MULTISPECIES: DEAD/DEAH box helicase family protein [Escherichia]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||||
| HsdR super family | cl34711 | Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
6-624 | 4.05e-126 | ||||||||||
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms]; The actual alignment was detected with superfamily member COG4096: Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 398.45 E-value: 4.05e-126
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| Name | Accession | Description | Interval | E-value | ||||||||||
| HsdR | COG4096 | Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
6-624 | 4.05e-126 | ||||||||||
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms]; Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 398.45 E-value: 4.05e-126
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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 ... |
190-344 | 8.07e-49 | ||||||||||
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: 170.05 E-value: 8.07e-49
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| hsdR | PRK11448 | type I restriction enzyme EcoKI subunit R; Provisional |
6-613 | 2.46e-46 | ||||||||||
type I restriction enzyme EcoKI subunit R; Provisional Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 179.76 E-value: 2.46e-46
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
190-343 | 1.30e-42 | ||||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 152.44 E-value: 1.30e-42
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
182-348 | 9.48e-25 | ||||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 102.57 E-value: 9.48e-25
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| hsdR | TIGR00348 | type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
73-407 | 1.74e-13 | ||||||||||
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I restriction and modification system which is composed of three polypeptides R (restriction endonuclease), M (modification) and S (specificity). This group of enzymes recognize specific short DNA sequences and have an absolute requirement for ATP (or dATP) and S-adenosyl-L-methionine. They also catalyse the reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar site specificity.(J. Mol. Biol. 271 (3), 342-348 (1997)). Members of this family are assumed to differ from each other in DNA site specificity. [DNA metabolism, Restriction/modification] Pssm-ID: 273028 [Multi-domain] Cd Length: 667 Bit Score: 74.36 E-value: 1.74e-13
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| Name | Accession | Description | Interval | E-value | ||||||||||
| HsdR | COG4096 | Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
6-624 | 4.05e-126 | ||||||||||
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms]; Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 398.45 E-value: 4.05e-126
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
167-617 | 1.21e-49 | ||||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 184.46 E-value: 1.21e-49
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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 ... |
190-344 | 8.07e-49 | ||||||||||
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: 170.05 E-value: 8.07e-49
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| hsdR | PRK11448 | type I restriction enzyme EcoKI subunit R; Provisional |
6-613 | 2.46e-46 | ||||||||||
type I restriction enzyme EcoKI subunit R; Provisional Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 179.76 E-value: 2.46e-46
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
190-343 | 1.30e-42 | ||||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 152.44 E-value: 1.30e-42
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
190-341 | 6.10e-34 | ||||||||||
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: 127.04 E-value: 6.10e-34
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
182-348 | 9.48e-25 | ||||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 102.57 E-value: 9.48e-25
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| SF2_C_EcoAI-like | cd18799 | C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
470-614 | 3.64e-20 | ||||||||||
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: 86.46 E-value: 3.64e-20
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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 ... |
190-344 | 9.91e-18 | ||||||||||
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: 82.66 E-value: 9.91e-18
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
212-340 | 1.69e-17 | ||||||||||
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: 80.14 E-value: 1.69e-17
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| COG0610 | COG0610 | Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
73-405 | 8.61e-16 | ||||||||||
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: 82.22 E-value: 8.61e-16
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
191-341 | 1.79e-15 | ||||||||||
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: 74.97 E-value: 1.79e-15
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| DEXHc_dicer | cd18034 | DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
216-341 | 6.53e-14 | ||||||||||
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: 71.14 E-value: 6.53e-14
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| hsdR | TIGR00348 | type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
