pp1ab polyprotein [Alphamesonivirus 1]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||
| Mesoniviridae_RdRp | cd23187 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the Mesoniviridae family of ... |
3115-3538 | 0e+00 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the Mesoniviridae family of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Mesoniviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The family is named after the size of the genomes relative to other nidoviruses, which is intermediate between that of the families Arteriviridae and Coronaviridae, with meso- coming from the Greek word mesos, which means medium, while -ni is an abbreviation of nido. The family Mesoniviridae comprises of mosquito-specific viruses with extensive geographic distribution and host range. The family has only one subfamily, Hexponivirinae, which contains only one genus, Alphamesonivirus. There are 8 subgenera (Casualivirus, Enselivirus, Hanalivirus, Kadilivirus, Karsalivirus, Menolivirus, Namcalivirus, and Ofalivirus) and 10 species in Alphamesonivirus. The structure of Mesoniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. : Pssm-ID: 438037 Cd Length: 424 Bit Score: 875.76 E-value: 0e+00
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| Peptidase_C107 super family | cl28872 | Viral cysteine endopeptidase C107; This is a family of viral cysteine endopeptidases that ... |
1391-1704 | 0e+00 | |||||||
Viral cysteine endopeptidase C107; This is a family of viral cysteine endopeptidases that process RNA polyproteins. Site directed mutagenesis suggest that H1434 and C1539 form the catalytic dyad. The actual alignment was detected with superfamily member pfam17222: Pssm-ID: 407341 Cd Length: 314 Bit Score: 649.85 E-value: 0e+00
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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; ... |
3612-3721 | 1.60e-66 | |||||||
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: 221.23 E-value: 1.60e-66
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| DNA2 super family | cl34114 | Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
4034-4280 | 7.31e-31 | |||||||
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; The actual alignment was detected with superfamily member COG1112: Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 134.10 E-value: 7.31e-31
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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 ... |
3930-4091 | 4.89e-12 | |||||||
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 cd17933: Pssm-ID: 475120 [Multi-domain] Cd Length: 155 Bit Score: 66.81 E-value: 4.89e-12
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| capping_2-OMTase_viral super family | cl41719 | viral Cap-0 specific (nucleoside-2'-O-)-methyltransferase; Cap-0 specific (nucleoside-2'-O-) ... |
4969-5053 | 4.47e-04 | |||||||
viral Cap-0 specific (nucleoside-2'-O-)-methyltransferase; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Some dsDNA and dsRNA viruses, like the bluetongue virus (BTV), a member of the Reoviridae family, and Vaccinia virus, a member of the Poxviridae family, as well as some ss(+)RNA viruses, like Flaviviridae and Nidovirales, cap their mRNAs and encode their own 2'OMTase. In BTV, all four reactions are catalyzed by a single protein, VP4. In Vaccinia, the activity is located in the processing factor of the poly(A) polymerase, VP39. The actual alignment was detected with superfamily member cd20762: Pssm-ID: 477759 Cd Length: 175 Bit Score: 44.23 E-value: 4.47e-04
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| Name | Accession | Description | Interval | E-value | |||||||
| Mesoniviridae_RdRp | cd23187 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the Mesoniviridae family of ... |
3115-3538 | 0e+00 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the Mesoniviridae family of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Mesoniviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The family is named after the size of the genomes relative to other nidoviruses, which is intermediate between that of the families Arteriviridae and Coronaviridae, with meso- coming from the Greek word mesos, which means medium, while -ni is an abbreviation of nido. The family Mesoniviridae comprises of mosquito-specific viruses with extensive geographic distribution and host range. The family has only one subfamily, Hexponivirinae, which contains only one genus, Alphamesonivirus. There are 8 subgenera (Casualivirus, Enselivirus, Hanalivirus, Kadilivirus, Karsalivirus, Menolivirus, Namcalivirus, and Ofalivirus) and 10 species in Alphamesonivirus. The structure of Mesoniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438037 Cd Length: 424 Bit Score: 875.76 E-value: 0e+00
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| Peptidase_C107 | pfam17222 | Viral cysteine endopeptidase C107; This is a family of viral cysteine endopeptidases that ... |
1391-1704 | 0e+00 | |||||||
