DNA repair protein (rad1); All proteins in this family for which functions are known are ...
97-908
0e+00
DNA repair protein (rad1); 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 recombinational repair in some species. Most Archaeal species also have homologs of these genes, but the function of these Archaeal genes is not known, so we have set our cutoff to only pick up the eukaryotic genes.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA metabolism, DNA replication, recombination, and repair]
The actual alignment was detected with superfamily member TIGR00596:
Pssm-ID: 273163 [Multi-domain] Cd Length: 814 Bit Score: 1139.54 E-value: 0e+00
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
21-165
1.43e-03
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.
The actual alignment was detected with superfamily member cd18035:
Pssm-ID: 475120 [Multi-domain] Cd Length: 181 Bit Score: 40.58 E-value: 1.43e-03
DNA repair protein (rad1); All proteins in this family for which functions are known are ...
97-908
0e+00
DNA repair protein (rad1); 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 recombinational repair in some species. Most Archaeal species also have homologs of these genes, but the function of these Archaeal genes is not known, so we have set our cutoff to only pick up the eukaryotic genes.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273163 [Multi-domain] Cd Length: 814 Bit Score: 1139.54 E-value: 0e+00
nuclease domain of XPF found in eukaryotes; XPF, also called DNA excision repair protein ...
685-819
1.89e-83
nuclease domain of XPF found in eukaryotes; XPF, also called DNA excision repair protein ERCC-4, or DNA repair protein complementing XP-F cells, or Xeroderma pigmentosum group F-complementing protein, is a DNA repair endonuclease that is a catalytic component of a structure-specific DNA repair endonuclease responsible for the 5-prime incision during DNA repair. It is involved in homologous recombination that assists in removing interstrand cross-link. The nuclease domains of the catalytic subunits XPF have the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity but not for DNA junction binding. 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.
Pssm-ID: 410854 [Multi-domain] Cd Length: 136 Bit Score: 263.96 E-value: 1.89e-83
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
687-817
1.72e-27
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.
Pssm-ID: 426945 [Multi-domain] Cd Length: 139 Bit Score: 108.67 E-value: 1.72e-27
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, ...
685-762
4.04e-21
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases, and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.
Pssm-ID: 214888 [Multi-domain] Cd Length: 98 Bit Score: 88.95 E-value: 4.04e-21
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350793 [Multi-domain] Cd Length: 181 Bit Score: 40.58 E-value: 1.43e-03
DNA repair protein (rad1); All proteins in this family for which functions are known are ...
97-908
0e+00
DNA repair protein (rad1); 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 recombinational repair in some species. Most Archaeal species also have homologs of these genes, but the function of these Archaeal genes is not known, so we have set our cutoff to only pick up the eukaryotic genes.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273163 [Multi-domain] Cd Length: 814 Bit Score: 1139.54 E-value: 0e+00
nuclease domain of XPF found in eukaryotes; XPF, also called DNA excision repair protein ...
685-819
1.89e-83
nuclease domain of XPF found in eukaryotes; XPF, also called DNA excision repair protein ERCC-4, or DNA repair protein complementing XP-F cells, or Xeroderma pigmentosum group F-complementing protein, is a DNA repair endonuclease that is a catalytic component of a structure-specific DNA repair endonuclease responsible for the 5-prime incision during DNA repair. It is involved in homologous recombination that assists in removing interstrand cross-link. The nuclease domains of the catalytic subunits XPF have the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity but not for DNA junction binding. 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.
Pssm-ID: 410854 [Multi-domain] Cd Length: 136 Bit Score: 263.96 E-value: 1.89e-83
XPF family DNA repair endonuclease; (Xeroderma Pigmentosum group F) DNA repair gene homologs ...
685-804
4.75e-47
XPF family DNA repair endonuclease; (Xeroderma Pigmentosum group F) DNA repair gene homologs are members of the XPF/Rad1/Mus81-dependent nuclease family which specifically cleave branched structures generated during DNA repair, replication, and recombination, and they are essential for maintaining genome stability. They belong to a wider 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: 411771 [Multi-domain] Cd Length: 123 Bit Score: 163.58 E-value: 4.75e-47
nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap ...
684-819
3.19e-37
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: 135.97 E-value: 3.19e-37
nuclease domain of XPF found in archaea; XPF, also called DNA excision repair protein ERCC-4, ...
685-813
4.88e-30
nuclease domain of XPF found in archaea; XPF, also called DNA excision repair protein ERCC-4, or DNA repair protein complementing XP-F cells, or Xeroderma pigmentosum group F-complementing protein, is a 3'-flap repair endonuclease that cleaves 5' of ds/ssDNA interfaces in 3' flap structures, although it also cuts bubble, Y-DNA structures and mobile and immobile Holliday junctions. XPF cuts preferentially after pyrimidines, may continue to progressively cleave substrate upstream of the initial cleavage, at least in vitro. It may be involved in nucleotide excision repair. The nuclease domains of the catalytic subunits XPF have the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity but not for DNA junction binding. 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.
Pssm-ID: 410851 [Multi-domain] Cd Length: 127 Bit Score: 115.17 E-value: 4.88e-30
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
687-817
1.72e-27
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.
Pssm-ID: 426945 [Multi-domain] Cd Length: 139 Bit Score: 108.67 E-value: 1.72e-27
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, ...
685-762
4.04e-21
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases, and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.
Pssm-ID: 214888 [Multi-domain] Cd Length: 98 Bit Score: 88.95 E-value: 4.04e-21
XPF-like nuclease domain of Mus81; Mus81 is a crossover junction endonuclease that interacts ...
686-792
6.15e-10
XPF-like nuclease domain of Mus81; Mus81 is a crossover junction endonuclease that interacts with Eme1 and Eme2 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. The typical substrates include 3'-flap structures, replication forks and nicked Holliday junctions. Mus81 may be required in mitosis for the processing of stalled or collapsed replication forks. Mus81 consists of the active nuclease domain with the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity and two helix-hairpin-helix (HhH2) domains.
Pssm-ID: 410850 [Multi-domain] Cd Length: 150 Bit Score: 58.65 E-value: 6.15e-10
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also ...
683-767
4.99e-07
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also called Fanconi anemia-associated polypeptide of 250 kDa (FAAP250), or protein Hef ortholog, or ATP-dependent RNA helicase FANCM, is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA) and Holliday junction substrates. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, FANCM strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA.
Pssm-ID: 410853 [Multi-domain] Cd Length: 139 Bit Score: 49.96 E-value: 4.99e-07
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350793 [Multi-domain] Cd Length: 181 Bit Score: 40.58 E-value: 1.43e-03
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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