viral nonstructural polyprotein [Simian hemorrhagic fever virus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| Arteriviridae_RdRp | cd23189 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ... |
2419-2741 | 0e+00 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Arteriviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The overall genome organization of the Arteriviruses are highly similar to the Coronaviruses; however, they lack the spike proteins of the coronaviruses. The family members include equine arteritis virus (EAV), porcine reproductive and respiratory syndrome virus (PRRSV), lactate dehydrogenase elevating virus of mice, and simian hemorrhagic fever virus (SHFV). The structure of Arteriviridae 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: 438039 [Multi-domain] Cd Length: 323 Bit Score: 615.81 E-value: 0e+00
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| Peptidase_S32 | pfam05579 | Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing ... |
1368-1665 | 2.39e-147 | ||||||
Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing nidovirus polyprotein. : Pssm-ID: 253263 Cd Length: 297 Bit Score: 460.40 E-value: 2.39e-147
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| NendoU_av_Nsp11-like | cd21160 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ... |
3299-3418 | 3.55e-78 | ||||||
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV Nonstructural protein 11 (Nsp11), and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Mn2+ is dispensable, and to some extent inhibits the activity of arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11. This Nsp11 exists as a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. : Pssm-ID: 394911 Cd Length: 120 Bit Score: 254.55 E-value: 3.55e-78
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| Arteri_nsp7a | pfam16749 | Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a ... |
1845-1971 | 1.60e-59 | ||||||
Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a role in viral RNA synthesis. : Pssm-ID: 374774 Cd Length: 128 Bit Score: 201.48 E-value: 1.60e-59
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| Peptidase_C32 | pfam05411 | Equine arteritis virus putative proteinase; These proteins are characterized by a region that ... |
224-356 | 1.39e-56 | ||||||
Equine arteritis virus putative proteinase; These proteins are characterized by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication. : Pssm-ID: 398854 Cd Length: 127 Bit Score: 193.15 E-value: 1.39e-56
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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 ... |
2892-3026 | 3.73e-54 | ||||||
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 cd17937: Pssm-ID: 475120 [Multi-domain] Cd Length: 137 Bit Score: 186.49 E-value: 3.73e-54
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| NTD_av_Nsp11-like | cd21166 | N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ... |
3199-3301 | 1.34e-52 | ||||||
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain and a C-terminal catalytic (NendoU) domain. Arterivirus Nsp11 has an N-terminal domain (NTD) and a C-terminal NendoU catalytic domain. The NTD of Nsp11 superimposes onto the M-domain of coronavirus Nsp15. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and Murine Hepatitis Virus (MHV) form a functional hexamer. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of the other coronaviruses; it has been shown to exist as a dimer and a monomer in solution. Nsp11 from the arterivirus PRRSV functions as a dimer. PRRSV Nsp11 has been shown to induce STAT2 degradation to inhibit interferon signaling; mutagenesis revealed that the amino acid residue K59 located at the NTD of Nsp11 is indispensable for inducing STAT2 reduction. : Pssm-ID: 394904 Cd Length: 100 Bit Score: 180.61 E-value: 1.34e-52
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| ZBD_av_Nsp10-like | cd21405 | Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 helicase and related ... |
2750-2812 | 1.02e-26 | ||||||
Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 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. Members of this arterivirus group belong to helicase superfamily 1 (SF1) and include helicases such Equine arteritis virus (EAV) Nsp10 helicase encoded on ORF1b. 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: 439169 Cd Length: 62 Bit Score: 105.10 E-value: 1.02e-26
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| av_Nsp3_ER-remodelling | cd22528 | intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This ... |
1256-1312 | 7.77e-26 | ||||||
intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This domain is present in subunit Nsp3 of RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV. Nsp3 proteins are localized to the ER and appear to be essential for formation of double-membrane vesicles that originate from the ER during the life-cycle of the virus. Arterivirus Nsp3 is a predicted tetra-spanning transmembrane protein containing four transmembrane helices, with the N- and C-termini of the protein residing in the cytoplasm. It contains a cluster of four highly conserved cysteine residues that are predicted to reside in the first luminal domain of the protein. These conserved cysteines play a key role in the formation of double-membrane vesicles (DMVs); mutagenesis of each completely blocked DMV formation. : Pssm-ID: 412095 Cd Length: 57 Bit Score: 102.40 E-value: 7.77e-26
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| 1B_av_Nsp10-like | cd21410 | 1B domain of arterivirus EAV Nsp10 helicase and related proteins; Helicases catalyze ... |
2825-2873 | 1.19e-20 | ||||||
1B domain of arterivirus EAV Nsp10 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. Members of this subfamily belong to helicase superfamily 1 (SF1) and include arterivirus helicases such Equine arteritis virus (EAV) Nsp10 helicase encoded on ORF1b. EAV Nsp10 is a multidomain protein; its other domains include an N-terminal Cys/His rich zinc-binding domain (CH/ZBD) 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: 439172 Cd Length: 49 Bit Score: 87.30 E-value: 1.19e-20
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| SF1_C | cd18786 | C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
3063-3122 | 1.05e-17 | ||||||
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: 80.56 E-value: 1.05e-17
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| Peptidase_C33 super family | cl05135 | Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These ... |
633-730 | 3.40e-08 | ||||||
Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These peptidases are involved in viral polyprotein processing in replication. The actual alignment was detected with superfamily member pfam05412: Pssm-ID: 114153 Cd Length: 108 Bit Score: 54.15 E-value: 3.40e-08
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| Peptidase_C32 super family | cl05134 | Equine arteritis virus putative proteinase; These proteins are characterized by a region that ... |
368-448 | 5.75e-05 | ||||||
Equine arteritis virus putative proteinase; These proteins are characterized by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication. The actual alignment was detected with superfamily member pfam05411: Pssm-ID: 398854 Cd Length: 127 Bit Score: 45.23 E-value: 5.75e-05
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| Name | Accession | Description | Interval | E-value | |||||||
| Arteriviridae_RdRp | cd23189 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ... |
2419-2741 | 0e+00 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Arteriviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The overall genome organization of the Arteriviruses are highly similar to the Coronaviruses; however, they lack the spike proteins of the coronaviruses. The family members include equine arteritis virus (EAV), porcine reproductive and respiratory syndrome virus (PRRSV), lactate dehydrogenase elevating virus of mice, and simian hemorrhagic fever virus (SHFV). The structure of Arteriviridae 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: 438039 [Multi-domain] Cd Length: 323 Bit Score: 615.81 E-value: 0e+00
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| Peptidase_S32 | pfam05579 | Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing ... |
1368-1665 | 2.39e-147 | |||||||
Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing nidovirus polyprotein. Pssm-ID: 253263 Cd Length: 297 Bit Score: 460.40 E-value: 2.39e-147
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| RdRP_1 | pfam00680 | Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ... |
2295-2717 | 5.57e-88 | |||||||
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases. Pssm-ID: 425815 Cd Length: 450 Bit Score: 296.24 E-value: 5.57e-88
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| NendoU_av_Nsp11-like | cd21160 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ... |
3299-3418 | 3.55e-78 | |||||||
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV Nonstructural protein 11 (Nsp11), and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Mn2+ is dispensable, and to some extent inhibits the activity of arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11. This Nsp11 exists as a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. Pssm-ID: 394911 Cd Length: 120 Bit Score: 254.55 E-value: 3.55e-78
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| Arteri_nsp7a | pfam16749 | Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a ... |
1845-1971 | 1.60e-59 | |||||||
Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a role in viral RNA synthesis. Pssm-ID: 374774 Cd Length: 128 Bit Score: 201.48 E-value: 1.60e-59
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| Peptidase_C32 | pfam05411 | Equine arteritis virus putative proteinase; These proteins are characterized by a region that ... |
224-356 | 1.39e-56 | |||||||
Equine arteritis virus putative proteinase; These proteins are characterized by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication. Pssm-ID: 398854 Cd Length: 127 Bit Score: 193.15 E-value: 1.39e-56
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| DEXXYc_viral_SF1-N | cd17937 | DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ... |
2892-3026 | 3.73e-54 | |||||||
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. The members here contain arterivirus equine arteritis virus (EAV) non-structural protein (nsp)10. Nsp10 is composed of two domains, ZBD (ATPase) and HEL1 (helicase) along with 2 additional non-enzymatic domains that are thought to regulate HEL1 function. The helicase activity depends on the extensive relay of interactions between the ZBD and HEL1 domains. The arterivirus helicase structurally resembles the cellular Upf1 helicase, suggesting that nidoviruses may also use their helicases for post-transcriptional quality control of their large RNA genomes. The proteins here 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: 350695 [Multi-domain] Cd Length: 137 Bit Score: 186.49 E-value: 3.73e-54
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| NTD_av_Nsp11-like | cd21166 | N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ... |
3199-3301 | 1.34e-52 | |||||||
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain and a C-terminal catalytic (NendoU) domain. Arterivirus Nsp11 has an N-terminal domain (NTD) and a C-terminal NendoU catalytic domain. The NTD of Nsp11 superimposes onto the M-domain of coronavirus Nsp15. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and Murine Hepatitis Virus (MHV) form a functional hexamer. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of the other coronaviruses; it has been shown to exist as a dimer and a monomer in solution. Nsp11 from the arterivirus PRRSV functions as a dimer. PRRSV Nsp11 has been shown to induce STAT2 degradation to inhibit interferon signaling; mutagenesis revealed that the amino acid residue K59 located at the NTD of Nsp11 is indispensable for inducing STAT2 reduction. Pssm-ID: 394904 Cd Length: 100 Bit Score: 180.61 E-value: 1.34e-52
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| ZBD_av_Nsp10-like | cd21405 | Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 helicase and related ... |
2750-2812 | 1.02e-26 | |||||||
Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 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. Members of this arterivirus group belong to helicase superfamily 1 (SF1) and include helicases such Equine arteritis virus (EAV) Nsp10 helicase encoded on ORF1b. 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: 439169 Cd Length: 62 Bit Score: 105.10 E-value: 1.02e-26
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| av_Nsp3_ER-remodelling | cd22528 | intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This ... |
1256-1312 | 7.77e-26 | |||||||
intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This domain is present in subunit Nsp3 of RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV. Nsp3 proteins are localized to the ER and appear to be essential for formation of double-membrane vesicles that originate from the ER during the life-cycle of the virus. Arterivirus Nsp3 is a predicted tetra-spanning transmembrane protein containing four transmembrane helices, with the N- and C-termini of the protein residing in the cytoplasm. It contains a cluster of four highly conserved cysteine residues that are predicted to reside in the first luminal domain of the protein. These conserved cysteines play a key role in the formation of double-membrane vesicles (DMVs); mutagenesis of each completely blocked DMV formation. Pssm-ID: 412095 Cd Length: 57 Bit Score: 102.40 E-value: 7.77e-26
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| 1B_av_Nsp10-like | cd21410 | 1B domain of arterivirus EAV Nsp10 helicase and related proteins; Helicases catalyze ... |
2825-2873 | 1.19e-20 | |||||||
1B domain of arterivirus EAV Nsp10 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. Members of this subfamily belong to helicase superfamily 1 (SF1) and include arterivirus helicases such Equine arteritis virus (EAV) Nsp10 helicase encoded on ORF1b. EAV Nsp10 is a multidomain protein; its other domains include an N-terminal Cys/His rich zinc-binding domain (CH/ZBD) 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: 439172 Cd Length: 49 Bit Score: 87.30 E-value: 1.19e-20
