RECQ helicase SIM [Arabidopsis thaliana]
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]; |
155-684 | 1.76e-132 | ||||||||
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: 404.52 E-value: 1.76e-132
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| UBA_like_SF super family | cl21463 | UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains ... |
8-42 | 7.38e-05 | ||||||||
UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains alpha-helical structural homology ubiquitin-binding domains, including UBA domains and coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domains which share a common three-helical bundle architecture. UBA domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only bind the UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains. CUE domain containing proteins are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. This superfamily also includes many UBA-like domains found in AMP-activated protein kinase (AMPK) related kinases, the NXF family of mRNA nuclear export factors, elongation factor Ts (EF-Ts), nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins. Although many UBA-like domains may have a conserved TG but not GF/Y-loop, they still show a high level of structural and sequence similarity with three-helical ubiquitin binding domains. The actual alignment was detected with superfamily member cd14327: Pssm-ID: 473871 [Multi-domain] Cd Length: 38 Bit Score: 40.75 E-value: 7.38e-05
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| Name | Accession | Description | Interval | E-value | ||||||||
| RecQ | COG0514 | Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
155-684 | 1.76e-132 | ||||||||
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 404.52 E-value: 1.76e-132
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| recQ_fam | TIGR00614 | ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are ... |
158-663 | 2.86e-113 | ||||||||
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: 354.08 E-value: 2.86e-113
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| DEXHc_RecQ | cd17920 | DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
158-360 | 1.63e-85 | ||||||||
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: 270.94 E-value: 1.63e-85
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| PRK11057 | PRK11057 | ATP-dependent DNA helicase RecQ; Provisional |
159-677 | 5.77e-81 | ||||||||
ATP-dependent DNA helicase RecQ; Provisional Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 272.74 E-value: 5.77e-81
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| DpdF | NF041063 | protein DpdF; |
159-602 | 2.23e-32 | ||||||||
protein DpdF; Pssm-ID: 468990 [Multi-domain] Cd Length: 813 Bit Score: 135.04 E-value: 2.23e-32
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
170-341 | 4.50e-29 | ||||||||
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: 113.88 E-value: 4.50e-29
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
162-355 | 3.24e-25 | ||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 104.11 E-value: 3.24e-25
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| UBA_atUPL1_2_like | cd14327 | UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 ... |
8-42 | 7.38e-05 | ||||||||
UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 (atUPL2) and similar proteins; The family includes two highly similar 405-kDa HECT E3 ubiquitin-protein ligases (UPLs), UPL1 and UPL2, from Arabidopsis thaliana. The HECT E3 UPL family plays a prominent role in the ubiquitination of plant proteins. The biological functions of UPL1 and UPL2 remain unclear. Both of them contain a ubiquitin-associated (UBA) domain and a C-terminal HECT domain. UBA domain may be involved in ubiquitin metabolism. HECT domain is necessary and sufficient for their E3 catalytic activity, but requires ATP, E1 and an E2 of the Arabidopsis UBC8 family to ubiquitinate proteins. Pssm-ID: 270512 [Multi-domain] Cd Length: 38 Bit Score: 40.75 E-value: 7.38e-05
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| Name | Accession | Description | Interval | E-value | ||||||||
| RecQ | COG0514 | Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
155-684 | 1.76e-132 | ||||||||
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 404.52 E-value: 1.76e-132
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| recQ_fam | TIGR00614 | ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are ... |
158-663 | 2.86e-113 | ||||||||
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: 354.08 E-value: 2.86e-113
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| recQ | TIGR01389 | ATP-dependent DNA helicase RecQ; The ATP-dependent DNA helicase RecQ of E. coli is about 600 ... |
159-677 | 2.71e-102 | ||||||||
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: 329.34 E-value: 2.71e-102
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| DEXHc_RecQ | cd17920 | DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
158-360 | 1.63e-85 | ||||||||