Viral cysteine endopeptidase C107; This is a family of viral cysteine endopeptidases that process RNA polyproteins. Site directed mutagenesis suggest that H1434 and C1539 form the catalytic dyad. Pssm-ID: 407341 Cd Length: 314 Bit Score: 649.85 E-value: 0e+00
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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; ... |
3612-3721 | 1.60e-66 | |||||||
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: 221.23 E-value: 1.60e-66
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| DNA2 | COG1112 | Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
4034-4280 | 7.31e-31 | |||||||
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 134.10 E-value: 7.31e-31
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| SF1_C_Upf1 | cd18808 | C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ... |
4125-4280 | 2.46e-21 | |||||||
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350195 [Multi-domain] Cd Length: 184 Bit Score: 94.61 E-value: 2.46e-21
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| AAA_12 | pfam13087 | AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
4112-4280 | 2.59e-18 | |||||||
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: 463780 [Multi-domain] Cd Length: 196 Bit Score: 86.45 E-value: 2.59e-18
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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. ... |
3930-4091 | 4.89e-12 | |||||||
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: 66.81 E-value: 4.89e-12
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| AAA_30 | pfam13604 | AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
3947-4091 | 1.51e-06 | |||||||
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: 51.80 E-value: 1.51e-06
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| capping_2-OMTase_Nidovirales | cd20762 | Cap-0 specific (nucleoside-2'-O-)-methyltransferase of nidovirales; Cap-0 specific ... |
4969-5053 | 4.47e-04 | |||||||
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of nidovirales; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Nidovirales viruses, which comprise a family of ss(+)RNA viruses, cap their mRNAs. For one member, coronavirus, the 2'OMTase activity is located in the non-structural protein 16 (Nsp16). For others, the 2'OMTase activity may be located in replicase polyprotein 1ab. Pssm-ID: 467737 Cd Length: 175 Bit Score: 44.23 E-value: 4.47e-04
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| Name | Accession | Description | Interval | E-value | |||||||
| Mesoniviridae_RdRp | cd23187 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the Mesoniviridae family of ... |
3115-3538 | 0e+00 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the Mesoniviridae family of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Mesoniviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The family is named after the size of the genomes relative to other nidoviruses, which is intermediate between that of the families Arteriviridae and Coronaviridae, with meso- coming from the Greek word mesos, which means medium, while -ni is an abbreviation of nido. The family Mesoniviridae comprises of mosquito-specific viruses with extensive geographic distribution and host range. The family has only one subfamily, Hexponivirinae, which contains only one genus, Alphamesonivirus. There are 8 subgenera (Casualivirus, Enselivirus, Hanalivirus, Kadilivirus, Karsalivirus, Menolivirus, Namcalivirus, and Ofalivirus) and 10 species in Alphamesonivirus. The structure of Mesoniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438037 Cd Length: 424 Bit Score: 875.76 E-value: 0e+00
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| Peptidase_C107 | pfam17222 | Viral cysteine endopeptidase C107; This is a family of viral cysteine endopeptidases that ... |
1391-1704 | 0e+00 | |||||||
Viral cysteine endopeptidase C107; This is a family of viral cysteine endopeptidases that process RNA polyproteins. Site directed mutagenesis suggest that H1434 and C1539 form the catalytic dyad. Pssm-ID: 407341 Cd Length: 314 Bit Score: 649.85 E-value: 0e+00
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| ps-ssRNAv_Nidovirales_RdRp | cd23168 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of ... |
3151-3538 | 3.85e-87 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRP of Nidovirales, an order of enveloped, (+)ssRNA viruses which infect vertebrates and invertebrates. Host organisms include mammals, birds, reptiles, amphibians, fish, arthropods, mollusks, and helminths. The order Nidovirales currently comprises 88 formally recognized virus species of (+)ssRNA viruses which are classified into nine virus families: Abyssoviridae, Arteriviridae, Coronaviridae, Euroniviridae, Medioniviridae, Mesoniviridae, Mononiviridae, Roniviridae, and Tobaniviridae. Based on the genome size, the members of the order Nidovirales can be divided into two groups, large and small nidoviruses. The genomes of the large nidoviruses are well over 25 kb in length with size differences in the 5 kb range. Planarian secretory cell nidovirus (PSCNV), only member of the Mononiviridae family, has the largest known non-segmented RNA genome of 41.1 kb; its host is the planarian flatworm. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438018 [Multi-domain] Cd Length: 310 Bit Score: 288.49 E-value: 3.85e-87
