polyprotein, partial [Hepacivirus hominis]
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 ... |
825-1342 | 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: 1156.91 E-value: 0e+00
|
||||||||||||
| HCV_NS5a_C super family | cl15181 | HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ... |
570-811 | 6.56e-144 | ||||||||
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: 437.06 E-value: 6.56e-144
|
||||||||||||
| HCV_NS4b | pfam01001 | Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ... |
119-312 | 1.01e-76 | ||||||||
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: 251.91 E-value: 1.01e-76
|
||||||||||||
| HCV_NS5a_1b | pfam08301 | Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ... |
459-559 | 8.15e-51 | ||||||||
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: 174.09 E-value: 8.15e-51
|
||||||||||||
| HCV_NS4a | pfam01006 | Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ... |
49-102 | 1.52e-22 | ||||||||
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: 91.76 E-value: 1.52e-22
|
||||||||||||
| HCV_NS5a | pfam01506 | Hepatitis C virus non-structural 5a protein membrane anchor; The molecular function of the ... |
365-387 | 1.73e-08 | ||||||||
Hepatitis C virus non-structural 5a protein membrane anchor; 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 N-terminal region of the NS5a protein has been used in the construction of the alignment for this family. The C-terminal region has not been included because it is too heterogeneous. : Pssm-ID: 366682 Cd Length: 23 Bit Score: 51.05 E-value: 1.73e-08
|
||||||||||||
| Name | Accession | Description | Interval | E-value | ||||||||
| Hepacivirus_RdRp | cd23202 | RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ... |
825-1342 | 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: 1156.91 E-value: 0e+00
|
||||||||||||
| RdRP_3 | pfam00998 | Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ... |
814-1325 | 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: 593.44 E-value: 0e+00
|
||||||||||||
| HCV_NS5a_C | pfam12941 | HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ... |
570-811 | 6.56e-144 | ||||||||
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: 437.06 E-value: 6.56e-144
|
||||||||||||
| HCV_NS4b | pfam01001 | Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ... |
119-312 | 1.01e-76 | ||||||||
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: 251.91 E-value: 1.01e-76
|
||||||||||||
| HCV_NS5a_1b | pfam08301 | Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ... |
459-559 | 8.15e-51 | ||||||||
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: 174.09 E-value: 8.15e-51
|
||||||||||||
| HCV_NS4a | pfam01006 | Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ... |
49-102 | 1.52e-22 | ||||||||
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: 91.76 E-value: 1.52e-22
|
||||||||||||
| HCV_NS5a | pfam01506 | Hepatitis C virus non-structural 5a protein membrane anchor; The molecular function of the ... |
365-387 | 1.73e-08 | ||||||||
Hepatitis C virus non-structural 5a protein membrane anchor; 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 N-terminal region of the NS5a protein has been used in the construction of the alignment for this family. The C-terminal region has not been included because it is too heterogeneous. Pssm-ID: 366682 Cd Length: 23 Bit Score: 51.05 E-value: 1.73e-08
|
||||||||||||
| Name | Accession | Description | Interval | E-value | ||||||||
| Hepacivirus_RdRp | cd23202 | RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ... |
825-1342 | 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: 1156.91 E-value: 0e+00
|
||||||||||||
| RdRP_3 | pfam00998 | Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ... |
814-1325 | 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: 593.44 E-value: 0e+00
|
||||||||||||
| ps-ssRNAv_Flaviviridae_RdRp | cd23178 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ... |
945-1229 | 5.13e-152 | ||||||||
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: 460.06 E-value: 5.13e-152
|
||||||||||||
| HCV_NS5a_C | pfam12941 | HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ... |
570-811 | 6.56e-144 | ||||||||
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: 437.06 E-value: 6.56e-144
|
||||||||||||
| Pegivirus_RdRp | cd23203 | RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ... |
