polyprotein [Hepatitis C virus subtype 1b]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||
| Hepacivirus_RdRp | cd23202 | RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ... |
2433-2950 | 0e+00 | ||||||||
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: 1159.61 E-value: 0e+00
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| HCV_NS1 | pfam01560 | Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ... |
386-729 | 0e+00 | ||||||||
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region of hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein. : Pssm-ID: 110557 Cd Length: 344 Bit Score: 741.28 E-value: 0e+00
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| HCV_env super family | cl03255 | Hepatitis C virus envelope glycoprotein E1; |
193-382 | 1.88e-111 | ||||||||
Hepatitis C virus envelope glycoprotein E1; The actual alignment was detected with superfamily member pfam01539: Pssm-ID: 110536 Cd Length: 190 Bit Score: 352.64 E-value: 1.88e-111
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| HCV_NS5a_C super family | cl15181 | HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ... |
2179-2419 | 1.71e-105 | ||||||||
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. The actual alignment was detected with superfamily member pfam12941: Pssm-ID: 289693 Cd Length: 242 Bit Score: 337.68 E-value: 1.71e-105
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| HCV_NS2 | pfam01538 | Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ... |
811-1005 | 1.81e-102 | ||||||||
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases. Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3. : Pssm-ID: 366698 Cd Length: 195 Bit Score: 326.94 E-value: 1.81e-102
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| Peptidase_S29 | pfam02907 | Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ... |
1056-1204 | 2.33e-84 | ||||||||
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A. : Pssm-ID: 427049 Cd Length: 149 Bit Score: 273.15 E-value: 2.33e-84
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| HCV_NS4b | pfam01001 | Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ... |
1728-1921 | 1.18e-75 | ||||||||
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. However, it is known that NS4b interacts with NS4a and NS3 to form a large replicase complex to direct the viral RNA replication. : Pssm-ID: 110032 Cd Length: 192 Bit Score: 249.99 E-value: 1.18e-75
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| HCV_capsid | pfam01543 | Hepatitis C virus capsid protein; |
2-115 | 2.33e-72 | ||||||||
Hepatitis C virus capsid protein; : Pssm-ID: 144947 Cd Length: 121 Bit Score: 237.67 E-value: 2.33e-72
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| SF2_C_viral | cd18806 | C-terminal helicase domain of viral helicase; Viral helicases in this family here are ... |
1362-1503 | 5.62e-55 | ||||||||
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: 189.01 E-value: 5.62e-55
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| DEXHc_viral_Ns3 | cd17931 | DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ... |
1223-1366 | 1.59e-53 | ||||||||
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: 185.06 E-value: 1.59e-53
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| HCV_NS5a_1b | pfam08301 | Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ... |
2068-2168 | 1.65e-49 | ||||||||
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain. : Pssm-ID: 149382 Cd Length: 102 Bit Score: 171.39 E-value: 1.65e-49
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| HCV_core super family | cl46603 | Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ... |
116-190 | 2.45e-31 | ||||||||
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression. The actual alignment was detected with superfamily member pfam01542: Pssm-ID: 480943 Cd Length: 75 Bit Score: 118.63 E-value: 2.45e-31
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| HCV_p7 | cd20903 | Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ... |
747-794 | 8.40e-24 | ||||||||
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for virus production. The p7 monomer is comprised of 2 trans-membrane helices connected by a cytosolic loop, and oligomerizes to form cation-specific ion channels. These ion channels dissipate pH gradients in secretory vesicles potentially protecting acid-labile intracellular virions during egress (the rupturing of the infected cell and release of viral contents). p7 protein has at least two different functions in culture, one via the formation of these ion channels, the other through its specific interaction with the non-structural viral protein NS2. Several compounds targeting p7 have been investigated as anti-HCV drugs. : Pssm-ID: 411017 Cd Length: 58 Bit Score: 96.53 E-value: 8.40e-24
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| HCV_NS4a | pfam01006 | Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ... |
1658-1711 | 1.30e-21 | ||||||||
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine protease, as it is required in a number of cases as a cofactor of cleavage. It has also been reported that NS4a interacts with NS4b and NS3 to form a multi-subunit replicase complex. : Pssm-ID: 366414 Cd Length: 55 Bit Score: 90.21 E-value: 1.30e-21
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| Name | Accession | Description | Interval | E-value | ||||||||
| Hepacivirus_RdRp | cd23202 | RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ... |
2433-2950 | 0e+00 | ||||||||
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: 1159.61 E-value: 0e+00
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| HCV_NS1 | pfam01560 | Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ... |
386-729 | 0e+00 | ||||||||
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region of hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein. Pssm-ID: 110557 Cd Length: 344 Bit Score: 741.28 E-value: 0e+00
