helicase [Brucella phage Iz]
Protein Classification
DEAD/DEAH box helicase( domain architecture ID 11437466)
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]; |
2-337 | 5.96e-68 | ||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; : Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 230.30 E-value: 5.96e-68
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| DZR super family | cl25536 | Double zinc ribbon; This family consists of a pair of zinc ribbon domains. |
415-456 | 1.19e-03 | ||||||
Double zinc ribbon; This family consists of a pair of zinc ribbon domains. The actual alignment was detected with superfamily member pfam12773: Pssm-ID: 432773 [Multi-domain] Cd Length: 45 Bit Score: 36.97 E-value: 1.19e-03
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| Name | Accession | Description | Interval | E-value | ||||||
| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
2-337 | 5.96e-68 | ||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 230.30 E-value: 5.96e-68
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| SF2_C_EcoAI-like | cd18799 | C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
235-334 | 9.08e-26 | ||||||
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: 101.87 E-value: 9.08e-26
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
3-129 | 5.73e-15 | ||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 73.68 E-value: 5.73e-15
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
3-129 | 2.47e-12 | ||||||
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: 65.34 E-value: 2.47e-12
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| uvsW | PHA02558 | UvsW helicase; Provisional |
3-334 | 1.54e-10 | ||||||
UvsW helicase; Provisional Pssm-ID: 222875 [Multi-domain] Cd Length: 501 Bit Score: 63.49 E-value: 1.54e-10
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| DZR | pfam12773 | Double zinc ribbon; This family consists of a pair of zinc ribbon domains. |
415-456 | 1.19e-03 | ||||||
Double zinc ribbon; This family consists of a pair of zinc ribbon domains. Pssm-ID: 432773 [Multi-domain] Cd Length: 45 Bit Score: 36.97 E-value: 1.19e-03
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| Name | Accession | Description | Interval | E-value | ||||||
| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
2-337 | 5.96e-68 | ||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 230.30 E-value: 5.96e-68
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| SF2_C_EcoAI-like | cd18799 | C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
235-334 | 9.08e-26 | ||||||
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: 101.87 E-value: 9.08e-26
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
3-129 | 5.73e-15 | ||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 73.68 E-value: 5.73e-15
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
4-129 | 1.24e-12 | ||||||
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: 65.40 E-value: 1.24e-12
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
3-129 | 2.47e-12 | ||||||
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: 65.34 E-value: 2.47e-12
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| HsdR | COG4096 | Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
199-338 | 5.79e-12 | ||||||
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms]; Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 68.71 E-value: 5.79e-12
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| uvsW | PHA02558 | UvsW helicase; Provisional |
3-334 | 1.54e-10 | ||||||
UvsW helicase; Provisional Pssm-ID: 222875 [Multi-domain] Cd Length: 501 Bit Score: 63.49 E-value: 1.54e-10
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
219-320 | 6.09e-10 | ||||||
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: 56.84 E-value: 6.09e-10
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
5-128 | 3.17e-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: 55.87 E-value: 3.17e-09
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
4-131 | 3.23e-09 | ||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 56.14 E-value: 3.23e-09
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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 ... |
4-139 | 3.43e-09 | ||||||
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: 56.03 E-value: 3.43e-09
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
257-320 | 3.41e-08 | ||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 51.06 E-value: 3.41e-08
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| hsdR | PRK11448 | type I restriction enzyme EcoKI subunit R; Provisional |
235-332 | 1.15e-07 | ||||||
type I restriction enzyme EcoKI subunit R; Provisional Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 54.96 E-value: 1.15e-07
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| BRR2 | COG1204 | Replicative superfamily II helicase [Replication, recombination and repair]; |
4-317 | 1.35e-06 | ||||||
Replicative superfamily II helicase [Replication, recombination and repair]; Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 51.05 E-value: 1.35e-06
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
234-334 | 1.61e-06 | ||||||
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: 46.16 E-value: 1.61e-06
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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 ... |
3-129 | 4.54e-06 | ||||||
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: 47.81 E-value: 4.54e-06
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| DEXHc_dicer | cd18034 | DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
8-130 | 5.42e-06 | ||||||
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: 47.26 E-value: 5.42e-06
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| DEXHc_Hef | cd18035 | DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
3-99 | 5.47e-06 | ||||||
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: 47.12 E-value: 5.47e-06
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| DEXHc_archSki2 | cd18028 | DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
4-146 | 7.55e-06 | ||||||
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: 46.56 E-value: 7.55e-06
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| DEXHc_Ski2 | cd17921 | DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
4-128 | 9.86e-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: 46.49 E-value: 9.86e-06
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| SF2_C_UvrB | cd18790 | C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ... |
215-320 | 3.99e-05 | ||||||
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB 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: 350177 [Multi-domain] Cd Length: 171 Bit Score: 44.54 E-value: 3.99e-05
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| MPH1 | COG1111 | ERCC4-related helicase [Replication, recombination and repair]; |
3-99 | 9.46e-05 | ||||||
ERCC4-related helicase [Replication, recombination and repair]; Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 45.49 E-value: 9.46e-05
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| DZR | pfam12773 | Double zinc ribbon; This family consists of a pair of zinc ribbon domains. |
415-456 | 1.19e-03 | ||||||
Double zinc ribbon; This family consists of a pair of zinc ribbon domains. Pssm-ID: 432773 [Multi-domain] Cd Length: 45 Bit Score: 36.97 E-value: 1.19e-03
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| DEXHc_UvsW | cd18031 | DEXH-box helicase domain of bacteriophage UvsW; Bacteriophage UvsW is part of the WXY system ... |
4-129 | 2.16e-03 | ||||||
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: 39.34 E-value: 2.16e-03
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| DEXDc_ComFA | cd17925 | DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
1-100 | 3.41e-03 | ||||||
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon protein 1) is part of the complex mediating the binding and uptake of single-stranded DNA. ComFA is required for DNA uptake but not for binding. It 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: 350683 [Multi-domain] Cd Length: 143 Bit Score: 38.05 E-value: 3.41e-03
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| DEXDc_FANCM | cd18033 | DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ... |
3-129 | 7.56e-03 | ||||||
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: 37.69 E-value: 7.56e-03
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| Blast search parameters | ||||
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