polyprotein [Classical swine fever virus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||
| Pestivirus_RdRp | cd23201 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, within ... |
3277-3855 | 0e+00 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Pestivirus genus within the family Flaviviridae, order Amarillovirales. Members of the genus Pestivirus infect pigs and ruminants, including cattle, sheep, goats and wild ruminants, and are transmitted through contact with infected secretions (respiratory droplets, urine or feces). Infections may be subclinical or cause enteric, hemorrhagic or wasting diseases, including those by the economically important bovine viral diarrhea virus and classical swine fever virus. Virions of Pestivirus have a single, small, basic capsid (C) protein and three envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438051 Cd Length: 579 Bit Score: 1278.42 E-value: 0e+00
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| Pestivirus_E2 super family | cl24788 | Pestivirus envelope glycoprotein E2; |
691-1060 | 4.79e-165 | |||||||||
Pestivirus envelope glycoprotein E2; The actual alignment was detected with superfamily member pfam16329: Pssm-ID: 318535 Cd Length: 372 Bit Score: 514.63 E-value: 4.79e-165
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| Peptidase_S31 | pfam05578 | Pestivirus NS3 polyprotein peptidase S31; These serine peptidases are involved in processing ... |
1590-1800 | 9.86e-150 | |||||||||
Pestivirus NS3 polyprotein peptidase S31; These serine peptidases are involved in processing of the flavivirus polyprotein. : Pssm-ID: 398938 Cd Length: 211 Bit Score: 463.45 E-value: 9.86e-150
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| Peptidase_C74 super family | cl13778 | Pestivirus NS2 peptidase; The pestivirus NS2 peptidase is responsible for single cleavage ... |
1323-1522 | 2.91e-94 | |||||||||
Pestivirus NS2 peptidase; The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the bovine viral diarrhea virus polyprotein, a cleavage that is correlated with cytopathogenicity. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. The actual alignment was detected with superfamily member pfam12387: Pssm-ID: 289175 Cd Length: 200 Bit Score: 303.93 E-value: 2.91e-94
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| Peptidase_C53 super family | cl05226 | Pestivirus Npro endopeptidase C53; Unique to pestiviruses, the N-terminal protein encoded by ... |
1-168 | 5.18e-84 | |||||||||
Pestivirus Npro endopeptidase C53; Unique to pestiviruses, the N-terminal protein encoded by the bovine viral diarrhoea virus genome is a cysteine protease (Npro) responsible for a self-cleavage that releases the N terminus of the core protein. This unique protease is dispensable for viral replication, and its coding region can be replaced by a ubiquitin gene directly fused in frame to the core. The actual alignment was detected with superfamily member pfam05550: Pssm-ID: 283255 Cd Length: 168 Bit Score: 273.48 E-value: 5.18e-84
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| DEXHc_viral_Ns3 | cd17931 | DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ... |
1808-1959 | 3.01e-60 | |||||||||
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 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: 350689 [Multi-domain] Cd Length: 151 Bit Score: 204.71 E-value: 3.01e-60
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| Capsid_pestivir super family | cl13348 | Capsid protein C, pestivirus; This domain is found in the genome polyprotein from Pestivirus. ... |
170-218 | 5.26e-20 | |||||||||
Capsid protein C, pestivirus; This domain is found in the genome polyprotein from Pestivirus. It covers part of the capsid protein C region in the polyprotein. The actual alignment was detected with superfamily member pfam11889: Pssm-ID: 288721 Cd Length: 56 Bit Score: 86.12 E-value: 5.26e-20
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| P-loop_NTPase super family | cl38936 | P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ... |
1953-2106 | 4.85e-11 | |||||||||
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families. The actual alignment was detected with superfamily member cd18791: Pssm-ID: 476819 [Multi-domain] Cd Length: 171 Bit Score: 64.09 E-value: 4.85e-11
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| RNase_T2 super family | cl00208 | Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism ... |
289-351 | 4.67e-03 | |||||||||
Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. S-RNases are thought to prevent self-fertilization by acting as selective cytotoxins of "self" pollen. The actual alignment was detected with superfamily member cd01062: Pssm-ID: 469659 Cd Length: 184 Bit Score: 41.21 E-value: 4.67e-03
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| Name | Accession | Description | Interval | E-value | |||||||||
| Pestivirus_RdRp | cd23201 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, within ... |
