nonstructural protein [Human astrovirus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| ps-ssRNAv_Astroviridae_RdRp | cd23172 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of ... |
1094-1333 | 5.52e-149 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Astroviridae, order, Stellavirales. Astrovirus has a non-segmented, (+)ssRNA genome within a non-enveloped icosahedral capsid. The family Astroviridae comprises two genera, Mamastrovirus, which infect mammals, and Avastrovirus, which infect birds. Astroviruses have been isolated from stools from a wide variety of mammals and birds. Human astroviruses have been shown to be an important cause of gastroenteritis in young children. Duck astrovirus causes an often-fatal hepatitis in ducklings. Astroviruses infecting turkeys, guinea fowl and chickens affect multiple organs, including the kidney and thymus. 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: 438022 Cd Length: 243 Bit Score: 451.92 E-value: 5.52e-149
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| Astrovir_pp_1 super family | cl13689 | Astroviridae polyprotein 1; This family of proteins is found in non-structural polyprotein 1 A ... |
757-917 | 1.72e-88 | |||||
Astroviridae polyprotein 1; This family of proteins is found in non-structural polyprotein 1 A/AB from Astroviridae. They are typically between 49 and 62 amino acids in length. There are two conserved sequence motifs: QPLDLS and EQQ. The actual alignment was detected with superfamily member pfam12285: Pssm-ID: 432454 Cd Length: 171 Bit Score: 284.44 E-value: 1.72e-88
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| Astro_VPg | pfam19416 | Astrovirus VPg protein; This entry represents the presumed VPg protein from human astrovirus. ... |
664-755 | 1.63e-38 | |||||
Astrovirus VPg protein; This entry represents the presumed VPg protein from human astrovirus. Viral genome-linked proteins (VPgs) are virus-encoded small proteins that are covalently linked to the 5' terminus of many RNA viral genomes through a phosphodiester bond. Viral genome-linked proteins (VPgs) have been identified in several single-stranded positive-sense RNA virus families. The protein resulting from this putative VPg coding region is a highly disordered protein. A common feature of VPgs is that they are rich in basic amino acids (mostly Lys (K), Gly (G), Thr (T), and Arg (R)), which favors the interaction with the negatively charged RNA. Tyr-693 at the conserved TEEEY-like motif has been postulated to be the residue responsible for the covalent linkage to viral RNA. Mutagenesis of Tyr-693 in the VPg protein is lethal for HAstV replication. : Pssm-ID: 437248 Cd Length: 104 Bit Score: 139.49 E-value: 1.63e-38
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| Trypsin_2 | pfam13365 | Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains. |
447-565 | 1.64e-13 | |||||
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains. : Pssm-ID: 433149 [Multi-domain] Cd Length: 142 Bit Score: 68.99 E-value: 1.64e-13
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| hsdR super family | cl36022 | type I restriction enzyme EcoKI subunit R; Provisional |
553-701 | 9.25e-03 | |||||
type I restriction enzyme EcoKI subunit R; Provisional The actual alignment was detected with superfamily member PRK11448: Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 40.71 E-value: 9.25e-03
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| Name | Accession | Description | Interval | E-value | ||||||
| ps-ssRNAv_Astroviridae_RdRp | cd23172 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of ... |
1094-1333 | 5.52e-149 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Astroviridae, order, Stellavirales. Astrovirus has a non-segmented, (+)ssRNA genome within a non-enveloped icosahedral capsid. The family Astroviridae comprises two genera, Mamastrovirus, which infect mammals, and Avastrovirus, which infect birds. Astroviruses have been isolated from stools from a wide variety of mammals and birds. Human astroviruses have been shown to be an important cause of gastroenteritis in young children. Duck astrovirus causes an often-fatal hepatitis in ducklings. Astroviruses infecting turkeys, guinea fowl and chickens affect multiple organs, including the kidney and thymus. 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: 438022 Cd Length: 243 Bit Score: 451.92 E-value: 5.52e-149
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| Astrovir_pp_1 | pfam12285 | Astroviridae polyprotein 1; This family of proteins is found in non-structural polyprotein 1 A ... |
757-917 | 1.72e-88 | ||||||
Astroviridae polyprotein 1; This family of proteins is found in non-structural polyprotein 1 A/AB from Astroviridae. They are typically between 49 and 62 amino acids in length. There are two conserved sequence motifs: QPLDLS and EQQ. Pssm-ID: 432454 Cd Length: 171 Bit Score: 284.44 E-value: 1.72e-88
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| Astro_VPg | pfam19416 | Astrovirus VPg protein; This entry represents the presumed VPg protein from human astrovirus. ... |
