replicase polyprotein/mCherry [Cloning vector pEAVsVBSmCherry]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| IFR3_antag super family | cl20679 | Papain-like auto-proteinase; The replicase polyproteins of the Nidoviruses such as, porcine ... |
1-249 | 1.01e-174 | ||||||
Papain-like auto-proteinase; The replicase polyproteins of the Nidoviruses such as, porcine arterivirus PRRSV, equine arterivirus EAV, human coronavirus 229E, and severe acute respiratory syndrome coronavirus (SARS-CoV), are predicted to be cleaved into 14 non-structural proteins (nsps) by the nsp4 main proteinase pfam05579 and three accessory proteinases residing in nsp1-alpha, nsp1-beta and nsp2. This family is the two nsp1 proteins that together act in a papain-like way to separate off the rest of the various functional domains of the polyprotein. Once inside the host cell, this nsp1 interferes with the regulation of interferon, thereby enabling the virus to replicate. The actual alignment was detected with superfamily member pfam14754: Pssm-ID: 291424 Cd Length: 249 Bit Score: 536.56 E-value: 1.01e-174
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| Arteriviridae_RdRp | cd23189 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ... |
2308-2634 | 4.95e-171 | ||||||
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: 529.52 E-value: 4.95e-171
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| Peptidase_S32 | pfam05579 | Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing ... |
1227-1533 | 5.18e-142 | ||||||
Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing nidovirus polyprotein. : Pssm-ID: 253263 Cd Length: 297 Bit Score: 444.99 E-value: 5.18e-142
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| Nsp2_AV | pfam14755 | Nsp2, transmembrane domain; This domain is found in Nsp2 protein of the RNA-arteriviruses, ... |
625-772 | 6.03e-87 | ||||||
Nsp2, transmembrane domain; This domain is found in Nsp2 protein of the RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV, which is a tetraspanning transmembrane protein. This domain resides adjacent to the peptidase C33 catalytic domain of Nsp2. : Pssm-ID: 373271 [Multi-domain] Cd Length: 148 Bit Score: 280.72 E-value: 6.03e-87
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| NendoU_av_Nsp11-like | cd21160 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ... |
3201-3320 | 1.73e-68 | ||||||
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: 226.82 E-value: 1.73e-68
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| DEXXYc_viral_SF1-N | cd17937 | DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ... |
2785-2929 | 3.04e-58 | ||||||
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: 198.04 E-value: 3.04e-58
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| NTD_av_Nsp11-like | cd21166 | N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ... |
3105-3203 | 2.06e-54 | ||||||
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: 185.61 E-value: 2.06e-54
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| Arteri_nsp7a | pfam16749 | Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a ... |
1718-1837 | 2.89e-48 | ||||||
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: 169.12 E-value: 2.89e-48
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| zf-RING_13 | pfam17977 | RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. ... |
2635-2702 | 2.11e-45 | ||||||
RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. It includes includes 12 or 13 conserved Cys/His residues. Amino acid substitutions in ZBD or the adjacent spacer that connects it to the downstream domain can profoundly affect EAV (equine arteritis virus) helicase activity and RNA synthesis, with most replacements of conserved Cys or His residues yielding replication-negative virus phenotypes. : Pssm-ID: 375459 Cd Length: 68 Bit Score: 158.72 E-value: 2.11e-45
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| GFP | pfam01353 | Green fluorescent protein; |
282-485 | 7.31e-44 | ||||||
Green fluorescent protein; : Pssm-ID: 426217 Cd Length: 211 Bit Score: 160.04 E-value: 7.31e-44
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| Rep_1B | pfam17873 | Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase ... |
2717-2769 | 1.18e-30 | ||||||
Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase polyprotein 1ab found in Arterivirus. Structural studies of arterivirus helicase (nsp10), indicate that this domain undergoes conformational changes on substrate binding. Besides the large conformational change, it is suggested that the regions at the surface of domain 1B not directly involved in DNA binding may become flexible. For example, domain 1B residues Arg95, Gly125 and Ala131 become disordered after DNA binding. Together with domains 1A and 2A it forms a nucleic acid-binding channel where the single-stranded part of the DNA substrate is bound to. : Pssm-ID: 375396 Cd Length: 53 Bit Score: 115.96 E-value: 1.18e-30
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| av_Nsp3_ER-remodelling | cd22528 | intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This ... |
1110-1166 | 4.09e-22 | ||||||