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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; ... |
3612-3721 | 1.60e-66 | |||||||
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: 221.23 E-value: 1.60e-66
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| DNA2 | COG1112 | Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
4034-4280 | 7.31e-31 | |||||||
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 134.10 E-value: 7.31e-31
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| HCoV_HKU1-like_RdRp | cd21593 | human coronavirus HKU1 RNA-dependent RNA polymerase, also known as non-structural protein 12, ... |
3105-3520 | 2.43e-28 | |||||||
human coronavirus HKU1 RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the A lineage: responsible for replication and transcription of the viral RNA genome; This group contains the RNA-dependent RNA polymerase (RdRp) of human coronavirus HKU1, murine hepatitis virus, and similar proteins from betacoronaviruses in the embecovirus subgenera (A lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394897 Cd Length: 925 Bit Score: 126.23 E-value: 2.43e-28
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| CoV_RdRp | cd21530 | coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible ... |
3105-3489 | 7.23e-26 | |||||||
coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This family contains the RNA-dependent RNA polymerase of alpha-, beta-, gamma-, delta-coronaviruses, including three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438015 Cd Length: 928 Bit Score: 118.01 E-value: 7.23e-26
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| ZBD_nv_SF1_Hel-like | cd21399 | Cys/His rich zinc-binding domain (CH/ZBD) of nidovirus helicases including coronavirus Nsp13 ... |
3612-3688 | 7.84e-24 | |||||||
Cys/His rich zinc-binding domain (CH/ZBD) of nidovirus 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. This nidovirus family includes Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13) and equine arteritis virus (EAV) Nsp10 helicase, and belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. 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. SARS-Nsp13 and EAV Nsp10 are multidomain proteins; their other domains include a 1B regulatory domain and a SF1 helicase core. Pssm-ID: 394806 Cd Length: 71 Bit Score: 97.64 E-value: 7.84e-24
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| MERS-CoV-like_RdRp | cd21592 | Middle East respiratory syndrome-related coronavirus RNA-dependent RNA polymerase, also known ... |
3105-3489 | 8.41e-24 | |||||||
Middle East respiratory syndrome-related coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the C lineage: responsible for replication and transcription of the viral RNA genome; This group contains the RNA-dependent RNA polymerase (RdRp) of Middle East respiratory syndrome (MERS)-related CoV, bat-CoV HKU5, and similar proteins from betacoronaviruses in the merbecovirus subgenera (C lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which has been shown to potently inhibit MERS RdRp. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394896 Cd Length: 931 Bit Score: 111.29 E-value: 8.41e-24
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| betaCoV_RdRp | cd21589 | betacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ... |
3105-3520 | 1.07e-23 | |||||||
betacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This subfamily contains the RNA-dependent RNA polymerase (RdRp) of betacoronaviruses, including the RdRps from three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438016 Cd Length: 925 Bit Score: 111.02 E-value: 1.07e-23
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| deltaCoV_RdRp | cd21590 | deltacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ... |
3046-3489 | 8.65e-22 | |||||||
deltacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This subfamily contains the RNA-dependent RNA polymerase (RdRp) of deltacoronaviruses. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which has been shown to inhibit human endemic and zoonotic deltacoronaviruses with a highly divergent RdRp. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394894 Cd Length: 928 Bit Score: 104.94 E-value: 8.65e-22
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| SF1_C_Upf1 | cd18808 | C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ... |
4125-4280 | 2.46e-21 | |||||||
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350195 [Multi-domain] Cd Length: 184 Bit Score: 94.61 E-value: 2.46e-21
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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 ... |
3613-3688 | 5.69e-21 | |||||||
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: 89.47 E-value: 5.69e-21
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| gammaCoV_RdRp | cd21587 | gammacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ... |
