RNA helicase-domain-containing protein, partial [Endogone sp. FLAS-F59071]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||
| UPF1_Zn_bind | pfam09416 | RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ... |
124-275 | 4.05e-115 | |||
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD). : Pssm-ID: 401391 Cd Length: 152 Bit Score: 339.61 E-value: 4.05e-115
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| DEAD-like_helicase_N super family | cl28899 | N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ... |
474-611 | 9.87e-87 | |||
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region. The actual alignment was detected with superfamily member cd18039: Pssm-ID: 475120 [Multi-domain] Cd Length: 234 Bit Score: 269.50 E-value: 9.87e-87
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| 1B_UPF1-like | cd21407 | 1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze ... |
328-417 | 5.54e-55 | |||
1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. UPF1 belongs to helicase superfamily 1 (SF1). It participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. UPF1 is a multidomain protein; it includes an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a regulatory 1B domain, and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of the related Equine arteritis virus (EAV) Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids. : Pssm-ID: 394815 Cd Length: 90 Bit Score: 181.19 E-value: 5.54e-55
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| Name | Accession | Description | Interval | E-value | |||||
| UPF1_Zn_bind | pfam09416 | RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ... |
124-275 | 4.05e-115 | |||||
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD). Pssm-ID: 401391 Cd Length: 152 Bit Score: 339.61 E-value: 4.05e-115
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| DEXXQc_UPF1 | cd18039 | DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ... |
474-611 | 9.87e-87 | |||||
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 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: 350797 [Multi-domain] Cd Length: 234 Bit Score: 269.50 E-value: 9.87e-87
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| ZBD_UPF1-like | cd21400 | Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; ... |
125-245 | 3.33e-82 | |||||
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. UPF1 belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. The N-terminal CH/ZBD of UPF1 interacts with UPF2, a factor also involved in NMD. UPF1 has an N-terminal CH/ZBD, a 1B domain, and a SF1 helicase core. Pssm-ID: 439167 Cd Length: 120 Bit Score: 253.71 E-value: 3.33e-82
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| 1B_UPF1-like | cd21407 | 1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze ... |
328-417 | 5.54e-55 | |||||
1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. UPF1 belongs to helicase superfamily 1 (SF1). It participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. UPF1 is a multidomain protein; it includes an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a regulatory 1B domain, and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of the related Equine arteritis virus (EAV) Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids. Pssm-ID: 394815 Cd Length: 90 Bit Score: 181.19 E-value: 5.54e-55
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| UPF1_1B_dom | pfam18141 | RNA helicase UPF1, 1B domain; UPF1 (or regulator of nonsense transcripts 1 homolog) is an ... |
327-418 | 5.40e-50 | |||||
RNA helicase UPF1, 1B domain; UPF1 (or regulator of nonsense transcripts 1 homolog) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. Together with UPF2 and UPF3, forms a surveillance complex, in which UPF2 acts as a bridge between UPF1 and UPF3. UPF2 and UPF3 are non-enzymatic components of the complex that stimulate the activity of UPF1. UPF1 has a N-terminal cysteine/histidine-rich zinc-binding domain (CH/ZBD), a regulatory 1B domain, followed by a helicase core that belongs to superfamily 1 (SF1). This entry represents 1B domain of UPF1 which has a regulatory role. It suffers conformational changes from an inhibitory state to a transition-state complex that modulate RNA binding. Pssm-ID: 407973 Cd Length: 93 Bit Score: 167.88 E-value: 5.40e-50
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| AAA_11 | pfam13086 | AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
478-588 | 3.94e-20 | |||||
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. Pssm-ID: 404072 [Multi-domain] Cd Length: 248 Bit Score: 90.10 E-value: 3.94e-20
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| TIGR00376 | TIGR00376 | DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ... |
357-600 | 9.03e-19 | |||||
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273041 [Multi-domain] Cd Length: 636 Bit Score: 90.26 E-value: 9.03e-19
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
428-538 | 1.14e-10 | |||||
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]; Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 64.23 E-value: 1.14e-10
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
467-538 | 7.58e-07 | |||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 50.18 E-value: 7.58e-07
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| recD | PRK10875 | exodeoxyribonuclease V subunit alpha; |
