polyprotein [Grapevine Syrah virus 1]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| Tymoviridae_RdRp | cd23247 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tymoviridae of ... |
1413-1793 | 0e+00 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tymoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tymoviridae, order Tymovirales. Virions of the family Tymoviridae are isometric, non-enveloped, about 30 nm in diameter, and contain a single molecule of (+)ssRNA constituting 25#35% of the particle weight. There are 42 species in this family, assigned to three genera (Maculavirus, Marafivirus, and Tymovirus), with two species unassigned to a genus. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. 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: 438097 Cd Length: 373 Bit Score: 703.95 E-value: 0e+00
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| Vmethyltransf | pfam01660 | Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ... |
116-397 | 1.22e-74 | ||||||
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily. : Pssm-ID: 396298 Cd Length: 308 Bit Score: 251.45 E-value: 1.22e-74
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| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
985-1216 | 1.13e-48 | ||||||
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. : Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 173.72 E-value: 1.13e-48
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| Tymo_coat super family | cl03052 | Tymovirus coat protein; |
1905-2079 | 9.80e-36 | ||||||
Tymovirus coat protein; The actual alignment was detected with superfamily member pfam00983: Pssm-ID: 395782 Cd Length: 179 Bit Score: 134.77 E-value: 9.80e-36
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| Peptidase_C21 super family | cl05113 | Tymovirus endopeptidase; Corresponds to Merops family C21. The best-studied plant alpha-like ... |
793-891 | 3.21e-18 | ||||||
Tymovirus endopeptidase; Corresponds to Merops family C21. The best-studied plant alpha-like virus proteolytic enzyme is the proteinase of turnip yellow mosaic virus (TYMV). The TYMV replicase protein undergoes auto-cleavage to yield two products. The auto-peptidase activity has been mapped to the central part of this polyprotein. The actual alignment was detected with superfamily member pfam05381: Pssm-ID: 398836 Cd Length: 100 Bit Score: 81.70 E-value: 3.21e-18
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| Salyut super family | cl41199 | Salyut domain; This entry represents the Salyut domain found in the replicase of all viruses ... |
554-600 | 6.96e-07 | ||||||
Salyut domain; This entry represents the Salyut domain found in the replicase of all viruses of the viral family Tymoviridae, composed of viruses that infect plants and insects. it is located within a long, hypervariable, Proline-rich hinge region located between the Alphavirus-like methyltransferase (pfam01660) and the pfam01443. It is located 150-20aa downstream the Iceberg region that forms the C-terminus of Vmethyltransf. The function of this family is unknown. The actual alignment was detected with superfamily member pfam19227: Pssm-ID: 408996 [Multi-domain] Cd Length: 51 Bit Score: 47.83 E-value: 6.96e-07
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| PHA03247 super family | cl33720 | large tegument protein UL36; Provisional |
588-794 | 1.69e-04 | ||||||
large tegument protein UL36; Provisional The actual alignment was detected with superfamily member PHA03247: Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 47.24 E-value: 1.69e-04
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| Name | Accession | Description | Interval | E-value | ||||||
| Tymoviridae_RdRp | cd23247 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tymoviridae of ... |
1413-1793 | 0e+00 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tymoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tymoviridae, order Tymovirales. Virions of the family Tymoviridae are isometric, non-enveloped, about 30 nm in diameter, and contain a single molecule of (+)ssRNA constituting 25#35% of the particle weight. There are 42 species in this family, assigned to three genera (Maculavirus, Marafivirus, and Tymovirus), with two species unassigned to a genus. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. 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: 438097 Cd Length: 373 Bit Score: 703.95 E-value: 0e+00
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| Vmethyltransf | pfam01660 | Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ... |
116-397 | 1.22e-74 | ||||||
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily. Pssm-ID: 396298 Cd Length: 308 Bit Score: 251.45 E-value: 1.22e-74
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| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
985-1216 | 1.13e-48 | ||||||
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 173.72 E-value: 1.13e-48
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| Tymo_coat | pfam00983 | Tymovirus coat protein; |
1905-2079 | 9.80e-36 | ||||||
Tymovirus coat protein; Pssm-ID: 395782 Cd Length: 179 Bit Score: 134.77 E-value: 9.80e-36
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| Peptidase_C21 | pfam05381 | Tymovirus endopeptidase; Corresponds to Merops family C21. The best-studied plant alpha-like ... |
793-891 | 3.21e-18 | ||||||
Tymovirus endopeptidase; Corresponds to Merops family C21. The best-studied plant alpha-like virus proteolytic enzyme is the proteinase of turnip yellow mosaic virus (TYMV). The TYMV replicase protein undergoes auto-cleavage to yield two products. The auto-peptidase activity has been mapped to the central part of this polyprotein. Pssm-ID: 398836 Cd Length: 100 Bit Score: 81.70 E-value: 3.21e-18
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| Salyut | pfam19227 | Salyut domain; This entry represents the Salyut domain found in the replicase of all viruses ... |
554-600 | 6.96e-07 | ||||||