73-407 | 1.74e-13 | ||||||||||
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I restriction and modification system which is composed of three polypeptides R (restriction endonuclease), M (modification) and S (specificity). This group of enzymes recognize specific short DNA sequences and have an absolute requirement for ATP (or dATP) and S-adenosyl-L-methionine. They also catalyse the reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar site specificity.(J. Mol. Biol. 271 (3), 342-348 (1997)). Members of this family are assumed to differ from each other in DNA site specificity. [DNA metabolism, Restriction/modification] Pssm-ID: 273028 [Multi-domain] Cd Length: 667 Bit Score: 74.36 E-value: 1.74e-13
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| MPH1 | COG1111 | ERCC4-related helicase [Replication, recombination and repair]; |
191-341 | 3.64e-12 | ||||||||||
ERCC4-related helicase [Replication, recombination and repair]; Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 70.14 E-value: 3.64e-12
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| SWI2_SNF2 | pfam18766 | SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. |
218-393 | 6.69e-12 | ||||||||||
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. Pssm-ID: 465860 [Multi-domain] Cd Length: 222 Bit Score: 65.92 E-value: 6.69e-12
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| DEXDc_RapA | cd18011 | DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
190-341 | 8.39e-11 | ||||||||||
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: 62.31 E-value: 8.39e-11
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| uvsW | PHA02558 | UvsW helicase; Provisional |
191-357 | 2.47e-10 | ||||||||||
UvsW helicase; Provisional Pssm-ID: 222875 [Multi-domain] Cd Length: 501 Bit Score: 63.88 E-value: 2.47e-10
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| PRK13766 | PRK13766 | Hef nuclease; Provisional |
191-341 | 2.87e-10 | ||||||||||
Hef nuclease; Provisional Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 64.12 E-value: 2.87e-10
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
190-341 | 1.51e-09 | ||||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 61.78 E-value: 1.51e-09
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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 ... |
218-341 | 2.22e-09 | ||||||||||
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: 58.21 E-value: 2.22e-09
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| DEXHc_Hef | cd18035 | DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
216-341 | 2.24e-09 | ||||||||||
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: 57.52 E-value: 2.24e-09
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| DEXHc_priA | cd17929 | DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
194-318 | 3.00e-09 | ||||||||||
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA 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: 350687 [Multi-domain] Cd Length: 178 Bit Score: 57.22 E-value: 3.00e-09
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| DEXHc_Snf | cd17919 | DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
190-341 | 1.65e-08 | ||||||||||
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: 54.88 E-value: 1.65e-08
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| DEXHc_RecG | cd17918 | DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
194-317 | 1.33e-07 | ||||||||||
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the 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: 350676 [Multi-domain] Cd Length: 180 Bit Score: 52.42 E-value: 1.33e-07
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| COG4889 | COG4889 | Predicted helicase [General function prediction only]; |
190-344 | 2.53e-07 | ||||||||||
Predicted helicase [General function prediction only]; Pssm-ID: 443917 [Multi-domain] Cd Length: 1571 Bit Score: 54.58 E-value: 2.53e-07
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| DEXDc_FANCM | cd18033 | DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ... |
190-341 | 6.19e-07 | ||||||||||
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: 50.40 E-value: 6.19e-07
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| DEXHc_XPB | cd18029 | DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ... |
190-340 | 8.29e-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: 49.99 E-value: 8.29e-07
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| BRR2 | COG1204 | Replicative superfamily II helicase [Replication, recombination and repair]; |
181-324 | 1.09e-06 | ||||||||||
Replicative superfamily II helicase [Replication, recombination and repair]; Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 52.20 E-value: 1.09e-06
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| DEXHc_Ski2 | cd17921 | DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
218-326 | 1.73e-06 | ||||||||||
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: 49.18 E-value: 1.73e-06
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| ResIII | COG3421 | Type III restriction endonuclease [Defense mechanisms]; |
183-317 | 4.09e-06 | ||||||||||
Type III restriction endonuclease [Defense mechanisms]; Pssm-ID: 442647 [Multi-domain] Cd Length: 883 Bit Score: 50.78 E-value: 4.09e-06
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| ComFA | COG4098 | Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
193-347 | 1.81e-05 | ||||||||||