3277-3855 | 0e+00 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Pestivirus genus within the family Flaviviridae, order Amarillovirales. Members of the genus Pestivirus infect pigs and ruminants, including cattle, sheep, goats and wild ruminants, and are transmitted through contact with infected secretions (respiratory droplets, urine or feces). Infections may be subclinical or cause enteric, hemorrhagic or wasting diseases, including those by the economically important bovine viral diarrhea virus and classical swine fever virus. Virions of Pestivirus have a single, small, basic capsid (C) protein and three envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438051 Cd Length: 579 Bit Score: 1278.42 E-value: 0e+00
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| Pestivirus_E2 | pfam16329 | Pestivirus envelope glycoprotein E2; |
691-1060 | 4.79e-165 | |||||||||
Pestivirus envelope glycoprotein E2; Pssm-ID: 318535 Cd Length: 372 Bit Score: 514.63 E-value: 4.79e-165
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| Peptidase_S31 | pfam05578 | Pestivirus NS3 polyprotein peptidase S31; These serine peptidases are involved in processing ... |
1590-1800 | 9.86e-150 | |||||||||
Pestivirus NS3 polyprotein peptidase S31; These serine peptidases are involved in processing of the flavivirus polyprotein. Pssm-ID: 398938 Cd Length: 211 Bit Score: 463.45 E-value: 9.86e-150
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| Peptidase_C74 | pfam12387 | Pestivirus NS2 peptidase; The pestivirus NS2 peptidase is responsible for single cleavage ... |
1323-1522 | 2.91e-94 | |||||||||
Pestivirus NS2 peptidase; The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the bovine viral diarrhea virus polyprotein, a cleavage that is correlated with cytopathogenicity. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. Pssm-ID: 289175 Cd Length: 200 Bit Score: 303.93 E-value: 2.91e-94
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| Peptidase_C53 | pfam05550 | Pestivirus Npro endopeptidase C53; Unique to pestiviruses, the N-terminal protein encoded by ... |
1-168 | 5.18e-84 | |||||||||
Pestivirus Npro endopeptidase C53; Unique to pestiviruses, the N-terminal protein encoded by the bovine viral diarrhoea virus genome is a cysteine protease (Npro) responsible for a self-cleavage that releases the N terminus of the core protein. This unique protease is dispensable for viral replication, and its coding region can be replaced by a ubiquitin gene directly fused in frame to the core. Pssm-ID: 283255 Cd Length: 168 Bit Score: 273.48 E-value: 5.18e-84
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| DEXHc_viral_Ns3 | cd17931 | DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ... |
1808-1959 | 3.01e-60 | |||||||||
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 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: 350689 [Multi-domain] Cd Length: 151 Bit Score: 204.71 E-value: 3.01e-60
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| Capsid_pestivir | pfam11889 | Capsid protein C, pestivirus; This domain is found in the genome polyprotein from Pestivirus. ... |
170-218 | 5.26e-20 | |||||||||
Capsid protein C, pestivirus; This domain is found in the genome polyprotein from Pestivirus. It covers part of the capsid protein C region in the polyprotein. Pssm-ID: 288721 Cd Length: 56 Bit Score: 86.12 E-value: 5.26e-20
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| RdRP_3 | pfam00998 | Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ... |
3427-3705 | 3.89e-18 | |||||||||
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses. Pssm-ID: 395794 [Multi-domain] Cd Length: 486 Bit Score: 91.14 E-value: 3.89e-18
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
1813-1976 | 3.94e-15 | |||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 76.76 E-value: 3.94e-15
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| SF2_C_RHA | cd18791 | C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ... |
1953-2106 | 4.85e-11 | |||||||||
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family members are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350178 [Multi-domain] Cd Length: 171 Bit Score: 64.09 E-value: 4.85e-11
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| HrpA | COG1643 | HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]; |
1817-2106 | 2.68e-08 | |||||||||
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]; Pssm-ID: 441249 [Multi-domain] Cd Length: 836 Bit Score: 60.09 E-value: 2.68e-08
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
1984-2100 | 7.51e-08 | |||||||||
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 53.37 E-value: 7.51e-08
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
1813-2102 | 1.08e-07 | |||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 58.11 E-value: 1.08e-07
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| PRK11664 | PRK11664 | ATP-dependent RNA helicase HrpB; Provisional |
1812-2102 | 1.40e-07 | |||||||||
