RdRp [Beihai barnacle virus 2]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| Kitaviridae_RdRp | cd23254 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of ... |
1907-2173 | 5.36e-145 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Kitaviridae, order Martellivirales. The family Kitaviridae is composed of five recognized species among the three genera: Blueberry necrotic ring blotch virus and Tea plant necrotic ring blotch virus (genus Blunervirus); Citrus leprosis virus C and Citrus leprosis virus C2 (genus Cilevirus); and Hibiscus green spot virus 2 (genus Higrevirus). Although related, there are considerable physical and genetic distinctions between members of the different genera. For example, cile- and higreviruses are associated with a bacilliform virion, whereas a spherical virion has been observed for the lone blunervirus for which microscopy has been reported. Moreover, the replication-associated polyproteins are encoded by a single genomic RNA for cile- and higreviruses, but are split between two genomic RNAs for blunerviruses. 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: 438104 Cd Length: 267 Bit Score: 451.22 E-value: 5.36e-145
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| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
1353-1599 | 8.99e-37 | ||||||
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. : Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 139.44 E-value: 8.99e-37
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| FtsJ | pfam01728 | FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ... |
763-942 | 1.19e-21 | ||||||
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping. : Pssm-ID: 426399 Cd Length: 179 Bit Score: 94.19 E-value: 1.19e-21
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| Vmethyltransf super family | cl46422 | Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ... |
85-413 | 6.06e-21 | ||||||
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily. The actual alignment was detected with superfamily member pfam01660: Pssm-ID: 480762 Cd Length: 308 Bit Score: 95.83 E-value: 6.06e-21
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| OTU super family | cl45892 | OTU (ovarian tumor) domain family; The OTU family of cysteine proteases use a conserved ... |
593-700 | 4.67e-10 | ||||||
OTU (ovarian tumor) domain family; The OTU family of cysteine proteases use a conserved cysteine and histidine, and in most cases an aspartate, as the catalytic triad. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. The actual alignment was detected with superfamily member cd22792: Pssm-ID: 459237 [Multi-domain] Cd Length: 108 Bit Score: 58.77 E-value: 4.67e-10
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| Name | Accession | Description | Interval | E-value | |||||||
| Kitaviridae_RdRp | cd23254 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of ... |
1907-2173 | 5.36e-145 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Kitaviridae, order Martellivirales. The family Kitaviridae is composed of five recognized species among the three genera: Blueberry necrotic ring blotch virus and Tea plant necrotic ring blotch virus (genus Blunervirus); Citrus leprosis virus C and Citrus leprosis virus C2 (genus Cilevirus); and Hibiscus green spot virus 2 (genus Higrevirus). Although related, there are considerable physical and genetic distinctions between members of the different genera. For example, cile- and higreviruses are associated with a bacilliform virion, whereas a spherical virion has been observed for the lone blunervirus for which microscopy has been reported. Moreover, the replication-associated polyproteins are encoded by a single genomic RNA for cile- and higreviruses, but are split between two genomic RNAs for blunerviruses. 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: 438104 Cd Length: 267 Bit Score: 451.22 E-value: 5.36e-145
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| RdRP_2 | pfam00978 | RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ... |
1784-2221 | 3.33e-97 | |||||||
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses Pssm-ID: 395779 Cd Length: 440 Bit Score: 321.90 E-value: 3.33e-97
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| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
1353-1599 | 8.99e-37 | |||||||
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 139.44 E-value: 8.99e-37
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| FtsJ | pfam01728 | FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ... |
763-942 | 1.19e-21 | |||||||
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping. Pssm-ID: 426399 Cd Length: 179 Bit Score: 94.19 E-value: 1.19e-21
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| Vmethyltransf | pfam01660 | Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ... |
85-413 | 6.06e-21 | |||||||
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily. Pssm-ID: 396298 Cd Length: 308 Bit Score: 95.83 E-value: 6.06e-21
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| OTU_RDRP-like | cd22792 | OTU (ovarian tumor) domain of the potexviruses/carlaviruses RNA replication protein family; ... |
593-700 | 4.67e-10 | |||||||