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair]; Pssm-ID: 443274 [Multi-domain] Cd Length: 451 Bit Score: 47.95 E-value: 1.81e-05
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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 ... |
190-341 | 2.37e-05 | ||||||||||
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: 46.00 E-value: 2.37e-05
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| DEXQc_arch_SWI2_SNF2 | cd18012 | DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ... |
190-341 | 4.54e-05 | ||||||||||
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: 45.63 E-value: 4.54e-05
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| DEXHc_RIG-I_DDX58 | cd18073 | DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ... |
218-320 | 6.07e-05 | ||||||||||
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called DEAD box protein 58 (DDX58), is a pathogen-recognition receptor that recognizes viral 5'-triphosphates carrying double-stranded RNA. Upon binding to these microbe-associated molecular patterns (MAMPs), RIG-I forms oligomers and promotes downstream processes that result in type I interferon production and induction of an antiviral state. The optimal ligand for RIG-I has been found to be base-paired or double-stranded RNA (dsRNA) molecules containing a 5' triphosphate (5'-ppp-dsRNA). RIG-I contains two N-terminal caspase activation and recruitment domains (CARDs), which are required for interaction with IPS-1, a superfamily 2 helicase/translocase/ATPase (SF2) domain and a C-terminal regulatory/repressor domain (RD). RIG-I 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: 350831 [Multi-domain] Cd Length: 202 Bit Score: 44.81 E-value: 6.07e-05
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| DEXHc_RLR | cd18036 | DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
218-341 | 6.55e-05 | ||||||||||
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: 44.77 E-value: 6.55e-05
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| DEXHc_archSki2 | cd18028 | DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
200-316 | 2.40e-04 | ||||||||||
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: 42.71 E-value: 2.40e-04
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| DEXHc_RAD54 | cd18004 | DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ... |
190-317 | 3.93e-04 | ||||||||||
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They 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: 350762 [Multi-domain] Cd Length: 240 Bit Score: 43.04 E-value: 3.93e-04
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| COG2810 | COG2810 | Predicted type IV restriction endonuclease [Defense mechanisms]; |
2-110 | 3.96e-04 | ||||||||||
Predicted type IV restriction endonuclease [Defense mechanisms]; Pssm-ID: 442059 [Multi-domain] Cd Length: 340 Bit Score: 43.43 E-value: 3.96e-04
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| DEAHc_XPD-like | cd17915 | DEAH-box helicase domain of XPD family DEAD-like helicases; The xeroderma pigmentosum group D ... |
213-316 | 5.52e-04 | ||||||||||
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: 40.88 E-value: 5.52e-04
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| SNF2-rel_dom | pfam00176 | SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
187-341 | 5.58e-04 | ||||||||||
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: 42.67 E-value: 5.58e-04
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| HSDR_N_2 | pfam13588 | Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N ... |
57-123 | 7.37e-04 | ||||||||||
Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA. Pssm-ID: 433331 [Multi-domain] Cd Length: 110 Bit Score: 39.88 E-value: 7.37e-04
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| DEXQc_bact_SNF2 | cd18013 | DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ... |
190-341 | 8.86e-04 | ||||||||||
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the 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 comprise a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. The bacterial SNF2 present in this family 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: 350771 [Multi-domain] Cd Length: 218 Bit Score: 41.57 E-value: 8.86e-04
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| DDXDc_reverse_gyrase | cd17924 | DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
218-315 | 1.16e-03 | ||||||||||
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs 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: 350682 [Multi-domain] Cd Length: 189 Bit Score: 40.77 E-value: 1.16e-03
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| PriA | COG1198 | Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
169-316 | 1.84e-03 | ||||||||||
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair]; Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 42.03 E-value: 1.84e-03
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| HSDR_N | pfam04313 | Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N ... |
6-118 | 2.98e-03 | ||||||||||
Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA. Pssm-ID: 427858 [Multi-domain] Cd Length: 151 Bit Score: 39.21 E-value: 2.98e-03
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
546-588 | 7.86e-03 | ||||||||||
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: 36.14 E-value: 7.86e-03
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