DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ...
56-762
1.21e-112
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
The actual alignment was detected with superfamily member TIGR00604:
Pssm-ID: 273169 [Multi-domain] Cd Length: 705 Bit Score: 364.81 E-value: 1.21e-112
harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL); ...
928-1032
9.19e-29
harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL); Mouse Rtel is an essential protein required for the maintenance of both telomeric and genomic stability. RTEL1 appears to maintain genome stability by suppressing homologous recombination (HR). In vitro, purified human and insect RTEL1 have been shown to promote the disassembly of D loop recombination intermediates, in a reaction dependent upon ATP hydrolysis. Human RTEL1 is implicated in the etiology of Dyskeratosis congenital (DC, is an inherited bone marrow failure and cancer predisposition syndrome). Point mutations in its helicase domains, and truncations which result in loss of its C-terminus have been discovered in DC families. RTEL1 is also a candidate gene influencing glioma susceptibility. The C-terminal domain of RTEL1, represented here, appears similar to the N-terminal domain of the scaffolding protein harmonin.
:
Pssm-ID: 259826 [Multi-domain] Cd Length: 99 Bit Score: 110.83 E-value: 9.19e-29
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ...
56-762
1.21e-112
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. 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: 273169 [Multi-domain] Cd Length: 705 Bit Score: 364.81 E-value: 1.21e-112
DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases ...
147-311
7.09e-74
DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast.
Pssm-ID: 399602 [Multi-domain] Cd Length: 168 Bit Score: 241.01 E-value: 7.09e-74
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; ...
519-734
8.99e-62
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; The xeroderma pigmentosum group D (XPD)-like family members are DEAD-box helicases belonging to superfamily (SF)2. This family includes DDX11 (also called ChlR1), a protein involved in maintaining chromosome transmission fidelity and genome stability, the TFIIH basal transcription factor complex XPD subunit, and FANCJ (also known as BRIP1), a DNA helicase required for the maintenance of chromosomal stability. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350175 [Multi-domain] Cd Length: 159 Bit Score: 207.07 E-value: 8.99e-62
harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL); ...
928-1032
9.19e-29
harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL); Mouse Rtel is an essential protein required for the maintenance of both telomeric and genomic stability. RTEL1 appears to maintain genome stability by suppressing homologous recombination (HR). In vitro, purified human and insect RTEL1 have been shown to promote the disassembly of D loop recombination intermediates, in a reaction dependent upon ATP hydrolysis. Human RTEL1 is implicated in the etiology of Dyskeratosis congenital (DC, is an inherited bone marrow failure and cancer predisposition syndrome). Point mutations in its helicase domains, and truncations which result in loss of its C-terminus have been discovered in DC families. RTEL1 is also a candidate gene influencing glioma susceptibility. The C-terminal domain of RTEL1, represented here, appears similar to the N-terminal domain of the scaffolding protein harmonin.
Pssm-ID: 259826 [Multi-domain] Cd Length: 99 Bit Score: 110.83 E-value: 9.19e-29
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ...
56-762
1.21e-112
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. 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: 273169 [Multi-domain] Cd Length: 705 Bit Score: 364.81 E-value: 1.21e-112
DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases ...
147-311
7.09e-74
DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast.
Pssm-ID: 399602 [Multi-domain] Cd Length: 168 Bit Score: 241.01 E-value: 7.09e-74
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; ...
519-734
8.99e-62
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; The xeroderma pigmentosum group D (XPD)-like family members are DEAD-box helicases belonging to superfamily (SF)2. This family includes DDX11 (also called ChlR1), a protein involved in maintaining chromosome transmission fidelity and genome stability, the TFIIH basal transcription factor complex XPD subunit, and FANCJ (also known as BRIP1), a DNA helicase required for the maintenance of chromosomal stability. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350175 [Multi-domain] Cd Length: 159 Bit Score: 207.07 E-value: 8.99e-62
DEAH-box helicase domain of Fanconi anemia group J protein and similar proteins; Fanconi ...
