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Conserved domains on  [gi|1774855415|ref|YP_009553013|]
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187 kDa hypothetical polymerase [Opuntia virus 2]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 1135-1566 0e+00

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.


The actual alignment was detected with superfamily member cd23251:

Pssm-ID: 477363  Cd Length: 427  Bit Score: 637.36  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1135 LPGNSFVLNDFDQWQVQVGDVALNVADCKLTLSKDDPVrnaLKEPTFLRPVLRTAHERPRRANLKENLLALIKRNFNAPE 1214
Cdd:cd23251      1 FPGNSTRDSDFDGYTVATSDINLNVEDCTLDPSKSVKV---WQEKEGLKPVLRTAMPEKRQNGLLESLLALIKRNMAAPK 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1215 LTGIVDIEASASFAVDRFFECFIDKS--DNSlgslRLRCRETLQRWLDNQEPATLKRLANFD-TSALPAIDQYSHMIKSQ 1291
Cdd:cd23251     78 LQGAVNEFETIERVIKKAKDVFFDEDliDRS----PLSTRESFLRWWDKQSTTARAQLLADDrVLDEIDVCTYNFMIKND 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1292 PKCRLDTSVQSEYGALQTIVFHSKEVNSIFGPIFQELTRVLLSSIDQnRFLFYTRKSASDVEGFFSGISTNSNYEVLELD 1371
Cdd:cd23251    154 VKPKLDLSPQSEYAALQTVVYPDKIVNALFGPIFKEINERILSALDP-HVVFNTRMTAEELNETVEFLDPDEEYDALEID 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1372 ISKYDKSQNDFHCAVEYEIWKRLGFDDFLLSVWEMGHRKTFLTDFKAGIKACIWYQRKSGDVTTFIGNTVLVATCLATLI 1451
Cdd:cd23251    233 FSKFDKSKTSLHIRAVIELYKLFGLDGMLAFLWEKSQCQTTVKDRQNGIKAYLLYQQKSGNCDTYGSNTWSAALALLSML 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1452 PLENCLKAAFCGDDSLIFMPKGFNSDDVQVRANLAWNFEAKLFKKRIGYFCGKYVIIHDSGCTIYPDPLKLISKLGAKSI 1531
Cdd:cd23251    313 PLEKAIFMIFGGDDSLILFPKGLVIPDPCRRLASLWNFECKLFKFKYGYFCGKFLLKHGDGYIFYPDPLKLITKLGRKDI 392

                          410       420       430
                   ....*....|....*....|....*....|....*
gi 1774855415 1532 KDWSHLEETRVSLMDNAGNYGNCAYFPHLDEAIAE 1566
Cdd:cd23251    393 KDGEHLSEIFVSICDNYKSYRDYRVLEALDVAVVE 427
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 814-1069 1.35e-50

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: 178.73  E-value: 1.35e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  814 TLIDGVPGCGKSKEIIESADLvndlvLTPGREAVSMLRRRFnshygrPVATKENVRTIDSFTMNPKPRTFKTLWIDEGLM 893
Cdd:pfam01443    1 IVVHGVPGCGKSTLIRKLLRT-----SRVIRPTAELRTEGK------PDLPNLNVRTVDTFLMALLKPTGKILILDEYTL 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  894 VHPGLINFCIVLSQASSVKVFGDRKQIPFISRVFEFDYPleLRNIVCDSVENRDVTRRCPLDITSFLAKQYDRgvlstss 973
Cdd:pfam01443   70 LPPGYILLLAAISGAKLVILFGDPLQIPYHSRAPSFLIP--HFPSSLSHRVGRRTTYLLPSLRAPILSAKGFE------- 140

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  974 vshSVSVDSVKGAAVFDPVSKPLeGKIVTFTQSDKLLLQRkgykDVNTVHEIQGETFPKVHLVRATSTPISIISqRDKPH 1053
Cdd:pfam01443  141 ---VVVERSGEYKVDYDPNGVLV-LVYLTFTQALKESLGV----RVTTVHEVQGLTFDSVTLVLDTDTDLLIIS-DSPEH 211

                          250
                   ....*....|....*.
gi 1774855415 1054 IIVALSRHTQCLVYHT 1069
Cdd:pfam01443  212 LYVALTRHRKSLHILT 227
Vmethyltransf pfam01660
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ...
 50-432 5.52e-40

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: 150.91  E-value: 5.52e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415   50 FSRVISQDATRVVTDSypEFRVS-FSNTVNSvHPLAGGLRGLELEWMMMQVPFGHLTYDIGGTFSAHLLKGRDYVHCCSP 128
Cdd:pfam01660    1 FPYALSPEAQELLENL--GIEFSpYSVTPHS-HPAAKALENLLLEVLPSYLPNPSTVLDIKGSKLRHLKRGNPNVHCCNP 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  129 ALSMRDLMRYQSQAQslecymakrhtlpefqrpaFELYSNSPRHIHCFDRFQECTLQAPDgvKPFAVALHSLYDIPVEEF 208
Cdd:pfam01660   78 ILDPRDVARYPEAFS-------------------LEKSLGNGEDLRPTNTFEDCRVLAPT--TSYAFMHDSLHDWSPEEL 136

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  209 APALLRKNV-ECCYAAFHFSEDLLLDEEfcSGELDPIGGRFERDGdrlSFYFKDESTL--VYEHSFkNVIGYVLRTFFVA 285
Cdd:pfam01660  137 ADLFLRKPKlERLYATLVFPPELLFGDK--ESLYPELYTFWYKGD---RFHFYPDGHLggSYTHPL-NLLSWLTTSKIHL 210