664-755 | 1.63e-38 | ||||||
Astrovirus VPg protein; This entry represents the presumed VPg protein from human astrovirus. Viral genome-linked proteins (VPgs) are virus-encoded small proteins that are covalently linked to the 5' terminus of many RNA viral genomes through a phosphodiester bond. Viral genome-linked proteins (VPgs) have been identified in several single-stranded positive-sense RNA virus families. The protein resulting from this putative VPg coding region is a highly disordered protein. A common feature of VPgs is that they are rich in basic amino acids (mostly Lys (K), Gly (G), Thr (T), and Arg (R)), which favors the interaction with the negatively charged RNA. Tyr-693 at the conserved TEEEY-like motif has been postulated to be the residue responsible for the covalent linkage to viral RNA. Mutagenesis of Tyr-693 in the VPg protein is lethal for HAstV replication. Pssm-ID: 437248 Cd Length: 104 Bit Score: 139.49 E-value: 1.63e-38
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| RdRP_1 | pfam00680 | Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ... |
991-1337 | 4.92e-27 | ||||||
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases. Pssm-ID: 425815 Cd Length: 450 Bit Score: 116.36 E-value: 4.92e-27
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| Trypsin_2 | pfam13365 | Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains. |
447-565 | 1.64e-13 | ||||||
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains. Pssm-ID: 433149 [Multi-domain] Cd Length: 142 Bit Score: 68.99 E-value: 1.64e-13
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| PspC_subgroup_2 | NF033839 | pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ... |
757-822 | 1.21e-04 | ||||||
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A. Pssm-ID: 468202 [Multi-domain] Cd Length: 557 Bit Score: 46.69 E-value: 1.21e-04
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| hsdR | PRK11448 | type I restriction enzyme EcoKI subunit R; Provisional |
553-701 | 9.25e-03 | ||||||
type I restriction enzyme EcoKI subunit R; Provisional Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 40.71 E-value: 9.25e-03
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| Name | Accession | Description | Interval | E-value | ||||||
| ps-ssRNAv_Astroviridae_RdRp | cd23172 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of ... |
1094-1333 | 5.52e-149 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Astroviridae, order, Stellavirales. Astrovirus has a non-segmented, (+)ssRNA genome within a non-enveloped icosahedral capsid. The family Astroviridae comprises two genera, Mamastrovirus, which infect mammals, and Avastrovirus, which infect birds. Astroviruses have been isolated from stools from a wide variety of mammals and birds. Human astroviruses have been shown to be an important cause of gastroenteritis in young children. Duck astrovirus causes an often-fatal hepatitis in ducklings. Astroviruses infecting turkeys, guinea fowl and chickens affect multiple organs, including the kidney and thymus. 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: 438022 Cd Length: 243 Bit Score: 451.92 E-value: 5.52e-149
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| Astrovir_pp_1 | pfam12285 | Astroviridae polyprotein 1; This family of proteins is found in non-structural polyprotein 1 A ... |
757-917 | 1.72e-88 | ||||||
Astroviridae polyprotein 1; This family of proteins is found in non-structural polyprotein 1 A/AB from Astroviridae. They are typically between 49 and 62 amino acids in length. There are two conserved sequence motifs: QPLDLS and EQQ. Pssm-ID: 432454 Cd Length: 171 Bit Score: 284.44 E-value: 1.72e-88
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| Astro_VPg | pfam19416 | Astrovirus VPg protein; This entry represents the presumed VPg protein from human astrovirus. ... |
664-755 | 1.63e-38 | ||||||
Astrovirus VPg protein; This entry represents the presumed VPg protein from human astrovirus. Viral genome-linked proteins (VPgs) are virus-encoded small proteins that are covalently linked to the 5' terminus of many RNA viral genomes through a phosphodiester bond. Viral genome-linked proteins (VPgs) have been identified in several single-stranded positive-sense RNA virus families. The protein resulting from this putative VPg coding region is a highly disordered protein. A common feature of VPgs is that they are rich in basic amino acids (mostly Lys (K), Gly (G), Thr (T), and Arg (R)), which favors the interaction with the negatively charged RNA. Tyr-693 at the conserved TEEEY-like motif has been postulated to be the residue responsible for the covalent linkage to viral RNA. Mutagenesis of Tyr-693 in the VPg protein is lethal for HAstV replication. Pssm-ID: 437248 Cd Length: 104 Bit Score: 139.49 E-value: 1.63e-38
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| RdRP_1 | pfam00680 | Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ... |
991-1337 | 4.92e-27 | ||||||
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases. Pssm-ID: 425815 Cd Length: 450 Bit Score: 116.36 E-value: 4.92e-27
