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Conserved domains on  [gi|19112907|ref|NP_596115|]
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DNA repair endonuclease non-catalytic (ERCC1) subunit Swi10 [Schizosaccharomyces pombe]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RAD10 COG5241
Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, ...
 1-236 1.02e-117

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


:

Pssm-ID: 227566 [Multi-domain]  Cd Length: 224  Bit Score: 335.43  E-value: 1.02e-117
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907   1 MSDIDDEEFEQLAVSALEEVEKKAGFAQQPTpqkvsrvTAHSILVNPRQKGNPLLPHVRNVPWEYTD-IVPDFVMGTGIC 79
Cdd:COG5241   1 MNNTDPTSFESILAGVAKLRKEKSGADTTGS-------QSLEIDVSPLQKGNPQLSRRINSNWVYNAfIKPDEWTDSKAT 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907  80 SLFLSLKYHHLHPEYIYSRISKLgKSYNLRILLILVDVENHQASIQELVKTSIVNqyTLILAWSSEEAARYLETYKAYEN 159
Cdd:COG5241  74 DLFLSLRFHSTRPEYIVLRISKL-KSYKERPLLNHVDSTNWRASIQELVSTTGIN--TIYLDYSVEERSRYFLTLTYHKL 150

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19112907 160 MSPALIMEKPSTDYlsqVQSFLTSIRGINKSDSLSLLSKFGSLERALVASRDELEQLEGWGPTKVNRFLEAVQQPFM 236
Cdd:COG5241 151 YSDYIIRRMQSLDR---SNEFLILIFIVNKSDSEDTLNDIGKLCRFNGASRDEFELLLGFGFEKAAKYIEYLNLPFM 224
 
Name Accession Description Interval E-value
RAD10 COG5241
Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, ...
 1-236 1.02e-117

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


Pssm-ID: 227566 [Multi-domain]  Cd Length: 224  Bit Score: 335.43  E-value: 1.02e-117
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907   1 MSDIDDEEFEQLAVSALEEVEKKAGFAQQPTpqkvsrvTAHSILVNPRQKGNPLLPHVRNVPWEYTD-IVPDFVMGTGIC 79
Cdd:COG5241   1 MNNTDPTSFESILAGVAKLRKEKSGADTTGS-------QSLEIDVSPLQKGNPQLSRRINSNWVYNAfIKPDEWTDSKAT 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907  80 SLFLSLKYHHLHPEYIYSRISKLgKSYNLRILLILVDVENHQASIQELVKTSIVNqyTLILAWSSEEAARYLETYKAYEN 159
Cdd:COG5241  74 DLFLSLRFHSTRPEYIVLRISKL-KSYKERPLLNHVDSTNWRASIQELVSTTGIN--TIYLDYSVEERSRYFLTLTYHKL 150

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19112907 160 MSPALIMEKPSTDYlsqVQSFLTSIRGINKSDSLSLLSKFGSLERALVASRDELEQLEGWGPTKVNRFLEAVQQPFM 236
Cdd:COG5241 151 YSDYIIRRMQSLDR---SNEFLILIFIVNKSDSEDTLNDIGKLCRFNGASRDEFELLLGFGFEKAAKYIEYLNLPFM 224
ERCC1_C-like cd22325
Central domain of ERCC1; ERCC1 is a subunit of the DNA structure-specific endonuclease ...
 41-168 1.50e-79

Central domain of ERCC1; ERCC1 is a subunit of the DNA structure-specific endonuclease XPF-ERCC1, which incises a damaged DNA strand on the 5' side of a lesion during nucleotide excision repair. It also plays roles in DNA interstrand crosslink repair and homologous recombination. The ERCC1 central domain modeled here interacts tightly with XPF and may be involved in binding to single-stranded DNA. It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411729  Cd Length: 128  Bit Score: 235.10  E-value: 1.50e-79
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907  41 HSILVNPRQKGNPLLPHVRNVPWEYTDIVPDFVMGTGICSLFLSLKYHHLHPEYIYSRISKLGKSYNLRILLILVDVENH 120
Cdd:cd22325   1 NSIIVSPRQKGNPVLKHIRNVPWEYGDIVPDYVLGKSTCALFLSLKYHRLHPEYIHERIKELGKSYKLRILLVLVDVEDP 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 19112907 121 QASIQELVKTSIVNQYTLILAWSSEEAARYLETYKAYENMSPALIMEK 168
Cdd:cd22325  81 HSALKELTKLAILNDCTLILAWSPEEAARYLETYKSYENKPADLIKER 128
Rad10 pfam03834
Binding domain of DNA repair protein Ercc1 (rad10/Swi10); Ercc1 and XPF (xeroderma pigmentosum ...
 42-155 1.42e-73