ATP-dependent RNA helicase HrpB; Provisional Pssm-ID: 236950 [Multi-domain] Cd Length: 812 Bit Score: 58.01 E-value: 1.40e-07
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
2004-2100 | 3.22e-06 | |||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 47.59 E-value: 3.22e-06
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| PHA02653 | PHA02653 | RNA helicase NPH-II; Provisional |
2034-2106 | 4.02e-05 | |||||||||
RNA helicase NPH-II; Provisional Pssm-ID: 177443 [Multi-domain] Cd Length: 675 Bit Score: 49.59 E-value: 4.02e-05
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
1817-1946 | 4.24e-05 | |||||||||
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 46.85 E-value: 4.24e-05
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| RNase_T2_prok | cd01062 | Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism ... |
289-351 | 4.67e-03 | |||||||||
Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. S-RNases are thought to prevent self-fertilization by acting as selective cytotoxins of "self" pollen. Generally, RNases have two distinct binding sites: the primary site (B1 site) and the subsite (B2 site), for nucleotides located at the 5'- and 3'- terminal ends of the sessil bond, respectively. This CD includes the prokaryotic RNase T2 family members. Pssm-ID: 238513 Cd Length: 184 Bit Score: 41.21 E-value: 4.67e-03
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| Name | Accession | Description | Interval | E-value | |||||||||
| Pestivirus_RdRp | cd23201 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, within ... |
3277-3855 | 0e+00 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Pestivirus genus within the family Flaviviridae, order Amarillovirales. Members of the genus Pestivirus infect pigs and ruminants, including cattle, sheep, goats and wild ruminants, and are transmitted through contact with infected secretions (respiratory droplets, urine or feces). Infections may be subclinical or cause enteric, hemorrhagic or wasting diseases, including those by the economically important bovine viral diarrhea virus and classical swine fever virus. Virions of Pestivirus have a single, small, basic capsid (C) protein and three envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438051 Cd Length: 579 Bit Score: 1278.42 E-value: 0e+00
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| Pestivirus_E2 | pfam16329 | Pestivirus envelope glycoprotein E2; |
691-1060 | 4.79e-165 | |||||||||
Pestivirus envelope glycoprotein E2; Pssm-ID: 318535 Cd Length: 372 Bit Score: 514.63 E-value: 4.79e-165
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| Peptidase_S31 | pfam05578 | Pestivirus NS3 polyprotein peptidase S31; These serine peptidases are involved in processing ... |
1590-1800 | 9.86e-150 | |||||||||
Pestivirus NS3 polyprotein peptidase S31; These serine peptidases are involved in processing of the flavivirus polyprotein. Pssm-ID: 398938 Cd Length: 211 Bit Score: 463.45 E-value: 9.86e-150
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| ps-ssRNAv_Flaviviridae_RdRp | cd23178 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ... |
3436-3732 | 3.93e-102 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Flaviviridae, order Amarillovirales. Flaviviridae, is a family of small, enveloped viruses with RNA genomes of 9-13 kb. Most infect mammals and birds. Many flaviviruses are host-specific and pathogenic, such as hepatitis C virus in the genus Hepacivirus. The majority of known members in the genus Flavivirus are arthropod borne, and many are important human and veterinary pathogens (e.g., yellow fever virus, dengue virus). Virions are typically spherical in shape with a lipid envelope. Virions have a single, small, basic capsid (C) protein and two (genera Flavivirus, Hepacivirus and Pegivirus) or three (genus Pestivirus) envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. Translational initiation of genomic RNA is cap dependent in the case of members of the genus Flavivirus. 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: 438028 Cd Length: 284 Bit Score: 330.25 E-value: 3.93e-102
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| Peptidase_C74 | pfam12387 | Pestivirus NS2 peptidase; The pestivirus NS2 peptidase is responsible for single cleavage ... |
1323-1522 | 2.91e-94 | |||||||||
Pestivirus NS2 peptidase; The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the bovine viral diarrhea virus polyprotein, a cleavage that is correlated with cytopathogenicity. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. Pssm-ID: 289175 Cd Length: 200 Bit Score: 303.93 E-value: 2.91e-94
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| Peptidase_C53 | pfam05550 | Pestivirus Npro endopeptidase C53; Unique to pestiviruses, the N-terminal protein encoded by ... |
1-168 | 5.18e-84 | |||||||||
