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Conserved domains on  [gi|755521198|ref|XP_011249187|]
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bifunctional polynucleotide phosphatase/kinase isoform X8 [Mus musculus]

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 ...
 17-500 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: 737.99  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198   17 QLGSRGRLWLQS----PTGGPPPIFLPSDGQALVLGRGPLTQVTDRKCSRNQVELIADPESRTVAVKQLGVNPSTVGVQE 92
Cdd:TIGR01663   2 EVEAAGKDVAARictlKPGEAEHHFIHLDAGALFLGRGPETGIRDRKCSKRQIELQADLEKATVALKQLGVNPCGTGGLE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198   93 LKPGLSGSLSLGDVLYLVNGLYPLTLRWEELSTSGSQPDAPPDTP-GDPEEGEDTEPQKKRVRKSSLGWESLKKLLVFTA 171
Cdd:TIGR01663  82 LKPGGEGELGHGDLLEIVNGLHPLTLQFEETFNPEPEPDKEKAEPlSSQDEKRDAEKPEKRDRKGNPGWENLEKLLIFTA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  172 SGVKPQGKVAAFDLDGTLITTRSGKVFPTSPSDWRILYPEIPKKLQELAAEGYK-------------------------- 225
Cdd:TIGR01663 162 AGVKGQEKIAGFDLDGTIIKTKSGKVFPKGPDDWQIIFPEIPEKLKELEADGFKiciftnqggiargkinaddfkakiea 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  226 ----------VLVATHAGLNRKPVSGMWDHLQEQANEGIPISVEDSVFVGDAAGRLAN-WAPGRKKKDFSCADRLFALNV 294
Cdd:TIGR01663 242 ivaklgvpfqVFIAIGAGFYRKPLTGMWDHLKEEANDGTEIQEDDCFFVGDAAGRPANgKAAGKKKKDFSCADRLFAANL 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  295 GLPFATPEEFFLKWPAARFELPAFDPRTISSAGPLYLPESSSLLSPNPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNRD 374
Cdd:TIGR01663 322 GIPFATPEEFFLGKPAAGFEKPAFDPRSVQDQGPLCDPDDLALDDAPCEMVIAVGFPGAGKSHFCKKFFQPAGYKHVNAD 401

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  375 TLGSWQRCVSSCQAALRQGKRVVIDNTNPDVPSRARYIQCAKDAGVPCRCFNFCATIEQARHNNRFREMTDPSHAPVSDM 454
Cdd:TIGR01663 402 TLGSTQNCLTACERALDQGKRCAIDNTNPDAASRAKFLQCARAAGIPCRCFLFNAPLAQAKHNIAFRELSDSAHIKIKDM 481

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*.
gi 755521198  455 VMFSYRKQFEPPTLAEGFLEILEIPFRlQEHLDPALQRLYRQFSEG 500
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 ...
 17-500 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: 737.99  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198   17 QLGSRGRLWLQS----PTGGPPPIFLPSDGQALVLGRGPLTQVTDRKCSRNQVELIADPESRTVAVKQLGVNPSTVGVQE 92
Cdd:TIGR01663   2 EVEAAGKDVAARictlKPGEAEHHFIHLDAGALFLGRGPETGIRDRKCSKRQIELQADLEKATVALKQLGVNPCGTGGLE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198   93 LKPGLSGSLSLGDVLYLVNGLYPLTLRWEELSTSGSQPDAPPDTP-GDPEEGEDTEPQKKRVRKSSLGWESLKKLLVFTA 171
Cdd:TIGR01663  82 LKPGGEGELGHGDLLEIVNGLHPLTLQFEETFNPEPEPDKEKAEPlSSQDEKRDAEKPEKRDRKGNPGWENLEKLLIFTA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  172 SGVKPQGKVAAFDLDGTLITTRSGKVFPTSPSDWRILYPEIPKKLQELAAEGYK-------------------------- 225
Cdd:TIGR01663 162 AGVKGQEKIAGFDLDGTIIKTKSGKVFPKGPDDWQIIFPEIPEKLKELEADGFKiciftnqggiargkinaddfkakiea 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  226 ----------VLVATHAGLNRKPVSGMWDHLQEQANEGIPISVEDSVFVGDAAGRLAN-WAPGRKKKDFSCADRLFALNV 294
Cdd:TIGR01663 242 ivaklgvpfqVFIAIGAGFYRKPLTGMWDHLKEEANDGTEIQEDDCFFVGDAAGRPANgKAAGKKKKDFSCADRLFAANL 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  295 GLPFATPEEFFLKWPAARFELPAFDPRTISSAGPLYLPESSSLLSPNPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNRD 374
Cdd:TIGR01663 322 GIPFATPEEFFLGKPAAGFEKPAFDPRSVQDQGPLCDPDDLALDDAPCEMVIAVGFPGAGKSHFCKKFFQPAGYKHVNAD 401