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| SF1_C | cd18786 | C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
3063-3122 | 1.05e-17 | |||||||
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: 80.56 E-value: 1.05e-17
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| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
2897-3122 | 8.35e-11 | |||||||
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 64.71 E-value: 8.35e-11
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
3078-3121 | 1.24e-08 | |||||||
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: 60.76 E-value: 1.24e-08
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| CoV_NSP15_C | pfam19215 | Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ... |
3296-3415 | 2.91e-08 | |||||||
Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the C-terminal domain of coronavirus non-structural protein 15 (NSP15 or nsp15). NSP15 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. This domain exhibits endoribonuclease activity designated EndoU, highly conserved in all known CoVs and is part of the replicase-transcriptase complex that plays important roles in virus replication and transcription. NSP15 is a Uridylate-specific endoribonuclease that cleaves the 5'-polyuridines from negative-sense viral RNA, termed PUN RNA either upstream or downstream of uridylates, at GUU or GU to produce molecules with 2',3'-cyclic phosphate ends. PUN RNA is a CoV MDA5-dependent pathogen-associated molecular pattern (PAMP). Pssm-ID: 465999 Cd Length: 155 Bit Score: 55.80 E-value: 2.91e-08
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| Peptidase_C33 | pfam05412 | Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These ... |
633-730 | 3.40e-08 | |||||||
Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These peptidases are involved in viral polyprotein processing in replication. Pssm-ID: 114153 Cd Length: 108 Bit Score: 54.15 E-value: 3.40e-08
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| Peptidase_C32 | pfam05411 | Equine arteritis virus putative proteinase; These proteins are characterized by a region that ... |
368-448 | 5.75e-05 | |||||||
Equine arteritis virus putative proteinase; These proteins are characterized by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication. Pssm-ID: 398854 Cd Length: 127 Bit Score: 45.23 E-value: 5.75e-05
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| recD | PRK10875 | exodeoxyribonuclease V subunit alpha; |
3078-3121 | 2.70e-03 | |||||||
exodeoxyribonuclease V subunit alpha; Pssm-ID: 236783 [Multi-domain] Cd Length: 615 Bit Score: 43.39 E-value: 2.70e-03
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| Name | Accession | Description | Interval | E-value | |||||||
| Arteriviridae_RdRp | cd23189 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ... |
2419-2741 | 0e+00 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Arteriviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The overall genome organization of the Arteriviruses are highly similar to the Coronaviruses; however, they lack the spike proteins of the coronaviruses. The family members include equine arteritis virus (EAV), porcine reproductive and respiratory syndrome virus (PRRSV), lactate dehydrogenase elevating virus of mice, and simian hemorrhagic fever virus (SHFV). The structure of Arteriviridae 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: 438039 [Multi-domain] Cd Length: 323 Bit Score: 615.81 E-value: 0e+00
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| Peptidase_S32 | pfam05579 | Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing ... |
1368-1665 | 2.39e-147 | |||||||
Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing nidovirus polyprotein. Pssm-ID: 253263 Cd Length: 297 Bit Score: 460.40 E-value: 2.39e-147
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| RdRP_1 | pfam00680 | Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ... |
2295-2717 | 5.57e-88 | |||||||
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases. Pssm-ID: 425815 Cd Length: 450 Bit Score: 296.24 E-value: 5.57e-88
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| NendoU_av_Nsp11-like | cd21160 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ... |
3299-3418 | 3.55e-78 | |||||||
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV Nonstructural protein 11 (Nsp11), and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Mn2+ is dispensable, and to some extent inhibits the activity of arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11. This Nsp11 exists as a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. Pssm-ID: 394911 Cd Length: 120 Bit Score: 254.55 E-value: 3.55e-78
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| Arteri_nsp7a | pfam16749 | Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a ... |
