RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
2760-3272
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: 764.78 E-value: 0e+00
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
1127-1268
4.25e-28
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: 112.26 E-value: 4.25e-28
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
1264-1385
9.87e-26
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: 105.42 E-value: 9.87e-26
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ...
453-632
1.59e-06
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.
The actual alignment was detected with superfamily member pfam01560:
Pssm-ID: 110557 Cd Length: 344 Bit Score: 53.32 E-value: 1.59e-06
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
2760-3272
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: 764.78 E-value: 0e+00
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
1127-1268
4.25e-28
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: 112.26 E-value: 4.25e-28
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
1264-1385
9.87e-26
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: 105.42 E-value: 9.87e-26
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ...
453-632
1.59e-06
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: 53.32 E-value: 1.59e-06
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
2760-3272
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: 764.78 E-value: 0e+00
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
2781-3238
3.25e-95
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: 318.05 E-value: 3.25e-95
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
2884-3160
8.75e-76
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: 254.36 E-value: 8.75e-76
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
2887-3139
3.87e-28
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: 116.61 E-value: 3.87e-28
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
1127-1268
4.25e-28
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: 112.26 E-value: 4.25e-28
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
1264-1385
9.87e-26
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: 105.42 E-value: 9.87e-26
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
2883-3092
3.43e-10
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: 62.92 E-value: 3.43e-10
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
1131-1252
2.99e-07
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.
Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 52.41 E-value: 2.99e-07
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ...
453-632
1.59e-06
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: 53.32 E-value: 1.59e-06
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, within ...
2863-3134
2.71e-06
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: 53.10 E-value: 2.71e-06
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
1130-1253
5.42e-06
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: 48.84 E-value: 5.42e-06
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
1131-1252
7.06e-06
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 438711 [Multi-domain] Cd Length: 174 Bit Score: 49.25 E-value: 7.06e-06
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
1130-1254
1.39e-03
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 42.23 E-value: 1.39e-03
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
3024-3072
7.81e-03
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: 37.70 E-value: 7.81e-03
RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense ...
2954-3113
8.21e-03
RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Betanecrosvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. In the Betanecrosvirus genus plants serve as natural hosts, and transmission routes are mechanical, seed borne, and by contact. There are three species in this genus: Beet black scorch virus, Leek white stripe virus, and Tobacco necrosis virus D. Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription, using the premature termination model of subgenomic RNA transcription is the method of transcription. The virus exits the host cell by tubule-guided viral movement. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.
Pssm-ID: 438094 Cd Length: 500 Bit Score: 41.81 E-value: 8.21e-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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