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  286 SSRYVYMKEAMCTRVNTMFMKFVKVDTFQLhrscfshqidtdalisgmndswelkRSLMLQSASRNIFKDkakvhvwfpg 365
Cdd:pfam01660  211 PGGFTYTVERLESRGAHHLFKITRGDGLTP-------------------------KVIVPDSRTFGPFEA---------- 255

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1774855415  366 lrnkllvpifrgivsrpgkvkkgnLLIDAEFFHTVSNHVRTYQGKQLTYESVLSLIESLRSRIVING 432
Cdd:pfam01660  256 ------------------------VLLPKIFVPRVLNYIRGKPIPLTVVNKLFSYLRSLKKRVVING 298
 
Name Accession Description Interval E-value
Virgaviridae_RdRp cd23251
RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense ...
 1135-1566 0e+00

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: 637.36  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1135 LPGNSFVLNDFDQWQVQVGDVALNVADCKLTLSKDDPVrnaLKEPTFLRPVLRTAHERPRRANLKENLLALIKRNFNAPE 1214
Cdd:cd23251      1 FPGNSTRDSDFDGYTVATSDINLNVEDCTLDPSKSVKV---WQEKEGLKPVLRTAMPEKRQNGLLESLLALIKRNMAAPK 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1215 LTGIVDIEASASFAVDRFFECFIDKS--DNSlgslRLRCRETLQRWLDNQEPATLKRLANFD-TSALPAIDQYSHMIKSQ 1291
Cdd:cd23251     78 LQGAVNEFETIERVIKKAKDVFFDEDliDRS----PLSTRESFLRWWDKQSTTARAQLLADDrVLDEIDVCTYNFMIKND 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1292 PKCRLDTSVQSEYGALQTIVFHSKEVNSIFGPIFQELTRVLLSSIDQnRFLFYTRKSASDVEGFFSGISTNSNYEVLELD 1371
Cdd:cd23251    154 VKPKLDLSPQSEYAALQTVVYPDKIVNALFGPIFKEINERILSALDP-HVVFNTRMTAEELNETVEFLDPDEEYDALEID 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1372 ISKYDKSQNDFHCAVEYEIWKRLGFDDFLLSVWEMGHRKTFLTDFKAGIKACIWYQRKSGDVTTFIGNTVLVATCLATLI 1451
Cdd:cd23251    233 FSKFDKSKTSLHIRAVIELYKLFGLDGMLAFLWEKSQCQTTVKDRQNGIKAYLLYQQKSGNCDTYGSNTWSAALALLSML 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1452 PLENCLKAAFCGDDSLIFMPKGFNSDDVQVRANLAWNFEAKLFKKRIGYFCGKYVIIHDSGCTIYPDPLKLISKLGAKSI 1531
Cdd:cd23251    313 PLEKAIFMIFGGDDSLILFPKGLVIPDPCRRLASLWNFECKLFKFKYGYFCGKFLLKHGDGYIFYPDPLKLITKLGRKDI 392

                          410       420       430
                   ....*....|....*....|....*....|....*
gi 1774855415 1532 KDWSHLEETRVSLMDNAGNYGNCAYFPHLDEAIAE 1566
Cdd:cd23251    393 KDGEHLSEIFVSICDNYKSYRDYRVLEALDVAVVE 427
RdRP_2 pfam00978
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...
 1153-1594 9.92e-157

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: 483.68  E-value: 9.92e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1153 GDVALNVADCKLTLSKDDPVRNalKEPTFLRPVLRTAHERPRRANLKENLLALIKRNFNAPELTGIVDIEASASFAVDRF 1232
Cdd:pfam00978    2 SDISLDLDDCRLDPSKSKPKPK--DKEPYLVPVLRTAAPSPRQNTLKEVLLALKKRNFNVPELQESVDLDDTAERVAERF 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1233 FECFIDKSDNSLGSLRLRCRETLQRWLDNQEPATLKRLANFDTSALPAID--QYSHMIKSQPKCRLDTSVQSEYGALQTI 1310
Cdd:pfam00978   80 KKSFLDKEKLDKLDPIINTTENVSRWLDKQSGKKAAQLKLDDLVPLHEVDldRYKHMIKSDVKPKLDLSPQSERPALQTI 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1311 VFHSKEVNSIFGPIFQELTRVLLSSIDQNrFLFYTRKSASDVEGFFSgiSTNSNYEVLELDISKYDKSQNDFHCAVEYEI 1390
Cdd:pfam00978  160 TYHDKGVTAYFSPIFRELFERLLYVLKPK-IVFPTGMTSSLIAEHFE--FLDASEDFLEIDFSKFDKSQGELHLLVQLEI 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1391 WKRLGFDDFLLSVWEMGHRKTFLTDFKAGIKACIWYQRKSGDVTTFIGNTVLVATCLATLIPLENCLKAAFCGDDSLIFM 1470
Cdd:pfam00978  237 LKLLGLDPELADLWFKFHRQSYIKDRKNGVGFSVDYQRKSGDANTYLGNTLVTMAMLASVYDLEKIDCAAFSGDDSLIFS 316

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1471 PKGFnsDDVQVRANLAWNFEAKLFKKRIGYFCGKYVIIHDSGCTIYPDPLKLISKLGAKSIKD-WSHLEETRVSLMDNAG 1549
Cdd:pfam00978  317 PKPI--EDPASRFATLFNMEAKVFDPSVPYFCSKFLLEVDGGAFFVPDPLKLLQKLGKKKIPDdEQHLDEIFTSLCDLTK 394