1845-1971 | 1.60e-59 | |||||||
Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a role in viral RNA synthesis. Pssm-ID: 374774 Cd Length: 128 Bit Score: 201.48 E-value: 1.60e-59
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| Peptidase_C32 | pfam05411 | Equine arteritis virus putative proteinase; These proteins are characterized by a region that ... |
224-356 | 1.39e-56 | |||||||
Equine arteritis virus putative proteinase; These proteins are characterized by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication. Pssm-ID: 398854 Cd Length: 127 Bit Score: 193.15 E-value: 1.39e-56
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| DEXXYc_viral_SF1-N | cd17937 | DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ... |
2892-3026 | 3.73e-54 | |||||||
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. The members here contain arterivirus equine arteritis virus (EAV) non-structural protein (nsp)10. Nsp10 is composed of two domains, ZBD (ATPase) and HEL1 (helicase) along with 2 additional non-enzymatic domains that are thought to regulate HEL1 function. The helicase activity depends on the extensive relay of interactions between the ZBD and HEL1 domains. The arterivirus helicase structurally resembles the cellular Upf1 helicase, suggesting that nidoviruses may also use their helicases for post-transcriptional quality control of their large RNA genomes. The proteins here 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: 350695 [Multi-domain] Cd Length: 137 Bit Score: 186.49 E-value: 3.73e-54
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| NTD_av_Nsp11-like | cd21166 | N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ... |
3199-3301 | 1.34e-52 | |||||||
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain and a C-terminal catalytic (NendoU) domain. Arterivirus Nsp11 has an N-terminal domain (NTD) and a C-terminal NendoU catalytic domain. The NTD of Nsp11 superimposes onto the M-domain of coronavirus Nsp15. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and Murine Hepatitis Virus (MHV) form a functional hexamer. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of the other coronaviruses; it has been shown to exist as a dimer and a monomer in solution. Nsp11 from the arterivirus PRRSV functions as a dimer. PRRSV Nsp11 has been shown to induce STAT2 degradation to inhibit interferon signaling; mutagenesis revealed that the amino acid residue K59 located at the NTD of Nsp11 is indispensable for inducing STAT2 reduction. Pssm-ID: 394904 Cd Length: 100 Bit Score: 180.61 E-value: 1.34e-52
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| ps-ssRNAv_Nidovirales_RdRp | cd23168 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of ... |
2425-2679 | 8.35e-31 | |||||||
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: 125.55 E-value: 8.35e-31
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| ZBD_av_Nsp10-like | cd21405 | Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 helicase and related ... |
2750-2812 | 1.02e-26 | |||||||
Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 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. Members of this arterivirus group belong to helicase superfamily 1 (SF1) and include helicases such Equine arteritis virus (EAV) Nsp10 helicase encoded on ORF1b. 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: 439169 Cd Length: 62 Bit Score: 105.10 E-value: 1.02e-26
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| av_Nsp3_ER-remodelling | cd22528 | intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This ... |
1256-1312 | 7.77e-26 | |||||||
intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This domain is present in subunit Nsp3 of RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV. Nsp3 proteins are localized to the ER and appear to be essential for formation of double-membrane vesicles that originate from the ER during the life-cycle of the virus. Arterivirus Nsp3 is a predicted tetra-spanning transmembrane protein containing four transmembrane helices, with the N- and C-termini of the protein residing in the cytoplasm. It contains a cluster of four highly conserved cysteine residues that are predicted to reside in the first luminal domain of the protein. These conserved cysteines play a key role in the formation of double-membrane vesicles (DMVs); mutagenesis of each completely blocked DMV formation. Pssm-ID: 412095 Cd Length: 57 Bit Score: 102.40 E-value: 7.77e-26
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| NendoU_nv | cd21158 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural ... |
3299-3417 | 1.30e-25 | |||||||
