ATP-dependent DNA helicase Q4 isoform X1 [Rattus norvegicus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| RecQ super family | cl33925 | Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
491-856 | 8.53e-115 | ||||||
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; The actual alignment was detected with superfamily member COG0514: Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 366.77 E-value: 8.53e-115
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| RecQL4_SLD2_NTD | cd22289 | N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA ... |
2-50 | 5.22e-19 | ||||||
N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA replication regulator SLD2 and similar proteins; RecQL4, also called ATP-dependent DNA helicase Q4, or DNA helicase, RecQ-like type 4 (RecQ4), or RTS, is a DNA-dependent ATPase that may modulate chromosome segregation. This family also includes fungal DNA replication regulator SLD2, also known as DNA replication and checkpoint protein 1 (DRC1), which functions with DPB11 to control DNA replication and the S-phase checkpoint. It is also required for the proper activation of RAD53 in response to DNA damage and replication blocks. This model corresponds to the N-terminal domain of RecQL4 and SLD2, which is a homeodomain-like DNA interaction motif. : Pssm-ID: 412085 Cd Length: 49 Bit Score: 81.52 E-value: 5.22e-19
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| Drc1-Sld2 super family | cl44400 | DNA replication and checkpoint protein; Genome duplication is precisely regulated by ... |
4-170 | 6.83e-10 | ||||||
DNA replication and checkpoint protein; Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent re-licensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5. Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication. The actual alignment was detected with superfamily member pfam11719: Pssm-ID: 371692 [Multi-domain] Cd Length: 391 Bit Score: 62.54 E-value: 6.83e-10
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| ZnF_C2HC | smart00343 | zinc finger; |
394-408 | 2.37e-03 | ||||||
zinc finger; : Pssm-ID: 197667 [Multi-domain] Cd Length: 17 Bit Score: 36.27 E-value: 2.37e-03
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| Name | Accession | Description | Interval | E-value | ||||||
| RecQ | COG0514 | Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
491-856 | 8.53e-115 | ||||||
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 366.77 E-value: 8.53e-115
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| DEXHc_RecQ4-like | cd18018 | DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ... |
494-696 | 3.22e-99 | ||||||
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: 313.81 E-value: 3.22e-99
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| recQ_fam | TIGR00614 | ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are ... |
501-849 | 1.76e-88 | ||||||
ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. 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: 129701 [Multi-domain] Cd Length: 470 Bit Score: 294.76 E-value: 1.76e-88
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| PRK11057 | PRK11057 | ATP-dependent DNA helicase RecQ; Provisional |
485-849 | 9.21e-79 | ||||||
ATP-dependent DNA helicase RecQ; Provisional Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 271.97 E-value: 9.21e-79
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| DpdF | NF041063 | protein DpdF; |
500-850 | 1.87e-34 | ||||||
protein DpdF; Pssm-ID: 468990 [Multi-domain] Cd Length: 813 Bit Score: 142.74 E-value: 1.87e-34
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
497-700 | 5.79e-25 | ||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 103.73 E-value: 5.79e-25
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
506-679 | 1.61e-24 | ||||||
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: 101.17 E-value: 1.61e-24
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| RecQL4_SLD2_NTD | cd22289 | N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA ... |
2-50 | 5.22e-19 | ||||||
N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA replication regulator SLD2 and similar proteins; RecQL4, also called ATP-dependent DNA helicase Q4, or DNA helicase, RecQ-like type 4 (RecQ4), or RTS, is a DNA-dependent ATPase that may modulate chromosome segregation. This family also includes fungal DNA replication regulator SLD2, also known as DNA replication and checkpoint protein 1 (DRC1), which functions with DPB11 to control DNA replication and the S-phase checkpoint. It is also required for the proper activation of RAD53 in response to DNA damage and replication blocks. This model corresponds to the N-terminal domain of RecQL4 and SLD2, which is a homeodomain-like DNA interaction motif. Pssm-ID: 412085 Cd Length: 49 Bit Score: 81.52 E-value: 5.22e-19
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| Drc1-Sld2 | pfam11719 | DNA replication and checkpoint protein; Genome duplication is precisely regulated by ... |