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*.
gi 1774855415 1550 NYGN-CAYFPHLDEAIAEVFPAAVGGRFAFCALYKFLSDKVLFRSL 1594
Cdd:pfam00978  395 SFNDdCVVLELLDLAVARYYKYAPEGYAALCALHKALSSFTLFFSL 440
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 814-1069 1.35e-50

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: 178.73  E-value: 1.35e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  814 TLIDGVPGCGKSKEIIESADLvndlvLTPGREAVSMLRRRFnshygrPVATKENVRTIDSFTMNPKPRTFKTLWIDEGLM 893
Cdd:pfam01443    1 IVVHGVPGCGKSTLIRKLLRT-----SRVIRPTAELRTEGK------PDLPNLNVRTVDTFLMALLKPTGKILILDEYTL 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  894 VHPGLINFCIVLSQASSVKVFGDRKQIPFISRVFEFDYPleLRNIVCDSVENRDVTRRCPLDITSFLAKQYDRgvlstss 973
Cdd:pfam01443   70 LPPGYILLLAAISGAKLVILFGDPLQIPYHSRAPSFLIP--HFPSSLSHRVGRRTTYLLPSLRAPILSAKGFE------- 140

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  974 vshSVSVDSVKGAAVFDPVSKPLeGKIVTFTQSDKLLLQRkgykDVNTVHEIQGETFPKVHLVRATSTPISIISqRDKPH 1053
Cdd:pfam01443  141 ---VVVERSGEYKVDYDPNGVLV-LVYLTFTQALKESLGV----RVTTVHEVQGLTFDSVTLVLDTDTDLLIIS-DSPEH 211

                          250
                   ....*....|....*.
gi 1774855415 1054 IIVALSRHTQCLVYHT 1069
Cdd:pfam01443  212 LYVALTRHRKSLHILT 227
Vmethyltransf pfam01660
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ...
 50-432 5.52e-40

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: 150.91  E-value: 5.52e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415   50 FSRVISQDATRVVTDSypEFRVS-FSNTVNSvHPLAGGLRGLELEWMMMQVPFGHLTYDIGGTFSAHLLKGRDYVHCCSP 128
Cdd:pfam01660    1 FPYALSPEAQELLENL--GIEFSpYSVTPHS-HPAAKALENLLLEVLPSYLPNPSTVLDIKGSKLRHLKRGNPNVHCCNP 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  129 ALSMRDLMRYQSQAQslecymakrhtlpefqrpaFELYSNSPRHIHCFDRFQECTLQAPDgvKPFAVALHSLYDIPVEEF 208
Cdd:pfam01660   78 ILDPRDVARYPEAFS-------------------LEKSLGNGEDLRPTNTFEDCRVLAPT--TSYAFMHDSLHDWSPEEL 136

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  209 APALLRKNV-ECCYAAFHFSEDLLLDEEfcSGELDPIGGRFERDGdrlSFYFKDESTL--VYEHSFkNVIGYVLRTFFVA 285
Cdd:pfam01660  137 ADLFLRKPKlERLYATLVFPPELLFGDK--ESLYPELYTFWYKGD---RFHFYPDGHLggSYTHPL-NLLSWLTTSKIHL 210

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  286 SSRYVYMKEAMCTRVNTMFMKFVKVDTFQLhrscfshqidtdalisgmndswelkRSLMLQSASRNIFKDkakvhvwfpg 365
Cdd:pfam01660  211 PGGFTYTVERLESRGAHHLFKITRGDGLTP-------------------------KVIVPDSRTFGPFEA---------- 255

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1774855415  366 lrnkllvpifrgivsrpgkvkkgnLLIDAEFFHTVSNHVRTYQGKQLTYESVLSLIESLRSRIVING 432
Cdd:pfam01660  256 ------------------------VLLPKIFVPRVLNYIRGKPIPLTVVNKLFSYLRSLKKRVVING 298
 
Name Accession Description Interval E-value
Virgaviridae_RdRp cd23251
RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense ...
 1135-1566 0e+00

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: 637.36  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1135 LPGNSFVLNDFDQWQVQVGDVALNVADCKLTLSKDDPVrnaLKEPTFLRPVLRTAHERPRRANLKENLLALIKRNFNAPE 1214
Cdd:cd23251      1 FPGNSTRDSDFDGYTVATSDINLNVEDCTLDPSKSVKV---WQEKEGLKPVLRTAMPEKRQNGLLESLLALIKRNMAAPK 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1215 LTGIVDIEASASFAVDRFFECFIDKS--DNSlgslRLRCRETLQRWLDNQEPATLKRLANFD-TSALPAIDQYSHMIKSQ 1291
Cdd:cd23251     78 LQGAVNEFETIERVIKKAKDVFFDEDliDRS----PLSTRESFLRWWDKQSTTARAQLLADDrVLDEIDVCTYNFMIKND 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1292 PKCRLDTSVQSEYGALQTIVFHSKEVNSIFGPIFQELTRVLLSSIDQnRFLFYTRKSASDVEGFFSGISTNSNYEVLELD 1371
Cdd:cd23251    154 VKPKLDLSPQSEYAALQTVVYPDKIVNALFGPIFKEINERILSALDP-HVVFNTRMTAEELNETVEFLDPDEEYDALEID 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1372 ISKYDKSQNDFHCAVEYEIWKRLGFDDFLLSVWEMGHRKTFLTDFKAGIKACIWYQRKSGDVTTFIGNTVLVATCLATLI 1451
Cdd:cd23251    233 FSKFDKSKTSLHIRAVIELYKLFGLDGMLAFLWEKSQCQTTVKDRQNGIKAYLLYQQKSGNCDTYGSNTWSAALALLSML 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1452 PLENCLKAAFCGDDSLIFMPKGFNSDDVQVRANLAWNFEAKLFKKRIGYFCGKYVIIHDSGCTIYPDPLKLISKLGAKSI 1531
Cdd:cd23251    313 PLEKAIFMIFGGDDSLILFPKGLVIPDPCRRLASLWNFECKLFKFKYGYFCGKFLLKHGDGYIFYPDPLKLITKLGRKDI 392