OTU (ovarian tumor) domain of the potexviruses/carlaviruses RNA replication protein family; RNA replication polyprotein (RDRP) is a viral homolog of ovarian tumor protease (vOTU), which displays RNA helicase (EC 3.6.4.13), RNA-directed RNA polymerase (EC 2.7.7.48), viral methyltransferase, Fe(2+) 2-oxoglutarate dioxygenase and protease activities. The central part of this protein possibly functions as an ATP-binding helicase. It is an RNA-directed RNA polymerase involved in viral RNA replication. It also acts as a thiol protease that cleaves the polyprotein. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. Pssm-ID: 438613 [Multi-domain] Cd Length: 108 Bit Score: 58.77 E-value: 4.67e-10
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| RlmE | COG0293 | 23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and ... |
762-942 | 7.99e-10 | |||||||
23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and biogenesis]; 23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ is part of the Pathway/BioSystem: 23S rRNA modification Pssm-ID: 440062 [Multi-domain] Cd Length: 208 Bit Score: 60.85 E-value: 7.99e-10
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| rrmJ | PRK11188 | 23S rRNA (uridine(2552)-2'-O)-methyltransferase RlmE; |
762-941 | 1.19e-08 | |||||||
23S rRNA (uridine(2552)-2'-O)-methyltransferase RlmE; Pssm-ID: 183025 Cd Length: 209 Bit Score: 57.44 E-value: 1.19e-08
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
1544-1615 | 2.93e-03 | |||||||
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]; Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 42.66 E-value: 2.93e-03
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| Name | Accession | Description | Interval | E-value | |||||||
| Kitaviridae_RdRp | cd23254 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of ... |
1907-2173 | 5.36e-145 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Kitaviridae, order Martellivirales. The family Kitaviridae is composed of five recognized species among the three genera: Blueberry necrotic ring blotch virus and Tea plant necrotic ring blotch virus (genus Blunervirus); Citrus leprosis virus C and Citrus leprosis virus C2 (genus Cilevirus); and Hibiscus green spot virus 2 (genus Higrevirus). Although related, there are considerable physical and genetic distinctions between members of the different genera. For example, cile- and higreviruses are associated with a bacilliform virion, whereas a spherical virion has been observed for the lone blunervirus for which microscopy has been reported. Moreover, the replication-associated polyproteins are encoded by a single genomic RNA for cile- and higreviruses, but are split between two genomic RNAs for blunerviruses. 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: 438104 Cd Length: 267 Bit Score: 451.22 E-value: 5.36e-145
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| RdRP_2 | pfam00978 | RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ... |
1784-2221 | 3.33e-97 | |||||||
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses Pssm-ID: 395779 Cd Length: 440 Bit Score: 321.90 E-value: 3.33e-97
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| Virgaviridae_RdRp | cd23251 | RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense ... |
1767-2193 | 8.22e-95 | |||||||
RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Virgaviridae, order Martellivirales. The Virgaviridae is a family of plant viruses with rod-shaped virions, a (+)ssRNA genome with a 3'-terminal tRNA-like structure and a replication protein similar to those of the alpha-like supergroup. Plants serve as natural hosts. The name of the family is derived from the Latin word virga (rod), as all viruses in this family are rod-shaped. There are currently 59 species in this family, divided among seven genera: Goravirus, Furovirus, Hordeivirus, Pecluvirus, Pomovirus, Tobamovirus, and Tobravirus. 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: 438101 Cd Length: 427 Bit Score: 314.17 E-value: 8.22e-95
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| Closteroviridae_RdRp | cd23253 | RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense ... |
1907-2155 | 1.36e-58 | |||||||
RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Closteroviridae, order Martellivirales. Viruses in the family Closteroviridae have a mono-, bi- or tripartite (+)ssRNA genome of 13-19 kb, and non-enveloped, filamentous particles 650-2200 nm long and 12 nm in diameter. They infect plants, mainly dicots, many of which are fruit crops. Members of the family are classified into four genera: Ampelovirus, Closterovirus, Crinivirus and Velarivirus. Their genetic diversity is primarily influenced by strong negative selection and recombination. Closteroviridae viruses are mostly phloem-restricted and induce specific cytoplasmic aggregates of virus particles intermingled with membranous vesicles derived from the endoplasmic reticulum and possibly mitochondria. Their transmission is by aphids, whiteflies, pseudococcid mealybugs or soft scale insects in a semi-persistent manner. 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: 438103 Cd Length: 266 Bit Score: 203.56 E-value: 1.36e-58
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| ps-ssRNAv_Martellivirales_RdRp | cd23208 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of ... |
1907-2098 | 6.55e-52 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Martellivirales, class Alsuviricetes. The order Martellivirales consists of seven families: Bromoviridae, Closteroviridae, Endornaviridae, Kitaviridae, Mayoviridae, Togaviridae, and Virgaviridae. 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: 438058 [Multi-domain] Cd Length: 190 Bit Score: 181.41 E-value: 6.55e-52