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: 92.00 E-value: 4.09e-22
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| SF1_C | cd18786 | C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
2965-3024 | 1.18e-19 | ||||||
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: 85.95 E-value: 1.18e-19
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| DUF3756 | pfam12581 | Protein of unknown function (DUF3756); This domain family is found in viruses, and is ... |
3348-3388 | 5.99e-17 | ||||||
Protein of unknown function (DUF3756); This domain family is found in viruses, and is approximately 40 amino acids in length. : Pssm-ID: 315289 Cd Length: 41 Bit Score: 76.75 E-value: 5.99e-17
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| Peptidase_C33 super family | cl05135 | Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These ... |
526-621 | 2.86e-14 | ||||||
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: 71.48 E-value: 2.86e-14
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| Name | Accession | Description | Interval | E-value | ||||||
| IFR3_antag | pfam14754 | Papain-like auto-proteinase; The replicase polyproteins of the Nidoviruses such as, porcine ... |
1-249 | 1.01e-174 | ||||||
Papain-like auto-proteinase; The replicase polyproteins of the Nidoviruses such as, porcine arterivirus PRRSV, equine arterivirus EAV, human coronavirus 229E, and severe acute respiratory syndrome coronavirus (SARS-CoV), are predicted to be cleaved into 14 non-structural proteins (nsps) by the nsp4 main proteinase pfam05579 and three accessory proteinases residing in nsp1-alpha, nsp1-beta and nsp2. This family is the two nsp1 proteins that together act in a papain-like way to separate off the rest of the various functional domains of the polyprotein. Once inside the host cell, this nsp1 interferes with the regulation of interferon, thereby enabling the virus to replicate. Pssm-ID: 291424 Cd Length: 249 Bit Score: 536.56 E-value: 1.01e-174
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| Arteriviridae_RdRp | cd23189 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ... |
2308-2634 | 4.95e-171 | ||||||
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: 529.52 E-value: 4.95e-171
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| Peptidase_S32 | pfam05579 | Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing ... |
1227-1533 | 5.18e-142 | ||||||
Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing nidovirus polyprotein. Pssm-ID: 253263 Cd Length: 297 Bit Score: 444.99 E-value: 5.18e-142
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| Nsp2_AV | pfam14755 | Nsp2, transmembrane domain; This domain is found in Nsp2 protein of the RNA-arteriviruses, ... |
625-772 | 6.03e-87 | ||||||
Nsp2, transmembrane domain; This domain is found in Nsp2 protein of the RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV, which is a tetraspanning transmembrane protein. This domain resides adjacent to the peptidase C33 catalytic domain of Nsp2. Pssm-ID: 373271 [Multi-domain] Cd Length: 148 Bit Score: 280.72 E-value: 6.03e-87
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| NendoU_av_Nsp11-like | cd21160 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ... |
3201-3320 | 1.73e-68 | ||||||
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: 226.82 E-value: 1.73e-68
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| DEXXYc_viral_SF1-N | cd17937 | DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ... |
2785-2929 | 3.04e-58 | ||||||
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: 198.04 E-value: 3.04e-58
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| NTD_av_Nsp11-like | cd21166 | N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ... |
3105-3203 | 2.06e-54 | ||||||
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: 185.61 E-value: 2.06e-54
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| Arteri_nsp7a | pfam16749 | Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a ... |
1718-1837 | 2.89e-48 | ||||||
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: 169.12 E-value: 2.89e-48
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| zf-RING_13 | pfam17977 | RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. ... |
2635-2702 | 2.11e-45 | ||||||
RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. It includes includes 12 or 13 conserved Cys/His residues. Amino acid substitutions in ZBD or the adjacent spacer that connects it to the downstream domain can profoundly affect EAV (equine arteritis virus) helicase activity and RNA synthesis, with most replacements of conserved Cys or His residues yielding replication-negative virus phenotypes. Pssm-ID: 375459 Cd Length: 68 Bit Score: 158.72 E-value: 2.11e-45
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| GFP | pfam01353 | Green fluorescent protein; |
282-485 | 7.31e-44 | ||||||
Green fluorescent protein; Pssm-ID: 426217 Cd Length: 211 Bit Score: 160.04 E-value: 7.31e-44
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| RdRP_1 | pfam00680 | Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ... |
