLNAvhaKMLELLAAEGGRIdAIYYCPHHPddncDCRKPKPGMLLQAAERLG----IDLSN 121

                 ....*.
gi 564328074 237 SVFVGD 242
Cdd:COG0241  122 SYMIGD 127
HAD_HisB-N cd07503
histidinol phosphate phosphatase and related phosphatases; This family includes the N-terminal ...
165-252 1.73e-06

histidinol phosphate phosphatase and related phosphatases; This family includes the N-terminal domain of the Escherichia coli bifunctional enzyme histidinol-phosphate phosphatase/imidazole-glycerol-phosphate dehydratase, HisB. The N-terminal histidinol-phosphate phosphatase domain catalyzes the dephosphorylation of histidinol phosphate, the eight step of L-histidine biosynthesis. This family also includes Escherichia coli GmhB phosphatase which is highly specific for D-glycero-D-manno-heptose-1,7-bisphosphate, it removes the C(7)phosphate and not the C(1)phosphate, and this is the third essential step of lipopolysaccharide heptose biosynthesis. 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: 319806 [Multi-domain]  Cd Length: 142  Bit Score: 47.53  E-value: 1.73e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074 165 KLVILTNQMGIGRGKLPAEVFKA---KVEAVLEKLGVPF-QVLVATHA----GLNRKPVSGMWDHLQEKGNegipISIGD 236
Cdd:cd07503   43 LVVVVTNQSGIARGYFSEADFEAlhdKMRELLASQGVEIdDIYYCPHHpddgCPCRKPKPGMLLDAAKELG----IDLAR 118
                         90       100
                 ....*....|....*....|.
gi 564328074 237 SVFVGDA-----AGRPANWAP 252
Cdd:cd07503  119 SFVIGDRlsdiqAARNAGCKG 139
pseT PHA02530
polynucleotide kinase; Provisional
318-439 5.13e-06

polynucleotide kinase; Provisional


Pssm-ID: 222856 [Multi-domain]  Cd Length: 300  Bit Score: 48.09  E-value: 5.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074 318 PEVVVAVGFPGAGKST----FIQKhlvSAGYVHVNRDTL-------GSW---------QRCVNSCQ-----AALRQGKQV 372
Cdd:PHA02530   2 MKIILTVGVPGSGKSTwareFAAK---NPKAVNVNRDDLrqslfghGEWgeykftkekEDLVTKAQeaaalAALKSGKSV 78
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564328074 373 VIDNTNPDIQSRARYIQCAKDAGVPCRCFSFCATIEQARHNNRFR-EMTDPSHAPVSdmvMFSYRKQF 439
Cdd:PHA02530  79 IISDTNLNPERRRKWKELAKELGAEFEEKVFDVPVEELVKRNRKRgERAVPEDVLRS---MFKQMKEY 143
Histidinol-ppas TIGR01656
histidinol-phosphate phosphatase family domain; This domain is found in authentic ...
166-252 1.97e-04

histidinol-phosphate phosphatase family domain; This domain is found in authentic histidinol-phosphate phosphatases which are sometimes found as stand-alone entities and sometimes as fusions with imidazoleglycerol-phosphate dehydratase (TIGR01261). Additionally, a family of proteins including YaeD from E. coli (TIGR00213) and various other proteins are closely related but may not have the same substrate specificity. This domain is a member of the haloacid-dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. This superfamily is distinguished by the presence of three motifs: an N-terminal motif containing the nucleophilic aspartate, a central motif containing an conserved serine or threonine, and a C-terminal motif containing a conserved lysine (or arginine) and conserved aspartates. More specifically, the domian modelled here is a member of subfamily III of the HAD-superfamily by virtue of lacking a "capping" domain in either of the two common positions, between motifs 1 and 2, or between motifs 2 and 3.


Pssm-ID: 273737  Cd Length: 147  Bit Score: 41.62  E-value: 1.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074  166 LVILTNQMGIGRGKLPAE---VFKAKVEAVLEKLGVPFQ-VLVATH--AGLN--RKPVSGMWDHLQEKGNEGIPIS--IG 235
Cdd:TIGR01656  46 VVVVTNQSGIGRGYFSAEafrAPNGRLLELLRQLGVAVDgVLFCPHhpADNCscRKPKPGLILEALKRLGVDASRSlvVG 125
                          90       100
                  ....*....|....*....|
gi 564328074  236 DS---VFVGDAAGRPANWAP 252
Cdd:TIGR01656 126 DRlrdLQAARNAGAAAGLLV 145
PRK08942 PRK08942
D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase;
165-242 9.08e-04

D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase;


Pssm-ID: 236354 [Multi-domain]  Cd Length: 181  Bit Score: 40.19  E-value: 9.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564328074 165 KLVILTNQMGIGRGKLPAEVFKA---KVEAVLEKLGVPFQVLV----ATHAGLN-RKPVSGMWDHLQEKGNegipISIGD 236
Cdd:PRK08942  47 RVVVATNQSGIARGLFTEAQLNAlheKMDWSLADRGGRLDGIYycphHPEDGCDcRKPKPGMLLSIAERLN----IDLAG 122

                 ....*.
gi 564328074 237 SVFVGD 242
Cdd:PRK08942 123 SPMVGD 128
FHA_APLF cd22717
forkhead associated (FHA) domain found in aprataxin and PNK-like factor (APLF) and similar ...
15-81 1.32e-03

forkhead associated (FHA) domain found in aprataxin and PNK-like factor (APLF) and similar proteins; APLF, also called apurinic-apyrimidinic endonuclease APLF, PNK and APTX-like FHA domain-containing protein, or XRCC1-interacting protein 1 (XIP1), is a novel apurinic-apyrimidinic (AP) endonuclease and 3'-5' exonuclease with conserved zinc-finger-like motifs involved in single-strand and double-strand DNA break repair. It is recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. It can introduce nicks at hydroxyuracil and other types of pyrimidine base damage. Together with PARP3, APLF promotes the retention of the LIG4-XRCC4 complex on chromatin and accelerate DNA ligation during non-homologous end-joining (NHEJ). APLF contains an FHA domain at its N-terminus. The FHA domain is a small phosphopeptide recognition module.


Pssm-ID: 438769 [Multi-domain]  Cd Length: 99  Bit Score: 38.03  E-value: 1.32e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564328074  15 PTGGPPPIFLPSDgqALVLGRGPLTQVMDRKCSRNQVEL-IADPETRtvaVKQLGVNP---STVGVQELKP 81
Cdd:cd22717    6 PVDGGKRIELPPG--ETTIGRGPFLGITDKRVSRNHAILeVVDGKLR---IKPTHTNPcfyQPSGKSKLIP 71
 
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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