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  375 TLGSWQRCVSSCQAALRQGKRVVIDNTNPDVPSRARYIQCAKDAGVPCRCFNFCATIEQARHNNRFREMTDPSHAPVSDM 454
Cdd:TIGR01663 402 TLGSTQNCLTACERALDQGKRCAIDNTNPDAASRAKFLQCARAAGIPCRCFLFNAPLAQAKHNIAFRELSDSAHIKIKDM 481

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*.
gi 755521198  455 VMFSYRKQFEPPTLAEGFLEILEIPFRlQEHLDPALQRLYRQFSEG 500
Cdd:TIGR01663 482 VFNGMKKKFEAPALAEGFIAIHEINFK-PLFADEKLEKLYCMFLEE 526
HAD_PNP cd01625
polynucleotide 3'-phosphatase domain similar to the phosphatase domain of the bifunctional ...
 179-305 4.12e-64

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: 204.89  E-value: 4.12e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198 179 KVAAFDLDGTLITTRSGKVFPTSPSDWRILYPEIPKKLQELAAEGYK--------------------------------- 225
Cdd:cd01625    1 KVAAFDLDGTLIKTKSGKVFPTNASDWQILYPSVPEKLKALHKDGYKiviftnqggivrgkltpevfkgkieaileklgv 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198 226 ---VLVATHAGLNRKPVSGMWDHLQEQANEGIPISVEDSVFVGDAAGRlanwapgrkKKDFSCADRLFALNVGLPFATPE 302
Cdd:cd01625   81 piqVYAATKKGKYRKPVTGMWDHLKEDLNSGIPINLKDSFYVGDAAGR---------PKDFSDSDRLFAENVGLKFFTPE 151


                 ...
gi 755521198 303 EFF 305
Cdd:cd01625  152 EFF 154
PNK3P pfam08645
Polynucleotide kinase 3 phosphatase; Polynucleotide kinase 3 phosphatases play a role in the ...
 179-305 2.80e-60

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: 195.17  E-value: 2.80e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  179 KVAAFDLDGTLITTRSGKVFPTSPSDWRILYPEIPKKLQELAAEGYKV-------------------------------- 226
Cdd:pfam08645   1 KIAAFDLDGTLIKTKSGKVFPRNPDDWKWLYPSVPEKLKKLHEDGYKIviftnqggigrkgkkslekfknkieailkklg 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  227 -----LVATHAGLNRKPVSGMWDHLQEQANEGIPISVEDSVFVGDAAGRLanwAPGRKKKDFSCADRLFALNVGLPFATP 301
Cdd:pfam08645  81 vplqvYAATKKDIYRKPNTGMWDEMKKDYNDGVEIDLEKSFYVGDAAGRP---YDTRRKKDFSDSDRKFALNVGIKFKTP 157


                  ....
gi 755521198  302 EEFF 305
Cdd:pfam08645 158 EEFF 161
COG4639 COG4639
Predicted kinase [General function prediction only];
342-476 3.06e-17

Predicted kinase [General function prediction only];