                          410       420       430
                   ....*....|....*....|....*....|....*
gi 1774855415 1532 KDWSHLEETRVSLMDNAGNYGNCAYFPHLDEAIAE 1566
Cdd:cd23251    393 KDGEHLSEIFVSICDNYKSYRDYRVLEALDVAVVE 427
RdRP_2 pfam00978
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...
 1153-1594 9.92e-157

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: 483.68  E-value: 9.92e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1153 GDVALNVADCKLTLSKDDPVRNalKEPTFLRPVLRTAHERPRRANLKENLLALIKRNFNAPELTGIVDIEASASFAVDRF 1232
Cdd:pfam00978    2 SDISLDLDDCRLDPSKSKPKPK--DKEPYLVPVLRTAAPSPRQNTLKEVLLALKKRNFNVPELQESVDLDDTAERVAERF 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1233 FECFIDKSDNSLGSLRLRCRETLQRWLDNQEPATLKRLANFDTSALPAID--QYSHMIKSQPKCRLDTSVQSEYGALQTI 1310
Cdd:pfam00978   80 KKSFLDKEKLDKLDPIINTTENVSRWLDKQSGKKAAQLKLDDLVPLHEVDldRYKHMIKSDVKPKLDLSPQSERPALQTI 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1311 VFHSKEVNSIFGPIFQELTRVLLSSIDQNrFLFYTRKSASDVEGFFSgiSTNSNYEVLELDISKYDKSQNDFHCAVEYEI 1390
Cdd:pfam00978  160 TYHDKGVTAYFSPIFRELFERLLYVLKPK-IVFPTGMTSSLIAEHFE--FLDASEDFLEIDFSKFDKSQGELHLLVQLEI 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1391 WKRLGFDDFLLSVWEMGHRKTFLTDFKAGIKACIWYQRKSGDVTTFIGNTVLVATCLATLIPLENCLKAAFCGDDSLIFM 1470
Cdd:pfam00978  237 LKLLGLDPELADLWFKFHRQSYIKDRKNGVGFSVDYQRKSGDANTYLGNTLVTMAMLASVYDLEKIDCAAFSGDDSLIFS 316

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1471 PKGFnsDDVQVRANLAWNFEAKLFKKRIGYFCGKYVIIHDSGCTIYPDPLKLISKLGAKSIKD-WSHLEETRVSLMDNAG 1549
Cdd:pfam00978  317 PKPI--EDPASRFATLFNMEAKVFDPSVPYFCSKFLLEVDGGAFFVPDPLKLLQKLGKKKIPDdEQHLDEIFTSLCDLTK 394

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*.
gi 1774855415 1550 NYGN-CAYFPHLDEAIAEVFPAAVGGRFAFCALYKFLSDKVLFRSL 1594
Cdd:pfam00978  395 SFNDdCVVLELLDLAVARYYKYAPEGYAALCALHKALSSFTLFFSL 440
Kitaviridae_RdRp cd23254
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of ...
 1283-1546 1.70e-85

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: 280.57  E-value: 1.70e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1283 QYSHMIKSQPKCRLDTSVQSEYGALQTIVFHSKEVNSIFGPIFQELTRVLLSSIDqNRFLFYTRKSASDVE----GFFSG 1358
Cdd:cd23254      2 VYSFMIKRNPKPNLTVDAAYKYPALQTIAYHDKDINAIFCPIFRELKKRLLAVLK-PNFVIFTDMSPEDFEellnRRFPP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1359 ISTNSNYEVLELDISKYDKSQNDFHCAVEYEIWKRLGFDDFLLSVWEMGHRKTFLTDFKAGIKACIWYQRKSGDVTTFIG 1438
Cdd:cd23254     81 EVLSKLLHKLEIDISKYDKSQGELALLFECKLMRRFGVPEELVELWFNAHVLTTLYDRTNKLKALVEYQRKSGDASTFFG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1439 NTVLVATCLATLIPLENCLKAAFCGDDSLIFMPKGFNSDDVQVRANLaWNFEAKLFKKRIGYFCGKYVIIHDSGCTIYPD 1518
Cdd:cd23254    161 NTLFLMAVLADLFDLSDLELALFSGDDSLLFGRNLLDYDDSQHFALK-FNLESKFLNYKYPYFCSKFLLPVGGRWYFVPD 239

                          250       260
                   ....*....|....*....|....*...
gi 1774855415 1519 PLKLISKLGAKSIKDWSHLEETRVSLMD 1546
Cdd:cd23254    240 PVKLLTKLGRHDLVNWEHVEEYRISLKD 267
ps-ssRNAv_Martellivirales_RdRp cd23208
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of ...
 1282-1471 1.28e-61