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural protein 15 (Nsp15), arterivirus Nsp11, torovirus endoribonuclease, and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. This family also includes torovirus NendoUs. Except for turkey coronavirus (TCoV) Nsp15, Mn2+ is generally essential for the catalytic activity of coronavirus Nsp15. Mn2+ is dispensable, and to some extent inhibits the activity of arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and murine hepatitis virus (MHV) form a functional hexamer while Porcine DeltaCoronavirus (PDCoV) Nsp15 has been shown to exist as a dimer and monomer in solution. Nsp11 from the arterivirus PRRSV is a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. Pssm-ID: 439157 Cd Length: 151 Bit Score: 105.42 E-value: 1.30e-25
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| M_cv_Nsp15-NTD_av_Nsp11-like | cd21163 | middle (M) domain of coronavirus Nonstructural protein 15 (Nsp15) and the N-terminal domain ... |
3199-3301 | 8.27e-24 | |||||||
middle (M) domain of coronavirus Nonstructural protein 15 (Nsp15) and the N-terminal domain (NTD) of arterivirus Nsp11 and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain, and a C-terminal catalytic (NendoU) domain. Arterivirus Nsp11 has an N-terminal domain (NTD) and a C-terminal catalytic (NendoU) domain. The NTD of Nsp11 superimposes onto the M-domain of coronavirus Nsp15. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and Murine Hepatitis Virus (MHV) form a functional hexamer. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of other coronavirus members; it has been shown to exist as a dimer and a monomer in solution. Nsp11 from the arterivirus PRRSV functions as a dimer. Pssm-ID: 439159 Cd Length: 123 Bit Score: 99.33 E-value: 8.27e-24
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| 1B_av_Nsp10-like | cd21410 | 1B domain of arterivirus EAV Nsp10 helicase and related proteins; Helicases catalyze ... |
2825-2873 | 1.19e-20 | |||||||
1B domain of arterivirus EAV Nsp10 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. Members of this subfamily belong to helicase superfamily 1 (SF1) and include arterivirus helicases such Equine arteritis virus (EAV) Nsp10 helicase encoded on ORF1b. EAV Nsp10 is a multidomain protein; its other domains include an N-terminal Cys/His rich zinc-binding domain (CH/ZBD) 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: 439172 Cd Length: 49 Bit Score: 87.30 E-value: 1.19e-20
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| SF1_C | cd18786 | C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
3063-3122 | 1.05e-17 | |||||||
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: 80.56 E-value: 1.05e-17
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| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
2897-3122 | 8.35e-11 | |||||||
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 64.71 E-value: 8.35e-11
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| SF1_C_RecD | cd18809 | C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ... |
3066-3121 | 1.55e-10 | |||||||
C-terminal helicase domain of RecD family helicases; 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 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: 350196 [Multi-domain] Cd Length: 80 Bit Score: 59.88 E-value: 1.55e-10
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
3078-3121 | 1.24e-08 | |||||||
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: 60.76 E-value: 1.24e-08
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| CoV_NSP15_C | pfam19215 | Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ... |
3296-3415 | 2.91e-08 | |||||||
Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the C-terminal domain of coronavirus non-structural protein 15 (NSP15 or nsp15). NSP15 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. This domain exhibits endoribonuclease activity designated EndoU, highly conserved in all known CoVs and is part of the replicase-transcriptase complex that plays important roles in virus replication and transcription. NSP15 is a Uridylate-specific endoribonuclease that cleaves the 5'-polyuridines from negative-sense viral RNA, termed PUN RNA either upstream or downstream of uridylates, at GUU or GU to produce molecules with 2',3'-cyclic phosphate ends. PUN RNA is a CoV MDA5-dependent pathogen-associated molecular pattern (PAMP). Pssm-ID: 465999 Cd Length: 155 Bit Score: 55.80 E-value: 2.91e-08
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| NendoU_cv_Nsp15-like | cd21161 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural ... |
3303-3415 | 3.27e-08 | |||||||
