MULTISPECIES: DEAD/DEAH box helicase [Serratia]
Protein Classification
DEAD/DEAH box helicase( domain architecture ID 11437332)
DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||
| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
1-530 | 2.03e-105 | ||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; : Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 328.91 E-value: 2.03e-105
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| Name | Accession | Description | Interval | E-value | ||||||||
| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
1-530 | 2.03e-105 | ||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 328.91 E-value: 2.03e-105
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
3-155 | 7.21e-35 | ||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 128.94 E-value: 7.21e-35
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| SF2_C_EcoAI-like | cd18799 | C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
248-356 | 8.77e-34 | ||||||||
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins 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: 350186 [Multi-domain] Cd Length: 116 Bit Score: 124.59 E-value: 8.77e-34
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
3-153 | 1.27e-21 | ||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 92.94 E-value: 1.27e-21
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| hsdR | PRK11448 | type I restriction enzyme EcoKI subunit R; Provisional |
3-347 | 1.54e-16 | ||||||||
type I restriction enzyme EcoKI subunit R; Provisional Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 83.46 E-value: 1.54e-16
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| rad25 | TIGR00603 | DNA repair helicase rad25; All proteins in this family for which functions are known are ... |
5-56 | 7.69e-03 | ||||||||
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: 39.40 E-value: 7.69e-03
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| Name | Accession | Description | Interval | E-value | ||||||||
| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
1-530 | 2.03e-105 | ||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 328.91 E-value: 2.03e-105
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
3-155 | 7.21e-35 | ||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 128.94 E-value: 7.21e-35
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| HsdR | COG4096 | Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
3-385 | 1.24e-34 | ||||||||
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms]; Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 139.59 E-value: 1.24e-34
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| SF2_C_EcoAI-like | cd18799 | C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
248-356 | 8.77e-34 | ||||||||
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins 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: 350186 [Multi-domain] Cd Length: 116 Bit Score: 124.59 E-value: 8.77e-34
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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 ... |
5-164 | 1.51e-30 | ||||||||
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: 117.28 E-value: 1.51e-30
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
5-153 | 2.74e-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: 110.09 E-value: 2.74e-28
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
3-153 | 1.27e-21 | ||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 92.94 E-value: 1.27e-21
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| hsdR | PRK11448 | type I restriction enzyme EcoKI subunit R; Provisional |
3-347 | 1.54e-16 | ||||||||
type I restriction enzyme EcoKI subunit R; Provisional Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 83.46 E-value: 1.54e-16
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
28-152 | 3.46e-16 | ||||||||
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: 75.90 E-value: 3.46e-16
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| MPH1 | COG1111 | ERCC4-related helicase [Replication, recombination and repair]; |
6-153 | 7.90e-15 | ||||||||
ERCC4-related helicase [Replication, recombination and repair]; Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 77.85 E-value: 7.90e-15
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| DEXHc_RIG-I | cd17927 | DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
3-153 | 1.29e-14 | ||||||||
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex 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. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family 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: 350685 [Multi-domain] Cd Length: 201 Bit Score: 72.85 E-value: 1.29e-14
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
6-153 | 3.30e-14 | ||||||||
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 70.73 E-value: 3.30e-14
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| DEXHc_RLR | cd18036 | DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
3-153 | 1.09e-13 | ||||||||
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) 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: 350794 [Multi-domain] Cd Length: 204 Bit Score: 70.20 E-value: 1.09e-13
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| RPL40A | COG1552 | Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]; Ribosomal protein ... |
417-466 | 2.03e-13 | ||||||||
Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]; Ribosomal protein L40E is part of the Pathway/BioSystem: Archaeal ribosomal proteins Pssm-ID: 441161 [Multi-domain] Cd Length: 50 Bit Score: 64.57 E-value: 2.03e-13
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
239-343 | 7.26e-13 | ||||||||
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: 64.92 E-value: 7.26e-13
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| DEXDc_FANCM | cd18033 | DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ... |
3-153 | 1.23e-12 | ||||||||
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein 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. Its ATP-dependent DNA branch migration activity can process branched DNA structures such as a movable replication fork. This activity is strongly stimulated in the presence of CENPS and CENPX. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, it strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA. FANCM 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: 350791 [Multi-domain] Cd Length: 182 Bit Score: 66.58 E-value: 1.23e-12
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| DEXHc_dicer | cd18034 | DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
3-153 | 3.18e-11 | ||||||||
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: 62.67 E-value: 3.18e-11
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| DEXHc_RE_I_HsdR | cd18030 | DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
5-153 | 1.41e-10 | ||||||||
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of type I restriction-modification enzymes contains the DNA cleavage and ATP-dependent DNA translocation activities of the heteromeric complex. It 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: 350788 [Multi-domain] Cd Length: 208 Bit Score: 61.09 E-value: 1.41e-10
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
276-343 | 3.00e-10 | ||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 56.84 E-value: 3.00e-10