487-566 | 1.23e-04 | |||||
exodeoxyribonuclease V subunit alpha; Pssm-ID: 236783 [Multi-domain] Cd Length: 615 Bit Score: 44.93 E-value: 1.23e-04
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| Name | Accession | Description | Interval | E-value | |||||
| UPF1_Zn_bind | pfam09416 | RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ... |
124-275 | 4.05e-115 | |||||
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD). Pssm-ID: 401391 Cd Length: 152 Bit Score: 339.61 E-value: 4.05e-115
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| DEXXQc_UPF1 | cd18039 | DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ... |
474-611 | 9.87e-87 | |||||
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 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: 350797 [Multi-domain] Cd Length: 234 Bit Score: 269.50 E-value: 9.87e-87
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| ZBD_UPF1-like | cd21400 | Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; ... |
125-245 | 3.33e-82 | |||||
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. UPF1 belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. The N-terminal CH/ZBD of UPF1 interacts with UPF2, a factor also involved in NMD. UPF1 has an N-terminal CH/ZBD, a 1B domain, and a SF1 helicase core. Pssm-ID: 439167 Cd Length: 120 Bit Score: 253.71 E-value: 3.33e-82
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| 1B_UPF1-like | cd21407 | 1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze ... |
328-417 | 5.54e-55 | |||||
1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. UPF1 belongs to helicase superfamily 1 (SF1). It participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. UPF1 is a multidomain protein; it includes an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a regulatory 1B domain, and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of the related Equine arteritis virus (EAV) Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids. Pssm-ID: 394815 Cd Length: 90 Bit Score: 181.19 E-value: 5.54e-55
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| UPF1_1B_dom | pfam18141 | RNA helicase UPF1, 1B domain; UPF1 (or regulator of nonsense transcripts 1 homolog) is an ... |
327-418 | 5.40e-50 | |||||
RNA helicase UPF1, 1B domain; UPF1 (or regulator of nonsense transcripts 1 homolog) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. Together with UPF2 and UPF3, forms a surveillance complex, in which UPF2 acts as a bridge between UPF1 and UPF3. UPF2 and UPF3 are non-enzymatic components of the complex that stimulate the activity of UPF1. UPF1 has a N-terminal cysteine/histidine-rich zinc-binding domain (CH/ZBD), a regulatory 1B domain, followed by a helicase core that belongs to superfamily 1 (SF1). This entry represents 1B domain of UPF1 which has a regulatory role. It suffers conformational changes from an inhibitory state to a transition-state complex that modulate RNA binding. Pssm-ID: 407973 Cd Length: 93 Bit Score: 167.88 E-value: 5.40e-50
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| DEXXc_HELZ2-C | cd18040 | C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ... |
475-602 | 3.54e-23 | |||||
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA. It belongs to 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: 350798 [Multi-domain] Cd Length: 271 Bit Score: 99.52 E-value: 3.54e-23
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| DEXXQc_SMUBP2 | cd18044 | DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ... |
474-548 | 5.80e-23 | |||||
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 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: 350802 [Multi-domain] Cd Length: 191 Bit Score: 96.52 E-value: 5.80e-23
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| AAA_11 | pfam13086 | AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
478-588 | 3.94e-20 | |||||
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. Pssm-ID: 404072 [Multi-domain] Cd Length: 248 Bit Score: 90.10 E-value: 3.94e-20
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| TIGR00376 | TIGR00376 | DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ... |
357-600 | 9.03e-19 | |||||
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273041 [Multi-domain] Cd Length: 636 Bit Score: 90.26 E-value: 9.03e-19
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| 1B_UPF1_nv_SF1_Hel-like | cd21344 | 1B domain of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and ... |
330-416 | 1.23e-16 | |||||
1B domain of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and arterivirus Nsp10, and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Members of this family belong to helicase superfamily 1 (SF1) and include nidoviral helicases such as Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13), Equine arteritis virus (EAV) Nsp10, and eukaryotic UPF1 RNA helicase. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. UPF1, EAV Nsp10 and SARS-Nsp13 are multidomain proteins with an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a 1B domain and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of EAV Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids. Pssm-ID: 439170 Cd Length: 86 Bit Score: 75.04 E-value: 1.23e-16
