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Conserved domains on  [gi|564335590|ref|XP_006232120|]
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cell cycle checkpoint protein RAD1 isoform X1 [Rattus norvegicus]

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;
17-257 2.10e-115

Repair protein Rad1/Rec1/Rad17;


:

Pssm-ID: 396631  Cd Length: 257  Bit Score: 331.93  E-value: 2.10e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590   17 LVASLDNVRNLSTVLKAIHFKEHATCFATKNGIKVTVENAKCVQANAFIQADVFQEFII-----------QEESVTFRIN 85
Cdd:pfam02144   1 FSATTSNVRHLYTLLKCIGFVDKALVQISSDGLKFTVEDNRVIQAQAFLDKALFSSYNFnpptaqdddddEEDSPSFCLN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590   86 LTILLDCLSIFGSSPTPGTLTALRMCYQGYGHPLMLFLEEGGVVTVCKITTQEPEDTLDFDFCSTNVMNKIILQSEGLRE 165
Cdd:pfam02144  81 LSALLDCLNIFGGNDDSSVKTSCRMSYKGEGSPLVLILEEDGVTTTCELSTYEPEDDLDLDLDRDEVVFKVILKSDWLHN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590  166 AFSELDMTGDVLQITVSP-DKPYFRLSTFGNAGNSHLDYPKDSDLVEAFHC----NKTQINRYKLSLLKPSTKALALSCK 240
Cdd:pfam02144 161 ALRELDETSEELYISASPtDAPHFALSSFGELGSSKVEFPNESSVLETFECydlgDEIVISRYKFSLLKKARKALALASK 240

                         250
                  ....*....|....*..
gi 564335590  241 VSIRTDNRGFLSLQYMI 257
Cdd:pfam02144 241 VSIRMDVRGLLSLQFMI 257
 
Name Accession Description Interval E-value
Rad1 pfam02144
Repair protein Rad1/Rec1/Rad17;
17-257 2.10e-115

Repair protein Rad1/Rec1/Rad17;


Pssm-ID: 396631  Cd Length: 257  Bit Score: 331.93  E-value: 2.10e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590   17 LVASLDNVRNLSTVLKAIHFKEHATCFATKNGIKVTVENAKCVQANAFIQADVFQEFII-----------QEESVTFRIN 85
Cdd:pfam02144   1 FSATTSNVRHLYTLLKCIGFVDKALVQISSDGLKFTVEDNRVIQAQAFLDKALFSSYNFnpptaqdddddEEDSPSFCLN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590   86 LTILLDCLSIFGSSPTPGTLTALRMCYQGYGHPLMLFLEEGGVVTVCKITTQEPEDTLDFDFCSTNVMNKIILQSEGLRE 165
Cdd:pfam02144  81 LSALLDCLNIFGGNDDSSVKTSCRMSYKGEGSPLVLILEEDGVTTTCELSTYEPEDDLDLDLDRDEVVFKVILKSDWLHN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590  166 AFSELDMTGDVLQITVSP-DKPYFRLSTFGNAGNSHLDYPKDSDLVEAFHC----NKTQINRYKLSLLKPSTKALALSCK 240
Cdd:pfam02144 161 ALRELDETSEELYISASPtDAPHFALSSFGELGSSKVEFPNESSVLETFECydlgDEIVISRYKFSLLKKARKALALASK 240

                         250
                  ....*....|....*..
gi 564335590  241 VSIRTDNRGFLSLQYMI 257
Cdd:pfam02144 241 VSIRMDVRGLLSLQFMI 257
PCNA cd00577
Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These ...
 19-276 2.26e-59

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: 189.38  E-value: 2.26e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590  19 ASLDNVRNLSTVLKAIHFKEHATCF-ATKNGIKVTVENAKCV-QANAFIQADVFQEFIIQEEsVTFRINLTILLDCLSIF 96
Cdd:cd00577    1 ATLSNAKLLKKIVDALSKLVDEANFdITEDGISLQAMDSSHVaLVSLFLPKELFEEYRCDEE-ISLGVNLKSLLKILKCA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590  97 GSSptpgtlTALRMCYQGyGHPLMLFLEE--GGVVTVCKITTQEPeDTLDFDFCSTNVMNKIILQSEGLREAFSELDMTG 174
Cdd:cd00577   80 GNE------DCVTLRADD-EDPLKILFESskGDVTSEFSLKLMDI-DSEQLPIPELEYDATVTLPSDELKDIVRDLESIS 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590 175 DVLQITVSPDKpyFRLSTFGNAGN-SHLDYPKDSDLVEAFHCNKTQINRYKLSLLKPSTKALALSCKVSIRTDNRGFLSL 253
Cdd:cd00577  152 DSVTISASKDG--FKFSAEGELGGaSVTLLPKDSDLLVTIECSEPVSSTYSLKYLKDFTKAAPLSDKVTLSFGSDGPLSL 229

                        250       260
                 ....*....|....*....|...
gi 564335590 254 QYMIRNEdgqiCFVEYYCCPDEE 276
Cdd:cd00577  230 EFKIADG----GHLTFYLAPKIE 248
PRK01115 PRK01115
DNA polymerase sliding clamp; Validated
 45-266 6.21e-06