Pestivirus Npro endopeptidase C53; Unique to pestiviruses, the N-terminal protein encoded by the bovine viral diarrhoea virus genome is a cysteine protease (Npro) responsible for a self-cleavage that releases the N terminus of the core protein. This unique protease is dispensable for viral replication, and its coding region can be replaced by a ubiquitin gene directly fused in frame to the core. Pssm-ID: 283255 Cd Length: 168 Bit Score: 273.48 E-value: 5.18e-84
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| DEXHc_viral_Ns3 | cd17931 | DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ... |
1808-1959 | 3.01e-60 | |||||||||
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 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: 350689 [Multi-domain] Cd Length: 151 Bit Score: 204.71 E-value: 3.01e-60
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| RNA_dep_RNAP | cd01699 | RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ... |
3419-3707 | 2.25e-44 | |||||||||
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: 163.99 E-value: 2.25e-44
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| ps_ssRNAv_Tolivirales_RdRp | cd23179 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ... |
3443-3678 | 4.91e-21 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of positive-sense single-stranded RNA (+ssRNA) viruses; This family contains the catalytic core domain of RdRp of Tolivirales, an order of (+)ssRNA viruses which infect insects and plants. The virions are non-enveloped, spherical, and have an icosahedral capsid. The name Tolivirales, is derived from "tombusvirus-like" with the suffix -virales indicating a virus order. This order includes two families: Carmotetraviridae and Tombusviridae. 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: 438029 Cd Length: 227 Bit Score: 94.90 E-value: 4.91e-21
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| Capsid_pestivir | pfam11889 | Capsid protein C, pestivirus; This domain is found in the genome polyprotein from Pestivirus. ... |
170-218 | 5.26e-20 | |||||||||
Capsid protein C, pestivirus; This domain is found in the genome polyprotein from Pestivirus. It covers part of the capsid protein C region in the polyprotein. Pssm-ID: 288721 Cd Length: 56 Bit Score: 86.12 E-value: 5.26e-20
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| RdRP_3 | pfam00998 | Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ... |
3427-3705 | 3.89e-18 | |||||||||
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses. Pssm-ID: 395794 [Multi-domain] Cd Length: 486 Bit Score: 91.14 E-value: 3.89e-18
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
1813-1976 | 3.94e-15 | |||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 76.76 E-value: 3.94e-15
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| Calvusvirinae_RdRp | cd23234 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae of ... |
3422-3682 | 1.06e-13 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the subfamily Calvusvirinae, family Tombusviridae, order Tolivirales. Umbravirus is a genus of plant viruses assigned to this subfamily. The genus includes nine distinct virus species: Carrot mottle mimic virus (CMoMV), Groundnut rosette virus (GRV), Ethiopian tobacco bushy top virus (ETBTV), Lettuce speckles mottle virus (LSMV), Opium poppy mosaic virus (OPMV), Pea enation mosaic virus-2 (PEMV-2), Tobacco mottle virus (TMoV), and Tobacco bushy top virus (TBTV). Umbraviruses differ from other plant viruses in that they do not encode a coat protein (CP), and thus no conventional virus particles are formed in the infected plants. However, they encode RdRp domain typical to that of other members of the family Tombusviridae, allowing to classify the genus Umbravirus within this family. 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: 438084 Cd Length: 471 Bit Score: 77.09 E-value: 1.06e-13
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| Tombusviridae_RdRp | cd23206 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of ... |
3509-3677 | 3.55e-12 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tombusviridae, order Tolivirales. The family Tombusviridae comprises plant viruses, and is classified into 3 subfamilies (Calvusvirinae, Procedovirinae, and Regressovirinae), 17 genera, and 95 species. One genus is unassigned to a subfamily: Luteovirus. The name of the family is derived from Tomato bushy stunt virus (TBSV). Members of Tombusviridae replicate in the cytoplasm, by use of negative strand templates. The replication process leaves a surplus of positive- sense (+)RNA strands, and it is thought that not only does the viral RNA act as a template for replication, but is also able to manipulate and regulate RNA synthesis. 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: 438056 Cd Length: 231 Bit Score: 69.06 E-value: 3.55e-12
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| Gammacarmovirus_RdRp | cd23242 | RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ... |
3431-3705 | 8.19e-12 | |||||||||