4-170 | 6.83e-10 | ||||||
DNA replication and checkpoint protein; Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent re-licensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5. Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication. Pssm-ID: 371692 [Multi-domain] Cd Length: 391 Bit Score: 62.54 E-value: 6.83e-10
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| ZnF_C2HC | smart00343 | zinc finger; |
394-408 | 2.37e-03 | ||||||
zinc finger; Pssm-ID: 197667 [Multi-domain] Cd Length: 17 Bit Score: 36.27 E-value: 2.37e-03
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| zf-CCHC | pfam00098 | Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ... |
393-410 | 9.77e-03 | ||||||
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. Pssm-ID: 395050 [Multi-domain] Cd Length: 18 Bit Score: 34.81 E-value: 9.77e-03
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| Name | Accession | Description | Interval | E-value | |||||||
| RecQ | COG0514 | Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
491-856 | 8.53e-115 | |||||||
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 366.77 E-value: 8.53e-115
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| DEXHc_RecQ4-like | cd18018 | DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ... |
494-696 | 3.22e-99 | |||||||
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: 313.81 E-value: 3.22e-99
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| recQ_fam | TIGR00614 | ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are ... |
501-849 | 1.76e-88 | |||||||
ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. 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: 129701 [Multi-domain] Cd Length: 470 Bit Score: 294.76 E-value: 1.76e-88
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| recQ | TIGR01389 | ATP-dependent DNA helicase RecQ; The ATP-dependent DNA helicase RecQ of E. coli is about 600 ... |
494-850 | 4.18e-88 | |||||||
ATP-dependent DNA helicase RecQ; The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ. [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273594 [Multi-domain] Cd Length: 591 Bit Score: 297.75 E-value: 4.18e-88
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| PRK11057 | PRK11057 | ATP-dependent DNA helicase RecQ; Provisional |
485-849 | 9.21e-79 | |||||||
ATP-dependent DNA helicase RecQ; Provisional Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 271.97 E-value: 9.21e-79
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| DEXHc_RecQ | cd17920 | DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
498-696 | 5.31e-66 | |||||||
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: 221.25 E-value: 5.31e-66
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| SF2_C_RecQ | cd18794 | C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
702-846 | 6.27e-56 | |||||||
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350181 [Multi-domain] Cd Length: 134 Bit Score: 190.11 E-value: 6.27e-56
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| PLN03137 | PLN03137 | ATP-dependent DNA helicase; Q4-like; Provisional |
501-846 | 3.27e-52 | |||||||
ATP-dependent DNA helicase; Q4-like; Provisional Pssm-ID: 215597 [Multi-domain] Cd Length: 1195 Bit Score: 200.89 E-value: 3.27e-52
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| DEXHc_RecQ1 | cd18015 | DEXH-box helicase domain of RecQ1; ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ ... |
484-696 | 5.07e-38 | |||||||
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: 141.73 E-value: 5.07e-38
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| DpdF | NF041063 | protein DpdF; |
500-850 | 1.87e-34 | |||||||
protein DpdF; Pssm-ID: 468990 [Multi-domain] Cd Length: 813 Bit Score: 142.74 E-value: 1.87e-34
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| DEXHc_RecQ5 | cd18014 | DEAH-box helicase domain of RecQ5; ATP-dependent DNA helicase Q5 (RecQ5) is part of the RecQ ... |
501-687 | 4.01e-32 | |||||||
DEAH-box helicase domain of RecQ5; ATP-dependent DNA helicase Q5 (RecQ5) 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: 350772 [Multi-domain] Cd Length: 205 Bit Score: 124.51 E-value: 4.01e-32
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| DEXHc_RecQ3 | cd18017 | DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ... |
498-687 | 4.46e-32 | |||||||
DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ATP-dependent helicase or WRN) 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 Werner's syndrome. Pssm-ID: 350775 [Multi-domain] Cd Length: 193 Bit Score: 124.12 E-value: 4.46e-32
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| DEXHc_RecQ2_BLM | cd18016 | DEAH-box helicase domain of RecQ2; ATP-dependent DNA helicase Q2 (RecQ2, also called Bloom ... |
499-687 | 3.92e-28 | |||||||
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: 113.00 E-value: 3.92e-28
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
497-700 | 5.79e-25 | |||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 103.73 E-value: 5.79e-25