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: 461070  Cd Length: 114  Bit Score: 219.65  E-value: 1.42e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907    42 SILVNPRQKGNPLLPHVRNVPWEYTDIVPDFVMGTGICSLFLSLKYHHLHPEYIYSRISKLGKSYNLRILLILVDVENHQ 121
Cdd:pfam03834   1 TILVNPRQKGNPLLKHIRNVPWEYGDIVPDYVIGSTTCVLFLSLKYHRLHPEYIHTRIKKLGKSYKLRILLVLVDVEDHE 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 19112907   122 ASIQELVKTSIVNQYTLILAWSSEEAARYLETYK 155
Cdd:pfam03834  81 DALRELTKICILNNLTLILAWSFEEAARYLETYK 114
rad10 TIGR00597
DNA repair protein rad10; All proteins in this family for which functions are known are ...
 41-152 4.44e-70

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: 210.85  E-value: 4.44e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907    41 HSILVNPRQKGNPLLPHVRNVPWEYTDIVPDFVMGTGICSLFLSLKYHHLHPEYIYSRISKLGKSYNLRILLILVDVENH 120
Cdd:TIGR00597   1 NSILVNPRQKGNPLLKHVRNVPWEYGDVIPDYVLGQGTCALFLSLRYHNLHPDYIHRRLQSLGKNFNLRILLVQVDVKNP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 19112907   121 QASIQELVKTSIVNQYTLILAWSSEEAARYLE 152
Cdd:TIGR00597  81 QQALKELAKMCILNDCTLILAWSFEEAARYLE 112
 
Name Accession Description Interval E-value
RAD10 COG5241
Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, ...
 1-236 1.02e-117

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


Pssm-ID: 227566 [Multi-domain]  Cd Length: 224  Bit Score: 335.43  E-value: 1.02e-117
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907   1 MSDIDDEEFEQLAVSALEEVEKKAGFAQQPTpqkvsrvTAHSILVNPRQKGNPLLPHVRNVPWEYTD-IVPDFVMGTGIC 79
Cdd:COG5241   1 MNNTDPTSFESILAGVAKLRKEKSGADTTGS-------QSLEIDVSPLQKGNPQLSRRINSNWVYNAfIKPDEWTDSKAT 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907  80 SLFLSLKYHHLHPEYIYSRISKLgKSYNLRILLILVDVENHQASIQELVKTSIVNqyTLILAWSSEEAARYLETYKAYEN 159
Cdd:COG5241  74 DLFLSLRFHSTRPEYIVLRISKL-KSYKERPLLNHVDSTNWRASIQELVSTTGIN--TIYLDYSVEERSRYFLTLTYHKL 150

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19112907 160 MSPALIMEKPSTDYlsqVQSFLTSIRGINKSDSLSLLSKFGSLERALVASRDELEQLEGWGPTKVNRFLEAVQQPFM 236
Cdd:COG5241 151 YSDYIIRRMQSLDR---SNEFLILIFIVNKSDSEDTLNDIGKLCRFNGASRDEFELLLGFGFEKAAKYIEYLNLPFM 224
ERCC1_C-like cd22325
Central domain of ERCC1; ERCC1 is a subunit of the DNA structure-specific endonuclease ...
 41-168 1.50e-79

Central domain of ERCC1; ERCC1 is a subunit of the DNA structure-specific endonuclease XPF-ERCC1, which incises a damaged DNA strand on the 5' side of a lesion during nucleotide excision repair. It also plays roles in DNA interstrand crosslink repair and homologous recombination. The ERCC1 central domain modeled here interacts tightly with XPF and may be involved in binding to single-stranded DNA. It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411729  Cd Length: 128  Bit Score: 235.10  E-value: 1.50e-79
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907  41 HSILVNPRQKGNPLLPHVRNVPWEYTDIVPDFVMGTGICSLFLSLKYHHLHPEYIYSRISKLGKSYNLRILLILVDVENH 120
Cdd:cd22325   1 NSIIVSPRQKGNPVLKHIRNVPWEYGDIVPDYVLGKSTCALFLSLKYHRLHPEYIHERIKELGKSYKLRILLVLVDVEDP 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 19112907 121 QASIQELVKTSIVNQYTLILAWSSEEAARYLETYKAYENMSPALIMEK 168
Cdd:cd22325  81 HSALKELTKLAILNDCTLILAWSPEEAARYLETYKSYENKPADLIKER 128
XPF_nuclease_ERCC1 cd20079
XPF-like nuclease domain of DNA excision repair protein ERCC1; ERCC1 is a non-catalytic ...
 42-156 4.76e-75

XPF-like nuclease domain of DNA excision repair protein ERCC1; ERCC1 is a non-catalytic component of a structure-specific DNA repair endonuclease responsible for the 5'-incision during DNA repair. In conjunction with SLX4, ERCC1 is responsible for the first step in the repair of interstrand cross-links (ICL), as well as for homology-directed repair (HDR) of DNA double-strand breaks. ERCC1 participates in the processing of anaphase bridge-generating DNA structures, which consist in incompletely processed DNA lesions arising during S or G2 phase, and can result in cytokinesis failure. ERCC1 also plays a critical role in targeting the XPF-ERCC1 complex to DNA. XPF-ERRC1 and its yeast homolog Rad1-Rad10 play key roles in the excision of DNA lesions and are required for certain types of homologous recombination events and for the repair of DNA cross-links. The critical motif, DX(n)ERKX(3)D, for endonuclease activity is absent in the nuclease domain of ERCC1.