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Gammacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The single genus Carmovirus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Most species have a narrow natural host range. However, different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 4 species in the genus Gammacarmovirus: Cowpea mottle virus, Melon necrotic spot virus, Pea stem necrosis virus, and Soybean yellow mottle mosaic virus. 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: 438092 Cd Length: 476 Bit Score: 70.93 E-value: 8.19e-12
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| Tombusvirus-like_RdRp | cd23236 | RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded ... |
3431-3705 | 1.59e-11 | |||||||||
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within Procedovirinae subfamily; and related RdRps; This group contains the RdRp of RNA viruses belonging to the Tombusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Tombusvirus is a genus of plant viruses. There are 17 species in the Tombusvirus genus: Artichoke mottled crinkle virus, Carnation Italian ringspot virus, Cucumber Bulgarian virus, Cucumber necrosis virus, Cymbidium ringspot virus, Eggplant mottled crinkle virus, Grapevine Algerian latent virus, Havel River virus, Lato River virus, Limonium flower distortion virus, Moroccan pepper virus, Neckar River virus, Pelargonium leaf curl virus, Pelargonium necrotic spot virus, Petunia asteroid mosaic virus, Sikte waterborne virus, and Tomato bushy stunt virus. Symptoms associated with this genus include mosaic. The name of the genus comes from Tomato bushy stunt virus. 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: 438086 [Multi-domain] Cd Length: 474 Bit Score: 70.04 E-value: 1.59e-11
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| SF2_C_RHA | cd18791 | C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ... |
1953-2106 | 4.85e-11 | |||||||||
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family members are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350178 [Multi-domain] Cd Length: 171 Bit Score: 64.09 E-value: 4.85e-11
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| Hepacivirus_RdRp | cd23202 | RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ... |
3462-3678 | 7.11e-11 | |||||||||
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Hepacivirus genus within the family Flaviviridae, order Amarillovirales. The genus Hepacivirus includes hepatitis C virus, a major human pathogen causing progressive liver disease, and several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows and primates. Infections are typically persistent and target the liver. Virions of Hepacivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438052 Cd Length: 518 Bit Score: 67.95 E-value: 7.11e-11
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| Alphanecrovirus_RdRp | cd23237 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of ... |
3464-3710 | 8.91e-10 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Alphanecrovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Alphanecroviruses are non-enveloped, with icosahedral and spherical geometries, and T=3 symmetry, and a diameter of around 28 nm. Their genomes are linear, around 4 kb in length. In the Alphanecrovirus genus plants serve as natural hosts. There are 4 species in this genus: Olive latent virus 1, Olive mild mosaic virus, Potato necrosis virus, and Tobacco necrosis virus A. 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: 438087 Cd Length: 439 Bit Score: 64.28 E-value: 8.91e-10
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| Pegivirus_RdRp | cd23203 | RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ... |
3332-3757 | 3.03e-09 | |||||||||
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Pegivirus genus within the family Flaviviridae, order Amarillovirales. Members of the Pegivirus genus are widely distributed in a range of mammalian species, in which they cause persistent infections. To date, they have not been clearly associated with disease. Virions of Pegivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438053 Cd Length: 476 Bit Score: 62.67 E-value: 3.03e-09
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| HrpA | COG1643 | HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]; |
1817-2106 | 2.68e-08 | |||||||||
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]; Pssm-ID: 441249 [Multi-domain] Cd Length: 836 Bit Score: 60.09 E-value: 2.68e-08
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
1984-2100 | 7.51e-08 | |||||||||
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 53.37 E-value: 7.51e-08
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
1813-2102 | 1.08e-07 | |||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 58.11 E-value: 1.08e-07
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| Betanecrovirus_RdRp | cd23244 | RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense ... |
3431-3684 | 1.11e-07 | |||||||||
RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Betanecrosvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. In the Betanecrosvirus genus plants serve as natural hosts, and transmission routes are mechanical, seed borne, and by contact. There are three species in this genus: Beet black scorch virus, Leek white stripe virus, and Tobacco necrosis virus D. Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription, using the premature termination model of subgenomic RNA transcription is the method of transcription. The virus exits the host cell by tubule-guided viral movement. 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: 438094 Cd Length: 500 Bit Score: 57.60 E-value: 1.11e-07
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| DEXHc_RHA-like | cd17917 | DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ... |
1813-1942 | 1.23e-07 | |||||||||
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 438707 [Multi-domain] Cd Length: 159 Bit Score: 54.00 E-value: 1.23e-07
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| PRK11664 | PRK11664 | ATP-dependent RNA helicase HrpB; Provisional |
1812-2102 | 1.40e-07 | |||||||||
ATP-dependent RNA helicase HrpB; Provisional Pssm-ID: 236950 [Multi-domain] Cd Length: 812 Bit Score: 58.01 E-value: 1.40e-07
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| Luteovirus_RdRp | cd23233 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of ... |
3465-3684 | 4.91e-07 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Luteovirus genus within the family Tombusviridae, order Tolivirales. There are 13 species in the Luteovirus genus: Apple associated luteovirus, Apple luteovirus 1, Barley yellow dwarf virus kerII, Barley yellow dwarf virus kerIII, Barley yellow dwarf virus MAV, Barley yellow dwarf virus PAS, Barley yellow dwarf virus PAV, Bean leafroll virus, Cherry associated luteovirus, Nectarine stem pitting associated virus, Red clover associated luteovirus, Rose spring dwarf-associated virus, and Soybean dwarf virus. Plants serve as natural hosts. The geographical distribution of Luteoviruses is widespread, with the virus primarily infecting plants via transmission by aphid vectors. The virus only replicates within the host cell and not within the vector. The name 'luteovirus' is derived from the Latin luteus (yellow) due to the symptomatic yellowing of the plant that occurs as a result of infection. 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: 438083 Cd Length: 407 Bit Score: 55.51 E-value: 4.91e-07
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
1808-1941 | 6.30e-07 | |||||||||
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region. Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 51.64 E-value: 6.30e-07
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| ps-ssRNAv-Picornavirales | cd23169 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ... |
3511-3703 | 9.65e-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: 53.75 E-value: 9.65e-07
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| Carmotetraviridae_RdRp | cd23205 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae ... |
3462-3681 | 1.65e-06 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, and related Erinaceus virus H14; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Carmotetraviridae, and related Erinaceus virus H14, order Tolivirales. Carmotetraviridae includes only one genus, Alphacarmotetravirus, which has one species: Providence virus. Lepidopteran insects serve as the natural host. Recent studies indicated that Providence virus, a non-enveloped insect RNA virus, isolated from a lepidopteran midgut cell line can establish a productive infection in plants as well as in animal cells. 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: 438055 Cd Length: 268 Bit Score: 52.71 E-value: 1.65e-06
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| SF2_C_viral | cd18806 | C-terminal helicase domain of viral helicase; Viral helicases in this family here are ... |
1991-2098 | 1.71e-06 | |||||||||
C-terminal helicase domain of viral helicase; Viral helicases in this family here are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350193 [Multi-domain] Cd Length: 145 Bit Score: 50.34 E-value: 1.71e-06
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| ps-ssRNAv_RdRp-like | cd23167 | conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ... |
3577-3635 | 2.12e-06 | |||||||||
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model. Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 48.10 E-value: 2.12e-06
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
2004-2100 | 3.22e-06 | |||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 47.59 E-value: 3.22e-06
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| DEXHc_HrpB | cd17990 | DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ... |
1817-1941 | 2.09e-05 | |||||||||
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 438711 [Multi-domain] Cd Length: 174 Bit Score: 47.71 E-value: 2.09e-05
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| Aureusvirus_RdRp | cd23243 | RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded ... |
3515-3683 | 2.45e-05 | |||||||||
RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Aureusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. In the Aureusvirus genus plants serve as natural hosts. There are six species in this genus: Cucumber leaf spot virus (CLSV), Elderberry aureusvirus 1, Johnsongrass chlorotic stripe mosaic virus (JCSMV), Maize white line mosaic virus (MWLMV), Pothos latent virus (PoLV), and Yam spherical virus (YSV). Aureusviruses infect various natural host plants but their individual range is generally restricted to a few species, pothos and pigeon pea or lisianthus for PoLV, yam for YSV, sesame for SNMV, cucumber, melon or squash for CLSV and various Poaceae species, mainly maize (MWLMV) or johnsongrass (JCSMV). Aureusviruses are transmitted mechanically and by seeds. Transmission through the soil or by the water circulating in hydroponic systems for PoLV, CLSV and MWLMV, or by the fungus Olpidium bornovanus (for CLSV) have also been reported. 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: 438093 Cd Length: 488 Bit Score: 50.22 E-value: 2.45e-05
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| Pelarspovirus_RdRp | cd23241 | RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense ... |
3490-3705 | 3.39e-05 | |||||||||
RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Pelarspovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The genus name "Pelarspovirus" is derived from the pelargonium ringspot virus, which was the first virus to be named. There are 8 species in the Pelarspovirus genus: Clematis chlorotic mottle virus, Elderberry latent virus, Jasmine mosaic-associated virus, Jasmine virus H, Pelargonium chlorotic ring pattern virus, Pelargonium line pattern virus, Pelargonium ringspot virus, and Rosa rugosa leaf distortion virus. Members of the Pelarspovirus have monopartite genomes encoding five open reading frames (ORFs) that include two 5'-proximal replication proteins, two centrally located movement proteins (MP1 and MP2) and a 3'-proximal coat protein that, at least for pelargonium line pattern virus (PLPV), has been shown to act also as suppressor of RNA silencing. 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: 438091 [Multi-domain] Cd Length: 497 Bit Score: 49.74 E-value: 3.39e-05
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| Regressovirinae_RdRp | cd23235 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae ... |
3492-3687 | 3.70e-05 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the subfamily Regressovirinae, family Tombusviridae, order Tolivirales. Dianthovirus is a genus of plant viruses within this subfamily. All the genera in the family Tombusviridae have monopartite (+)ssRNA genomes, except the dianthoviruses which have bipartite (+)ssRNA genomes. The dianthoviruses are distributed worldwide. The genus Dianthovirus is composed of three viruses: Carnation ringspot virus, Red clover necrotic mosaic virus, and Sweet clover necrotic mosaic virus. The amino acid (aa) sequence of dianthovirus RdRp has higher homology with that of the luteoviruses, while the amino acid sequence of dianthovirus coat protein (CP) has high homology with those of the tombusviruses and aureusviruses that belong to the subfamily Procedovirinae. 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: 438085 [Multi-domain] Cd Length: 472 Bit Score: 49.54 E-value: 3.70e-05
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| PHA02653 | PHA02653 | RNA helicase NPH-II; Provisional |
2034-2106 | 4.02e-05 | |||||||||
RNA helicase NPH-II; Provisional Pssm-ID: 177443 [Multi-domain] Cd Length: 675 Bit Score: 49.59 E-value: 4.02e-05
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
1817-1946 | 4.24e-05 | |||||||||
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 46.85 E-value: 4.24e-05
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| Betacarmovirus_RdRp | cd23240 | RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense ... |
3428-3682 | 8.60e-05 | |||||||||
RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Betacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The single genus Carmovirus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 4 species in the genus Betacarmovirus: Cardamine chlorotic fleck virus, Hibiscus chlorotic ringspot virus, Japanese iris necrotic ring virus, and Turnip crinkle virus. 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: 438090 Cd Length: 451 Bit Score: 48.31 E-value: 8.60e-05
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| Fipivirus_RdRp | cd23229 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus of ... |
3558-3629 | 1.40e-04 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus 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 Fipivirus genus within the family Picornaviridae, order Picornavirales. The Fipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains five species: Fipivirus A (Wuhan sharpbelly picornavirus 2), Fipivirus B (Wuhan sharpbelly picornavirus 3), Fipivirus C (Wenling crossorhombus picornavirus), Fipivirus D (Wenling jack mackerels picornavirus) and Fipivirus E (Wenling banjofish picornavirus 1). All contain viruses from fish. 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: 438079 Cd Length: 394 Bit Score: 47.49 E-value: 1.40e-04