817-1308 | 3.93e-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: 322.68 E-value: 3.93e-98
|
||||||||||||
| HCV_NS4b | pfam01001 | Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ... |
119-312 | 1.01e-76 | ||||||||
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: 251.91 E-value: 1.01e-76
|
||||||||||||
| HCV_NS5a_1b | pfam08301 | Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ... |
459-559 | 8.15e-51 | ||||||||
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: 174.09 E-value: 8.15e-51
|
||||||||||||
| RNA_dep_RNAP | cd01699 | RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ... |
928-1209 | 1.43e-44 | ||||||||
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage. Pssm-ID: 238843 [Multi-domain] Cd Length: 278 Bit Score: 163.22 E-value: 1.43e-44
|
||||||||||||
| HCV_NS4a | pfam01006 | Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ... |
49-102 | 1.52e-22 | ||||||||
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: 91.76 E-value: 1.52e-22
|
||||||||||||
| ps_ssRNAv_Tolivirales_RdRp | cd23179 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ... |
1006-1149 | 7.90e-13 | ||||||||
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: 69.47 E-value: 7.90e-13
|
||||||||||||
| HCV_NS5a | pfam01506 | Hepatitis C virus non-structural 5a protein membrane anchor; The molecular function of the ... |
365-387 | 1.73e-08 | ||||||||
Hepatitis C virus non-structural 5a protein membrane anchor; 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 N-terminal region of the NS5a protein has been used in the construction of the alignment for this family. The C-terminal region has not been included because it is too heterogeneous. Pssm-ID: 366682 Cd Length: 23 Bit Score: 51.05 E-value: 1.73e-08
|
||||||||||||
| ps-ssRNAv_RdRp-like | cd23167 | conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ... |
1090-1136 | 2.58e-08 | ||||||||
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: 51.96 E-value: 2.58e-08
|
||||||||||||
| RT_like | cd00304 | RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ... |
1091-1181 | 2.68e-08 | ||||||||
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: 52.74 E-value: 2.68e-08
|
||||||||||||
| Tombusvirus-like_RdRp | cd23236 | RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded ... |
1019-1213 | 5.18e-05 | ||||||||
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within Procedovirinae subfamily; and related RdRps; This group contains the RdRp of RNA viruses belonging to the Tombusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Tombusvirus is a genus of plant viruses. There are 17 species in the Tombusvirus genus: Artichoke mottled crinkle virus, Carnation Italian ringspot virus, Cucumber Bulgarian virus, Cucumber necrosis virus, Cymbidium ringspot virus, Eggplant mottled crinkle virus, Grapevine Algerian latent virus, Havel River virus, Lato River virus, Limonium flower distortion virus, Moroccan pepper virus, Neckar River virus, Pelargonium leaf curl virus, Pelargonium necrotic spot virus, Petunia asteroid mosaic virus, Sikte waterborne virus, and Tomato bushy stunt virus. Symptoms associated with this genus include mosaic. The name of the genus comes from Tomato bushy stunt virus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438086 [Multi-domain] Cd Length: 474 Bit Score: 47.32 E-value: 5.18e-05
|
||||||||||||
| Gammacarmovirus_RdRp | cd23242 | RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ... |
1018-1223 | 5.42e-05 | ||||||||
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: 47.43 E-value: 5.42e-05
|
||||||||||||
| Carmotetraviridae_RdRp | cd23205 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae ... |
1010-1138 | 6.30e-04 | ||||||||
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: 6.30e-04
|
||||||||||||
| Betacarmovirus_RdRp | cd23240 | RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense ... |
1006-1223 | 1.37e-03 | ||||||||
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: 42.91 E-value: 1.37e-03
|
||||||||||||
| Tombusviridae_RdRp | cd23206 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of ... |
1006-1157 | 1.72e-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: 41.71 E-value: 1.72e-03
|
||||||||||||
| Regressovirinae_RdRp | cd23235 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae ... |
1014-1148 | 4.43e-03 | ||||||||
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: 41.06 E-value: 4.43e-03
|
||||||||||||
| Blast search parameters | ||||
|