Pssm-ID: 410855  Cd Length: 115  Bit Score: 223.40  E-value: 4.76e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907  42 SILVNPRQKGNPLLPHVRNVPWEYTDIVPDFVMGTGICSLFLSLKYHHLHPEYIYSRISKLGKSYNLRILLILVDVENHQ 121
Cdd:cd20079   1 SILVNPRQRGNPILKFVRNVPWEFGDIVPDYVLGQTTCALFLSLRYHNLHPDYIHERLKQLGKSYELRVLLVQVDVKDPH 80

                        90       100       110
                ....*....|....*....|....*....|....*
gi 19112907 122 ASIQELVKTSIVNQYTLILAWSSEEAARYLETYKA 156
Cdd:cd20079  81 HALKELAKICILADCTLILAWSPEEAGRYLETYKA 115
Rad10 pfam03834
Binding domain of DNA repair protein Ercc1 (rad10/Swi10); Ercc1 and XPF (xeroderma pigmentosum ...
 42-155 1.42e-73

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: 461070  Cd Length: 114  Bit Score: 219.65  E-value: 1.42e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907    42 SILVNPRQKGNPLLPHVRNVPWEYTDIVPDFVMGTGICSLFLSLKYHHLHPEYIYSRISKLGKSYNLRILLILVDVENHQ 121
Cdd:pfam03834   1 TILVNPRQKGNPLLKHIRNVPWEYGDIVPDYVIGSTTCVLFLSLKYHRLHPEYIHTRIKKLGKSYKLRILLVLVDVEDHE 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 19112907   122 ASIQELVKTSIVNQYTLILAWSSEEAARYLETYK 155
Cdd:pfam03834  81 DALRELTKICILNNLTLILAWSFEEAARYLETYK 114
rad10 TIGR00597
DNA repair protein rad10; All proteins in this family for which functions are known are ...
 41-152 4.44e-70

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: 210.85  E-value: 4.44e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907    41 HSILVNPRQKGNPLLPHVRNVPWEYTDIVPDFVMGTGICSLFLSLKYHHLHPEYIYSRISKLGKSYNLRILLILVDVENH 120
Cdd:TIGR00597   1 NSILVNPRQKGNPLLKHVRNVPWEYGDVIPDYVLGQGTCALFLSLRYHNLHPDYIHRRLQSLGKNFNLRILLVQVDVKNP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 19112907   121 QASIQELVKTSIVNQYTLILAWSSEEAARYLE 152
Cdd:TIGR00597  81 QQALKELAKMCILNDCTLILAWSFEEAARYLE 112
XPF_nuclease-like cd19940
nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap ...
 42-156 1.91e-18

nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap endonuclease that act upon 3'-flap structures and involved in DNA repair pathways that are necessary for the removal of UV-light-induced DNA lesions and cross-links between DNA strands. Family members exist either as heterodimers or as homodimers in their functionally competent states which consist of a catalytic and a noncatalytic subunit. The catalytic subunits have a DX(n)RKX(3)D motif. This motif is required for metal-dependent endonuclease activity but not for DNA junction binding. The equivalent regions of the noncatalytic subunits (ERCC1, EME1, and FAAP24) have diverged. The noncatalytic subunits have roles such as binding ssDNA or an ability to target the endonuclease to defined DNA structures or sites of DNA damage.


Pssm-ID: 410849 [Multi-domain]  Cd Length: 126  Bit Score: 78.58  E-value: 1.91e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112907  42 SILVNPRQKGNPLLPHVRN--VPWEYTD-IVPDFVMGTGICSLFLSLKYHHLHP--EYIYSRISKLGKSYNLRILLILVD 116
Cdd:cd19940   1 SIVVDPRERRSELLSELQRlgVQVEFEDlAVGDYVLSNRTCVERKSLSDLVSSInkGRLREQLQRLTRKFERRVLLVEKD 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 19112907 117 VENHQASI------QELVKTSIVNQYTLILAWSSEEAARYLETYKA 156
Cdd:cd19940  81 RSKFRSMVssvqalSALTKLQLLTGIRLLIVASPKETADLLEELTQ 126
HHH pfam00633
Helix-hairpin-helix motif; The helix-hairpin-helix DNA-binding motif is found to be duplicated ...
 201-230 4.78e-04

Helix-hairpin-helix motif; The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.


Pssm-ID: 425789 [Multi-domain]  Cd Length: 30  Bit Score: 36.63  E-value: 4.78e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 19112907   201 SLERALVASRDELEQLEGWGPTKVNRFLEA 230
Cdd:pfam00633   1 SLEGLIPASVEELLALPGVGPKTAEAILSY 30
HHH_5 pfam14520
Helix-hairpin-helix domain;
181-232 1.25e-03

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 36.31  E-value: 1.25e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 19112907   181 LTSIRGINKSDSLSLLSK-FGSLERALVASRDELEQLEGWGPTKVNRFLEAVQ 232
Cdd:pfam14520   4 LLSISGIGPKTALALLSAgIGTVEDLAEADVDELAEIPGIGEKTAQRIILELR 56
 
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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