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Conserved domains on  [gi|62859563|ref|NP_001016045|]
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cell cycle checkpoint protein RAD1 [Xenopus tropicalis]

Protein Classification

Rad1/Rec1/Rad17 family repair protein( domain architecture ID 12031406)

Rad1/Rec1/Rad17 family repair protein similar to Homo sapiens cell cycle checkpoint protein RAD1, Saccharomyces cerevisiae DNA damage checkpoint control protein RAD17 and Ustilago maydis DNA repair exonuclease REC1

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rad1 pfam02144
Repair protein Rad1/Rec1/Rad17;
16-256 4.71e-114

Repair protein Rad1/Rec1/Rad17;


:

Pssm-ID: 396631  Cd Length: 257  Bit Score: 328.85  E-value: 4.71e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563    16 LTCSLDNARNLSNILKAIHFKDHASCFATNNGLKVTVENAKCLQANAFIQAGIFQEFNIR-----------EESVVFRIN 84
Cdd:pfam02144   1 FSATTSNVRHLYTLLKCIGFVDKALVQISSDGLKFTVEDNRVIQAQAFLDKALFSSYNFNpptaqdddddeEDSPSFCLN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563    85 LTVLLDCLTIFGASAGPGTPTALKMCYQGYGHPLVLFLEEGGVVTVCKIHTQEPEETLDFDFCSTNVLNKIILQSEGLRE 164
Cdd:pfam02144  81 LSALLDCLNIFGGNDDSSVKTSCRMSYKGEGSPLVLILEEDGVTTTCELSTYEPEDDLDLDLDRDEVVFKVILKSDWLHN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563   165 AFAELDMTSDFLQIIMSP-DKPYFRLSTFGNAGSAHLDYPKDSDLIEAFHC----TQTQTNRYKISLLKPSTKALALSCK 239
Cdd:pfam02144 161 ALRELDETSEELYISASPtDAPHFALSSFGELGSSKVEFPNESSVLETFECydlgDEIVISRYKFSLLKKARKALALASK 240

                         250
                  ....*....|....*..
gi 62859563   240 VSIRTDNRGFLSLQYMI 256
Cdd:pfam02144 241 VSIRMDVRGLLSLQFMI 257
 
Name Accession Description Interval E-value
Rad1 pfam02144
Repair protein Rad1/Rec1/Rad17;
16-256 4.71e-114

Repair protein Rad1/Rec1/Rad17;


Pssm-ID: 396631  Cd Length: 257  Bit Score: 328.85  E-value: 4.71e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563    16 LTCSLDNARNLSNILKAIHFKDHASCFATNNGLKVTVENAKCLQANAFIQAGIFQEFNIR-----------EESVVFRIN 84
Cdd:pfam02144   1 FSATTSNVRHLYTLLKCIGFVDKALVQISSDGLKFTVEDNRVIQAQAFLDKALFSSYNFNpptaqdddddeEDSPSFCLN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563    85 LTVLLDCLTIFGASAGPGTPTALKMCYQGYGHPLVLFLEEGGVVTVCKIHTQEPEETLDFDFCSTNVLNKIILQSEGLRE 164
Cdd:pfam02144  81 LSALLDCLNIFGGNDDSSVKTSCRMSYKGEGSPLVLILEEDGVTTTCELSTYEPEDDLDLDLDRDEVVFKVILKSDWLHN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563   165 AFAELDMTSDFLQIIMSP-DKPYFRLSTFGNAGSAHLDYPKDSDLIEAFHC----TQTQTNRYKISLLKPSTKALALSCK 239
Cdd:pfam02144 161 ALRELDETSEELYISASPtDAPHFALSSFGELGSSKVEFPNESSVLETFECydlgDEIVISRYKFSLLKKARKALALASK 240

                         250
                  ....*....|....*..
gi 62859563   240 VSIRTDNRGFLSLQYMI 256
Cdd:pfam02144 241 VSIRMDVRGLLSLQFMI 257
PCNA cd00577
Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These ...
 19-275 3.13e-58

Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY].


Pssm-ID: 238322 [Multi-domain]  Cd Length: 248  Bit Score: 186.30  E-value: 3.13e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563  19 SLDNARNLSNILKAIHFKDHASCF-ATNNGLKVTVENAKC-LQANAFIQAGIFQEFNIREEsVVFRINLTVLLDCLTIFG 96
Cdd:cd00577   2 TLSNAKLLKKIVDALSKLVDEANFdITEDGISLQAMDSSHvALVSLFLPKELFEEYRCDEE-ISLGVNLKSLLKILKCAG 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563  97 ASagpgtpTALKMCYQGyGHPLVLFLEE--GGVVTVCKIHTQEPEETLDfDFCSTNVLNKIILQSEGLREAFAELDMTSD 174
Cdd:cd00577  81 NE------DCVTLRADD-EDPLKILFESskGDVTSEFSLKLMDIDSEQL-PIPELEYDATVTLPSDELKDIVRDLESISD 152

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563 175 FLQIIMSPDKpyFRLSTFGN-AGSAHLDYPKDSDLIEAFHCTQTQTNRYKISLLKPSTKALALSCKVSIRTDNRGFLSLQ 253
Cdd:cd00577 153 SVTISASKDG--FKFSAEGElGGASVTLLPKDSDLLVTIECSEPVSSTYSLKYLKDFTKAAPLSDKVTLSFGSDGPLSLE 230