3105-3489 | 8.63e-21 | |||||||
gammacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This subfamily contains the RNA-dependent RNA polymerase (RdRp) of gammacoronaviruses, including the RdRp of avian infectious bronchitis virus (IBV) and similar proteins. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394891 Cd Length: 931 Bit Score: 101.50 E-value: 8.63e-21
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| SARS-CoV-like_RdRp | cd21591 | Severe acute respiratory syndrome coronavirus RNA-dependent RNA polymerase, also known as ... |
3105-3529 | 2.31e-20 | |||||||
Severe acute respiratory syndrome coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the B lineage: responsible for replication and transcription of the viral RNA genome; This group contains the RNA-dependent RNA polymerase (RdRp) of Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2 (also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus), and similar proteins from betacoronaviruses in the sarbecovirus subgenera (B lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. Recent studies have shown that the SARS-CoV-2 RdRp requires two iron-sulfur clusters to function optimally. Earlier studies had mistakenly identified these iron-sulfur cluster binding sites for zinc-binding sites, likely because iron-sulfur clusters degrade easily under standard experimental conditions.The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394895 Cd Length: 928 Bit Score: 100.16 E-value: 2.31e-20
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| Medioniviridae_RdRp | cd23188 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the Medioniviridae family of ... |
3115-3489 | 8.46e-20 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the Medioniviridae family of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Medioniviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The Medioniviridae subgenera includes Turrinivirus and Balbicanovirus. The structure of Medioniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438038 Cd Length: 391 Bit Score: 95.53 E-value: 8.46e-20
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| batCoV-HKU9-like_RdRp | cd21596 | Bat coronavirus HKU9 RNA-dependent RNA polymerase, also known as non-structural protein 12, ... |
3105-3489 | 2.80e-19 | |||||||
Bat coronavirus HKU9 RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the D lineage: responsible for replication and transcription of the viral RNA genome; This group contains the RNA-dependent RNA polymerase (RdRp) of bat coronavirus HKU9 and similar proteins from betacoronaviruses in the nobecovirus subgenera (D lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394898 Cd Length: 929 Bit Score: 96.64 E-value: 2.80e-19
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| AAA_12 | pfam13087 | AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
4112-4280 | 2.59e-18 | |||||||
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: 463780 [Multi-domain] Cd Length: 196 Bit Score: 86.45 E-value: 2.59e-18
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| alphaCoV_RdRp | cd21588 | alphacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ... |
3106-3353 | 5.40e-16 | |||||||
alphacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This subfamily contains the RNA-dependent RNA polymerase (RdRp) of alphacoronaviruses, including human coronaviruses (HCoVs), HCoV-NL63, and HCoV-229E. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394892 Cd Length: 924 Bit Score: 85.93 E-value: 5.40e-16
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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. ... |
3930-4091 | 4.89e-12 | |||||||
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: 66.81 E-value: 4.89e-12
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| Euroniviridae_RdRp | cd23191 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Eunroniviridae of ... |
3202-3489 | 4.95e-12 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Eunroniviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Eunroniviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. Eunroniviridae is a closely related family of crustacean nidoviruses, within the suborder Ronidovirineae, which also includes the family Roniviridae. Ronidovirineae, named "rod-shaped nidovirus", is 150-200 nm long and approximately 60 nm thick. There are 3 viral species in the Euroniviridae family, all of which have been detected in crustaceans. The structure of Euroniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438041 Cd Length: 345 Bit Score: 71.08 E-value: 4.95e-12
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| DEXXQc_Helz-like | cd18038 | DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ... |
3944-4097 | 1.25e-10 | |||||||
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: 64.95 E-value: 1.25e-10
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
3937-4284 | 3.96e-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: 66.15 E-value: 3.96e-10
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| DEXXQc_Mov10L1 | cd18078 | DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ... |
