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Conserved domains on  [gi|159470289|ref|XP_001693292|]
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predicted protein [Chlamydomonas reinhardtii]

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List of domain hits

Name Accession Description Interval E-value
Rad10 super family cl04283
Binding domain of DNA repair protein Ercc1 (rad10/Swi10); Ercc1 and XPF (xeroderma pigmentosum ...
2-111 5.77e-42

Binding domain of DNA repair protein Ercc1 (rad10/Swi10); Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA interstrand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex.


The actual alignment was detected with superfamily member TIGR00597:

Pssm-ID: 262083  Cd Length: 112  Bit Score: 138.81  E-value: 5.77e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159470289    2 ILVNKRQQGNPVLKHIRNVRWQFGDIIPDYQLGLNTAALFLSLRYHLLHPDYILHRIKEQQRLFRLTVLLCHVDVDDCIK 81
Cdd:TIGR00597   3 ILVNPRQKGNPLLKHVRNVPWEYGDVIPDYVLGQGTCALFLSLRYHNLHPDYIHRRLQSLGKNFNLRILLVQVDVKNPQQ 82
                          90       100       110
                  ....*....|....*....|....*....|
gi 159470289   82 PLGEVTRAAVVGDCTLVCAWSPEECARWLE 111
Cdd:TIGR00597  83 ALKELAKMCILNDCTLILAWSFEEAARYLE 112
 
Name Accession Description Interval E-value
rad10 TIGR00597
DNA repair protein rad10; All proteins in this family for which functions are known are ...
2-111 5.77e-42

DNA repair protein rad10; All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].


Pssm-ID: 129685  Cd Length: 112  Bit Score: 138.81  E-value: 5.77e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159470289    2 ILVNKRQQGNPVLKHIRNVRWQFGDIIPDYQLGLNTAALFLSLRYHLLHPDYILHRIKEQQRLFRLTVLLCHVDVDDCIK 81
Cdd:TIGR00597   3 ILVNPRQKGNPLLKHVRNVPWEYGDVIPDYVLGQGTCALFLSLRYHNLHPDYIHRRLQSLGKNFNLRILLVQVDVKNPQQ 82
                          90       100       110
                  ....*....|....*....|....*....|
gi 159470289   82 PLGEVTRAAVVGDCTLVCAWSPEECARWLE 111
Cdd:TIGR00597  83 ALKELAKMCILNDCTLILAWSFEEAARYLE 112
Rad10 pfam03834
Binding domain of DNA repair protein Ercc1 (rad10/Swi10); Ercc1 and XPF (xeroderma pigmentosum ...
1-67 5.60e-31

Binding domain of DNA repair protein Ercc1 (rad10/Swi10); Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA interstrand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex.


Pssm-ID: 252193  Cd Length: 68  Bit Score: 108.84  E-value: 5.60e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 159470289    1 MILVNKRQQGNPVLKHIRNVRWQFGDIIPDYQLGLNTAALFLSLRYHLLHPDYILHRIKEQQRLFRL 67
Cdd:pfam03834   2 SILVSPRQKGNPLLKHLKNVPWEYGDIVPDYVVGKTRCVLFLSLKYHRLHPEYIYRRLKKLQKNYNL 68
RAD10 COG5241
Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, ...
1-188 2.18e-33

Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]


Pssm-ID: 227566 [Multi-domain]  Cd Length: 224  Bit Score: 119.72  E-value: 2.18e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159470289   1 MILVNKRQQGNPVLKHIRNVRWQFGD-IIPDYQLGLNTAALFLSLRYHLLHPDYILHRIKeQQRLFRLTVLLCHVDVDDC 79
Cdd:COG5241   35 EIDVSPLQKGNPQLSRRINSNWVYNAfIKPDEWTDSKATDLFLSLRFHSTRPEYIVLRIS-KLKSYKERPLLNHVDSTNW 113
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159470289  80 IKPLGEVTRAAVVGdcTLVCAWSPEECARWLETYKSYESKSAtyfAVAQERVEADYISRLAAvlagSVRGINRTDTHTLG 159
Cdd:COG5241  114 RASIQELVSTTGIN--TIYLDYSVEERSRYFLTLTYHKLYSD---YIIRRMQSLDRSNEFLI----LIFIVNKSDSEDTL 184
                        170       180
                 ....*....|....*....|....*....
gi 159470289 160 TSFGSLADLMRCKDAEaFSACPGIGPTKV 188
Cdd:COG5241  185 NDIGKLCRFNGASRDE-FELLLGFGFEKA 212
 
Name Accession Description Interval E-value
rad10 TIGR00597
DNA repair protein rad10; All proteins in this family for which functions are known are ...
2-111 5.77e-42

DNA repair protein rad10; All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair].


Pssm-ID: 129685  Cd Length: 112  Bit Score: 138.81  E-value: 5.77e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159470289    2 ILVNKRQQGNPVLKHIRNVRWQFGDIIPDYQLGLNTAALFLSLRYHLLHPDYILHRIKEQQRLFRLTVLLCHVDVDDCIK 81
Cdd:TIGR00597   3 ILVNPRQKGNPLLKHVRNVPWEYGDVIPDYVLGQGTCALFLSLRYHNLHPDYIHRRLQSLGKNFNLRILLVQVDVKNPQQ 82
                          90       100       110
                  ....*....|....*....|....*....|
gi 159470289   82 PLGEVTRAAVVGDCTLVCAWSPEECARWLE 111
Cdd:TIGR00597  83 ALKELAKMCILNDCTLILAWSFEEAARYLE 112
Rad10 pfam03834
Binding domain of DNA repair protein Ercc1 (rad10/Swi10); Ercc1 and XPF (xeroderma pigmentosum ...
1-67 5.60e-31

Binding domain of DNA repair protein Ercc1 (rad10/Swi10); Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA interstrand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex.


Pssm-ID: 252193  Cd Length: 68  Bit Score: 108.84  E-value: 5.60e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 159470289    1 MILVNKRQQGNPVLKHIRNVRWQFGDIIPDYQLGLNTAALFLSLRYHLLHPDYILHRIKEQQRLFRL 67
Cdd:pfam03834   2 SILVSPRQKGNPLLKHLKNVPWEYGDIVPDYVVGKTRCVLFLSLKYHRLHPEYIYRRLKKLQKNYNL 68
RAD10 COG5241
Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, ...
1-188 2.18e-33

Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]


Pssm-ID: 227566 [Multi-domain]  Cd Length: 224  Bit Score: 119.72  E-value: 2.18e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159470289   1 MILVNKRQQGNPVLKHIRNVRWQFGD-IIPDYQLGLNTAALFLSLRYHLLHPDYILHRIKeQQRLFRLTVLLCHVDVDDC 79
Cdd:COG5241   35 EIDVSPLQKGNPQLSRRINSNWVYNAfIKPDEWTDSKATDLFLSLRFHSTRPEYIVLRIS-KLKSYKERPLLNHVDSTNW 113
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159470289  80 IKPLGEVTRAAVVGdcTLVCAWSPEECARWLETYKSYESKSAtyfAVAQERVEADYISRLAAvlagSVRGINRTDTHTLG 159
Cdd:COG5241  114 RASIQELVSTTGIN--TIYLDYSVEERSRYFLTLTYHKLYSD---YIIRRMQSLDRSNEFLI----LIFIVNKSDSEDTL 184
                        170       180
                 ....*....|....*....|....*....
gi 159470289 160 TSFGSLADLMRCKDAEaFSACPGIGPTKV 188
Cdd:COG5241  185 NDIGKLCRFNGASRDE-FELLLGFGFEKA 212
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.11
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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