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| RdRP_3 | pfam00998 | Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ... |
2422-2933 | 0e+00 | ||||||||
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: 624.26 E-value: 0e+00
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| HCV_env | pfam01539 | Hepatitis C virus envelope glycoprotein E1; |
193-382 | 1.88e-111 | ||||||||
Hepatitis C virus envelope glycoprotein E1; Pssm-ID: 110536 Cd Length: 190 Bit Score: 352.64 E-value: 1.88e-111
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| HCV_NS5a_C | pfam12941 | HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ... |
2179-2419 | 1.71e-105 | ||||||||
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. Pssm-ID: 289693 Cd Length: 242 Bit Score: 337.68 E-value: 1.71e-105
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| HCV_NS2 | pfam01538 | Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ... |
811-1005 | 1.81e-102 | ||||||||
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases. Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3. Pssm-ID: 366698 Cd Length: 195 Bit Score: 326.94 E-value: 1.81e-102
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| Peptidase_S29 | pfam02907 | Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ... |
1056-1204 | 2.33e-84 | ||||||||
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A. Pssm-ID: 427049 Cd Length: 149 Bit Score: 273.15 E-value: 2.33e-84
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| HCV_NS4b | pfam01001 | Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ... |
1728-1921 | 1.18e-75 | ||||||||
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. However, it is known that NS4b interacts with NS4a and NS3 to form a large replicase complex to direct the viral RNA replication. Pssm-ID: 110032 Cd Length: 192 Bit Score: 249.99 E-value: 1.18e-75
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| HCV_capsid | pfam01543 | Hepatitis C virus capsid protein; |
2-115 | 2.33e-72 | ||||||||
Hepatitis C virus capsid protein; Pssm-ID: 144947 Cd Length: 121 Bit Score: 237.67 E-value: 2.33e-72
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| SF2_C_viral | cd18806 | C-terminal helicase domain of viral helicase; Viral helicases in this family here are ... |
1362-1503 | 5.62e-55 | ||||||||
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: 189.01 E-value: 5.62e-55
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| DEXHc_viral_Ns3 | cd17931 | DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ... |
1223-1366 | 1.59e-53 | ||||||||
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: 185.06 E-value: 1.59e-53
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| HCV_NS5a_1b | pfam08301 | Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ... |
2068-2168 | 1.65e-49 | ||||||||
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain. Pssm-ID: 149382 Cd Length: 102 Bit Score: 171.39 E-value: 1.65e-49
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| HCV_core | pfam01542 | Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ... |
116-190 | 2.45e-31 | ||||||||
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression. Pssm-ID: 460245 Cd Length: 75 Bit Score: 118.63 E-value: 2.45e-31
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| HCV_p7 | cd20903 | Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ... |
747-794 | 8.40e-24 | ||||||||
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for virus production. The p7 monomer is comprised of 2 trans-membrane helices connected by a cytosolic loop, and oligomerizes to form cation-specific ion channels. These ion channels dissipate pH gradients in secretory vesicles potentially protecting acid-labile intracellular virions during egress (the rupturing of the infected cell and release of viral contents). p7 protein has at least two different functions in culture, one via the formation of these ion channels, the other through its specific interaction with the non-structural viral protein NS2. Several compounds targeting p7 have been investigated as anti-HCV drugs. Pssm-ID: 411017 Cd Length: 58 Bit Score: 96.53 E-value: 8.40e-24
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| HCV_NS4a | pfam01006 | Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ... |
1658-1711 | 1.30e-21 | ||||||||
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine protease, as it is required in a number of cases as a cofactor of cleavage. It has also been reported that NS4a interacts with NS4b and NS3 to form a multi-subunit replicase complex. Pssm-ID: 366414 Cd Length: 55 Bit Score: 90.21 E-value: 1.30e-21
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
1228-1355 | 9.87e-14 | ||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 72.52 E-value: 9.87e-14
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
1228-1351 | 1.11e-04 | ||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 47.71 E-value: 1.11e-04
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| Flavi_DEAD | pfam07652 | Flavivirus DEAD domain; |
1233-1361 | 4.66e-04 | ||||||||
Flavivirus DEAD domain; Pssm-ID: 400138 [Multi-domain] Cd Length: 146 Bit Score: 43.09 E-value: 4.66e-04
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| RecQ | COG0514 | Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
1382-1440 | 1.91e-03 | ||||||||
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 43.59 E-value: 1.91e-03
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| PRK11057 | PRK11057 | ATP-dependent DNA helicase RecQ; Provisional |
1382-1443 | 2.31e-03 | ||||||||
ATP-dependent DNA helicase RecQ; Provisional Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 43.55 E-value: 2.31e-03
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| Name | Accession | Description | Interval | E-value | ||||||||
| Hepacivirus_RdRp | cd23202 | RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ... |
2433-2950 | 0e+00 | ||||||||