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: 270.94 E-value: 1.63e-85
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| PRK11057 | PRK11057 | ATP-dependent DNA helicase RecQ; Provisional |
159-677 | 5.77e-81 | ||||||||
ATP-dependent DNA helicase RecQ; Provisional Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 272.74 E-value: 5.77e-81
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| PLN03137 | PLN03137 | ATP-dependent DNA helicase; Q4-like; Provisional |
152-665 | 8.42e-60 | ||||||||
ATP-dependent DNA helicase; Q4-like; Provisional Pssm-ID: 215597 [Multi-domain] Cd Length: 1195 Bit Score: 221.69 E-value: 8.42e-60
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| DEXHc_RecQ3 | cd18017 | DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ... |
160-360 | 1.18e-58 | ||||||||
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: 198.46 E-value: 1.18e-58
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| DEXHc_RecQ1 | cd18015 | DEXH-box helicase domain of RecQ1; ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ ... |
151-351 | 7.91e-55 | ||||||||
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: 188.34 E-value: 7.91e-55
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| DEXHc_RecQ2_BLM | cd18016 | DEAH-box helicase domain of RecQ2; ATP-dependent DNA helicase Q2 (RecQ2, also called Bloom ... |
154-360 | 1.43e-51 | ||||||||
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: 179.25 E-value: 1.43e-51
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| DEXHc_RecQ4-like | cd18018 | DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ... |
159-347 | 8.58e-47 | ||||||||
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: 165.89 E-value: 8.58e-47
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| SF2_C_RecQ | cd18794 | C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
492-600 | 2.22e-44 | ||||||||
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: 156.21 E-value: 2.22e-44
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| DEXHc_RecQ5 | cd18014 | DEAH-box helicase domain of RecQ5; ATP-dependent DNA helicase Q5 (RecQ5) is part of the RecQ ... |
158-361 | 9.71e-42 | ||||||||
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: 151.47 E-value: 9.71e-42
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| DpdF | NF041063 | protein DpdF; |
159-602 | 2.23e-32 | ||||||||
protein DpdF; Pssm-ID: 468990 [Multi-domain] Cd Length: 813 Bit Score: 135.04 E-value: 2.23e-32
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
170-341 | 4.50e-29 | ||||||||
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: 113.88 E-value: 4.50e-29
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
162-355 | 3.24e-25 | ||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 104.11 E-value: 3.24e-25
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
513-592 | 3.59e-18 | ||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 79.56 E-value: 3.59e-18
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
183-334 | 1.90e-16 | ||||||||
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region. Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 77.06 E-value: 1.90e-16
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
498-592 | 9.57e-15 | ||||||||
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: 71.09 E-value: 9.57e-15
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| SF2_C_Hrq | cd18797 | C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
500-593 | 6.66e-12 | ||||||||
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: 63.82 E-value: 6.66e-12
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| RecQ_Zn_bind | pfam16124 | RecQ zinc-binding; This domain is the zinc-binding domain of ATP-dependent DNA helicase RecQ. |
600-664 | 7.57e-12 | ||||||||
RecQ zinc-binding; This domain is the zinc-binding domain of ATP-dependent DNA helicase RecQ. Pssm-ID: 465031 [Multi-domain] Cd Length: 66 Bit Score: 61.15 E-value: 7.57e-12
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| SF2_C_Ski2 | cd18795 | C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
500-602 | 4.76e-10 | ||||||||
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: 58.72 E-value: 4.76e-10
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
168-588 | 6.94e-09 | ||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 59.27 E-value: 6.94e-09
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
169-305 | 1.17e-08 | ||||||||
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: 54.62 E-value: 1.17e-08
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| COG1202 | COG1202 | Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
498-627 | 1.36e-08 | ||||||||
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 58.75 E-value: 1.36e-08
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| YprA | COG1205 | ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
154-230 | 1.58e-08 | ||||||||
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: 58.31 E-value: 1.58e-08