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| DEXXQc_SETX | cd18042 | DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ... |
475-556 | 1.95e-16 | |||||
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX 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: 438712 [Multi-domain] Cd Length: 218 Bit Score: 78.41 E-value: 1.95e-16
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| DEXXQc_Upf1-like | cd17934 | DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ... |
491-534 | 2.76e-16 | |||||
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to 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: 438708 [Multi-domain] Cd Length: 121 Bit Score: 75.35 E-value: 2.76e-16
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| DEXXQc_Helz-like | cd18038 | DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ... |
474-565 | 3.01e-16 | |||||
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All 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: 350796 [Multi-domain] Cd Length: 229 Bit Score: 78.43 E-value: 3.01e-16
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| EEXXEc_NFX1 | cd17936 | EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ... |
475-551 | 1.47e-14 | |||||
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 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: 350694 [Multi-domain] Cd Length: 178 Bit Score: 72.19 E-value: 1.47e-14
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| ZBD_UPF1_nv_SF1_Hel-like | cd21343 | Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 helicase, nidovirus SF1 helicases ... |
125-214 | 4.91e-14 | |||||
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and arterivirus Nsp10, and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands, and are classified based on the arrangement of conserved motifs into six superfamilies. Members of this family belong to helicase superfamily 1 (SF1) and include nidoviral helicases such as Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13) and equine arteritis virus (EAV) Nsp10, as well as eukaryotic UPF1 helicase. The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. The CH/ZBD of UPF1 interacts with UPF2, a factor also involved in NMD. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. SARS-Nsp12 can enhance the helicase activity of SARS-Nsp13. UPF1, SARS-Nsp13 and EAV Nsp10 are multidomain proteins; their other domains include a 1B regulatory domain and a SF1 helicase core. Pssm-ID: 439166 Cd Length: 70 Bit Score: 67.13 E-value: 4.91e-14
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| DExxQc_SF1-N | cd17914 | DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ... |
491-536 | 4.88e-12 | |||||
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 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: 438706 [Multi-domain] Cd Length: 121 Bit Score: 63.27 E-value: 4.88e-12
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| DEXSc_RecD-like | cd17933 | DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ... |
479-538 | 3.45e-11 | |||||
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD 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: 350691 [Multi-domain] Cd Length: 155 Bit Score: 61.80 E-value: 3.45e-11
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
428-538 | 1.14e-10 | |||||
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]; Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 64.23 E-value: 1.14e-10
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| DEXXQc_DNA2 | cd18041 | DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ... |
475-583 | 1.65e-10 | |||||
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 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: 350799 [Multi-domain] Cd Length: 203 Bit Score: 60.71 E-value: 1.65e-10
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| EEXXQc_AQR | cd17935 | EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ... |
471-540 | 4.20e-10 | |||||
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds precursor-mRNA introns at a defined position and is part of a pentameric intron-binding complex (IBC). It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350693 [Multi-domain] Cd Length: 207 Bit Score: 59.75 E-value: 4.20e-10
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| DEXXQc_Mov10L1 | cd18078 | DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ... |
475-553 | 4.87e-10 | |||||
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. Mov10L1 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: 350836 [Multi-domain] Cd Length: 230 Bit Score: 60.08 E-value: 4.87e-10
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| DEXXQc_SF1 | cd18043 | DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ... |
476-532 | 6.25e-10 | |||||
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases 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: 350801 [Multi-domain] Cd Length: 127 Bit Score: 57.21 E-value: 6.25e-10
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| AAA_19 | pfam13245 | AAA domain; |
482-543 | 2.47e-08 | |||||
AAA domain; Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 52.99 E-value: 2.47e-08
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| AAA_30 | pfam13604 | AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
474-536 | 7.72e-08 | |||||
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B. Pssm-ID: 433343 [Multi-domain] Cd Length: 191 Bit Score: 52.95 E-value: 7.72e-08