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
506-679 | 1.61e-24 | |||||||
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: 101.17 E-value: 1.61e-24
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| YprA | COG1205 | ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
480-841 | 3.84e-20 | |||||||
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair]; Pssm-ID: 440818 [Multi-domain] Cd Length: 758 Bit Score: 96.83 E-value: 3.84e-20
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
770-838 | 7.77e-20 | |||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 84.96 E-value: 7.77e-20
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| RecQL4_SLD2_NTD | cd22289 | N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA ... |
2-50 | 5.22e-19 | |||||||
N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA replication regulator SLD2 and similar proteins; RecQL4, also called ATP-dependent DNA helicase Q4, or DNA helicase, RecQ-like type 4 (RecQ4), or RTS, is a DNA-dependent ATPase that may modulate chromosome segregation. This family also includes fungal DNA replication regulator SLD2, also known as DNA replication and checkpoint protein 1 (DRC1), which functions with DPB11 to control DNA replication and the S-phase checkpoint. It is also required for the proper activation of RAD53 in response to DNA damage and replication blocks. This model corresponds to the N-terminal domain of RecQL4 and SLD2, which is a homeodomain-like DNA interaction motif. Pssm-ID: 412085 Cd Length: 49 Bit Score: 81.52 E-value: 5.22e-19
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| SF2_C_Hrq | cd18797 | C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
733-841 | 4.19e-17 | |||||||
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases 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: 350184 [Multi-domain] Cd Length: 146 Bit Score: 79.22 E-value: 4.19e-17
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
715-838 | 3.78e-16 | |||||||
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: 75.32 E-value: 3.78e-16
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
506-846 | 2.04e-14 | |||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 77.76 E-value: 2.04e-14
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
711-847 | 2.21e-14 | |||||||
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: 71.00 E-value: 2.21e-14
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| SrmB | COG0513 | Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
490-839 | 2.60e-14 | |||||||
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 76.72 E-value: 2.60e-14
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
522-672 | 3.87e-14 | |||||||
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: 70.90 E-value: 3.87e-14
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| BRR2 | COG1204 | Replicative superfamily II helicase [Replication, recombination and repair]; |
485-852 | 2.44e-12 | |||||||
Replicative superfamily II helicase [Replication, recombination and repair]; Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 71.08 E-value: 2.44e-12
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| SF2_C_LHR | cd18796 | C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
739-841 | 3.76e-11 | |||||||
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases 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: 350183 [Multi-domain] Cd Length: 150 Bit Score: 62.28 E-value: 3.76e-11
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
797-846 | 6.05e-10 | |||||||
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: 56.56 E-value: 6.05e-10
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| Drc1-Sld2 | pfam11719 | DNA replication and checkpoint protein; Genome duplication is precisely regulated by ... |
4-170 | 6.83e-10 | |||||||
DNA replication and checkpoint protein; Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent re-licensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5. Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication. Pssm-ID: 371692 [Multi-domain] Cd Length: 391 Bit Score: 62.54 E-value: 6.83e-10
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| SF2_C_Ski2 | cd18795 | C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
731-838 | 7.67e-09 | |||||||
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases 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: 350182 [Multi-domain] Cd Length: 154 Bit Score: 56.02 E-value: 7.67e-09
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| PRK09751 | PRK09751 | putative ATP-dependent helicase Lhr; Provisional |
734-835 | 9.32e-09 | |||||||
putative ATP-dependent helicase Lhr; Provisional Pssm-ID: 137505 [Multi-domain] Cd Length: 1490 Bit Score: 59.94 E-value: 9.32e-09
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| PTZ00110 | PTZ00110 | helicase; Provisional |
490-849 | 3.10e-08 | |||||||
helicase; Provisional Pssm-ID: 240273 [Multi-domain] Cd Length: 545 Bit Score: 57.86 E-value: 3.10e-08