Pssm-ID: 443677 [Multi-domain]  Cd Length: 145  Bit Score: 78.33  E-value: 3.06e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198 342 PEVVVAVGFPGAGKSTFIQEHL-----VSA----GYVHVNRDTLGSWQRCV----SSCQAALRQGKRVVIDNTNPDVPSR 408
Cdd:COG4639    2 LSLVVLIGLPGSGKSTFARRLFaptevVSSddirALLGGDENDQSAWGDVFqlahEIARARLRAGRLTVVDATNLQREAR 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755521198 409 ARYIQCAKDAGVPCRCFNFCATIEQARHNNRFREmtdpshAPVSDMVMFSYRKQFE-PPTLAEGFLEIL 476
Cdd:COG4639   82 RRLLALARAYGALVVAVVLDVPLEVCLARNAARD------RQVPEEVIRRMLRRLRrPPLPEEGFRVVY 144
pseT PHA02530
polynucleotide kinase; Provisional
 342-463 8.70e-07

polynucleotide kinase; Provisional


Pssm-ID: 222856 [Multi-domain]  Cd Length: 300  Bit Score: 50.79  E-value: 8.70e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198 342 PEVVVAVGFPGAGKSTFIQEHL-VSAGYVHVNRDTL-------GSW---------QRCVSSCQ-----AALRQGKRVVID 399
Cdd:PHA02530   2 MKIILTVGVPGSGKSTWAREFAaKNPKAVNVNRDDLrqslfghGEWgeykftkekEDLVTKAQeaaalAALKSGKSVIIS 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755521198 400 NTNPdVPSRARYIQ-CAKDAGVPCRCFNFCATIEQARHNNRFR-EMTDPSHAPVSdmvMFSYRKQF 463
Cdd:PHA02530  82 DTNL-NPERRRKWKeLAKELGAEFEEKVFDVPVEELVKRNRKRgERAVPEDVLRS---MFKQMKEY 143
 
Name Accession Description Interval E-value
PNK-3'Pase TIGR01663
polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5 ...
 17-500 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: 737.99  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198   17 QLGSRGRLWLQS----PTGGPPPIFLPSDGQALVLGRGPLTQVTDRKCSRNQVELIADPESRTVAVKQLGVNPSTVGVQE 92
Cdd:TIGR01663   2 EVEAAGKDVAARictlKPGEAEHHFIHLDAGALFLGRGPETGIRDRKCSKRQIELQADLEKATVALKQLGVNPCGTGGLE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198   93 LKPGLSGSLSLGDVLYLVNGLYPLTLRWEELSTSGSQPDAPPDTP-GDPEEGEDTEPQKKRVRKSSLGWESLKKLLVFTA 171
Cdd:TIGR01663  82 LKPGGEGELGHGDLLEIVNGLHPLTLQFEETFNPEPEPDKEKAEPlSSQDEKRDAEKPEKRDRKGNPGWENLEKLLIFTA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  172 SGVKPQGKVAAFDLDGTLITTRSGKVFPTSPSDWRILYPEIPKKLQELAAEGYK-------------------------- 225
Cdd:TIGR01663 162 AGVKGQEKIAGFDLDGTIIKTKSGKVFPKGPDDWQIIFPEIPEKLKELEADGFKiciftnqggiargkinaddfkakiea 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  226 ----------VLVATHAGLNRKPVSGMWDHLQEQANEGIPISVEDSVFVGDAAGRLAN-WAPGRKKKDFSCADRLFALNV 294
Cdd:TIGR01663 242 ivaklgvpfqVFIAIGAGFYRKPLTGMWDHLKEEANDGTEIQEDDCFFVGDAAGRPANgKAAGKKKKDFSCADRLFAANL 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  295 GLPFATPEEFFLKWPAARFELPAFDPRTISSAGPLYLPESSSLLSPNPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNRD 374
Cdd:TIGR01663 322 GIPFATPEEFFLGKPAAGFEKPAFDPRSVQDQGPLCDPDDLALDDAPCEMVIAVGFPGAGKSHFCKKFFQPAGYKHVNAD 401