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
492-590 | 2.47e-07 | ||||||||
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: 50.58 E-value: 2.47e-07
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
546-600 | 2.78e-07 | ||||||||
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: 48.47 E-value: 2.78e-07
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
168-334 | 3.56e-07 | ||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 50.75 E-value: 3.56e-07
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| YprA | COG1205 | ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
500-593 | 1.34e-06 | ||||||||
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: 52.15 E-value: 1.34e-06
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| SrmB | COG0513 | Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
498-593 | 1.64e-06 | ||||||||
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 51.30 E-value: 1.64e-06
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| BRR2 | COG1204 | Replicative superfamily II helicase [Replication, recombination and repair]; |
163-590 | 3.67e-06 | ||||||||
Replicative superfamily II helicase [Replication, recombination and repair]; Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 50.66 E-value: 3.67e-06
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| DEXHc_Hrq1-like | cd17923 | DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ... |
169-224 | 5.38e-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: 47.58 E-value: 5.38e-06
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| UBA_atUPL1_2_like | cd14327 | UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 ... |
8-42 | 7.38e-05 | ||||||||
UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 (atUPL2) and similar proteins; The family includes two highly similar 405-kDa HECT E3 ubiquitin-protein ligases (UPLs), UPL1 and UPL2, from Arabidopsis thaliana. The HECT E3 UPL family plays a prominent role in the ubiquitination of plant proteins. The biological functions of UPL1 and UPL2 remain unclear. Both of them contain a ubiquitin-associated (UBA) domain and a C-terminal HECT domain. UBA domain may be involved in ubiquitin metabolism. HECT domain is necessary and sufficient for their E3 catalytic activity, but requires ATP, E1 and an E2 of the Arabidopsis UBC8 family to ubiquitinate proteins. Pssm-ID: 270512 [Multi-domain] Cd Length: 38 Bit Score: 40.75 E-value: 7.38e-05
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| DEADc_DDX42 | cd17952 | DEAD-box helicase domain of DEAD box protein 42; DDX42 (also called Splicing Factor ... |
173-290 | 8.59e-05 | ||||||||
DEAD-box helicase domain of DEAD box protein 42; DDX42 (also called Splicing Factor 3B-Associated 125 kDa Protein, RHELP, or RNAHP) is an NTPase with a preference for ATP, the hydrolysis of which is enhanced by various RNA substrates. It acts as a non-processive RNA helicase with protein displacement and RNA annealing activities. DDX42 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: 350710 [Multi-domain] Cd Length: 197 Bit Score: 44.33 E-value: 8.59e-05
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| DEADc_DDX51 | cd17956 | DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by ... |
185-365 | 1.26e-04 | ||||||||
DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by regulating multiple signalling pathways. Mammalian DEAD box protein Ddx51 acts in 3' end maturation of 28S rRNA by promoting the release of U8 snoRNA.It 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: 350714 [Multi-domain] Cd Length: 231 Bit Score: 44.16 E-value: 1.26e-04
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| DEADc_DDX52 | cd17957 | DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ... |
173-230 | 1.33e-04 | ||||||||
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ubiquitously expressed in testis, endometrium, and other tissues in humans. DDX52 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: 350715 [Multi-domain] Cd Length: 198 Bit Score: 43.73 E-value: 1.33e-04
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| DEADc | cd00268 | DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
162-290 | 1.34e-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: 43.97 E-value: 1.34e-04
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| PRK11634 | PRK11634 | ATP-dependent RNA helicase DeaD; Provisional |
500-619 | 1.70e-04 | ||||||||
ATP-dependent RNA helicase DeaD; Provisional Pssm-ID: 236941 [Multi-domain] Cd Length: 629 Bit Score: 45.22 E-value: 1.70e-04
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| PLN00206 | PLN00206 | DEAD-box ATP-dependent RNA helicase; Provisional |
521-593 | 2.51e-04 | ||||||||
DEAD-box ATP-dependent RNA helicase; Provisional Pssm-ID: 215103 [Multi-domain] Cd Length: 518 Bit Score: 44.39 E-value: 2.51e-04
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| SF2_C_TRCF | cd18810 | C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
522-626 | 4.80e-04 | ||||||||