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| PRK13767 | PRK13767 | ATP-dependent helicase; Provisional |
504-835 | 4.53e-08 | |||||||
ATP-dependent helicase; Provisional Pssm-ID: 237497 [Multi-domain] Cd Length: 876 Bit Score: 57.59 E-value: 4.53e-08
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| PTZ00424 | PTZ00424 | helicase 45; Provisional |
728-860 | 1.66e-07 | |||||||
helicase 45; Provisional Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 55.22 E-value: 1.66e-07
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| COG1202 | COG1202 | Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
770-836 | 6.83e-07 | |||||||
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 53.74 E-value: 6.83e-07
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| DEXHc_Hrq1-like | cd17923 | DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ... |
509-568 | 1.27e-06 | |||||||
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. Hrq1 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: 350681 [Multi-domain] Cd Length: 182 Bit Score: 49.89 E-value: 1.27e-06
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| Lhr | COG1201 | Lhr-like helicase [Replication, recombination and repair]; |
504-835 | 2.95e-06 | |||||||
Lhr-like helicase [Replication, recombination and repair]; Pssm-ID: 440814 [Multi-domain] Cd Length: 850 Bit Score: 51.64 E-value: 2.95e-06
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| DDXDc_reverse_gyrase | cd17924 | DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
515-604 | 3.51e-06 | |||||||
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: 48.86 E-value: 3.51e-06
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
505-672 | 4.21e-06 | |||||||
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: 47.69 E-value: 4.21e-06
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| PLN00206 | PLN00206 | DEAD-box ATP-dependent RNA helicase; Provisional |
780-855 | 7.34e-06 | |||||||
DEAD-box ATP-dependent RNA helicase; Provisional Pssm-ID: 215103 [Multi-domain] Cd Length: 518 Bit Score: 50.17 E-value: 7.34e-06
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| DEADc_DDX5 | cd18049 | DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, ... |
470-619 | 1.15e-05 | |||||||
DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, G17P1, or HUMP68) is involved in pathways that include the alteration of RNA structures, plays a role as a coregulator of transcription, a regulator of splicing, and in the processing of small noncoding RNAs. It synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. Dysregulation of this gene may play a role in cancer development. DDX5 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350807 [Multi-domain] Cd Length: 234 Bit Score: 48.08 E-value: 1.15e-05
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
503-672 | 1.31e-05 | |||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 46.51 E-value: 1.31e-05
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| DEXHc_Ski2 | cd17921 | DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
504-692 | 2.84e-05 | |||||||
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: 46.10 E-value: 2.84e-05
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| PRK04837 | PRK04837 | ATP-dependent RNA helicase RhlB; Provisional |
782-842 | 3.58e-05 | |||||||
ATP-dependent RNA helicase RhlB; Provisional Pssm-ID: 235314 [Multi-domain] Cd Length: 423 Bit Score: 47.66 E-value: 3.58e-05
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| DEXHc_LHR-like | cd17922 | DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ... |
519-608 | 6.79e-05 | |||||||
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases from 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: 350680 [Multi-domain] Cd Length: 166 Bit Score: 44.50 E-value: 6.79e-05
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| DEADc_DDX17 | cd18050 | DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or ... |
470-619 | 1.24e-04 | |||||||
DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or DEAD Box Protein P82) has a wide variety of functions including regulating the alternative splicing of exons exhibiting specific features such as the inclusion of AC-rich alternative exons in CD44 transcripts, playing a role in innate immunity, and promoting mRNA degradation mediated by the antiviral zinc-finger protein ZC3HAV1 in an ATPase-dependent manner. DDX17 synergizes with DDX5 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. DDX17 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350808 [Multi-domain] Cd Length: 271 Bit Score: 45.39 E-value: 1.24e-04
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| PRK01172 | PRK01172 | ATP-dependent DNA helicase; |
667-838 | 2.91e-04 | |||||||
ATP-dependent DNA helicase; Pssm-ID: 100801 [Multi-domain] Cd Length: 674 Bit Score: 45.26 E-value: 2.91e-04
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| SF2_C_dicer | cd18802 | C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