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: 208.76  E-value: 1.28e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1282 DQYSHMIKSQPKCRLDTSVQSEYGALQTIVFHSKEVNSIFGPIFQELTRVLLSSIDQnRFLFYTR-KSASDVEGFFSGIS 1360
Cdd:cd23208      1 DKYEMMIKSDVKPKLDLTAQQEYPKLQTIVYHDKNITAIFCPIFKELFERLLSCLKK-KVVIYTGmMTSAELNDFISALH 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1361 TNSNYEVLELDISKYDKSQNDFHCAVEYEIWKRLGFDDFLLSVWEMGHRKTFLTDFKAGIKACIWYQRKSGDVTTFIGNT 1440
Cdd:cd23208     80 LESGYYVLEIDFSKFDKSQGALHLLTELLILRRLGVDEPLLVLWEFAHTQSTTRDINNGISFETAYQRKSGDAFTYFGNT 159

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1774855415 1441 VLVATCLATLIPLENCLKAAFCGDDSLIFMP 1471
Cdd:cd23208    160 LVTMAALLDVLDLEKIVCIAFGGDDSLIFSK 190
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 814-1069 1.35e-50

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: 178.73  E-value: 1.35e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  814 TLIDGVPGCGKSKEIIESADLvndlvLTPGREAVSMLRRRFnshygrPVATKENVRTIDSFTMNPKPRTFKTLWIDEGLM 893
Cdd:pfam01443    1 IVVHGVPGCGKSTLIRKLLRT-----SRVIRPTAELRTEGK------PDLPNLNVRTVDTFLMALLKPTGKILILDEYTL 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  894 VHPGLINFCIVLSQASSVKVFGDRKQIPFISRVFEFDYPleLRNIVCDSVENRDVTRRCPLDITSFLAKQYDRgvlstss 973
Cdd:pfam01443   70 LPPGYILLLAAISGAKLVILFGDPLQIPYHSRAPSFLIP--HFPSSLSHRVGRRTTYLLPSLRAPILSAKGFE------- 140

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  974 vshSVSVDSVKGAAVFDPVSKPLeGKIVTFTQSDKLLLQRkgykDVNTVHEIQGETFPKVHLVRATSTPISIISqRDKPH 1053
Cdd:pfam01443  141 ---VVVERSGEYKVDYDPNGVLV-LVYLTFTQALKESLGV----RVTTVHEVQGLTFDSVTLVLDTDTDLLIIS-DSPEH 211

                          250
                   ....*....|....*.
gi 1774855415 1054 IIVALSRHTQCLVYHT 1069
Cdd:pfam01443  212 LYVALTRHRKSLHILT 227
Bromoviridae_RdRp cd23252
RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense ...
 1154-1527 1.01e-48

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: 177.03  E-value: 1.01e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1154 DVALNVADCKLTLSKddpVRNALKEPTFLRPVLRTAHERPRRANLKENLLALIKRNFNAPELTGIVDIEASASFAVDRFF 1233
Cdd:cd23252      1 DISLDVDHCRLDQSD---FNDWTKPDGYLEPVLNTGSGSKRVGTQREALLAIKKRNANVPELGDSVDLDRVSNAVANRFL 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1234 ECFIDKsdnslgslrlrcretlqrwldnqepatlkrlanfdtsalPAIDQYSHMIKSQPKCRLDTSVQSEYGALQTIVFH 1313
Cdd:cd23252     78 TTVIDV---------------------------------------DRLDKYMHMIKSDLKPVEDDSLHVERPVPATITYH 118

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1314 SKEVNSIFGPIF----QELTRVLLS--SIDQNRF--LFYTRKSASDVEGFFsgistnsnyevLELDISKYDKSQNDFHCA 1385
Cdd:cd23252    119 KKGIVMQFSPLFlaafERLLRCLRSkiVIPSGKIhqLFMIDPSVLNASKHF-----------KEIDFSKFDKSQGELHHE 187

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1386 VEYEIWKRLGFDDFLLSVWEMGHRKTFLTDFKAGIKACIWYQRKSGDVTTFIGNTVLVATCLATLIPLE--NCLKAAFCG 1463
Cdd:cd23252    188 IQEHILNALGCPAPFTKWWFDFHRRSYISDRRAGVGFSVDFQRRTGDAFTYLGNTLVTLAELAYVYDLDdpNFDFVVASG 267

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1774855415 1464 DDSLIFMPKGFNSDDVQVRANLaWNFEAKlFKKRIGYFCGKYVIIHDSGCT---IYPDPLKLISKLG 1527
Cdd:cd23252    268 DDSLIGSVEPLPRDDEDLFTTL-FNFEAK-FPHNQPFICSKFLLSDEFGDEnvfSVPDPLKLLQRLG 332
Closteroviridae_RdRp cd23253
RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense ...
 1287-1546 1.29e-47

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: 171.59  E-value: 1.29e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1287 MIKSQPKCRLDTSVQSEYGALQTIVFHSKEVNSIFGPIFQE----LTRVLLSSIdqnrfLFYTRKSASDvegfFSGISTN 1362
Cdd:cd23253      6 MVKGDMKPKLDSSSLSKYPPGQNIVYHERAINAFFSPIFLEvfdrIKYCLSDKI-----ILYSGMNLEE----LASLIRS 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1363 ------SNYEVLELDISKYDKSQNDFHCAVEYEIWKRLGFDDFLLSVWEMGHRKTFLTDFKAGIKACIWYQRKSGDVTTF 1436
Cdd:cd23253     77 klgdplDEYKTVEIDFSKFDKSQGVLFKVYEELVYKFFGFSEELYDNWKCSEYFSCRATSDSGVSLELGAQRRTGSPNTW 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1437 IGNTVLVATCLATLIPLENCLKAAFCGDDSLIFMPKGFNSDDVQVraNLAWNFEAKLFKKRIGYFCGKYVIIHDSGCTIY 1516
Cdd:cd23253    157 LGNTLVTLGILSSSYDLDDIDLLLVSGDDSLIFSKKPLPNKANEI--NLDFGFEAKFIENSVPYFCSKFIIEDRGKIKVV 234