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  375 TLGSWQRCVSSCQAALRQGKRVVIDNTNPDVPSRARYIQCAKDAGVPCRCFNFCATIEQARHNNRFREMTDPSHAPVSDM 454
Cdd:TIGR01663 402 TLGSTQNCLTACERALDQGKRCAIDNTNPDAASRAKFLQCARAAGIPCRCFLFNAPLAQAKHNIAFRELSDSAHIKIKDM 481

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*.
gi 755521198  455 VMFSYRKQFEPPTLAEGFLEILEIPFRlQEHLDPALQRLYRQFSEG 500
Cdd:TIGR01663 482 VFNGMKKKFEAPALAEGFIAIHEINFK-PLFADEKLEKLYCMFLEE 526
DNA-3'-Pase TIGR01664
DNA 3'-phosphatase; This model represents a family of proteins and protein domains which ...
 166-306 2.90e-64

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: 205.76  E-value: 2.90e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  166 LLVFTASGVKPQGKVAAFDLDGTLITTRSGKVFPTSPSDWRILYPEIPKKLQELAAEGYK-------------------- 225
Cdd:TIGR01664   1 LFVFTADGPKPQSKVAAFDLDGTLITTRSGKVFPTSASDWRFLYPEIPAKLQELDDEGYKiviftnqsgigrgklsaesf 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  226 ----------------VLVATHAGLNRKPVSGMWDHLQEQANEgiPISVEDSVFVGDAAGRlanwapgrkKKDFSCADRL 289
Cdd:TIGR01664  81 knkieafleklkvpiqVLAATHAGLYRKPMTGMWEYLQSQYNS--PIKMTRSFYVGDAAGR---------KLDFSDADIK 149

                         170
                  ....*....|....*..
gi 755521198  290 FALNVGLPFATPEEFFL 306
Cdd:TIGR01664 150 FAKNLGLEFKYPEEFFL 166
HAD_PNP cd01625
polynucleotide 3'-phosphatase domain similar to the phosphatase domain of the bifunctional ...
 179-305 4.12e-64

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: 204.89  E-value: 4.12e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198 179 KVAAFDLDGTLITTRSGKVFPTSPSDWRILYPEIPKKLQELAAEGYK--------------------------------- 225
Cdd:cd01625    1 KVAAFDLDGTLIKTKSGKVFPTNASDWQILYPSVPEKLKALHKDGYKiviftnqggivrgkltpevfkgkieaileklgv 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198 226 ---VLVATHAGLNRKPVSGMWDHLQEQANEGIPISVEDSVFVGDAAGRlanwapgrkKKDFSCADRLFALNVGLPFATPE 302
Cdd:cd01625   81 piqVYAATKKGKYRKPVTGMWDHLKEDLNSGIPINLKDSFYVGDAAGR---------PKDFSDSDRLFAENVGLKFFTPE 151


                 ...
gi 755521198 303 EFF 305
Cdd:cd01625  152 EFF 154
PNK3P pfam08645
Polynucleotide kinase 3 phosphatase; Polynucleotide kinase 3 phosphatases play a role in the ...
 179-305 2.80e-60

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: 195.17  E-value: 2.80e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  179 KVAAFDLDGTLITTRSGKVFPTSPSDWRILYPEIPKKLQELAAEGYKV-------------------------------- 226
Cdd:pfam08645   1 KIAAFDLDGTLIKTKSGKVFPRNPDDWKWLYPSVPEKLKKLHEDGYKIviftnqggigrkgkkslekfknkieailkklg 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  227 -----LVATHAGLNRKPVSGMWDHLQEQANEGIPISVEDSVFVGDAAGRLanwAPGRKKKDFSCADRLFALNVGLPFATP 301
Cdd:pfam08645  81 vplqvYAATKKDIYRKPNTGMWDEMKKDYNDGVEIDLEKSFYVGDAAGRP---YDTRRKKDFSDSDRKFALNVGIKFKTP 157


                  ....
gi 755521198  302 EEFF 305
Cdd:pfam08645 158 EEFF 161
FHA_PNKP cd22736
forkhead associated (FHA) domain found in bifunctional polynucleotide phosphatase/kinase (PNKP) ...
 23-122 2.28e-56