Salyut domain; This entry represents the Salyut domain found in the replicase of all viruses of the viral family Tymoviridae, composed of viruses that infect plants and insects. it is located within a long, hypervariable, Proline-rich hinge region located between the Alphavirus-like methyltransferase (pfam01660) and the pfam01443. It is located 150-20aa downstream the Iceberg region that forms the C-terminus of Vmethyltransf. The function of this family is unknown. Pssm-ID: 408996 [Multi-domain] Cd Length: 51 Bit Score: 47.83 E-value: 6.96e-07
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| RdRP_2 | pfam00978 | RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ... |
1522-1683 | 4.47e-05 | ||||||
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses Pssm-ID: 395779 Cd Length: 440 Bit Score: 48.41 E-value: 4.47e-05
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
588-794 | 1.69e-04 | ||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 47.24 E-value: 1.69e-04
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
1173-1225 | 8.45e-04 | ||||||
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]; Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 44.20 E-value: 8.45e-04
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| SF1_C_RecD | cd18809 | C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ... |
1173-1218 | 3.55e-03 | ||||||
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350196 [Multi-domain] Cd Length: 80 Bit Score: 38.31 E-value: 3.55e-03
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| Name | Accession | Description | Interval | E-value | ||||||
| Tymoviridae_RdRp | cd23247 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tymoviridae of ... |
1413-1793 | 0e+00 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tymoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tymoviridae, order Tymovirales. Virions of the family Tymoviridae are isometric, non-enveloped, about 30 nm in diameter, and contain a single molecule of (+)ssRNA constituting 25#35% of the particle weight. There are 42 species in this family, assigned to three genera (Maculavirus, Marafivirus, and Tymovirus), with two species unassigned to a genus. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. 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: 438097 Cd Length: 373 Bit Score: 703.95 E-value: 0e+00
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| Vmethyltransf | pfam01660 | Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ... |
116-397 | 1.22e-74 | ||||||
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily. Pssm-ID: 396298 Cd Length: 308 Bit Score: 251.45 E-value: 1.22e-74
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| ps-ssRNA_RdRp_Tymovirales | cd23207 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Tymovirales of ... |
1492-1684 | 2.11e-72 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Tymovirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Tymovirales. The Tymovirales order contains viruses that mostly infect plants, have a single molecule of (+)ssRNA, and which are united by the similarities in their replication-associated polyproteins. Tymovirales contains five families (Alpha-, Beta-, Delta- and Gammaflexiviridae and Tymoviridae) and groups mostly plant-infecting agents, although a few Tymovirales members have either fungal or insect hosts. Botrytis virus F (BVF), isolated from the fungus Botrytis cinerea, is a flexuous mycovirus that is typical of members of the genus Mycoflexivirus (family Gammaflexiviridae). 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: 438057 [Multi-domain] Cd Length: 188 Bit Score: 240.00 E-value: 2.11e-72
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| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
985-1216 | 1.13e-48 | ||||||
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 173.72 E-value: 1.13e-48
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| ps-ssRNAv_Alsuviricetes_RdRp | cd23182 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of ... |
1500-1684 | 1.86e-46 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the class Alsuviricetes, phylum: Kitrinoviricota. Alsuviricetes is a class of [(+)ssRNA] viruses which infect eukaryotes. The name of the group is a syllabic abbreviation of "alpha supergroup" with the suffix -viricetes indicating a virus class. The class Alsuviricetes includes three orders: Hepelivirales, Martellivirales, and Tymovirales. 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: 438032 [Multi-domain] Cd Length: 187 Bit Score: 165.85 E-value: 1.86e-46
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| Alphaflexiviridae_RdRp | cd23246 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Alphaflexiviridae ... |
1492-1780 | 1.03e-39 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Alphaflexiviridae of positive-sense single-stranded RNA (+ssRNA) viruses, in the order Tymovirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Alphaflexiviridae, order Tymovirales. Virions within the Alphaflexiviridae family are flexuous filaments, that are 470#800 nm long and 12#13 nm in diameter. They infect plants and plant-infecting fungi. 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: 438096 Cd Length: 294 Bit Score: 150.03 E-value: 1.03e-39
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| Gammaflexiviridae_RdRp | cd23249 | RNA-dependent RNA polymerase (RdRp) in the family Gammaflexiviridae of positive-sense ... |
1440-1784 | 7.71e-36 | ||||||
RNA-dependent RNA polymerase (RdRp) in the family Gammaflexiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the RdRp of RNA viruses belonging to the family Gammaflexiviridae, order Tymovirales. Virions within the Gammaflexiviridae family are flexuous filaments of 720 nm modal length and about 13 nm in diameter. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. 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: 438099 Cd Length: 354 Bit Score: 140.81 E-value: 7.71e-36