715-847 | 3.17e-04 | |||||||
C-terminal helicase domain of the 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. Dicer exists throughout eukaryotes, and a subset has 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 helicase domains 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: 350189 [Multi-domain] Cd Length: 142 Bit Score: 42.19 E-value: 3.17e-04
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| DEADc | cd00268 | DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
495-609 | 5.31e-04 | |||||||
DEAD-box helicase domain of 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350669 [Multi-domain] Cd Length: 196 Bit Score: 42.43 E-value: 5.31e-04
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
572-602 | 5.78e-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: 5.78e-04
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| PRK01297 | PRK01297 | ATP-dependent RNA helicase RhlB; Provisional |
690-838 | 6.44e-04 | |||||||
ATP-dependent RNA helicase RhlB; Provisional Pssm-ID: 234938 [Multi-domain] Cd Length: 475 Bit Score: 43.75 E-value: 6.44e-04
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
538-604 | 7.83e-04 | |||||||
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: 40.27 E-value: 7.83e-04
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| PRK11634 | PRK11634 | ATP-dependent RNA helicase DeaD; Provisional |
714-847 | 8.15e-04 | |||||||
ATP-dependent RNA helicase DeaD; Provisional Pssm-ID: 236941 [Multi-domain] Cd Length: 629 Bit Score: 43.68 E-value: 8.15e-04
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| PRK00254 | PRK00254 | ski2-like helicase; Provisional |
733-836 | 1.59e-03 | |||||||
ski2-like helicase; Provisional Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 42.88 E-value: 1.59e-03
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| DEADc_DDX43_DDX53 | cd17958 | DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis ... |
493-605 | 1.76e-03 | |||||||
DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis antigen 13 or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 is also called cancer/testis antigen 26 or DEAD-Box Protein CAGE. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350716 [Multi-domain] Cd Length: 197 Bit Score: 40.91 E-value: 1.76e-03
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| DEADc_DDX28 | cd17948 | DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ... |
509-608 | 2.35e-03 | |||||||
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350706 [Multi-domain] Cd Length: 231 Bit Score: 41.20 E-value: 2.35e-03
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| ZnF_C2HC | smart00343 | zinc finger; |
394-408 | 2.37e-03 | |||||||
zinc finger; Pssm-ID: 197667 [Multi-domain] Cd Length: 17 Bit Score: 36.27 E-value: 2.37e-03
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| DinG | COG1199 | Rad3-related DNA helicase DinG [Replication, recombination and repair]; |
498-547 | 2.45e-03 | |||||||
Rad3-related DNA helicase DinG [Replication, recombination and repair]; Pssm-ID: 440812 [Multi-domain] Cd Length: 629 Bit Score: 42.22 E-value: 2.45e-03
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| PRK02362 | PRK02362 | ATP-dependent DNA helicase; |
767-852 | 2.93e-03 | |||||||
ATP-dependent DNA helicase; Pssm-ID: 235032 [Multi-domain] Cd Length: 737 Bit Score: 41.87 E-value: 2.93e-03
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| PRK11776 | PRK11776 | ATP-dependent RNA helicase DbpA; Provisional |
710-839 | 3.53e-03 | |||||||
ATP-dependent RNA helicase DbpA; Provisional Pssm-ID: 236977 [Multi-domain] Cd Length: 460 Bit Score: 41.33 E-value: 3.53e-03
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| SF2_C_SNF | cd18793 | C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
773-847 | 6.27e-03 | |||||||
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350180 [Multi-domain] Cd Length: 135 Bit Score: 38.23 E-value: 6.27e-03
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| DEXHc_Snf | cd17919 | DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
529-672 | 6.65e-03 | |||||||
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: 39.09 E-value: 6.65e-03
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
572-604 | 7.14e-03 | |||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 36.81 E-value: 7.14e-03
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| SF2_C_RecG | cd18811 | C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
774-845 | 8.05e-03 | |||||||
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It 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: 350198 [Multi-domain] Cd Length: 159 Bit Score: 38.48 E-value: 8.05e-03
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| zf-CCHC | pfam00098 | Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ... |
393-410 | 9.77e-03 | |||||||
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. Pssm-ID: 395050 [Multi-domain] Cd Length: 18 Bit Score: 34.81 E-value: 9.77e-03
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