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| DEXHc_Ski2 | cd17921 | DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
4-152 | 4.08e-10 | ||||||||
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 59.20 E-value: 4.08e-10
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| COG0610 | COG0610 | Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
5-363 | 8.77e-10 | ||||||||
Type I site-specific restriction-modification system, R (restriction) subunit and related helicases ... [Defense mechanisms]; Pssm-ID: 440375 [Multi-domain] Cd Length: 936 Bit Score: 61.81 E-value: 8.77e-10
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| uvsW | PHA02558 | UvsW helicase; Provisional |
6-120 | 2.03e-09 | ||||||||
UvsW helicase; Provisional Pssm-ID: 222875 [Multi-domain] Cd Length: 501 Bit Score: 60.02 E-value: 2.03e-09
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| PRK13766 | PRK13766 | Hef nuclease; Provisional |
28-153 | 3.16e-09 | ||||||||
Hef nuclease; Provisional Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 59.89 E-value: 3.16e-09
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| DEXHc_archSki2 | cd18028 | DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
4-152 | 7.53e-09 | ||||||||
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 55.42 E-value: 7.53e-09
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| DEXHc_RLR-3 | cd18075 | DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ... |
5-153 | 8.85e-09 | ||||||||
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 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: 350833 [Multi-domain] Cd Length: 200 Bit Score: 55.63 E-value: 8.85e-09
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
304-355 | 1.85e-08 | ||||||||
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The 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: 350172 [Multi-domain] Cd Length: 77 Bit Score: 51.55 E-value: 1.85e-08
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| DEXHc_RecQ4-like | cd18018 | DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ... |
3-152 | 2.80e-08 | ||||||||
DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations cause Rothmund-Thomson/RAPADILINO/Baller-Gerold syndrome. Pssm-ID: 350776 [Multi-domain] Cd Length: 201 Bit Score: 54.18 E-value: 2.80e-08
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| DEXHc_Hef | cd18035 | DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
28-153 | 5.27e-08 | ||||||||
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: 52.90 E-value: 5.27e-08
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| DEXHc_RecQ | cd17920 | DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
4-152 | 7.82e-08 | ||||||||
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region. Pssm-ID: 350678 [Multi-domain] Cd Length: 200 Bit Score: 52.92 E-value: 7.82e-08
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| DEXHc_XPB | cd18029 | DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ... |
5-152 | 3.41e-07 | ||||||||
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: 50.38 E-value: 3.41e-07
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| DEXHc_Snf | cd17919 | DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
5-153 | 5.95e-07 | ||||||||
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: 49.87 E-value: 5.95e-07
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| COG4889 | COG4889 | Predicted helicase [General function prediction only]; |
3-153 | 8.11e-07 | ||||||||
Predicted helicase [General function prediction only]; Pssm-ID: 443917 [Multi-domain] Cd Length: 1571 Bit Score: 52.27 E-value: 8.11e-07
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| DEXHc_UvsW | cd18031 | DEXH-box helicase domain of bacteriophage UvsW; Bacteriophage UvsW is part of the WXY system ... |
8-164 | 9.73e-07 | ||||||||
DEXH-box helicase domain of bacteriophage UvsW; Bacteriophage UvsW is part of the WXY system that repairs DNA damage by a process that involves homologous recombination. UvsW 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: 350789 [Multi-domain] Cd Length: 161 Bit Score: 48.97 E-value: 9.73e-07
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| DEXDc_RapA | cd18011 | DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
5-153 | 1.13e-06 | ||||||||
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: 49.59 E-value: 1.13e-06
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| SWI2_SNF2 | pfam18766 | SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. |
8-153 | 4.34e-05 | ||||||||
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. Pssm-ID: 465860 [Multi-domain] Cd Length: 222 Bit Score: 45.11 E-value: 4.34e-05
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
1-153 | 1.96e-04 | ||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 44.45 E-value: 1.96e-04
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
255-322 | 2.56e-04 | ||||||||
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise 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. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain] Cd Length: 131 Bit Score: 41.34 E-value: 2.56e-04
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| RecQ | COG0514 | Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
4-40 | 9.55e-04 | ||||||||
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 42.05 E-value: 9.55e-04
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| DEXHc_RecQ2_BLM | cd18016 | DEAH-box helicase domain of RecQ2; ATP-dependent DNA helicase Q2 (RecQ2, also called Bloom ... |
6-152 | 1.60e-03 | ||||||||
DEAH-box helicase domain of RecQ2; ATP-dependent DNA helicase Q2 (RecQ2, also called Bloom syndrome protein homolog or BLM) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations in RecQ2 cause Bloom syndrome. Pssm-ID: 350774 [Multi-domain] Cd Length: 208 Bit Score: 40.20 E-value: 1.60e-03
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| Cas3_I | cd09696 | CRISPR/Cas system-associated protein Cas3; Distinct Cas3 family with HD domain fused to ... |
232-353 | 2.01e-03 | ||||||||
CRISPR/Cas system-associated protein Cas3; Distinct Cas3 family with HD domain fused to C-termus of Helicase domain; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DNA helicase Cas3; This protein includes both DEAH and HD motifs; signature gene for Type I Pssm-ID: 187827 [Multi-domain] Cd Length: 843 Bit Score: 41.16 E-value: 2.01e-03
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| DEXHc_RecQ1 | cd18015 | DEXH-box helicase domain of RecQ1; ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ ... |
4-152 | 2.32e-03 | ||||||||
DEXH-box helicase domain of RecQ1; ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350773 [Multi-domain] Cd Length: 209 Bit Score: 39.66 E-value: 2.32e-03
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| AAA | smart00382 | ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ... |
23-150 | 5.12e-03 | ||||||||
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 37.74 E-value: 5.12e-03
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| rad25 | TIGR00603 | DNA repair helicase rad25; All proteins in this family for which functions are known are ... |
5-56 | 7.69e-03 | ||||||||
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: 39.40 E-value: 7.69e-03
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