2226-2576 | 1.29e-34 | ||||||
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: 140.24 E-value: 1.29e-34
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| Rep_1B | pfam17873 | Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase ... |
2717-2769 | 1.18e-30 | ||||||
Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase polyprotein 1ab found in Arterivirus. Structural studies of arterivirus helicase (nsp10), indicate that this domain undergoes conformational changes on substrate binding. Besides the large conformational change, it is suggested that the regions at the surface of domain 1B not directly involved in DNA binding may become flexible. For example, domain 1B residues Arg95, Gly125 and Ala131 become disordered after DNA binding. Together with domains 1A and 2A it forms a nucleic acid-binding channel where the single-stranded part of the DNA substrate is bound to. Pssm-ID: 375396 Cd Length: 53 Bit Score: 115.96 E-value: 1.18e-30
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| av_Nsp3_ER-remodelling | cd22528 | intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This ... |
1110-1166 | 4.09e-22 | ||||||
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: 92.00 E-value: 4.09e-22
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| SF1_C | cd18786 | C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
2965-3024 | 1.18e-19 | ||||||
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: 85.95 E-value: 1.18e-19
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| ZBD_av_Nsp10-like | cd21405 | Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 helicase and related ... |
2636-2702 | 1.51e-19 | ||||||
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: 84.68 E-value: 1.51e-19
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| DUF3756 | pfam12581 | Protein of unknown function (DUF3756); This domain family is found in viruses, and is ... |
3348-3388 | 5.99e-17 | ||||||
Protein of unknown function (DUF3756); This domain family is found in viruses, and is approximately 40 amino acids in length. Pssm-ID: 315289 Cd Length: 41 Bit Score: 76.75 E-value: 5.99e-17
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| Peptidase_C33 | pfam05412 | Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These ... |
526-621 | 2.86e-14 | ||||||
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: 71.48 E-value: 2.86e-14
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| 1B_nv_SF1_Hel-like | cd21406 | 1B domain of nidovirus helicases including coronavirus Nsp13 and arterivirus Nsp10, and ... |
2721-2768 | 1.11e-10 | ||||||
1B domain 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. Members of this nidoviral 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. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). They belong to a larger SF1 helicase family which also includes eukaryotic UPF1-like helicases. UPF1, EAV Nsp10 and SARS-Nsp13 are multidomain proteins with an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a 1B domain and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of EAV Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids. Pssm-ID: 439171 Cd Length: 48 Bit Score: 59.11 E-value: 1.11e-10
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| CoV_NSP15_C | pfam19215 | Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ... |
3198-3319 | 1.67e-09 | ||||||
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: 59.27 E-value: 1.67e-09
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| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
2790-3024 | 1.22e-06 | ||||||
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: 52.38 E-value: 1.22e-06
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| Name | Accession | Description | Interval | E-value | ||||||
| IFR3_antag | pfam14754 | Papain-like auto-proteinase; The replicase polyproteins of the Nidoviruses such as, porcine ... |
1-249 | 1.01e-174 | ||||||
Papain-like auto-proteinase; The replicase polyproteins of the Nidoviruses such as, porcine arterivirus PRRSV, equine arterivirus EAV, human coronavirus 229E, and severe acute respiratory syndrome coronavirus (SARS-CoV), are predicted to be cleaved into 14 non-structural proteins (nsps) by the nsp4 main proteinase pfam05579 and three accessory proteinases residing in nsp1-alpha, nsp1-beta and nsp2. This family is the two nsp1 proteins that together act in a papain-like way to separate off the rest of the various functional domains of the polyprotein. Once inside the host cell, this nsp1 interferes with the regulation of interferon, thereby enabling the virus to replicate. Pssm-ID: 291424 Cd Length: 249 Bit Score: 536.56 E-value: 1.01e-174
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| Arteriviridae_RdRp | cd23189 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ... |
2308-2634 | 4.95e-171 | ||||||
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: 529.52 E-value: 4.95e-171
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| Peptidase_S32 | pfam05579 | Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing ... |
1227-1533 | 5.18e-142 | ||||||
Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing nidovirus polyprotein. Pssm-ID: 253263 Cd Length: 297 Bit Score: 444.99 E-value: 5.18e-142
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| ps-ssRNAv_Nidovirales_RdRp | cd23168 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of ... |
2314-2633 | 2.41e-89 | ||||||
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: 294.65 E-value: 2.41e-89
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| Nsp2_AV | pfam14755 | Nsp2, transmembrane domain; This domain is found in Nsp2 protein of the RNA-arteriviruses, ... |
625-772 | 6.03e-87 | ||||||
Nsp2, transmembrane domain; This domain is found in Nsp2 protein of the RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV, which is a tetraspanning transmembrane protein. This domain resides adjacent to the peptidase C33 catalytic domain of Nsp2. Pssm-ID: 373271 [Multi-domain] Cd Length: 148 Bit Score: 280.72 E-value: 6.03e-87
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| NendoU_av_Nsp11-like | cd21160 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ... |
3201-3320 | 1.73e-68 | ||||||
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: 226.82 E-value: 1.73e-68
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| DEXXYc_viral_SF1-N | cd17937 | DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ... |
2785-2929 | 3.04e-58 | ||||||
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: 198.04 E-value: 3.04e-58
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| NTD_av_Nsp11-like | cd21166 | N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ... |
3105-3203 | 2.06e-54 | ||||||
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: 185.61 E-value: 2.06e-54
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| Arteri_nsp7a | pfam16749 | Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a ... |
1718-1837 | 2.89e-48 | ||||||
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: 169.12 E-value: 2.89e-48
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| zf-RING_13 | pfam17977 | RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. ... |
2635-2702 | 2.11e-45 | ||||||
RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. It includes includes 12 or 13 conserved Cys/His residues. Amino acid substitutions in ZBD or the adjacent spacer that connects it to the downstream domain can profoundly affect EAV (equine arteritis virus) helicase activity and RNA synthesis, with most replacements of conserved Cys or His residues yielding replication-negative virus phenotypes. Pssm-ID: 375459 Cd Length: 68 Bit Score: 158.72 E-value: 2.11e-45
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| GFP | pfam01353 | Green fluorescent protein; |
282-485 | 7.31e-44 | ||||||
Green fluorescent protein; Pssm-ID: 426217 Cd Length: 211 Bit Score: 160.04 E-value: 7.31e-44
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| RdRP_1 | pfam00680 | Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ... |
2226-2576 | 1.29e-34 | ||||||
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: 140.24 E-value: 1.29e-34
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| Rep_1B | pfam17873 | Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase ... |
2717-2769 | 1.18e-30 | ||||||
Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase polyprotein 1ab found in Arterivirus. Structural studies of arterivirus helicase (nsp10), indicate that this domain undergoes conformational changes on substrate binding. Besides the large conformational change, it is suggested that the regions at the surface of domain 1B not directly involved in DNA binding may become flexible. For example, domain 1B residues Arg95, Gly125 and Ala131 become disordered after DNA binding. Together with domains 1A and 2A it forms a nucleic acid-binding channel where the single-stranded part of the DNA substrate is bound to. Pssm-ID: 375396 Cd Length: 53 Bit Score: 115.96 E-value: 1.18e-30
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| DExxQc_SF1-N | cd17914 | DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ... |
2787-2929 | 2.75e-26 | ||||||
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. Their helicase core is surrounded by C and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains or domains engaged in protein-protein interactions. SF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 438706 [Multi-domain] Cd Length: 121 Bit Score: 106.03 E-value: 2.75e-26
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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 ... |
3106-3202 | 1.38e-25 | ||||||
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: 104.34 E-value: 1.38e-25
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| av_Nsp3_ER-remodelling | cd22528 | intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This ... |
1110-1166 | 4.09e-22 | ||||||
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: 92.00 E-value: 4.09e-22
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| SF1_C | cd18786 | C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
2965-3024 | 1.18e-19 | ||||||
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: 85.95 E-value: 1.18e-19