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural Protein 15 (Nsp15) and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Except for turkey coronavirus (TCoV) Nsp15, Mn2+ is generally essential for the catalytic activity of coronavirus Nsp15. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and murine hepatitis virus (MHV) form a functional hexamer while Porcine DeltaCoronavirus (PDCoV) Nsp15 has been shown to exist as a dimer and a monomer in solution. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. Pssm-ID: 439158 Cd Length: 151 Bit Score: 55.35 E-value: 3.27e-08
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| Peptidase_C33 | pfam05412 | Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These ... |
633-730 | 3.40e-08 | |||||||
Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These peptidases are involved in viral polyprotein processing in replication. Pssm-ID: 114153 Cd Length: 108 Bit Score: 54.15 E-value: 3.40e-08
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| HCoV_HKU1-like_RdRp | cd21593 | human coronavirus HKU1 RNA-dependent RNA polymerase, also known as non-structural protein 12, ... |
2333-2602 | 3.46e-08 | |||||||
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: 59.97 E-value: 3.46e-08
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| batCoV-HKU9-like_RdRp | cd21596 | Bat coronavirus HKU9 RNA-dependent RNA polymerase, also known as non-structural protein 12, ... |
2333-2580 | 1.20e-06 | |||||||
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: 54.66 E-value: 1.20e-06
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| deltaCoV_RdRp | cd21590 | deltacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ... |
2412-2580 | 1.59e-06 | |||||||
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: 54.48 E-value: 1.59e-06
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| gammaCoV_RdRp | cd21587 | gammacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ... |
2412-2580 | 1.73e-05 | |||||||
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: 51.04 E-value: 1.73e-05
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| RNA_dep_RNAP | cd01699 | RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ... |
2440-2674 | 3.65e-05 | |||||||
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage. Pssm-ID: 238843 [Multi-domain] Cd Length: 278 Bit Score: 48.43 E-value: 3.65e-05
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| Peptidase_C32 | pfam05411 | Equine arteritis virus putative proteinase; These proteins are characterized by a region that ... |
368-448 | 5.75e-05 | |||||||
Equine arteritis virus putative proteinase; These proteins are characterized by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication. Pssm-ID: 398854 Cd Length: 127 Bit Score: 45.23 E-value: 5.75e-05
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| SARS-CoV-like_RdRp | cd21591 | Severe acute respiratory syndrome coronavirus RNA-dependent RNA polymerase, also known as ... |
2410-2591 | 3.56e-04 | |||||||
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: 46.62 E-value: 3.56e-04
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| MERS-CoV-like_RdRp | cd21592 | Middle East respiratory syndrome-related coronavirus RNA-dependent RNA polymerase, also known ... |
2412-2586 | 4.80e-04 | |||||||
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: 46.19 E-value: 4.80e-04
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| DEXXQc_Upf1-like | cd17934 | DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ... |
2894-2923 | 1.03e-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: 41.45 E-value: 1.03e-03
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| recD | PRK10875 | exodeoxyribonuclease V subunit alpha; |
3078-3121 | 2.70e-03 | |||||||
exodeoxyribonuclease V subunit alpha; Pssm-ID: 236783 [Multi-domain] Cd Length: 615 Bit Score: 43.39 E-value: 2.70e-03
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| NendoU_tv_PToV-like | cd21162 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) ... |
3299-3418 | 3.43e-03 | |||||||
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) endoribonuclease and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. The Porcine torovirus (PToV) strain PToV-NPL/2013 NendoU domain is located at the N-terminus of the ORF1ab replicase polyprotein, between regions annotated as Nonstructural proteins 11 (Nsp11) and 13 (Nsp13). This subfamily belongs to a family which includes Nsp15 from coronaviruses and Nsp11 from arteriviruses, which may participate in the viral replication process and in the evasion of the host immune system. These vary in their requirement for Mn2+. Coronavirus Nsp15 generally form functional hexamers, with the exception of Porcine DeltaCoronavirus (PDCoV) Nsp15 which exists as a dimer and a monomer in solution. Arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11 is a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. Pssm-ID: 394913 Cd Length: 133 Bit Score: 40.26 E-value: 3.43e-03
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