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF 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: 350197 [Multi-domain] Cd Length: 151 Bit Score: 41.56 E-value: 4.80e-04
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| Dob10 | COG4581 | Superfamily II RNA helicase [Replication, recombination and repair]; |
172-220 | 1.01e-03 | ||||||||
Superfamily II RNA helicase [Replication, recombination and repair]; Pssm-ID: 443638 [Multi-domain] Cd Length: 751 Bit Score: 42.62 E-value: 1.01e-03
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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 ... |
167-295 | 1.51e-03 | ||||||||
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: 40.88 E-value: 1.51e-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 ... |
185-249 | 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: 40.53 E-value: 1.76e-03
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| DEXHc_Ski2 | cd17921 | DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
172-294 | 1.79e-03 | ||||||||
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: 40.32 E-value: 1.79e-03
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| DEXDc_ComFA | cd17925 | DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
174-235 | 1.99e-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: 39.59 E-value: 1.99e-03
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| SF2_C_LHR | cd18796 | C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
500-590 | 2.13e-03 | ||||||||
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: 39.55 E-value: 2.13e-03
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| DEXHc_HFM1 | cd18023 | DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ... |
184-363 | 3.35e-03 | ||||||||
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box helicase, required for crossover formation and complete synapsis of homologous chromosomes during meiosis. HFM1 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: 350781 [Multi-domain] Cd Length: 206 Bit Score: 39.65 E-value: 3.35e-03
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| DEXHc_LHR-like | cd17922 | DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ... |
184-224 | 3.82e-03 | ||||||||
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: 39.10 E-value: 3.82e-03
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| DEADc_DDX31 | cd17949 | DEAD-box helicase domain of DEAD box protein 31; DDX31 (also called helicain or G2 helicase) ... |
160-205 | 4.22e-03 | ||||||||
DEAD-box helicase domain of DEAD box protein 31; DDX31 (also called helicain or G2 helicase) plays a role in ribosome biogenesis and TP53/p53 regulation through its interaction with NPM1. DDX31 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: 350707 [Multi-domain] Cd Length: 214 Bit Score: 39.49 E-value: 4.22e-03
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| DEADc_DDX46 | cd17953 | DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) ... |
162-290 | 5.30e-03 | ||||||||
DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) is a component of the 17S U2 snRNP complex. It plays an important role in pre-mRNA splicing and has a role in antiviral innate immunity. DDX46 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: 350711 [Multi-domain] Cd Length: 222 Bit Score: 39.28 E-value: 5.30e-03
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| Lhr | COG1201 | Lhr-like helicase [Replication, recombination and repair]; |
161-198 | 7.38e-03 | ||||||||
Lhr-like helicase [Replication, recombination and repair]; Pssm-ID: 440814 [Multi-domain] Cd Length: 850 Bit Score: 40.09 E-value: 7.38e-03
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| PTZ00110 | PTZ00110 | helicase; Provisional |
501-592 | 7.48e-03 | ||||||||
helicase; Provisional Pssm-ID: 240273 [Multi-domain] Cd Length: 545 Bit Score: 39.76 E-value: 7.48e-03
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| DEADc_DDX10 | cd17941 | DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin ... |
173-216 | 7.83e-03 | ||||||||
DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin gene, NUP98, by inversion 11 (p15q22) chromosome translocation is found in the patients with de novo or therapy-related myeloid malignancies. Diseases associated with DDX10 (also known as DDX10-NUP98 Fusion Protein Type 2) include myelodysplastic syndrome and leukemia, acute myeloid. DDX10 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: 350699 [Multi-domain] Cd Length: 198 Bit Score: 38.43 E-value: 7.83e-03
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| DEADc_DDX18 | cd17942 | DEAD-box helicase domain of DEAD box protein 18; This DDX18 gene encodes a DEAD box protein ... |
164-290 | 8.02e-03 | ||||||||
DEAD-box helicase domain of DEAD box protein 18; This DDX18 gene encodes a DEAD box protein and is activated by Myc protein. DDX18 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: 350700 [Multi-domain] Cd Length: 198 Bit Score: 38.50 E-value: 8.02e-03
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