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
467-538 | 7.58e-07 | |||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 50.18 E-value: 7.58e-07
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
474-538 | 1.48e-06 | |||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 48.44 E-value: 1.48e-06
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| recD | TIGR01447 | exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
471-566 | 6.74e-06 | |||||
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273631 [Multi-domain] Cd Length: 582 Bit Score: 48.99 E-value: 6.74e-06
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| DEXXQc_HELZ | cd18077 | DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ... |
475-532 | 1.19e-05 | |||||
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. HELZ is a member of the family I class of RNA helicases 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: 350835 [Multi-domain] Cd Length: 226 Bit Score: 46.71 E-value: 1.19e-05
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
493-538 | 7.75e-05 | |||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 45.79 E-value: 7.75e-05
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| recD | PRK10875 | exodeoxyribonuclease V subunit alpha; |
487-566 | 1.23e-04 | |||||
exodeoxyribonuclease V subunit alpha; Pssm-ID: 236783 [Multi-domain] Cd Length: 615 Bit Score: 44.93 E-value: 1.23e-04
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
493-536 | 1.48e-03 | |||||
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: 39.31 E-value: 1.48e-03
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| ZBD_mv_SF1_Hel-like | cd21402 | Cys/His rich zinc-binding domain (CH/ZBD) of mesnidovirus SF1 helicase and related proteins; ... |
126-168 | 1.63e-03 | |||||
Cys/His rich zinc-binding domain (CH/ZBD) of mesnidovirus SF1 helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. This mesnidovirus group includes the Bontag Baru virus (BBaV) replication helicase encoded on ORF1b and belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. Members of this group belong to a family of nindoviral replication helicases which include includes Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) non-structural protein 13 (SARS-Nsp13), a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. SARS-Nsp12 can enhance the helicase activity of SARS-Nsp13. Pssm-ID: 394809 Cd Length: 111 Bit Score: 38.65 E-value: 1.63e-03
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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 ... |
475-582 | 2.04e-03 | |||||
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: 39.08 E-value: 2.04e-03
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| DEXSMc_CoV_Nsp13 | cd22649 | DEXSM-box helicase domain of coronavirus Nsp13 helicase; Helicases catalyze the NTP-dependent ... |
456-553 | 4.03e-03 | |||||
DEXSM-box helicase domain of coronavirus Nsp13 helicase; Helicases catalyze the NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified into six superfamilies based on the arrangement of conserved motifs. This family contains coronavirus (CoV) non-structural protein 13 (Nsp13) helicase, including those from highly pathogenic human betaCoVs such as Severe Acute Respiratory Syndrome coronavirus (SARS) and SARS-CoV-2 (also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus). Nsp13 helicase is a component of the viral RNA synthesis replication and transcription complex (RTC). SARS-Nsp13 is strongly inhibited by natural flavonoids, myricetin and scutellarein, and is emerging as a target for development of anti-SARS medications. It contains an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B regulatory domain, and an SF1 helicase core that carries a DEAD-box helicase domain. Nsp13 belongs to 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: 438713 [Multi-domain] Cd Length: 202 Bit Score: 38.92 E-value: 4.03e-03
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| betaCoV_Nsp13-helicase | cd21722 | helicase domain of betacoronavirus non-structural protein 13; This model represents the ... |
467-539 | 4.19e-03 | |||||
helicase domain of betacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from betacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core. Pssm-ID: 409655 [Multi-domain] Cd Length: 340 Bit Score: 39.78 E-value: 4.19e-03
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| AAA | smart00382 | ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ... |
493-611 | 5.00e-03 | |||||
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 38.12 E-value: 5.00e-03
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| CoV_Nsp13-helicase | cd21718 | helicase domain of coronavirus non-structural protein 13; This model represents the helicase ... |
468-537 | 6.52e-03 | |||||
helicase domain of coronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alpha-, beta-, gamma-, and deltacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core. Pssm-ID: 409652 [Multi-domain] Cd Length: 341 Bit Score: 39.05 E-value: 6.52e-03
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
479-558 | 8.58e-03 | |||||
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: 37.29 E-value: 8.58e-03
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