                          250       260       270
                   ....*....|....*....|....*....|.
gi 1774855415 1517 PDPLKLISKLGA-KSIKDWSHLEETRVSLMD 1546
Cdd:cd23253    235 PDPVKLFEKLSVpIRLEDETLLKERFTSFKD 265
Mayoviridae_RdRp cd23256
RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense ...
 1277-1548 3.31e-44

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: 164.15  E-value: 3.31e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1277 ALPAIDQYSHMIKSQPKCRLDTSVQSEYGALQTIVFHSKEVNSIFGPIFQELTRVLLSSidQNRFLFYTRKSASDVEGFF 1356
Cdd:cd23256     28 ALTSLNKYSHMIKRDRKPVLTTAVQSEYTKAATITYHDKDITQVATPIFRQFKTRLLAC--KKSNLCIPLDHDHDISGWL 105

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1357 SGISTNS-NYEVLELDISKYDKSQNDFHCAVEYEIWKRLGFDDFLLSVWEMGHRKTFLTDFKAGIKACIWYQRKSGDVTT 1435
Cdd:cd23256    106 TNRHLGSeNGTFTEIDFSKFDKSQGELHQLIQDLILLRFGCDPEFVSLWSTAHRSSSIKDQNVGISFKTDFQRRTGDAFT 185

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1436 FIGNTVLVATCLATLIPLENCLKAAFC---GDDSLI--FMPKGFNSDDVQVranlAWNFEAKLFKKRIGYFCGKYVIIHD 1510
Cdd:cd23256    186 FLGNSLVTAVMLAYVLSFEDEKKIRYMlvgGDDSLIcsYGPISVPLEPLST----IFNMSCKLIQPSCPYFASRYIIRVG 261

                          250       260       270
                   ....*....|....*....|....*....|....*....
gi 1774855415 1511 SGCTIYPDPLKLISKLGAKSIKD-WSHLEETRVSLMDNA 1548
Cdd:cd23256    262 DEILCVPDPYKLLVKMGRKDIPDnEASLEEVRTGLADSA 300
Vmethyltransf pfam01660
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ...
 50-432 5.52e-40

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: 150.91  E-value: 5.52e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415   50 FSRVISQDATRVVTDSypEFRVS-FSNTVNSvHPLAGGLRGLELEWMMMQVPFGHLTYDIGGTFSAHLLKGRDYVHCCSP 128
Cdd:pfam01660    1 FPYALSPEAQELLENL--GIEFSpYSVTPHS-HPAAKALENLLLEVLPSYLPNPSTVLDIKGSKLRHLKRGNPNVHCCNP 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  129 ALSMRDLMRYQSQAQslecymakrhtlpefqrpaFELYSNSPRHIHCFDRFQECTLQAPDgvKPFAVALHSLYDIPVEEF 208
Cdd:pfam01660   78 ILDPRDVARYPEAFS-------------------LEKSLGNGEDLRPTNTFEDCRVLAPT--TSYAFMHDSLHDWSPEEL 136

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  209 APALLRKNV-ECCYAAFHFSEDLLLDEEfcSGELDPIGGRFERDGdrlSFYFKDESTL--VYEHSFkNVIGYVLRTFFVA 285
Cdd:pfam01660  137 ADLFLRKPKlERLYATLVFPPELLFGDK--ESLYPELYTFWYKGD---RFHFYPDGHLggSYTHPL-NLLSWLTTSKIHL 210

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415  286 SSRYVYMKEAMCTRVNTMFMKFVKVDTFQLhrscfshqidtdalisgmndswelkRSLMLQSASRNIFKDkakvhvwfpg 365
Cdd:pfam01660  211 PGGFTYTVERLESRGAHHLFKITRGDGLTP-------------------------KVIVPDSRTFGPFEA---------- 255

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1774855415  366 lrnkllvpifrgivsrpgkvkkgnLLIDAEFFHTVSNHVRTYQGKQLTYESVLSLIESLRSRIVING 432
Cdd:pfam01660  256 ------------------------VLLPKIFVPRVLNYIRGKPIPLTVVNKLFSYLRSLKKRVVING 298
ps-ssRNAv_Alsuviricetes_RdRp cd23182
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of ...
 1284-1468 4.35e-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: 115.39  E-value: 4.35e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1284 YSHMIKSQPKCRLDTSvQSEYGALQTIVFHSKEVNSIFGPIFQELTRVLLSSiDQNRFLFYTRKSASDVEGFFSGISTNS 1363
Cdd:cd23182      3 IDFLIKTQQKVSPKTP-FNTGKAGQTIAAHSKSINFVLGPWIRYLEERLRDG-SRTHRYSNGLMDEEEAMLSQWKINHVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1364 NYEVLELDISKYDKSQNDFHCAVEYEIWKRLGFDDFLLSVWEMGHRKTFLTDFKAGIKACIWYQRKSGDVTTFIGNTVLV 1443
Cdd:cd23182     81 HATFVSNDYTAFDKSHNGESLLLEAAIMRRIGTPAAAPNLFIELHGKRTLRAKVLGGSGELDGMRDSGAAWTYCRNTDYN 160

                          170       180
                   ....*....|....*....|....*
gi 1774855415 1444 ATCLATLIPLENCLkAAFCGDDSLI 1468
Cdd:cd23182    161 LAVMLSLYRLKVKP-AAFSGDDSLL 184
Endornaviridae_RdRp cd23255
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Endornaviridae of ...
 1310-1488 9.13e-17