3944-4101 | 2.16e-09 | |||||||
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: 61.23 E-value: 2.16e-09
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| CoV_Nsp13-helicase | cd21718 | helicase domain of coronavirus non-structural protein 13; This model represents the helicase ... |
3936-4280 | 2.29e-09 | |||||||
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: 62.55 E-value: 2.29e-09
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| SF1_C | cd18786 | C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
4208-4282 | 2.76e-08 | |||||||
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 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: 350173 [Multi-domain] Cd Length: 89 Bit Score: 53.98 E-value: 2.76e-08
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| alphaCoV_Nsp13-helicase | cd21723 | helicase domain of alphacoronavirus non-structural protein 13; This model represents the ... |
3925-4279 | 3.02e-08 | |||||||
helicase domain of alphacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alphacoronavirus, including Porcine epidemic diarrhea virus and Human coronavirus (CoV) NL63. 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: 409656 [Multi-domain] Cd Length: 340 Bit Score: 59.36 E-value: 3.02e-08
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| gammaCoV_Nsp13-helicase | cd21720 | helicase domain of gammacoronavirus non-structural protein 13; This model represents the ... |
3947-4275 | 4.77e-08 | |||||||
helicase domain of gammacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from gammacoronavirus, including Avian infectious bronchitis virus. 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. Coronavirus (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: 409653 [Multi-domain] Cd Length: 343 Bit Score: 58.78 E-value: 4.77e-08
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| betaCoV_Nsp13-helicase | cd21722 | helicase domain of betacoronavirus non-structural protein 13; This model represents the ... |
3914-4275 | 1.20e-07 | |||||||
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: 57.50 E-value: 1.20e-07
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| AAA_30 | pfam13604 | AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
3947-4091 | 1.51e-06 | |||||||
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: 51.80 E-value: 1.51e-06
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| deltaCoV_Nsp13-helicase | cd21721 | helicase domain of deltacoronavirus non-structural protein 13; This model represents the ... |
3936-4275 | 9.08e-06 | |||||||
helicase domain of deltacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from deltacoronavirus, including Bulbul coronavirus (CoV) HKU11 and Common moorhen CoV HKU21. 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: 409654 [Multi-domain] Cd Length: 342 Bit Score: 51.46 E-value: 9.08e-06
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| ZBD_UPF1-like | cd21400 | Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; ... |
3614-3676 | 1.32e-05 | |||||||
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: 47.63 E-value: 1.32e-05
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| Roniviridae_RdRp | cd23190 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Roniviridae of ... |
3202-3490 | 1.77e-05 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Roniviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Roniviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The family Roniviridae includes a single genus (Okavirus) for three species of viruses (Yellow head virus, Gill-associated virus and Okavirus 1) with enveloped, rod-shaped virions. Roniviruses infect penaeid and palaemonid shrimp. Natural infections are usually without apparent clinical signs. One member of the family (yellow head virus) is highly pathogenic for shrimp. Roniviruses are most closely related to other nidoviruses infecting arthropods, including members of the families Mesoniviridae (from mosquitoes) and Euroniviridae (from crustaceans). The structure of Roniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438040 Cd Length: 379 Bit Score: 50.81 E-value: 1.77e-05
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| DEXXQc_DNA2 | cd18041 | DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ... |
3933-4124 | 3.42e-05 | |||||||
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: 48.00 E-value: 3.42e-05
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| UvrD_C | pfam13361 | UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
4213-4281 | 8.66e-05 | |||||||
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold. Pssm-ID: 433145 [Multi-domain] Cd Length: 377 Bit Score: 48.56 E-value: 8.66e-05
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| SF1_C_UvrD | cd18807 | C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase ... |
4172-4281 | 2.64e-04 | |||||||
C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. This family also includes ATP-dependent helicase/nuclease AddA and helicase/nuclease RecBCD subunit RecB, among others. UvrD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350194 [Multi-domain] Cd Length: 150 Bit Score: 44.53 E-value: 2.64e-04