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| Bromoviridae_RdRp | cd23252 | RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense ... |
1811-2154 | 8.37e-44 | |||||||
RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Bromoviridae, order Martellivirales. The Bromoviridae family of plant viruses contains tri-segmented, (+)ssRNA viruses with a total genome size of about 8 kb. There are six genera in this family: Alfamovirus, Anulavirus, Bromovirus, Cucumovirus, Ilarvirus, and Oleavirus. Bromoviridae virions are variable in morphology (spherical or bacilliform) and are transmitted mechanically, in/on the pollen and non-persistently by insect vectors. Members of the family cause major disease epidemics in fruit, vegetable and fodder crops such as tomato, cucurbits, bananas, and alfalfa. 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: 438102 Cd Length: 332 Bit Score: 163.55 E-value: 8.37e-44
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| Mayoviridae_RdRp | cd23256 | RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense ... |
1891-2195 | 8.27e-40 | |||||||
RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Mayoviridae, order Martellivirales. The Mayoviridae family consists of two genera, Idaeovirus and Pteridovirus. The genus Idaeovirus contains Raspberry bushy dwarf virus (RBDV), named after the host with which it was first associated (red raspberry, Rubus idaeu) and the disease which is characterized by bushiness (stunting and proliferation of canes); RBDV has recently been found causing an infection in grapevines. RBDV occurs in all tissues of the plant, including seed and pollen, and is transmitted in association with pollen, both vertically to the seed and horizontally to the pollinated plant; this is the only known method of natural spread of RBDV. 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: 438106 Cd Length: 329 Bit Score: 151.82 E-value: 8.27e-40
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| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
1353-1599 | 8.99e-37 | |||||||
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 139.44 E-value: 8.99e-37
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| ps-ssRNAv_Alsuviricetes_RdRp | cd23182 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of ... |
1907-2098 | 1.01e-29 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the class Alsuviricetes, phylum: Kitrinoviricota. Alsuviricetes is a class of [(+)ssRNA] viruses which infect eukaryotes. The name of the group is a syllabic abbreviation of "alpha supergroup" with the suffix -viricetes indicating a virus class. The class Alsuviricetes includes three orders: Hepelivirales, Martellivirales, and Tymovirales. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438032 [Multi-domain] Cd Length: 187 Bit Score: 117.70 E-value: 1.01e-29
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| FtsJ | pfam01728 | FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ... |
763-942 | 1.19e-21 | |||||||
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping. Pssm-ID: 426399 Cd Length: 179 Bit Score: 94.19 E-value: 1.19e-21
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| Vmethyltransf | pfam01660 | Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ... |
85-413 | 6.06e-21 | |||||||
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily. Pssm-ID: 396298 Cd Length: 308 Bit Score: 95.83 E-value: 6.06e-21
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| ps-ssRNAv_Hepelivirales_RdRp | cd23209 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of ... |
1907-2098 | 7.40e-16 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Hepelivirales, class Alsuviricetes. This Hepelivirales order consists of four families: Alphatetraviridae, Benyviridae, Hepeviridae, and Matonaviridae. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438059 [Multi-domain] Cd Length: 183 Bit Score: 77.91 E-value: 7.40e-16
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| Hepeviridae_RdRp | cd23259 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of ... |
1939-2102 | 5.11e-15 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Hepeviridae, order Hepelivirales. The family Hepeviridae includes enterically transmitted small non-enveloped [(+)ssRNA viruses. It includes the genera Piscihepevirus, whose members infect fish, and Orthohepevirus, whose members infect mammals and birds. Members of the genus Orthohepevirus include hepatitis E virus, which is responsible for self-limiting acute hepatitis in humans and several mammalian species; the infection may become chronic in immunocompromised individuals. Avian hepatitis E virus causes hepatitis-splenomegaly syndrome in chickens. Hepeviridae genomes (approximately 7.2 kb) have 5' methyl G caps and 3' poly (A) tails, and contain three ORFS. They have two mRNAs, a genome length and a subgenomic mRNA: the genome-length mRNA is translated to produce proteins required for RNA replication while the subgenomic mRNA is used to produce the capsid protein. Some of the capsid protein is glycosylated, which is an unusual finding for an unenveloped virus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438109 Cd Length: 274 Bit Score: 77.48 E-value: 5.11e-15