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: 81.43  E-value: 9.13e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1310 IVFHSKEVNSIFGPIFQEL-TRvlLSSIDQNRFLFYTRKSASDVEGFFSGISTNSNyeVLELDISKYDKsQNDFHC-AVE 1387
Cdd:cd23255     61 IVWQRKGICAIFSPIFNEAkKR--LKSLLKPKVVYADGLTPDELSARLRLVKNVKY--FFEDDLSKQDR-QTDKPIiDVE 135

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1388 YEIWKRLGFDDFLLSVWEMGHRKtflTDFK-AGIKACIWYQRKSGDVTTFIGNtvlVATCLATL----IPLENCLKAA-F 1461
Cdd:cd23255    136 MELYKLLGVDPNVIELWREVHEN---WRFKgKGVRGVGDAMRLTGQATTALGN---VITNLLVHsrlvKRNGSNLKLMlV 209

                          170       180
                   ....*....|....*....|....*..
gi 1774855415 1462 CGDDSLIFMPKGFNSDDVQVRANLAWN 1488
Cdd:cd23255    210 LGDDNLILTDTKIDLENLRKEIAEYHN 236
ps-ssRNAv_Hepelivirales_RdRp cd23209
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of ...
 1308-1471 4.12e-14

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: 72.14  E-value: 4.12e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1308 QTIVFHSKEVNSIFGPIFQELTRVLLSSIDQNRFLFYTRKSASDVEGFFSGISTNsnyeVLELDISKYDKSQNDFHCAVE 1387
Cdd:cd23209     26 QGISAWSKELCFVFGPWFRALEKILRRALKPNVLYANGHEAEPFVDKINQAHSAV----FIENDFTEFDSTQNLFSLLVE 101

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1388 YEIWKRLGFDDFLLSVWEMGHRKTFLTDFKAGIKACiwYQRKSGDVTTFIGNTVLVATCLATLIPLENCLKAAFCGDDSL 1467
Cdd:cd23209    102 LEILEACGMPPALAELYRALRAKWTLQAREGSLEGT--CKKTSGEPGTLLHNTIWNMAVMMHMVRGGVRKAAAFKGDDSV 179


                   ....
gi 1774855415 1468 IFMP 1471
Cdd:cd23209    180 VCCS 183
Togaviridae_RdRp cd23250
RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense ...
 1160-1594 7.08e-14

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: 75.96  E-value: 7.08e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1160 ADCKLTLSKDDP--VRNALKEPTFLRPVLRTAHERPRRANLKENLLALIKRNFNAPELTGIVDIEaSASFAVDRF--FEC 1235
Cdd:cd23250      5 SECCLDTATFCPakLRSYPKKHAYHQPQIRSAVPSPFQNTLQNVLAAATKRNCNVTQMRELPTLD-SAAFNVECFkkFAC 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1236 -------FIDKSdnslgsLRLRCRETLQ---RWLDNQEPATLKRLANFDTSALPAIDQYSHMIKSQPKCRLDTSVQSEYG 1305
Cdd:cd23250     84 nneyweeFKEKP------IRLTTENVTTyvtKLKGPKAAALFAKTHNLVPLQEVPMDRFVMDMKRDVKVTPGTKHTEERP 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1306 ALQTIVFHSKEVNSIFGPIFQELTR----VLLSSIdqnRFLFytRKSASD-----VEGFFSGIStnsnyeVLELDISKYD 1376
Cdd:cd23250    158 KVQVIQAADPLATAYLCGIHRELVRrlnaVLLPNI---HTLF--DMSAEDfdaiiAEHFQPGDK------VLETDIASFD 226

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1377 KSQNDFHCAVEYEIWKRLGFDDFLLSVWEMG-------HRKTFlTDFKAGIkaciwyQRKSGDVTTFIGNTVLVATCLAT 1449
Cdd:cd23250    227 KSQDDAMALTALMILEDLGVDQELLDLIEAAfgeitsvHLPTG-TRFKFGA------MMKSGMFLTLFVNTVLNIVIASR 299

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1450 LIP--LENCLKAAFCGDDSLIfmpKGFNSDDVQVRANLAW-NFEAKLFKKRIG----YFCGKYVI---IHDSGCTIyPDP 1519
Cdd:cd23250    300 VLRerLTNSRCAAFIGDDNIV---HGVVSDKLMADRCATWlNMEVKIIDAVIGekppYFCGGFILydsVTGTACRV-ADP 375

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1774855415 1520 LKLISKLGAKSIKDWSHLEETRVSLMDNAGNYGNCAYFPHLDEAIAEVFpAAVGGRFAFCALYKFLSDKVLFRSL 1594
Cdd:cd23250    376 LKRLFKLGKPLPADDEQDEDRRRALHDEVKRWFRVGITSELEVAVESRY-EVNGLSNILLAMATLAQSVKNFKAL 449
Hepeviridae_RdRp cd23259
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of ...
 1308-1468 7.41e-09

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: 58.60  E-value: 7.41e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1308 QTIVFHSKEVNSIFGPIFQELTRVLLSSIDQNrfLFYTrkSASDVEGFFSGISTNSNYEVLELDISKYDKSQNDFHCAVE 1387
Cdd:cd23259     90 QGISAWSKTFCALFGPWFRAIEKAIVALLPPN--IFYG--DAYEESVFSAAVAGAGSCRVFENDFSEFDSTQNNFSLGLE 165