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| RNA_dep_RNAP | cd01699 | RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ... |
1117-1354 | 8.12e-23 | ||||||
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: 100.05 E-value: 8.12e-23
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| ps-ssRNAv_RdRp-like | cd23167 | conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ... |
1175-1293 | 4.39e-14 | ||||||
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: 68.52 E-value: 4.39e-14
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| ps-ssRNAv-Picornavirales | cd23169 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ... |
1166-1301 | 1.36e-13 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRp of Picornavirales, an order of (+)ssRNA viruses. The order Picornavirales comprises viruses that historically are referred to as picorna-like viruses and which are classified into eight virus families: Caliciviridae, Dicistroviridae, Iflaviridae, Marnaviridae, Picornaviridae, Polycipiviridae, Secoviridae, and Solinviviridae. All known genomes of Picornavirales members encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. The picornavirus genome is replicated via a negative-sense (-) RNA intermediate by the viral RdRp, named 3Dpol, which uses VPg (the product of 3B) as a primer to initiate the replication process. 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: 438019 Cd Length: 309 Bit Score: 73.40 E-value: 1.36e-13
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| Trypsin_2 | pfam13365 | Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains. |
447-565 | 1.64e-13 | ||||||
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains. Pssm-ID: 433149 [Multi-domain] Cd Length: 142 Bit Score: 68.99 E-value: 1.64e-13
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| ps-ssRNAv_Potyviridae_RdRp | cd23175 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ... |
1122-1289 | 7.16e-10 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Potyviridae, order: Patatavirales. Potyviridae, is the largest family of RNA plant viruses, members of which have (+)ssRNA genomes and flexuous filamentous particles. The family is divided into eight genera: Brambyvirus, Bymovirus, Ipomovirus, Macluravirus, Poacevirus, Potyvirus, Rymovirus, and Tritimovirus. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. 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: 438025 Cd Length: 236 Bit Score: 60.93 E-value: 7.16e-10
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| ps-ssRNA_Picornaviridae | cd23193 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ... |
1174-1319 | 7.87e-09 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Picornaviridae, order Picornavirales. The Picornaviridae family consists of small, icosahedral viruses with (+)ssRNA genomes. Characteristic features of all members of the family Picornaviridae are three capsid proteins with beta-barrel folding, polyprotein processing by virus-encoded cysteine proteinase(s), and replication by an RdRp with a YGDD sequence motif. The family Picornaviridae comprises 68 genera containing 158 species, but many viruses are presently awaiting classification. The established genera of the family include: Aphthovirus, Avisivirus, Crohivirus, Enterovirus, Teschovirus, Cardiovirus, Erbovirus, Kobuvirus, Hepatovirus, Parechovirus, Aquamavirus, Avihepatovirus, Avisivirus, Cosavirus, Dicipivirus, Fipivirus, Gallivirus, Hunnivirus, Kunsagivirus, Limnipivirus, Megrivirus, Mischivirus, Mosavirus, Oscivirus, Pasivirus, Passerivirus, Rabovirus, Rosavirus, Sakobuvirus, Salivirus, Sapelovirus, Senecavirus, Sicinivirus, and Tremovirus. The Picornaviridae contains many important human and animal pathogens including enteroviruses (such as poliovirus, enterovirus, coxsackievirus, and rhinovirus), cardioviruses (such as encephalomyocarditis virus and Theiler's virus), hepatitis A virus and foot-and-mouth disease virus. Infection with various picornaviruses may cause encephalitis, febrile rash illnesses (hand-foot-and-mouth disease), aseptic meningitis, hepatitis, conjunctivitis, herpangina, myositis and myocarditis, and the common cold. 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: 438043 Cd Length: 345 Bit Score: 59.10 E-value: 7.87e-09
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| Dicistroviridae_RdRp | cd23194 | RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense ... |
1138-1313 | 7.62e-07 | ||||||
RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the RdRp of RNA viruses belonging to the family Dicistroviridae, order Picornavirales. Dicistroviridae is a family of small non-enveloped viruses with a (+)ssRNA genome of approximately 8-10 kilobases. The family contains 3 genera: Aparavirus, Cripavirus, and Triatovirus. All members infect arthropod hosts with some having devastating economic consequences, such as acute bee paralysis virus, Kashmir bee virus, and Israeli acute paralysis virus in domesticated honeybees, and taura syndrome virus and mud crab virus in the seafood industry. On the contrary, host specificity and other desirable traits make several members of this group amenable to development as biopesticides for insect control, such as Solenopsis invicta virus 1 against fire ants, and triatoma virus against triatomine bugs that vector Chagas disease. Members in the family Dicistroviridae have similarity to viruses in the Picornavirales members (Iflaviridae, Picornaviridae, Marnaviridae and Secoviridae). The genomes of viruses of these taxa encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. 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: 438044 [Multi-domain] Cd Length: 315 Bit Score: 52.89 E-value: 7.62e-07