                       250       260
                ....*....|....*....|..
gi 62859563 254 YMIRNEdgqiCFVEYYCCPDEE 275
Cdd:cd00577 231 FKIADG----GHLTFYLAPKIE 248
PRK01115 PRK01115
DNA polymerase sliding clamp; Validated
 135-265 1.07e-04

DNA polymerase sliding clamp; Validated


Pssm-ID: 234903 [Multi-domain]  Cd Length: 247  Bit Score: 42.50  E-value: 1.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563  135 TQEPEE-TLDFDFcstnvlnKIILQSEGLREAFAELDMTSDFLQIIMSPDKpyFRLSTFGNaGSAHLDYPKDSDLIEAFH 213
Cdd:PRK01115 120 SEEPPEpNLELPV-------KAVILGDDLKDAIKDAELVSDHIELEADEDK--FYIEAEGE-GEDEVELSLDSGPLIELS 189

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 62859563  214 CTQTQTNRYKISLLKPSTKALALSCKVSIRTDNRGFLSLQYMIRNEdGQICF 265
Cdd:PRK01115 190 VEEPAKSSYSLDYLKDMVKATSASDEVTIEFGSDMPLKLEFEIAGG-GKVTY 240
 
Name Accession Description Interval E-value
Rad1 pfam02144
Repair protein Rad1/Rec1/Rad17;
16-256 4.71e-114

Repair protein Rad1/Rec1/Rad17;


Pssm-ID: 396631  Cd Length: 257  Bit Score: 328.85  E-value: 4.71e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563    16 LTCSLDNARNLSNILKAIHFKDHASCFATNNGLKVTVENAKCLQANAFIQAGIFQEFNIR-----------EESVVFRIN 84
Cdd:pfam02144   1 FSATTSNVRHLYTLLKCIGFVDKALVQISSDGLKFTVEDNRVIQAQAFLDKALFSSYNFNpptaqdddddeEDSPSFCLN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563    85 LTVLLDCLTIFGASAGPGTPTALKMCYQGYGHPLVLFLEEGGVVTVCKIHTQEPEETLDFDFCSTNVLNKIILQSEGLRE 164
Cdd:pfam02144  81 LSALLDCLNIFGGNDDSSVKTSCRMSYKGEGSPLVLILEEDGVTTTCELSTYEPEDDLDLDLDRDEVVFKVILKSDWLHN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563   165 AFAELDMTSDFLQIIMSP-DKPYFRLSTFGNAGSAHLDYPKDSDLIEAFHC----TQTQTNRYKISLLKPSTKALALSCK 239
Cdd:pfam02144 161 ALRELDETSEELYISASPtDAPHFALSSFGELGSSKVEFPNESSVLETFECydlgDEIVISRYKFSLLKKARKALALASK 240

                         250
                  ....*....|....*..
gi 62859563   240 VSIRTDNRGFLSLQYMI 256
Cdd:pfam02144 241 VSIRMDVRGLLSLQFMI 257
PCNA cd00577
Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These ...
 19-275 3.13e-58

Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY].


Pssm-ID: 238322 [Multi-domain]  Cd Length: 248  Bit Score: 186.30  E-value: 3.13e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563  19 SLDNARNLSNILKAIHFKDHASCF-ATNNGLKVTVENAKC-LQANAFIQAGIFQEFNIREEsVVFRINLTVLLDCLTIFG 96
Cdd:cd00577   2 TLSNAKLLKKIVDALSKLVDEANFdITEDGISLQAMDSSHvALVSLFLPKELFEEYRCDEE-ISLGVNLKSLLKILKCAG 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563  97 ASagpgtpTALKMCYQGyGHPLVLFLEE--GGVVTVCKIHTQEPEETLDfDFCSTNVLNKIILQSEGLREAFAELDMTSD 174
Cdd:cd00577  81 NE------DCVTLRADD-EDPLKILFESskGDVTSEFSLKLMDIDSEQL-PIPELEYDATVTLPSDELKDIVRDLESISD 152

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563 175 FLQIIMSPDKpyFRLSTFGN-AGSAHLDYPKDSDLIEAFHCTQTQTNRYKISLLKPSTKALALSCKVSIRTDNRGFLSLQ 253
Cdd:cd00577 153 SVTISASKDG--FKFSAEGElGGASVTLLPKDSDLLVTIECSEPVSSTYSLKYLKDFTKAAPLSDKVTLSFGSDGPLSLE 230

                       250       260
                ....*....|....*....|..
gi 62859563 254 YMIRNEdgqiCFVEYYCCPDEE 275
Cdd:cd00577 231 FKIADG----GHLTFYLAPKIE 248
PRK01115 PRK01115
DNA polymerase sliding clamp; Validated
 135-265 1.07e-04

DNA polymerase sliding clamp; Validated


Pssm-ID: 234903 [Multi-domain]  Cd Length: 247  Bit Score: 42.50  E-value: 1.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62859563  135 TQEPEE-TLDFDFcstnvlnKIILQSEGLREAFAELDMTSDFLQIIMSPDKpyFRLSTFGNaGSAHLDYPKDSDLIEAFH 213
Cdd:PRK01115 120 SEEPPEpNLELPV-------KAVILGDDLKDAIKDAELVSDHIELEADEDK--FYIEAEGE-GEDEVELSLDSGPLIELS 189

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 62859563  214 CTQTQTNRYKISLLKPSTKALALSCKVSIRTDNRGFLSLQYMIRNEdGQICF 265
Cdd:PRK01115 190 VEEPAKSSYSLDYLKDMVKATSASDEVTIEFGSDMPLKLEFEIAGG-GKVTY 240
 
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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