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| Endornaviridae_RdRp | cd23255 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Endornaviridae of ... |
1938-2113 | 1.12e-13 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Endornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Endornaviridae, order Martellivirales. The family Endornaviridae includes viruses with linear (+)ssRNA genomes that range from 9.7 to 17.6 kb. The family consists of two genera, Alphaendornavirus and Betaendornavirus. Alphaendornavirus includes species whose members infect plants, fungi and oomycetes, while the genus Betaendornavirus includes species whose members infect ascomycete fungi. Plant endornaviruses are transmitted only through the gametes. A conserved RNA-dependent RNA polymerase domain located in the C-terminal region of the polyprotein is a feature common to all endornaviruses. 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: 438105 Cd Length: 237 Bit Score: 72.95 E-value: 1.12e-13
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| ps-ssRNA_RdRp_Tymovirales | cd23207 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Tymovirales of ... |
1948-2099 | 6.03e-11 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Tymovirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Tymovirales. The Tymovirales order contains viruses that mostly infect plants, have a single molecule of (+)ssRNA, and which are united by the similarities in their replication-associated polyproteins. Tymovirales contains five families (Alpha-, Beta-, Delta- and Gammaflexiviridae and Tymoviridae) and groups mostly plant-infecting agents, although a few Tymovirales members have either fungal or insect hosts. Botrytis virus F (BVF), isolated from the fungus Botrytis cinerea, is a flexuous mycovirus that is typical of members of the genus Mycoflexivirus (family Gammaflexiviridae). The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438057 [Multi-domain] Cd Length: 188 Bit Score: 63.58 E-value: 6.03e-11
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| OTU_RDRP-like | cd22792 | OTU (ovarian tumor) domain of the potexviruses/carlaviruses RNA replication protein family; ... |
593-700 | 4.67e-10 | |||||||
OTU (ovarian tumor) domain of the potexviruses/carlaviruses RNA replication protein family; RNA replication polyprotein (RDRP) is a viral homolog of ovarian tumor protease (vOTU), which displays RNA helicase (EC 3.6.4.13), RNA-directed RNA polymerase (EC 2.7.7.48), viral methyltransferase, Fe(2+) 2-oxoglutarate dioxygenase and protease activities. The central part of this protein possibly functions as an ATP-binding helicase. It is an RNA-directed RNA polymerase involved in viral RNA replication. It also acts as a thiol protease that cleaves the polyprotein. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. Pssm-ID: 438613 [Multi-domain] Cd Length: 108 Bit Score: 58.77 E-value: 4.67e-10
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| RlmE | COG0293 | 23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and ... |
762-942 | 7.99e-10 | |||||||
23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and biogenesis]; 23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ is part of the Pathway/BioSystem: 23S rRNA modification Pssm-ID: 440062 [Multi-domain] Cd Length: 208 Bit Score: 60.85 E-value: 7.99e-10
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| Togaviridae_RdRp | cd23250 | RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense ... |
1805-2214 | 6.96e-09 | |||||||
RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Togaviridae, order Martellivirales. Togaviridae is a family of small, enveloped viruses with [(+)ssRNA] genomes of 10-12 kb, and contains a single genus, Alphavirus. Alphavirus includes a large number of species that are mostly mosquito-borne and pathogenic in their vertebrate hosts. Many are important human and veterinary pathogens (e.g., chikungunya virus, eastern equine encephalitis virus). The genus Alphavirus mainly consists of mosquito-borne viruses although other hematophagous insects, including ticks, lice, and cliff swallow bugs, have been implicated in transmission. Vertebrate hosts include humans, non-human primates, equids, birds, amphibians, reptiles, rodents, and pigs. There are two aquatic alphaviruses, southern elephant seal virus and salmon pancreas disease virus, infecting sea mammals and fish respectively. Interestingly, Eilat virus (EILV) has been shown to only infect insect cells and is incapable of replicating in vertebrate cells. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438100 Cd Length: 458 Bit Score: 60.55 E-value: 6.96e-09
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| rrmJ | PRK11188 | 23S rRNA (uridine(2552)-2'-O)-methyltransferase RlmE; |
762-941 | 1.19e-08 | |||||||
23S rRNA (uridine(2552)-2'-O)-methyltransferase RlmE; Pssm-ID: 183025 Cd Length: 209 Bit Score: 57.44 E-value: 1.19e-08
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| Gammaflexiviridae_RdRp | cd23249 | RNA-dependent RNA polymerase (RdRp) in the family Gammaflexiviridae of positive-sense ... |
1911-2099 | 2.45e-07 | |||||||
RNA-dependent RNA polymerase (RdRp) in the family Gammaflexiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the RdRp of RNA viruses belonging to the family Gammaflexiviridae, order Tymovirales. Virions within the Gammaflexiviridae family are flexuous filaments of 720 nm modal length and about 13 nm in diameter. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438099 Cd Length: 354 Bit Score: 55.29 E-value: 2.45e-07