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: 182.68  E-value: 2.28e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  23 RLWLQSPTGGPPPIFLPsDGQALVLGRGPLTQVTDRKCSRNQVELIADPESRTVAVKQLGVNPSTVGVQELKPGLSGSLS 102
Cdd:cd22736    1 RCWLVSVDGGHPPIFLP-DGQALVLGRGPETRVTDRKCSRTQVELVADYESRTVAVTQLGVNPSSVGEQELKPGLSGSLK 79

                         90       100
                 ....*....|....*....|
gi 755521198 103 LGDVLYLVNGLYPLTLRWEE 122
Cdd:cd22736   80 EGQTLYLVNGLYPLTLRFEE 99
FHA_APTX_PNKP cd22716
forkhead associated (FHA) domain found in aprataxin, bifunctional polynucleotide phosphatase ...
 25-122 3.62e-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: 140.11  E-value: 3.62e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  25 WLQSPTGGPPPIFLPsDGQALVLGRGPLTQVTDRKCSRNQVELIADPESRTVAVKQLGVNPSTVGVQELKPGLSGSLSLG 104
Cdd:cd22716    1 ILVCCSSSHPPIPLP-DGVPVILGRGPQTQITDKRCSRQQVELTANYEKRYVLVKQLGPNPSSVGGKLLEKGDEAELSPG 79

                         90
                 ....*....|....*...
gi 755521198 105 DVLYLVNGLYPLTLRWEE 122
Cdd:cd22716   80 ETLHLLNGKYPHTVYFEG 97
FHA_2 pfam17913
FHA domain; This entry represents a divergent FHA domain which in PNK binds to phosphorylated ...
 25-121 5.21e-39

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: 137.04  E-value: 5.21e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198   25 WLQSPTGGPPPIFLPsDGQALVLGRGPLTQVTDRKCSRNQVELIADPESRTVAVKQLGVNPSTVGVQELKPGLSGSLSLG 104
Cdd:pfam17913   2 YLVSLEGTHPPIPLP-HGQPVVIGRGPETGITDKKCSRNQVELKADCEKRYVKVKQLGANPSGLNGFKLKKGESYELKHG 80

                          90
                  ....*....|....*..
gi 755521198  105 DVLYLVNGLYPLTLRWE 121
Cdd:pfam17913  81 DVLELLNGKHPHRVEFN 97
HAD-SF-IIIA TIGR01662
HAD-superfamily hydrolase, subfamily IIIA; This subfamily falls within the Haloacid ...
 179-287 4.47e-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: 103.25  E-value: 4.47e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  179 KVAAFDLDGTLITtrsgKVFPTSPSDWRILYPEIPKKLQELAAEGYKVLVATH--------------------------- 231
Cdd:TIGR01662   1 KAVVLDLDGTLTD----DVPYVSDEDERILYPEVPDALAELKEAGYKVVIVTNqsgigrgyfsrsfsgrvarrleelgvp 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 755521198  232 ------AGLNRKPVSGMWDHLQEQANEgipISVEDSVFVGDAAGRLANWAPGRKKKDFSCAD 287
Cdd:TIGR01662  77 idilyaCPGCRKPKPGMFLEALKRFNE---IDPEESVYVGDQDLTDLQAAKRVGLATILVAP 135
FHA_APTX-like cd22671
forkhead associated (FHA) domain found in aprataxin, bifunctional polynucleotide phosphatase ...
 25-119 1.86e-25

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: 100.08  E-value: 1.86e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  25 WLQSPTGGP-PPIFLPsDGQALVLGRGPLTQVTDRKCSRNQVELIADPESRTVAVKQLGVNPSTVGV-----QELKPGLS 98
Cdd:cd22671    1 FLRPVDGGGgPPIELK-EGGPTVLGRGPLLGIRDKRVSRKQAEITVDDDTGSVTVTQLGTNPSFVNRadgegKVLKKGES 79

                         90       100
                 ....*....|....*....|.
gi 755521198  99 GSLSLGDVLYLVNGLYPLTLR 119
Cdd:cd22671   80 VELKDGDVISLLPGKYPFRVE 100
FHA_APTX cd22735
forkhead associated (FHA) domain found in aprataxin and similar proteins; Aprataxin (EC 3.6.1. ...
 25-122 8.41e-24