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| ZBD_av_Nsp10-like | cd21405 | Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 helicase and related ... |
2636-2702 | 1.51e-19 | ||||||
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: 84.68 E-value: 1.51e-19
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| NendoU_nv | cd21158 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural ... |
3201-3319 | 2.59e-19 | ||||||
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: 87.32 E-value: 2.59e-19
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| DUF3756 | pfam12581 | Protein of unknown function (DUF3756); This domain family is found in viruses, and is ... |
3348-3388 | 5.99e-17 | ||||||
Protein of unknown function (DUF3756); This domain family is found in viruses, and is approximately 40 amino acids in length. Pssm-ID: 315289 Cd Length: 41 Bit Score: 76.75 E-value: 5.99e-17
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| Peptidase_C33 | pfam05412 | Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These ... |
526-621 | 2.86e-14 | ||||||
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: 71.48 E-value: 2.86e-14
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| ZBD_nv_SF1_Hel-like | cd21399 | Cys/His rich zinc-binding domain (CH/ZBD) of nidovirus helicases including coronavirus Nsp13 ... |
2636-2693 | 1.76e-13 | ||||||
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: 67.98 E-value: 1.76e-13
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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 ... |
2637-2693 | 1.45e-11 | ||||||
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: 62.51 E-value: 1.45e-11
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| 1B_nv_SF1_Hel-like | cd21406 | 1B domain of nidovirus helicases including coronavirus Nsp13 and arterivirus Nsp10, and ... |
2721-2768 | 1.11e-10 | ||||||
1B domain 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. Members of this nidoviral 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. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). They belong to a larger SF1 helicase family which also includes eukaryotic UPF1-like helicases. UPF1, EAV Nsp10 and SARS-Nsp13 are multidomain proteins with an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a 1B domain and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of EAV Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids. Pssm-ID: 439171 Cd Length: 48 Bit Score: 59.11 E-value: 1.11e-10
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| CoV_NSP15_C | pfam19215 | Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ... |
3198-3319 | 1.67e-09 | ||||||
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: 59.27 E-value: 1.67e-09
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| RNA_dep_RNAP | cd01699 | RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ... |
2394-2571 | 3.03e-09 | ||||||
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: 61.15 E-value: 3.03e-09
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| NendoU_tv_PToV-like | cd21162 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) ... |
3201-3320 | 5.92e-08 | ||||||
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: 54.13 E-value: 5.92e-08
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| ps-ssRNAv-Picornavirales | cd23169 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ... |
2397-2571 | 1.11e-07 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRp of Picornavirales, an order of (+)ssRNA viruses. The order Picornavirales comprises viruses that historically are referred to as picorna-like viruses and which are classified into eight virus families: Caliciviridae, Dicistroviridae, Iflaviridae, Marnaviridae, Picornaviridae, Polycipiviridae, Secoviridae, and Solinviviridae. All known genomes of Picornavirales members encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. The picornavirus genome is replicated via a negative-sense (-) RNA intermediate by the viral RdRp, named 3Dpol, which uses VPg (the product of 3B) as a primer to initiate the replication process. 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: 438019 Cd Length: 309 Bit Score: 56.45 E-value: 1.11e-07
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| Caliciviridae_RdRp | cd23192 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ... |
2380-2554 | 7.17e-07 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Caliciviridae, order Picornavirales. Member viruses have a viral (+)ssRNA genome, which is not segmented. The family Caliciviridae, includes eleven genera: seven genera of which infect mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus, and Vesivirus), two genera of which infect birds (Bavovirus, Nacovirus), and two genera of which infect fish (Minovirus and Salovirus). Each genus includes 1-2 species. Human noroviruses are a leading cause of acute gastroenteritis in humans. Furthermore, unclassified caliciviruses have been detected in geese, yellowfin seabream, greater green snake, arctic lamprey, frogs and various Australian birds, highlighting the wide host range of viruses in the family Caliciviridae. 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: 438042 Cd Length: 310 Bit Score: 54.19 E-value: 7.17e-07