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| Tymoviridae_RdRp | cd23247 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tymoviridae of ... |
1962-2098 | 9.76e-07 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tymoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tymoviridae, order Tymovirales. Virions of the family Tymoviridae are isometric, non-enveloped, about 30 nm in diameter, and contain a single molecule of (+)ssRNA constituting 25#35% of the particle weight. There are 42 species in this family, assigned to three genera (Maculavirus, Marafivirus, and Tymovirus), with two species unassigned to a genus. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438097 Cd Length: 373 Bit Score: 53.35 E-value: 9.76e-07
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| OTU | cd22744 | OTU (ovarian tumor) domain family; The OTU family of cysteine proteases use a conserved ... |
595-678 | 4.86e-06 | |||||||
OTU (ovarian tumor) domain family; The OTU family of cysteine proteases use a conserved cysteine and histidine, and in most cases an aspartate, as the catalytic triad. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. Pssm-ID: 438581 [Multi-domain] Cd Length: 128 Bit Score: 47.82 E-value: 4.86e-06
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| Benyviridae_RdRp | cd23257 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Benyviridae of ... |
1909-2079 | 1.13e-05 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Benyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Benyviridae, order Hepelivirales. The Benyviridae is a family of plant viruses with rod-shaped virions. Their genomes are multipartite (+)ssRNAs with 5' m7G-cap and 3' poly(A) and there is post-translational cleavage of the viral replicase. Beet necrotic yellow vein virus belongs to the genus Benyvirus and is the cause of 'rhizomania' disease of sugar beet. This widespread soil-borne disease can severely reduce sugar beet growth and beet sucrose production. BNYVV RNA1 contains one open reading frame (ORF) encoding a replicase protein that harbors motifs for methyltransferase, helicase, papain-like protease, and RdRp. 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: 438107 [Multi-domain] Cd Length: 188 Bit Score: 48.38 E-value: 1.13e-05
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| Carmotetraviridae_RdRp | cd23205 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae ... |
2046-2152 | 8.21e-04 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, and related Erinaceus virus H14; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Carmotetraviridae, and related Erinaceus virus H14, order Tolivirales. Carmotetraviridae includes only one genus, Alphacarmotetravirus, which has one species: Providence virus. Lepidopteran insects serve as the natural host. Recent studies indicated that Providence virus, a non-enveloped insect RNA virus, isolated from a lepidopteran midgut cell line can establish a productive infection in plants as well as in animal cells. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438055 Cd Length: 268 Bit Score: 43.46 E-value: 8.21e-04
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| Alphacarmovirus_RdRp | cd23239 | RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense ... |
1999-2162 | 1.77e-03 | |||||||
RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Alphacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The Alphacarmovirus genus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 8 species in the genus Alphacarmovirus: Adonis mosaic virus, Angelonia flower break virus, Calibrachoa mottle virus, Carnation mottle virus, Honeysuckle ringspot virus, Nootka lupine vein clearing virus, Pelargonium flower break virus, and Saguaro cactus 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: 438089 [Multi-domain] Cd Length: 470 Bit Score: 43.20 E-value: 1.77e-03
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| OTU_RNAP_L_virus | cd21880 | OTU (ovarian tumor) domain of viral RNA-directed RNA polymerase L; RNA-directed RNA polymerase ... |
592-705 | 2.91e-03 | |||||||
OTU (ovarian tumor) domain of viral RNA-directed RNA polymerase L; RNA-directed RNA polymerase L is also called protein L, large structural protein, replicase, transcriptase, or ubiquitin thioesterase. It displays RNA-directed RNA polymerase (EC 2.7.7.48), deubiquitinase (DUB)/ubiquitin thiolesterase (EC 3.4.19.12), and deISGylating activities. It is a viral homolog of ovarian tumor protease (vOTU) that has been implicated in the downregulation of type I interferon immune response by removing post-translational modifying proteins ubiquitin (Ub) and the Ub-like interferon-simulated gene 15 (ISG15) from host cellular proteins. The attachment of Ub and ISG15 to cellular proteins mediates important innate antiviral responses, and their removal inhibits these antiviral pathways. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. Pssm-ID: 438580 Cd Length: 148 Bit Score: 40.28 E-value: 2.91e-03
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
1544-1615 | 2.93e-03 | |||||||
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]; Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 42.66 E-value: 2.93e-03
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