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: 95.63  E-value: 8.41e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  25 WLQSPTGGPPPIFLPSDgQALVLGRGPLTQVTDRKCSRNQVELIADPESRTVAVKQLGVNPSTVGVQELKPGLSGSLSLG 104
Cdd:cd22735    4 WLVSKDGRHLRIRLPHL-EAVVIGRGPETKITDKKCSRHQVQLKADCNKGYVKVKQLGVNPTSIDLVDIGKDEEVKLKPG 82

                         90
                 ....*....|....*...
gi 755521198 105 DVLYLVNGLYPLTLRWEE 122
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 ...
 344-466 1.81e-21

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: 90.45  E-value: 1.81e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  344 VVVAVGFPGAGKSTFIQEHLVSAGYVHVNRDTL-----------GSWQRCVSS---------CQAALRQGKRVVIDNTNP 403
Cdd:pfam13671   1 LILLVGLPGSGKSTLARRLLEELGAVRLSSDDErkrlfgegrpsISYYTDATDrtyerlhelARIALRAGRPVILDATNL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 755521198  404 DVPSRARYIQCAKDAGVPCRCFNFCATIEQARHNNRFREMTDPSHAPVSDMVMFSYRKQFEPP 466
Cdd:pfam13671  81 RRDERARLLALAREYGVPVRIVVFEAPEEVLRERLAARARAGGDPSDVPEEVLDRQKARFEPP 143
COG4639 COG4639
Predicted kinase [General function prediction only];
342-476 3.06e-17

Predicted kinase [General function prediction only];


Pssm-ID: 443677 [Multi-domain]  Cd Length: 145  Bit Score: 78.33  E-value: 3.06e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198 342 PEVVVAVGFPGAGKSTFIQEHL-----VSA----GYVHVNRDTLGSWQRCV----SSCQAALRQGKRVVIDNTNPDVPSR 408
Cdd:COG4639    2 LSLVVLIGLPGSGKSTFARRLFaptevVSSddirALLGGDENDQSAWGDVFqlahEIARARLRAGRLTVVDATNLQREAR 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755521198 409 ARYIQCAKDAGVPCRCFNFCATIEQARHNNRFREmtdpshAPVSDMVMFSYRKQFE-PPTLAEGFLEIL 476
Cdd:COG4639   82 RRLLALARAYGALVVAVVLDVPLEVCLARNAARD------RQVPEEVIRRMLRRLRrPPLPEEGFRVVY 144
COG0645 COG0645
Predicted kinase, contains AAA domain [General function prediction only];
344-493 4.94e-10

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


Pssm-ID: 440410 [Multi-domain]  Cd Length: 164  Bit Score: 58.39  E-value: 4.94e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198 344 VVVAVGFPGAGKSTF---IQEHLvsaGYVHVNRDT-----LGSW---------------QRCVSSCQAALRQGKRVVIDN 400
Cdd:COG0645    1 LILVCGLPGSGKSTLaraLAERL---GAVRLRSDVvrkrlFGAGlaplerspeatartyARLLALARELLAAGRSVILDA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198 401 TNPDVPSRARYIQCAKDAGVPCRCFNFCATIEQARHNNRFR-EMTDPSHApvSDMVMFSYRKQFEPPTLAEGFLEILEip 479
Cdd:COG0645   78 TFLRRAQREAFRALAEEAGAPFVLIWLDAPEEVLRERLEARnAEGGDSDA--TWEVLERQLAFEEPLTEDEGFLLVVD-- 153