82-295
1.19e-52
DEAH-box helicase domain of Fanconi anemia group J protein and similar proteins; Fanconi anemia group J protein (FACJ or FANCJ, also known as BRIP1) is a DNA helicase required for the maintenance of chromosomal stability. It plays a role in the repair of DNA double-strand breaks by homologous recombination dependent on its interaction with BRCA1. FANCJ belongs to the DEAD-box helicase family, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350728 [Multi-domain] Cd Length: 181 Bit Score: 182.16 E-value: 1.19e-52
harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL); ...
928-1032
9.19e-29
harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL); Mouse Rtel is an essential protein required for the maintenance of both telomeric and genomic stability. RTEL1 appears to maintain genome stability by suppressing homologous recombination (HR). In vitro, purified human and insect RTEL1 have been shown to promote the disassembly of D loop recombination intermediates, in a reaction dependent upon ATP hydrolysis. Human RTEL1 is implicated in the etiology of Dyskeratosis congenital (DC, is an inherited bone marrow failure and cancer predisposition syndrome). Point mutations in its helicase domains, and truncations which result in loss of its C-terminus have been discovered in DC families. RTEL1 is also a candidate gene influencing glioma susceptibility. The C-terminal domain of RTEL1, represented here, appears similar to the N-terminal domain of the scaffolding protein harmonin.
Pssm-ID: 259826 [Multi-domain] Cd Length: 99 Bit Score: 110.83 E-value: 9.19e-29
DEAH-box helicase domain of XPD family DEAD-like helicases; The xeroderma pigmentosum group D ...
82-295
7.02e-17
DEAH-box helicase domain of XPD family DEAD-like helicases; The xeroderma pigmentosum group D (XPD)-like family members are DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350673 [Multi-domain] Cd Length: 138 Bit Score: 78.24 E-value: 7.02e-17
DEAH-box helicase domain of ATP-dependent DNA helicase DDX11; DDX11 (also called ChlR1) ...
84-178
1.83e-08
DEAH-box helicase domain of ATP-dependent DNA helicase DDX11; DDX11 (also called ChlR1) encodes a protein of the conserved family of Iron-Sulfur (Fe-S) cluster DNA helicases and is thought to function in maintaining chromosome transmission fidelity and genome stability. Mutations in the Chl1 human homologs ChlR1/DDX11 and BACH1/BRIP1/FANCJ collectively result in Warsaw Breakage Syndrome, Fanconi anemia, cell aneuploidy and breast and ovarian cancers. DDX11 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350726 Cd Length: 134 Bit Score: 54.25 E-value: 1.83e-08
harmonin-homology domain (harmonin_N_like domain) of malcavernin (CCM2); CCM2 (also called ...
957-1029
3.82e-03
harmonin-homology domain (harmonin_N_like domain) of malcavernin (CCM2); CCM2 (also called malcavernin; C7orf22/chromosome 7 open reading frame 22; OSM) along with CCM1 and CCM3 constitutes a set of proteins which when mutated are responsible for cerebral cavernous malformations, an autosomal dominant neurovascular disease characterized by cerebral hemorrhages and vascular malformations in the central nervous system. CCM2 plays many functional roles. CCM2 functions as a scaffold involved in small GTPase Rac-dependent p38 mitogen-activated protein kinase (MAPK) activation when the cell is under hyperosmotic stress. It associates with CCM1 in the signaling cascades that regulate vascular integrity and participates in HEG1 (the transmembrane receptor heart of glass 1) mediated endothelial cell junctions. CCM proteins also inhibit the activation of small GTPase RhoA and its downstream effector Rho kinase (ROCK) to limit vascular permeability. CCM2 mediates TrkA-dependent cell death via its N-terminal PTB domain in pediatric neuroblastic tumours. CCM2 possesses an N-terminal PTB domain. The C-terminal domain of malcavernin, which is represented here, appears similar to the N-terminal domain of the scaffolding protein harmonin. It has also been referred to as the Karet domain.
Pssm-ID: 259825 Cd Length: 97 Bit Score: 37.62 E-value: 3.82e-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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