transcription factor TFIIH complex ERCC-3 subunit Ptr8 [Schizosaccharomyces pombe]
Protein Classification
rad25 family protein( domain architecture ID 11489419)
rad25 family protein
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||||
| rad25 | TIGR00603 | DNA repair helicase rad25; All proteins in this family for which functions are known are ... |
75-797 | 0e+00 | |||||||||||
DNA repair helicase rad25; All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription 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: 273168 [Multi-domain] Cd Length: 732 Bit Score: 1322.11 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | |||||||||||
| rad25 | TIGR00603 | DNA repair helicase rad25; All proteins in this family for which functions are known are ... |
75-797 | 0e+00 | |||||||||||
DNA repair helicase rad25; All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription 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: 273168 [Multi-domain] Cd Length: 732 Bit Score: 1322.11 E-value: 0e+00
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| ERCC3_RAD25_C | pfam16203 | ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 ... |
505-747 | 3.20e-174 | |||||||||||
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases. Pssm-ID: 406585 Cd Length: 248 Bit Score: 500.98 E-value: 3.20e-174
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| DEXHc_XPB | cd18029 | DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ... |
316-485 | 1.23e-113 | |||||||||||
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription factor complex helicase XPB subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB 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: 350787 [Multi-domain] Cd Length: 169 Bit Score: 341.97 E-value: 1.23e-113
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
323-740 | 3.05e-55 | |||||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 200.25 E-value: 3.05e-55
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
316-491 | 8.97e-20 | |||||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 88.32 E-value: 8.97e-20
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| PRK13766 | PRK13766 | Hef nuclease; Provisional |
318-455 | 9.10e-03 | |||||||||||
Hef nuclease; Provisional Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 39.47 E-value: 9.10e-03
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| Name | Accession | Description | Interval | E-value | |||||||||||
| rad25 | TIGR00603 | DNA repair helicase rad25; All proteins in this family for which functions are known are ... |
75-797 | 0e+00 | |||||||||||
DNA repair helicase rad25; All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription 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: 273168 [Multi-domain] Cd Length: 732 Bit Score: 1322.11 E-value: 0e+00
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| ERCC3_RAD25_C | pfam16203 | ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 ... |
505-747 | 3.20e-174 | |||||||||||
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases. Pssm-ID: 406585 Cd Length: 248 Bit Score: 500.98 E-value: 3.20e-174
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| DEXHc_XPB | cd18029 | DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ... |
316-485 | 1.23e-113 | |||||||||||
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription factor complex helicase XPB subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB 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: 350787 [Multi-domain] Cd Length: 169 Bit Score: 341.97 E-value: 1.23e-113
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| SF2_C_XPB | cd18789 | C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
516-671 | 9.57e-89 | |||||||||||
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. 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: 350176 [Multi-domain] Cd Length: 153 Bit Score: 276.44 E-value: 9.57e-89
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
323-740 | 3.05e-55 | |||||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 200.25 E-value: 3.05e-55
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| Helicase_C_3 | pfam13625 | Helicase conserved C-terminal domain; This domain family is found in a wide variety of ... |
91-215 | 4.74e-45 | |||||||||||
Helicase conserved C-terminal domain; This domain family is found in a wide variety of helicases and helicase-related proteins. Pssm-ID: 463939 [Multi-domain] Cd Length: 121 Bit Score: 157.66 E-value: 4.74e-45
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
325-479 | 1.54e-28 | |||||||||||
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part 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: 350684 [Multi-domain] Cd Length: 146 Bit Score: 111.63 E-value: 1.54e-28
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
316-491 | 8.97e-20 | |||||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 88.32 E-value: 8.97e-20
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
312-687 | 2.31e-17 | |||||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 86.82 E-value: 2.31e-17
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
323-481 | 6.56e-17 | |||||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 78.87 E-value: 6.56e-17
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| DEXHc_Snf | cd17919 | DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
325-478 | 1.46e-12 | |||||||||||
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350677 [Multi-domain] Cd Length: 182 Bit Score: 66.82 E-value: 1.46e-12
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
548-656 | 6.02e-12 | |||||||||||
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 63.00 E-value: 6.02e-12
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