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1388 YEIWKRLGFDDFLLSVWEMGHRKTFLTDFKAGIKACiwYQRKSGDVTTFIGNTVLVATCLATLIPLENCLKAAFCGDDSL 1467
Cdd:cd23259    166 CEIMEECGMPQWLVRLYHLVRSAWVLQAPKESLRGF--WKKHSGEPGTLLWNTVWNMAVIAHCYEFRDLAVAAFKGDDSV 243


                   .
gi 1774855415 1468 I 1468
Cdd:cd23259    244 V 244
Benyviridae_RdRp cd23257
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Benyviridae of ...
 1308-1465 1.06e-06

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: 50.69  E-value: 1.06e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1308 QTIVFHSKEVNSIFGPIFQELTRVLLSSIDQNRFLFYTRKSASDVEGFFSGISTNSNYEVLE-LDISKYDKSQNDFHCAV 1386
Cdd:cd23257     26 QGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYDNTMSETEFVGKINAAMNTVPDSAINGvIDAAACDSGQGVFTQLI 105

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1774855415 1387 EYEIWKRLGFDDFLLSvWEMGHRKTFLTDFKAgIKACIWYQRKSGDVTTFIGNTVLVATCLATLIPLENCLKAAFCGDD 1465
Cdd:cd23257    106 ERYIYAALGISDFFLD-WYFSFREKYVMQSRY-VRAHMSYVKTSGEPGTLLGNTILMGAMLNAMLRGTGPFCMAMKGDD 182
ps-ssRNA_RdRp_Tymovirales cd23207
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Tymovirales of ...
 1286-1468 3.72e-05

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: 46.24  E-value: 3.72e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1286 HMIKSQPKCRLDtSVQSEYGALQTIVFHSKEVNSIFGPIFQELTRVLLSSIDQNRFLfYTRKSASDVEGF-----FSGIS 1360
Cdd:cd23207     13 IFIKGQHKKKDE-KIFSDAKAGQTLALFHDQIILRFGPYARYMRRFINADLPPNIYI-HCGKTPEDLSKWckehwQHGPS 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1361 TNSNYEVleldiskYDKSQNdfHCAVEYEIW--KRLGFDDFL--LSVWEMGHRKTFLtdfkaGIKACIwyqRKSGDVTTF 1436
Cdd:cd23207     91 TANDYTA-------FDQSQD--GEFVVFEVLlmRHLHIPDDLieLYVDIKTNAYSHL-----GPLSIM---RLTGEPGTF 153

                          170       180       190
                   ....*....|....*....|....*....|..
gi 1774855415 1437 IGNTVLVATCLATLIPLENCLKAAFCGDDSLI 1468
Cdd:cd23207    154 DFNTDYNLALTYAKYDLPPGTPICFSGDDSVA 185
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
 1367-1499 4.47e-04

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: 43.66  E-value: 4.47e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1367 VLELDISKYDKSQNDFHCAVEYEIWKRL-GFDDFLLSVWEM-----GHrktfltdFKAGIKaciwYQRK----SGDVTTF 1436
Cdd:cd23179     85 VFSLDASRFDAHVSVELLRLEHSVYLACyPGDPELRKLLKWqlvnkGR-------TSNGVK----YKTRggrmSGDMNTG 153

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1774855415 1437 IGNTVLVATCLATLIPLENCLKAAFC-GDDSLIFMPKgfnSDDVQVRANLAWNFEAKLFKKRIG 1499
Cdd:cd23179    154 LGNCLIMLAMVYAVLRELGIKYDLLVdGDDALVFVER---EDLERLLEEFAEFFLEGGGEETVE 214
Aureusvirus_RdRp cd23243
RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded ...
 1370-1473 3.01e-03

RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Aureusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. In the Aureusvirus genus plants serve as natural hosts. There are six species in this genus: Cucumber leaf spot virus (CLSV), Elderberry aureusvirus 1, Johnsongrass chlorotic stripe mosaic virus (JCSMV), Maize white line mosaic virus (MWLMV), Pothos latent virus (PoLV), and Yam spherical virus (YSV). Aureusviruses infect various natural host plants but their individual range is generally restricted to a few species, pothos and pigeon pea or lisianthus for PoLV, yam for YSV, sesame for SNMV, cucumber, melon or squash for CLSV and various Poaceae species, mainly maize (MWLMV) or johnsongrass (JCSMV). Aureusviruses are transmitted mechanically and by seeds. Transmission through the soil or by the water circulating in hydroponic systems for PoLV, CLSV and MWLMV, or by the fungus Olpidium bornovanus (for CLSV) have also been reported. 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: 438093  Cd Length: 488  Bit Score: 42.13  E-value: 3.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774855415 1370 LDISKYDKsqndfHCAVEYEIWKRLGFDDFL-------LSVWEMGHRKT-FLTD--FKAGIKACiwyqRKSGDVTTFIGN 1439
Cdd:cd23243    209 LDASRFDQ-----HCSRQALEWEHSVYNAIFrdpylaeLLTWQIDNVGTaYLKDgfVRYRVDGC----RMSGDMNTSMGN 279

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1774855415 1440 tVLVATCLATLIPLENCLKA--AFCGDDSLIFMPKG 1473
Cdd:cd23243    280 -YLIMSCLVYQFCKEVGLDAslANCGDDCVLFLEKK 314
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 1421-1471 4.93e-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: 37.32  E-value: 4.93e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1774855415 1421 KACIWYQRKSGDVTTFIGNT----VLVATCLATL---IPLENCLKAAFCGDDSLIFMP 1471
Cdd:cd23167     16 PDLLKAGQPSGSPNTSADNSlinlLLARLALRKAcgrAEFLNSVGILVYGDDSLVSVP 73
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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.
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