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| Alphacarmovirus_RdRp | cd23239 | RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense ... |
3464-3682 | 2.05e-04 | |||||||||
RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Alphacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The Alphacarmovirus genus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 8 species in the genus Alphacarmovirus: Adonis mosaic virus, Angelonia flower break virus, Calibrachoa mottle virus, Carnation mottle virus, Honeysuckle ringspot virus, Nootka lupine vein clearing virus, Pelargonium flower break virus, and Saguaro cactus virus. 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: 438089 [Multi-domain] Cd Length: 470 Bit Score: 47.05 E-value: 2.05e-04
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| DEXHc_DHX40 | cd17984 | DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the ... |
1810-1941 | 6.65e-04 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350742 [Multi-domain] Cd Length: 178 Bit Score: 43.69 E-value: 6.65e-04
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| DEXHc_TDRD9 | cd17988 | DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also ... |
1816-1941 | 2.25e-03 | |||||||||
DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also known as HIG-1or NET54 or C14orf75) is a part of the nuclear PIWI-interacting RNA (piRNA) pathway essential for transposon silencing and male fertility TDRD9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350746 [Multi-domain] Cd Length: 180 Bit Score: 42.10 E-value: 2.25e-03
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| RNase_T2_prok | cd01062 | Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism ... |
289-351 | 4.67e-03 | |||||||||
Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. S-RNases are thought to prevent self-fertilization by acting as selective cytotoxins of "self" pollen. Generally, RNases have two distinct binding sites: the primary site (B1 site) and the subsite (B2 site), for nucleotides located at the 5'- and 3'- terminal ends of the sessil bond, respectively. This CD includes the prokaryotic RNase T2 family members. Pssm-ID: 238513 Cd Length: 184 Bit Score: 41.21 E-value: 4.67e-03
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| DEXHc_DHX33 | cd17978 | DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA ... |
1817-1941 | 5.61e-03 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA polymerase I transcription of the 47S precursor rRNA. DHX33 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 438710 [Multi-domain] Cd Length: 178 Bit Score: 40.80 E-value: 5.61e-03
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| Panicovirus_RdRp | cd23238 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Panicovirus of ... |
3464-3705 | 6.43e-03 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Panicovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Panicovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Viruses in Panicovirus are non-enveloped, with icosahedral and spherical geometries, and T=3 symmetry. Their host range is restricted to monocotyledonous plants. There are 3 species in this genus: Cocksfoot mild mosaic virus, Panicum mosaic virus, and Thin paspalum asymptomatic virus. The virus typically forms a systemic mosaic. 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: 438088 [Multi-domain] Cd Length: 692 Bit Score: 42.58 E-value: 6.43e-03
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| Iflaviridae_RdRp | cd23197 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Iflaviridae of ... |
3544-3680 | 6.86e-03 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Iflaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Iflaviridae, order Picornavirales. Iflaviridae is a family of small non-enveloped viruses with (+)ssRNA genomes of approximately 9-11 kilobases in length encoding a single polyprotein. All members infect arthropod hosts with the majority infecting insects. Beneficial and pest insects serve as hosts and infections can be symptomless (Nilaparvata lugens honeydew virus 1), cause developmental abnormalities (deformed wing virus, Varroa destructor virus 1, sacbrood virus), behavioral changes (deformed wing virus, Varroa destructor virus 1, slow bee paralysis virus, sacbrood virus) and premature mortality (deformed wing virus, Varroa destructor virus 1, slow bee paralysis virus, infectious flacherie virus, sacbrood virus). 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: 438047 Cd Length: 319 Bit Score: 41.78 E-value: 6.86e-03
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
1991-2106 | 7.94e-03 | |||||||||
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 38.07 E-value: 7.94e-03
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