587-656 | 6.29e-11 | |||||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 59.15 E-value: 6.29e-11
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| DEXHc_RE_I_III_res | cd18032 | DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
325-485 | 5.47e-10 | |||||||||||
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members 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: 350790 [Multi-domain] Cd Length: 163 Bit Score: 58.73 E-value: 5.47e-10
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| DEXHc_HARP_SMARCAL1 | cd18010 | DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ... |
351-453 | 2.44e-09 | |||||||||||
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1, also known as HARP) is recruited to stalled replication forks to promote repair and helps restart replication. It plays a role in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress. Mutations cause Schimke Immunoosseous Dysplasia. SMARCAL1 is part 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: 350768 [Multi-domain] Cd Length: 213 Bit Score: 57.99 E-value: 2.44e-09
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
344-478 | 3.15e-09 | |||||||||||
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region. Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 56.26 E-value: 3.15e-09
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| SNF2-rel_dom | pfam00176 | SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
327-478 | 2.52e-07 | |||||||||||
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 53.07 E-value: 2.52e-07
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| SF2_C_SNF | cd18793 | C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
549-654 | 3.29e-07 | |||||||||||
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. 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: 350180 [Multi-domain] Cd Length: 135 Bit Score: 50.17 E-value: 3.29e-07
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| DEXQc_arch_SWI2_SNF2 | cd18012 | DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ... |
323-478 | 6.98e-06 | |||||||||||
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members 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: 350770 [Multi-domain] Cd Length: 218 Bit Score: 47.95 E-value: 6.98e-06
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| DEXHc_HLTF1_SMARC3 | cd18071 | DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ... |
342-478 | 2.13e-05 | |||||||||||
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 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: 350829 [Multi-domain] Cd Length: 239 Bit Score: 46.69 E-value: 2.13e-05
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| DEXHc_dicer | cd18034 | DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
322-489 | 2.25e-05 | |||||||||||
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer 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: 350792 [Multi-domain] Cd Length: 200 Bit Score: 46.11 E-value: 2.25e-05
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| DEXHc_Mot1 | cd17999 | DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ... |
324-478 | 6.56e-05 | |||||||||||
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in eukaryotes) regulates transcription in association with TATA binding protein (TBP). Mot1, Ino80C, and NC2 function coordinately to regulate pervasive transcription in yeast and mammals. Mot1 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: 350757 [Multi-domain] Cd Length: 232 Bit Score: 45.03 E-value: 6.56e-05
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| MPH1 | COG1111 | ERCC4-related helicase [Replication, recombination and repair]; |
325-487 | 9.46e-05 | |||||||||||
ERCC4-related helicase [Replication, recombination and repair]; Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 45.88 E-value: 9.46e-05
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| DEXHc_ERCC6L | cd18001 | DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ... |
332-453 | 1.13e-04 | |||||||||||
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint helicase (ERCC6L, also known as RAD26L) is an essential component of the mitotic spindle assembly checkpoint, by acting as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase. ERCC6L is proposed to stimulate cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2. ERCC6L 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: 350759 [Multi-domain] Cd Length: 232 Bit Score: 44.28 E-value: 1.13e-04
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| DEXDc_RapA | cd18011 | DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
351-478 | 4.53e-04 | |||||||||||
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part 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: 350769 [Multi-domain] Cd Length: 207 Bit Score: 42.28 E-value: 4.53e-04
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| DEXHc_ERCC6 | cd18000 | DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ... |
344-453 | 4.69e-04 | |||||||||||
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 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: 350758 [Multi-domain] Cd Length: 193 Bit Score: 41.93 E-value: 4.69e-04
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| DEXHc_Hef | cd18035 | DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
345-486 | 7.93e-03 | |||||||||||
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: 38.26 E-value: 7.93e-03
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| PRK13766 | PRK13766 | Hef nuclease; Provisional |
318-455 | 9.10e-03 | |||||||||||
Hef nuclease; Provisional Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 39.47 E-value: 9.10e-03
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