DNA polymerase sliding clamp; Validated


Pssm-ID: 234903 [Multi-domain]  Cd Length: 247  Bit Score: 46.36  E-value: 6.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590  45 TKNGIKV-TVENAKCVQANAFIQADVFQEFIIQEEsVTFRINLTILLDCLSIFGSSPTpgtltaLRMCYQGYGHPLMLFL 123
Cdd:PRK01115  31 TEDGIRLrALDPAKVAMVDLELPKEAFEEYEVDEE-EKIGVDLEDLKKILKRAKKGDK------LELELDEEENKLKITF 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590 124 EEGGV----VTVCKITTQE-PEDTLDFDFcstnvmnKIILQSEGLREAFSELDMTGDVLQITVSPDKpyFRLSTFGNaGN 198
Cdd:PRK01115 104 GGEKTrefsLPLLDVSSEEpPEPNLELPV-------KAVILGDDLKDAIKDAELVSDHIELEADEDK--FYIEAEGE-GE 173

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564335590 199 SHLDYPKDSDLVEAFHCNKTQINRYKLSLLKPSTKALALSCKVSIRTDNRGFLSLQYMIRNEdGQICF 266
Cdd:PRK01115 174 DEVELSLDSGPLIELSVEEPAKSSYSLDYLKDMVKATSASDEVTIEFGSDMPLKLEFEIAGG-GKVTY 240
 
Name Accession Description Interval E-value
Rad1 pfam02144
Repair protein Rad1/Rec1/Rad17;
17-257 2.10e-115

Repair protein Rad1/Rec1/Rad17;


Pssm-ID: 396631  Cd Length: 257  Bit Score: 331.93  E-value: 2.10e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590   17 LVASLDNVRNLSTVLKAIHFKEHATCFATKNGIKVTVENAKCVQANAFIQADVFQEFII-----------QEESVTFRIN 85
Cdd:pfam02144   1 FSATTSNVRHLYTLLKCIGFVDKALVQISSDGLKFTVEDNRVIQAQAFLDKALFSSYNFnpptaqdddddEEDSPSFCLN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590   86 LTILLDCLSIFGSSPTPGTLTALRMCYQGYGHPLMLFLEEGGVVTVCKITTQEPEDTLDFDFCSTNVMNKIILQSEGLRE 165
Cdd:pfam02144  81 LSALLDCLNIFGGNDDSSVKTSCRMSYKGEGSPLVLILEEDGVTTTCELSTYEPEDDLDLDLDRDEVVFKVILKSDWLHN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590  166 AFSELDMTGDVLQITVSP-DKPYFRLSTFGNAGNSHLDYPKDSDLVEAFHC----NKTQINRYKLSLLKPSTKALALSCK 240
Cdd:pfam02144 161 ALRELDETSEELYISASPtDAPHFALSSFGELGSSKVEFPNESSVLETFECydlgDEIVISRYKFSLLKKARKALALASK 240

                         250
                  ....*....|....*..
gi 564335590  241 VSIRTDNRGFLSLQYMI 257
Cdd:pfam02144 241 VSIRMDVRGLLSLQFMI 257
PCNA cd00577
Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These ...
 19-276 2.26e-59

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: 189.38  E-value: 2.26e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590  19 ASLDNVRNLSTVLKAIHFKEHATCF-ATKNGIKVTVENAKCV-QANAFIQADVFQEFIIQEEsVTFRINLTILLDCLSIF 96
Cdd:cd00577    1 ATLSNAKLLKKIVDALSKLVDEANFdITEDGISLQAMDSSHVaLVSLFLPKELFEEYRCDEE-ISLGVNLKSLLKILKCA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590  97 GSSptpgtlTALRMCYQGyGHPLMLFLEE--GGVVTVCKITTQEPeDTLDFDFCSTNVMNKIILQSEGLREAFSELDMTG 174
Cdd:cd00577   80 GNE------DCVTLRADD-EDPLKILFESskGDVTSEFSLKLMDI-DSEQLPIPELEYDATVTLPSDELKDIVRDLESIS 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590 175 DVLQITVSPDKpyFRLSTFGNAGN-SHLDYPKDSDLVEAFHCNKTQINRYKLSLLKPSTKALALSCKVSIRTDNRGFLSL 253
Cdd:cd00577  152 DSVTISASKDG--FKFSAEGELGGaSVTLLPKDSDLLVTIECSEPVSSTYSLKYLKDFTKAAPLSDKVTLSFGSDGPLSL 229

                        250       260
                 ....*....|....*....|...
gi 564335590 254 QYMIRNEdgqiCFVEYYCCPDEE 276
Cdd:cd00577  230 EFKIADG----GHLTFYLAPKIE 248
PRK01115 PRK01115
DNA polymerase sliding clamp; Validated
 45-266 6.21e-06

DNA polymerase sliding clamp; Validated


Pssm-ID: 234903 [Multi-domain]  Cd Length: 247  Bit Score: 46.36  E-value: 6.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590  45 TKNGIKV-TVENAKCVQANAFIQADVFQEFIIQEEsVTFRINLTILLDCLSIFGSSPTpgtltaLRMCYQGYGHPLMLFL 123
Cdd:PRK01115  31 TEDGIRLrALDPAKVAMVDLELPKEAFEEYEVDEE-EKIGVDLEDLKKILKRAKKGDK------LELELDEEENKLKITF 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564335590 124 EEGGV----VTVCKITTQE-PEDTLDFDFcstnvmnKIILQSEGLREAFSELDMTGDVLQITVSPDKpyFRLSTFGNaGN 198
Cdd:PRK01115 104 GGEKTrefsLPLLDVSSEEpPEPNLELPV-------KAVILGDDLKDAIKDAELVSDHIELEADEDK--FYIEAEGE-GE 173

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564335590 199 SHLDYPKDSDLVEAFHCNKTQINRYKLSLLKPSTKALALSCKVSIRTDNRGFLSLQYMIRNEdGQICF 266
Cdd:PRK01115 174 DEVELSLDSGPLIELSVEEPAKSSYSLDYLKDMVKATSASDEVTIEFGSDMPLKLEFEIAGG-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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