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| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
2790-3024 | 1.22e-06 | ||||||
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: 52.38 E-value: 1.22e-06
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| 1B_av_Nsp10-like | cd21410 | 1B domain of arterivirus EAV Nsp10 helicase and related proteins; Helicases catalyze ... |
2719-2768 | 3.77e-06 | ||||||
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: 46.08 E-value: 3.77e-06
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| NendoU_cv_Nsp15-like | cd21161 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural ... |
3227-3319 | 5.31e-06 | ||||||
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: 48.80 E-value: 5.31e-06
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| ps-ssRNA_Picornaviridae | cd23193 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ... |
2406-2557 | 1.50e-04 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Picornaviridae, order Picornavirales. The Picornaviridae family consists of small, icosahedral viruses with (+)ssRNA genomes. Characteristic features of all members of the family Picornaviridae are three capsid proteins with beta-barrel folding, polyprotein processing by virus-encoded cysteine proteinase(s), and replication by an RdRp with a YGDD sequence motif. The family Picornaviridae comprises 68 genera containing 158 species, but many viruses are presently awaiting classification. The established genera of the family include: Aphthovirus, Avisivirus, Crohivirus, Enterovirus, Teschovirus, Cardiovirus, Erbovirus, Kobuvirus, Hepatovirus, Parechovirus, Aquamavirus, Avihepatovirus, Avisivirus, Cosavirus, Dicipivirus, Fipivirus, Gallivirus, Hunnivirus, Kunsagivirus, Limnipivirus, Megrivirus, Mischivirus, Mosavirus, Oscivirus, Pasivirus, Passerivirus, Rabovirus, Rosavirus, Sakobuvirus, Salivirus, Sapelovirus, Senecavirus, Sicinivirus, and Tremovirus. The Picornaviridae contains many important human and animal pathogens including enteroviruses (such as poliovirus, enterovirus, coxsackievirus, and rhinovirus), cardioviruses (such as encephalomyocarditis virus and Theiler's virus), hepatitis A virus and foot-and-mouth disease virus. Infection with various picornaviruses may cause encephalitis, febrile rash illnesses (hand-foot-and-mouth disease), aseptic meningitis, hepatitis, conjunctivitis, herpangina, myositis and myocarditis, and the common cold. 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: 438043 Cd Length: 345 Bit Score: 47.16 E-value: 1.50e-04
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| Dicistroviridae_RdRp | cd23194 | RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense ... |
2391-2505 | 4.08e-04 | ||||||
RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the RdRp of RNA viruses belonging to the family Dicistroviridae, order Picornavirales. Dicistroviridae is a family of small non-enveloped viruses with a (+)ssRNA genome of approximately 8-10 kilobases. The family contains 3 genera: Aparavirus, Cripavirus, and Triatovirus. All members infect arthropod hosts with some having devastating economic consequences, such as acute bee paralysis virus, Kashmir bee virus, and Israeli acute paralysis virus in domesticated honeybees, and taura syndrome virus and mud crab virus in the seafood industry. On the contrary, host specificity and other desirable traits make several members of this group amenable to development as biopesticides for insect control, such as Solenopsis invicta virus 1 against fire ants, and triatoma virus against triatomine bugs that vector Chagas disease. Members in the family Dicistroviridae have similarity to viruses in the Picornavirales members (Iflaviridae, Picornaviridae, Marnaviridae and Secoviridae). The genomes of viruses of these taxa encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. 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: 438044 [Multi-domain] Cd Length: 315 Bit Score: 45.57 E-value: 4.08e-04
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| Mosavirus_RdRp | cd23225 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of ... |
2379-2533 | 4.29e-03 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Mosavirus genus within the family Picornaviridae, order Picornavirales. The Mosavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus includes two species: Mosavirus A, which found in the feces of a canyon mouse (Peromyscus crinitus), and Mosavirus B, which contains marmot mosavirus. Mosavirus stands for mouse stool-associated picornavirus. 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: 438075 Cd Length: 378 Bit Score: 42.59 E-value: 4.29e-03
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| deltaCoV_RdRp | cd21590 | deltacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ... |
2386-2458 | 4.72e-03 | ||||||
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: 42.92 E-value: 4.72e-03
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