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| AAA_11 | pfam13086 | AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
3933-4017 | 3.36e-04 | |||||||
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: 45.80 E-value: 3.36e-04
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
3930-4189 | 3.80e-04 | |||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 46.94 E-value: 3.80e-04
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| capping_2-OMTase_Nidovirales | cd20762 | Cap-0 specific (nucleoside-2'-O-)-methyltransferase of nidovirales; Cap-0 specific ... |
4969-5053 | 4.47e-04 | |||||||
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of nidovirales; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Nidovirales viruses, which comprise a family of ss(+)RNA viruses, cap their mRNAs. For one member, coronavirus, the 2'OMTase activity is located in the non-structural protein 16 (Nsp16). For others, the 2'OMTase activity may be located in replicase polyprotein 1ab. Pssm-ID: 467737 Cd Length: 175 Bit Score: 44.23 E-value: 4.47e-04
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| Peptidase_C62 | pfam12380 | Gill-associated viral 3C-like peptidase; a positive-stranded RNA virus of prawns, that has ... |
1524-1674 | 5.29e-04 | |||||||
Gill-associated viral 3C-like peptidase; a positive-stranded RNA virus of prawns, that has been called yellow head virus protease and gill-associated virus 3C-like peptidase. The GAV cysteine protease is predicted to be the key enzyme in the processing of the GAV replicase polyprotein precursors, pp1a and pp1ab. This protease employs a Cys(2968)-His(2879) catalytic dyad. Pssm-ID: 289173 Cd Length: 284 Bit Score: 45.48 E-value: 5.29e-04
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| DEXXQc_SETX | cd18042 | DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ... |
3938-4087 | 1.35e-03 | |||||||
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: 43.74 E-value: 1.35e-03
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| DEXXQc_SMUBP2 | cd18044 | DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ... |
3937-4087 | 1.68e-03 | |||||||
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: 42.98 E-value: 1.68e-03
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
3930-4084 | 2.08e-03 | |||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 42.27 E-value: 2.08e-03
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| Polycipiviridae_RdRp | cd23198 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of ... |
3289-3353 | 2.73e-03 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Polycipiviridae (polycistronic picorna-like viruses), order Picornavirales. Polycipiviridae is a family of picorna-like viruses with non-segmented, linear, (+)ssRNA genomes of approximately 10-12 kb. Their genomes are polycistronic, with four (or more) consecutive 5'-proximal open reading frames (ORFs) encoding structural (and possibly other) proteins and a long 3' ORF encoding the replication polyprotein. Members of species within the family are typically found in ants, with Apple picorna-like virus 1 and the unnamed Polycipiviridae virus in fruit bat stool as exceptions. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438048 Cd Length: 317 Bit Score: 43.56 E-value: 2.73e-03
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
3949-4082 | 2.94e-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: 41.23 E-value: 2.94e-03
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| DEXXQc_Upf1-like | cd17934 | DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ... |
3947-4090 | 5.24e-03 | |||||||
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: 39.91 E-value: 5.24e-03
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| ZBD_cv_Nsp13-like | cd21401 | Cys/His rich zinc-binding domain (CH/ZBD) of coronavirus SARS NSP13 helicase and related ... |
3614-3700 | 7.83e-03 | |||||||
Cys/His rich zinc-binding domain (CH/ZBD) of coronavirus SARS NSP13 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 coronavirus family includes Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) non-structural protein 13 (SARS-Nsp13) and belongs to helicase superfamily 1 (SF1) and to a family of nindoviral replication helicases. SARS-Nsp13 has an N-terminal CH/ZBD, a stalk domain, a 1B regulatory domain, and SF1 helicase core. The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. 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 (RdRp). Structural studies of a stable SARS-CoV-2 RTC which included two molecules of Nsp13, the RdRp holoenzyme (Nsp7, two molecules of Nsp8, Nsp12), and an RNA template product, show that one Nsp13 CH/ZBD domain interacts with Nsp12, and both Nsp13-CH/ZBD domains interact with the Nsp8. This stable SARS-CoV-2 RTC suggests that the Nsp13 helicase may drive RTC backtracking, affecting proofreading and template switching. Pssm-ID: 439168 Cd Length: 95 Bit Score: 38.91 E-value: 7.83e-03
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