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| Tymo_coat | pfam00983 | Tymovirus coat protein; |
1905-2079 | 9.80e-36 | ||||||
Tymovirus coat protein; Pssm-ID: 395782 Cd Length: 179 Bit Score: 134.77 E-value: 9.80e-36
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| Betaflexiviridae_RdRp | cd23245 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Betaflexiviridae of ... |
1458-1769 | 6.17e-33 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Betaflexiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Betaflexiviridae, order Tymovirales. Virions within the Betaflexiviridae family are flexuous filaments, usually 12#13 nm in diameter (range 10#15 nm) and from 600 to over 1000 nm in length, depending on the genus. They infect plants which share a distinct lineage of alphavirus-like replication proteins. There are 108 species in the family Betaflexiviridae, assigned to 13 genera in two subfamilies (Quinvirinae and Trivirinae). Diseases associated with this family include: mosaic and ringspot symptoms. 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: 438095 Cd Length: 318 Bit Score: 131.43 E-value: 6.17e-33
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| Peptidase_C21 | pfam05381 | Tymovirus endopeptidase; Corresponds to Merops family C21. The best-studied plant alpha-like ... |
793-891 | 3.21e-18 | ||||||
Tymovirus endopeptidase; Corresponds to Merops family C21. The best-studied plant alpha-like virus proteolytic enzyme is the proteinase of turnip yellow mosaic virus (TYMV). The TYMV replicase protein undergoes auto-cleavage to yield two products. The auto-peptidase activity has been mapped to the central part of this polyprotein. Pssm-ID: 398836 Cd Length: 100 Bit Score: 81.70 E-value: 3.21e-18
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| Deltaflexiviridae_RdRp | cd23248 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Deltaflexiviridae ... |
1458-1675 | 2.18e-15 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Deltaflexiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Deltaflexiviridae, order Tymovirales. Deltaflexiviridae consists of one genus (Deltaflexivirus) and three species: Fusarium deltaflexivirus 1, Sclerotinia deltaflexivirus 1, and Soybean-associated deltaflexivirus 1. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. 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: 438098 Cd Length: 279 Bit Score: 78.68 E-value: 2.18e-15
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| ps-ssRNAv_Hepelivirales_RdRp | cd23209 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of ... |
1599-1688 | 2.57e-07 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Hepelivirales, class Alsuviricetes. This Hepelivirales order consists of four families: Alphatetraviridae, Benyviridae, Hepeviridae, and Matonaviridae. 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: 438059 [Multi-domain] Cd Length: 183 Bit Score: 52.88 E-value: 2.57e-07
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| Salyut | pfam19227 | Salyut domain; This entry represents the Salyut domain found in the replicase of all viruses ... |
554-600 | 6.96e-07 | ||||||
Salyut domain; This entry represents the Salyut domain found in the replicase of all viruses of the viral family Tymoviridae, composed of viruses that infect plants and insects. it is located within a long, hypervariable, Proline-rich hinge region located between the Alphavirus-like methyltransferase (pfam01660) and the pfam01443. It is located 150-20aa downstream the Iceberg region that forms the C-terminus of Vmethyltransf. The function of this family is unknown. Pssm-ID: 408996 [Multi-domain] Cd Length: 51 Bit Score: 47.83 E-value: 6.96e-07
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| Hepeviridae_RdRp | cd23259 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of ... |
1605-1676 | 4.60e-06 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Hepeviridae, order Hepelivirales. The family Hepeviridae includes enterically transmitted small non-enveloped [(+)ssRNA viruses. It includes the genera Piscihepevirus, whose members infect fish, and Orthohepevirus, whose members infect mammals and birds. Members of the genus Orthohepevirus include hepatitis E virus, which is responsible for self-limiting acute hepatitis in humans and several mammalian species; the infection may become chronic in immunocompromised individuals. Avian hepatitis E virus causes hepatitis-splenomegaly syndrome in chickens. Hepeviridae genomes (approximately 7.2 kb) have 5' methyl G caps and 3' poly (A) tails, and contain three ORFS. They have two mRNAs, a genome length and a subgenomic mRNA: the genome-length mRNA is translated to produce proteins required for RNA replication while the subgenomic mRNA is used to produce the capsid protein. Some of the capsid protein is glycosylated, which is an unusual finding for an unenveloped 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: 438109 Cd Length: 274 Bit Score: 50.52 E-value: 4.60e-06
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| RdRP_2 | pfam00978 | RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ... |
1522-1683 | 4.47e-05 | ||||||
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses Pssm-ID: 395779 Cd Length: 440 Bit Score: 48.41 E-value: 4.47e-05
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
588-794 | 1.69e-04 | ||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 47.24 E-value: 1.69e-04
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
1173-1225 | 8.45e-04 | ||||||
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]; Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 44.20 E-value: 8.45e-04
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| SF1_C_RecD | cd18809 | C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ... |
1173-1218 | 3.55e-03 | ||||||
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350196 [Multi-domain] Cd Length: 80 Bit Score: 38.31 E-value: 3.55e-03
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