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: 1159.61 E-value: 0e+00
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| HCV_NS1 | pfam01560 | Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ... |
386-729 | 0e+00 | ||||||||
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region of hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein. Pssm-ID: 110557 Cd Length: 344 Bit Score: 741.28 E-value: 0e+00
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| RdRP_3 | pfam00998 | Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ... |
2422-2933 | 0e+00 | ||||||||
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: 624.26 E-value: 0e+00
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| ps-ssRNAv_Flaviviridae_RdRp | cd23178 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ... |
2553-2837 | 2.54e-150 | ||||||||
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: 468.15 E-value: 2.54e-150
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| HCV_env | pfam01539 | Hepatitis C virus envelope glycoprotein E1; |
193-382 | 1.88e-111 | ||||||||
Hepatitis C virus envelope glycoprotein E1; Pssm-ID: 110536 Cd Length: 190 Bit Score: 352.64 E-value: 1.88e-111
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| HCV_NS5a_C | pfam12941 | HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ... |
2179-2419 | 1.71e-105 | ||||||||
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. Pssm-ID: 289693 Cd Length: 242 Bit Score: 337.68 E-value: 1.71e-105
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| HCV_NS2 | pfam01538 | Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ... |
811-1005 | 1.81e-102 | ||||||||
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases. Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3. Pssm-ID: 366698 Cd Length: 195 Bit Score: 326.94 E-value: 1.81e-102
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| Pegivirus_RdRp | cd23203 | RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ... |
2425-2916 | 5.29e-98 | ||||||||
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: 325.76 E-value: 5.29e-98
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| Peptidase_S29 | pfam02907 | Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ... |
1056-1204 | 2.33e-84 | ||||||||
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A. Pssm-ID: 427049 Cd Length: 149 Bit Score: 273.15 E-value: 2.33e-84
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| HCV_NS4b | pfam01001 | Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ... |
1728-1921 | 1.18e-75 | ||||||||
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. However, it is known that NS4b interacts with NS4a and NS3 to form a large replicase complex to direct the viral RNA replication. Pssm-ID: 110032 Cd Length: 192 Bit Score: 249.99 E-value: 1.18e-75
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| HCV_capsid | pfam01543 | Hepatitis C virus capsid protein; |
2-115 | 2.33e-72 | ||||||||
Hepatitis C virus capsid protein; Pssm-ID: 144947 Cd Length: 121 Bit Score: 237.67 E-value: 2.33e-72
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| SF2_C_viral | cd18806 | C-terminal helicase domain of viral helicase; Viral helicases in this family here are ... |
1362-1503 | 5.62e-55 | ||||||||
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: 189.01 E-value: 5.62e-55
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| DEXHc_viral_Ns3 | cd17931 | DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ... |
1223-1366 | 1.59e-53 | ||||||||
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: 185.06 E-value: 1.59e-53
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| HCV_NS5a_1b | pfam08301 | Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ... |
2068-2168 | 1.65e-49 | ||||||||
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain. Pssm-ID: 149382 Cd Length: 102 Bit Score: 171.39 E-value: 1.65e-49
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| RNA_dep_RNAP | cd01699 | RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ... |
2535-2817 | 9.65e-47 | ||||||||
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: 170.54 E-value: 9.65e-47
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| HCV_core | pfam01542 | Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ... |
1-75 | 5.98e-34 | ||||||||
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression. Pssm-ID: 460245 Cd Length: 75 Bit Score: 125.95 E-value: 5.98e-34
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| HCV_core | pfam01542 | Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ... |
116-190 | 2.45e-31 | ||||||||
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression. Pssm-ID: 460245 Cd Length: 75 Bit Score: 118.63 E-value: 2.45e-31
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| HCV_p7 | cd20903 | Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ... |
747-794 | 8.40e-24 | ||||||||
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for virus production. The p7 monomer is comprised of 2 trans-membrane helices connected by a cytosolic loop, and oligomerizes to form cation-specific ion channels. These ion channels dissipate pH gradients in secretory vesicles potentially protecting acid-labile intracellular virions during egress (the rupturing of the infected cell and release of viral contents). p7 protein has at least two different functions in culture, one via the formation of these ion channels, the other through its specific interaction with the non-structural viral protein NS2. Several compounds targeting p7 have been investigated as anti-HCV drugs. Pssm-ID: 411017 Cd Length: 58 Bit Score: 96.53 E-value: 8.40e-24
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| HCV_NS4a | pfam01006 | Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ... |
1658-1711 | 1.30e-21 | ||||||||
