RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
2456-2973
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: 1124.94 E-value: 0e+00
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ...
387-733
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: 719.71 E-value: 0e+00
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
815-1009
7.89e-98
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: 313.84 E-value: 7.89e-98
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
1733-1925
1.11e-88
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: 287.35 E-value: 1.11e-88
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ...
2183-2442
1.19e-65
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: 223.66 E-value: 1.19e-65
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
1228-1369
3.38e-43
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.
The actual alignment was detected with superfamily member cd17931:
Pssm-ID: 475120 [Multi-domain] Cd Length: 151 Bit Score: 155.40 E-value: 3.38e-43
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
2072-2172
5.88e-43
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: 152.90 E-value: 5.88e-43
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
1366-1487
7.87e-43
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.
The actual alignment was detected with superfamily member cd18806:
Pssm-ID: 476819 [Multi-domain] Cd Length: 145 Bit Score: 154.34 E-value: 7.87e-43
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
116-190
5.98e-29
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: 111.69 E-value: 5.98e-29
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ...
1662-1715
1.67e-08
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.
The actual alignment was detected with superfamily member pfam01006:
Pssm-ID: 366414 Cd Length: 55 Bit Score: 52.85 E-value: 1.67e-08
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
2456-2973
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: 1124.94 E-value: 0e+00
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ...
387-733
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: 719.71 E-value: 0e+00
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
815-1009
7.89e-98
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: 313.84 E-value: 7.89e-98
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
1733-1925
1.11e-88
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: 287.35 E-value: 1.11e-88
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ...
2183-2442
1.19e-65
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: 223.66 E-value: 1.19e-65
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
1228-1369
3.38e-43
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: 155.40 E-value: 3.38e-43
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
2072-2172
5.88e-43
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: 152.90 E-value: 5.88e-43
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
1366-1487
7.87e-43
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: 154.34 E-value: 7.87e-43
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
116-190
5.98e-29
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: 111.69 E-value: 5.98e-29
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ...
1662-1715
1.67e-08
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: 52.85 E-value: 1.67e-08
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
2456-2973
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: 1124.94 E-value: 0e+00
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ...
387-733
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: 719.71 E-value: 0e+00
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
2576-2860
1.46e-149
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: 465.84 E-value: 1.46e-149
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
815-1009
7.89e-98
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: 313.84 E-value: 7.89e-98
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
2448-2939
1.14e-94
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: 316.13 E-value: 1.14e-94
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
1733-1925
1.11e-88
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: 287.35 E-value: 1.11e-88
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ...
2183-2442
1.19e-65
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: 223.66 E-value: 1.19e-65
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
1228-1369
3.38e-43
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: 155.40 E-value: 3.38e-43
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
2072-2172
5.88e-43
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: 152.90 E-value: 5.88e-43
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
1366-1487
7.87e-43
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: 154.34 E-value: 7.87e-43
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
2559-2840
5.92e-42
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: 156.67 E-value: 5.92e-42
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
1-75
7.62e-30
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: 114.39 E-value: 7.62e-30
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
116-190
5.98e-29
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: 111.69 E-value: 5.98e-29
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
2637-2780
1.53e-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: 69.86 E-value: 1.53e-12
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ...
1662-1715
1.67e-08
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: 52.85 E-value: 1.67e-08
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ...
2637-2856
5.66e-06
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: 51.67 E-value: 5.66e-06
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
2721-2767
6.50e-06
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.
Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 46.18 E-value: 6.50e-06
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, within ...
2648-2767
5.75e-05
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Pestivirus genus within the family Flaviviridae, order Amarillovirales. Members of the genus Pestivirus infect pigs and ruminants, including cattle, sheep, goats and wild ruminants, and are transmitted through contact with infected secretions (respiratory droplets, urine or feces). Infections may be subclinical or cause enteric, hemorrhagic or wasting diseases, including those by the economically important bovine viral diarrhea virus and classical swine fever virus. Virions of Pestivirus have a single, small, basic capsid (C) protein and three envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.
Pssm-ID: 438051 Cd Length: 579 Bit Score: 48.86 E-value: 5.75e-05
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae ...
2645-2779
1.02e-04
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: 47.61 E-value: 1.02e-04
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of ...
2637-2788
1.08e-04
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: 46.33 E-value: 1.08e-04
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
1390-1443
1.33e-04
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: 44.12 E-value: 1.33e-04
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of ...
2648-2776
5.25e-04
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: 45.50 E-value: 5.25e-04
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded ...
2623-2811
8.44e-04
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: 44.62 E-value: 8.44e-04
RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense ...
2650-2842
8.75e-04
RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Pelarspovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The genus name "Pelarspovirus" is derived from the pelargonium ringspot virus, which was the first virus to be named. There are 8 species in the Pelarspovirus genus: Clematis chlorotic mottle virus, Elderberry latent virus, Jasmine mosaic-associated virus, Jasmine virus H, Pelargonium chlorotic ring pattern virus, Pelargonium line pattern virus, Pelargonium ringspot virus, and Rosa rugosa leaf distortion virus. Members of the Pelarspovirus have monopartite genomes encoding five open reading frames (ORFs) that include two 5'-proximal replication proteins, two centrally located movement proteins (MP1 and MP2) and a 3'-proximal coat protein that, at least for pelargonium line pattern virus (PLPV), has been shown to act also as suppressor of RNA silencing. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.
Pssm-ID: 438091 [Multi-domain] Cd Length: 497 Bit Score: 44.73 E-value: 8.75e-04
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
1230-1355
1.91e-03
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: 41.14 E-value: 1.91e-03
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
1230-1354
5.13e-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: 40.08 E-value: 5.13e-03
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
1386-1426
5.97e-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: 39.41 E-value: 5.97e-03
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
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Domains are color coded according to superfamilies
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if a domain or superfamily has been annotated with functional sites (conserved features),
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click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
or click on the triangles, if present, that represent functional sites (conserved features)
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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
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and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits
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the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
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