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| PspC_subgroup_2 | NF033839 | pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ... |
757-822 | 1.21e-04 | ||||||
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A. Pssm-ID: 468202 [Multi-domain] Cd Length: 557 Bit Score: 46.69 E-value: 1.21e-04
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| Nora-virus_RdRp | cd23200 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like ... |
1174-1344 | 1.28e-04 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like Drosophila virus, Nora virus; This group contains the catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the unclassified Nora virus, a new picorna-like virus family. Nora virus has a (+)ssRNA genome followed by a poly(A) tail. Unlike other picorna-like viruses, the genome has four open reading frames (ORFs). One ORF encodes a picornavirus-like cassette of proteins for virus replication, including an iflavirus-like RdRp and a helicase that is related to those of mammalian picornaviruses. The three other ORFs are not closely related to any previously described viruses. Nora virus is present as a persistent infection in several tested laboratory stocks and wild-caught flies. 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: 438050 Cd Length: 306 Bit Score: 45.68 E-value: 1.28e-04
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| Limnipivirus_RdRp | cd23228 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of ... |
1176-1317 | 1.23e-03 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Limnipivirus genus within the family Picornaviridae, order Picornavirales. The Limnipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains three species, Limnipivirus A (bluegill picornavirus 1), Limnipivirus B (carp picornavirus 1) and Limnipivirus C (fathead minnow picornavirus 1). Limnipiviruses infect freshwater fishes. The virus can be grown in various fish cell lines. Experimental infection of bluegills with bluegill picornavirus induces morbidity (inflammation and redness at the base of fins, exophthalmia, abdomen distension, internal hemorrhaging and ascites) and mortality. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438078 Cd Length: 390 Bit Score: 42.94 E-value: 1.23e-03
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| Crohivirus_RdRp | cd23232 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Crohivirus of ... |
1173-1318 | 2.15e-03 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Crohivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Crohivirus genus within the family Picornaviridae, order Picornavirales. The Crohivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Crohivirus is a new genus containing two species, Crohivirus A and Crohivirus B. Crohivirus A (Crohivirus 1, CroV-1) is a novel picornavirus found the lesser red musk shrew (Crocidura hirta) which is found in southern Africa. The genome sequence is most closely related to the parechoviruses. Crohivirus B consists of a virus which has been found in the straw-colored fruit bat (Eidolon helvum). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438082 Cd Length: 373 Bit Score: 42.01 E-value: 2.15e-03
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| Enterovirus_RdRp | cd23213 | RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded ... |
1175-1293 | 4.15e-03 | ||||||
RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Enterovirus genus within the family Picornaviridae, order Picornavirales. Enteroviruses have small, non-enveloped (+)ssRNA genomes, and replicate within the gastrointestinal tract or other mucosal surfaces. The genus Enterovirus has been divided into 15 species based on genetic divergence (EV A-L and Rhinovirus A-C), and its major members include poliovirus, coxsackievirus and rhinovirus. More than 100 enterovirus types have been associated with several human diseases, all of which are classified into four species (Enterovirus A, Enterovirus B, Enterovirus C, and Enterovirus D). RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of enteroviruses. 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: 438063 Cd Length: 453 Bit Score: 41.36 E-value: 4.15e-03
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| hsdR | PRK11448 | type I restriction enzyme EcoKI subunit R; Provisional |
553-701 | 9.25e-03 | ||||||
type I restriction enzyme EcoKI subunit R; Provisional Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 40.71 E-value: 9.25e-03
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