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine protease, as it is required in a number of cases as a cofactor of cleavage. It has also been reported that NS4a interacts with NS4b and NS3 to form a multi-subunit replicase complex. Pssm-ID: 366414 Cd Length: 55 Bit Score: 90.21 E-value: 1.30e-21
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
1228-1355 | 9.87e-14 | ||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 72.52 E-value: 9.87e-14
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| ps_ssRNAv_Tolivirales_RdRp | cd23179 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ... |
2614-2756 | 2.67e-12 | ||||||||
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: 69.09 E-value: 2.67e-12
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| RT_like | cd00304 | RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ... |
2699-2789 | 6.56e-09 | ||||||||
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Pssm-ID: 238185 [Multi-domain] Cd Length: 98 Bit Score: 55.43 E-value: 6.56e-09
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| ps-ssRNAv_RdRp-like | cd23167 | conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ... |
2698-2744 | 4.16e-07 | ||||||||
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: 49.64 E-value: 4.16e-07
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| Betacarmovirus_RdRp | cd23240 | RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense ... |
2596-2831 | 8.78e-07 | ||||||||
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: 54.47 E-value: 8.78e-07
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| SF2_C_RecQ | cd18794 | C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
1386-1439 | 3.90e-05 | ||||||||
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They 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: 350181 [Multi-domain] Cd Length: 134 Bit Score: 45.66 E-value: 3.90e-05
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| Regressovirinae_RdRp | cd23235 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae ... |
2622-2756 | 4.96e-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: 48.77 E-value: 4.96e-05
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
1228-1351 | 1.11e-04 | ||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 47.71 E-value: 1.11e-04
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| Alphanecrovirus_RdRp | cd23237 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of ... |
2614-2758 | 4.45e-04 | ||||||||
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: 45.79 E-value: 4.45e-04
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| Flavi_DEAD | pfam07652 | Flavivirus DEAD domain; |
1233-1361 | 4.66e-04 | ||||||||
Flavivirus DEAD domain; Pssm-ID: 400138 [Multi-domain] Cd Length: 146 Bit Score: 43.09 E-value: 4.66e-04
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| Gammacarmovirus_RdRp | cd23242 | RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ... |
2627-2831 | 6.11e-04 | ||||||||
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: 45.12 E-value: 6.11e-04
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
1230-1351 | 7.89e-04 | ||||||||
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 42.29 E-value: 7.89e-04
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| AAA_30 | pfam13604 | AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
1224-1344 | 1.22e-03 | ||||||||
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B. Pssm-ID: 433343 [Multi-domain] Cd Length: 191 Bit Score: 42.55 E-value: 1.22e-03
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| Tombusviridae_RdRp | cd23206 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of ... |
2614-2745 | 1.40e-03 | ||||||||
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: 42.87 E-value: 1.40e-03
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| Carmotetraviridae_RdRp | cd23205 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae ... |
2618-2762 | 1.53e-03 | ||||||||
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: 43.08 E-value: 1.53e-03
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| RecQ | COG0514 | Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
1382-1440 | 1.91e-03 | ||||||||
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 43.59 E-value: 1.91e-03
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
1382-1422 | 1.98e-03 | ||||||||
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain] Cd Length: 131 Bit Score: 40.95 E-value: 1.98e-03
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| PRK11057 | PRK11057 | ATP-dependent DNA helicase RecQ; Provisional |
1382-1443 | 2.31e-03 | ||||||||
ATP-dependent DNA helicase RecQ; Provisional Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 43.55 E-value: 2.31e-03
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| Betanecrovirus_RdRp | cd23244 | RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense ... |
2627-2819 | 2.35e-03 | ||||||||
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: 43.35 E-value: 2.35e-03
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
1230-1350 | 3.19e-03 | ||||||||
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region. Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 40.46 E-value: 3.19e-03
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| Alphacarmovirus_RdRp | cd23239 | RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense ... |
2627-2745 | 4.33e-03 | ||||||||
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: 42.43 E-value: 4.33e-03
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| DEXHc_HrpB | cd17990 | DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ... |
1228-1350 | 4.82e-03 | ||||||||
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: 40.39 E-value: 4.82e-03
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| Luteovirus_RdRp | cd23233 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of ... |
2625-2744 | 5.70e-03 | ||||||||
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: 42.03 E-value: 5.70e-03
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