                        170
                 ....*....|....
gi 755521198 480 frlQEHLDPALQRL 493
Cdd:COG0645  154 ---TSGLEEALAAL 164
pseT PHA02530
polynucleotide kinase; Provisional
 342-463 8.70e-07

polynucleotide kinase; Provisional


Pssm-ID: 222856 [Multi-domain]  Cd Length: 300  Bit Score: 50.79  E-value: 8.70e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198 342 PEVVVAVGFPGAGKSTFIQEHL-VSAGYVHVNRDTL-------GSW---------QRCVSSCQ-----AALRQGKRVVID 399
Cdd:PHA02530   2 MKIILTVGVPGSGKSTWAREFAaKNPKAVNVNRDDLrqslfghGEWgeykftkekEDLVTKAQeaaalAALKSGKSVIIS 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755521198 400 NTNPdVPSRARYIQ-CAKDAGVPCRCFNFCATIEQARHNNRFR-EMTDPSHAPVSdmvMFSYRKQF 463
Cdd:PHA02530  82 DTNL-NPERRRKWKeLAKELGAEFEEKVFDVPVEELVKRNRKRgERAVPEDVLRS---MFKQMKEY 143
HAD-SF-IIIC TIGR01681
HAD-superfamily phosphatase, subfamily IIIC; This model represents the IIIC subfamily of the ...
 179-230 5.73e-06

HAD-superfamily phosphatase, subfamily IIIC; This model represents the IIIC subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate nucleophile hydrolases. Subfamily III (also including IIIA - TIGR01662 and IIIB - pfam03767) contains sequences which do not contain either of the insert domains (between the 1st and 2nd conserved catalytic motifs, subfamily I - TIGR01493, TIGR01509, TIGR01549, TIGR01488, TIGR01494, TIGR01658, TIGR01544 and TIGR01545, or between the 2nd and 3rd, subfamily II - TIGR01460 and TIGR01484). Subfamily IIIC contains five relatively distantly related clades: a family of viral proteins (TIGR01684), a family of eukaryotic proteins called MDP-1 and a family of archaeal proteins most closely related to MDP-1 (TIGR01685), a family of bacteria including the Streptomyces FkbH protein (TIGR01686), and a small clade including the Pasteurella BcbF and EcbF proteins. The overall lack of species overlap among these clades may indicate a conserved function, but the degree of divergence between the clades and the differences in archetecture outside of the domain in some clades warns against such a conclusion. No member of this subfamily is characterized with respect to function, however the MDP-1 protein is a characterized phosphatase. All of the characterized enzymes within subfamily III are phosphatases, and all of the active site residues characteristic of HAD-superfamily phosphatases are present in subfamily IIIC.


Pssm-ID: 273752 [Multi-domain]  Cd Length: 128  Bit Score: 45.50  E-value: 5.73e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 755521198  179 KVAAFDLDGTLITTRSGKVFPTSPSDWRILYPEIPKKLQELAAEGYKVLVAT 230
Cdd:TIGR01681   1 KVIVFDLDNTLWTGENIVVGEDPIIDLEVTIKEIRDKLQTLKKNGFLLALAS 52
FHA_APLF cd22717
forkhead associated (FHA) domain found in aprataxin and PNK-like factor (APLF) and similar ...
 29-95 4.40e-05

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: 42.27  E-value: 4.40e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198  29 PTGGPPPIFLPSDgqALVLGRGPLTQVTDRKCSRNQVELiaDPESRTVAVKQLGVNP---STVGVQELKP 95
Cdd:cd22717    6 PVDGGKRIELPPG--ETTIGRGPFLGITDKRVSRNHAIL--EVVDGKLRIKPTHTNPcfyQPSGKSKLIP 71
HisB1/GmhB COG0241
Histidinol phosphatase/D-glycero-mannoheptose bisphosphatephosphatase, HAD superfamily [Amino ...
 183-264 1.93e-03

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: 39.31  E-value: 1.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755521198 183 FDLDGTLITtRSGKVfpTSPSDWRiLYPEIPKKLQELAAEGYKVLVATH-AGLNRK--PVSGMW---DHLQEQ-ANEGIP 255
Cdd:COG0241    8 LDRDGTINE-DVGYV--KSPEEFE-FLPGVLEALARLNEAGYRLVVVTNqSGIGRGlfTEEDLNavhAKMLELlAAEGGR 83


                 ....*....
gi 755521198 256 IsveDSVFV 264
Cdd:COG0241   84 I---DAIYY 89
 
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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