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Conserved domains on  [gi|556694|emb|CAA41362|]
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2a protein [Brome mosaic virus]

Protein Classification

BBMV_Gp1_N and Bromoviridae_RdRp domain-containing protein( domain architecture ID 10266827)

BBMV_Gp1_N and Bromoviridae_RdRp domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RdRP_2 pfam00978
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...
 256-688 0e+00

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: 573.82  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     256 NGDYSMDFDRIRLKQSDVDWY-KDPDKYFQPKMNIGSAQRRVGTQKEVLTALKKRNADVPEMGDAINMKETAKAIAKRFR 334
Cdd:pfam00978   1 TSDISLDLDDCRLDPSKSKPKpKDKEPYLVPVLRTAAPSPRQNTLKEVLLALKKRNFNVPELQESVDLDDTAERVAERFK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     335 STFLNVDGEDCLRASMDV---MTKCLEYHKKWG-KHMDLQGVNVAAETDLRRYQHMLKSDVKPVVTDTLHLERAVAATIT 410
Cdd:pfam00978  81 KSFLDKEKLDKLDPIINTtenVSRWLDKQSGKKaAQLKLDDLVPLHEVDLDRYKHMIKSDVKPKLDLSPQSERPALQTIT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     411 FHSKGVTSNFSPFFTACFEKLSLALKSRFIVPIGKISSLELKNVRLNN--RYFLEADLSKFDKSQGELHLEFQREILLAL 488
Cdd:pfam00978 161 YHDKGVTAYFSPIFRELFERLLYVLKPKIVFPTGMTSSLIAEHFEFLDasEDFLEIDFSKFDKSQGELHLLVQLEILKLL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     489 GFPAPLTNWWSDFHRDSYLSDPHAKVGMSVSFQRRTGDAFTYFGNTLVTMAMIAYASDLSDCDCAIFSGDDSLIISKVKP 568
Cdd:pfam00978 241 GLDPELADLWFKFHRQSYIKDRKNGVGFSVDYQRKSGDANTYLGNTLVTMAMLASVYDLEKIDCAAFSGDDSLIFSPKPI 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     569 VLDTDMFTSLFNMEIKVMDPSVPYVCSKFLVETEMGNlVSIPDPMREIQRLAKRKILRDEQMLRAHFVSFCDRMK-FINQ 647
Cdd:pfam00978 321 EDPASRFATLFNMEAKVFDPSVPYFCSKFLLEVDGGA-FFVPDPLKLLQKLGKKKIPDDEQHLDEIFTSLCDLTKsFNDD 399

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|.
gi 556694     648 LDEKMITMLCHFVYLKYGKEKPWIFEEVRAALAAFSLYSEN 688
Cdd:pfam00978 400 CVVLELLDLAVARYYKYAPEGYAALCALHKALSSFTLFFSL 440
BBMV_Gp1_N super family cl04563
Broad bean mottle virus, Gp1, N-terminal; This region represents the N terminus of Broad bean ...
 1-234 2.89e-136

Broad bean mottle virus, Gp1, N-terminal; This region represents the N terminus of Broad bean mottle virus, Gp1 (2a protein), and is always found N terminal to a predicted RNA-dependent RNA polymerase region (pfam00978).


The actual alignment was detected with superfamily member pfam04522:

Pssm-ID: 461342  Cd Length: 234  Bit Score: 403.74  E-value: 2.89e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694       1 MSSKTWDDDFVRQVPSFQWIIDQSLEDEVEAASLQVPEPADGVAIDGSLASFKLAIAPLEIGGVFDPPFDRVRWGSICDT 80
Cdd:pfam04522   1 MKSKDDDDDFQRPSFQFIIDIDLEDEDEAAAAQLQEPADADAIAGDGALAKFAIAIAEIEGGFDFDFDFDRVGSGCDCDQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694      81 VQQMVQQFTDRPLIPQAEMARMLYLDIPGSFVLEDEIDDWYPEDTSDGYGVTFAPDEDHASDLKLASDSSNCEIEEVRVT 160
Cdd:pfam04522  81 QMQMQFQDRDLILIAEAAMALMLDIDGPFSFEDEDDDDDPEDEDDGDGVGFAAAADEAHALDLALASDNCECEEEEVRGD 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556694     161 GDTPKELTLGDRYMGIDEEFQTTNTDYDITLQIMNPIEHRVSRVIDTHCHPDNPDISTGPIYVERVSLARTEAT 234
Cdd:pfam04522 161 GDKEKELGDGDMGIDEDEEFQNTDTDIDIQIMIMIEHEHRRSIDIDCHCDNDDIDIGPGPIEMERLALAEAEAH 234
 
Name Accession Description Interval E-value
RdRP_2 pfam00978
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...
 256-688 0e+00

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: 573.82  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     256 NGDYSMDFDRIRLKQSDVDWY-KDPDKYFQPKMNIGSAQRRVGTQKEVLTALKKRNADVPEMGDAINMKETAKAIAKRFR 334
Cdd:pfam00978   1 TSDISLDLDDCRLDPSKSKPKpKDKEPYLVPVLRTAAPSPRQNTLKEVLLALKKRNFNVPELQESVDLDDTAERVAERFK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     335 STFLNVDGEDCLRASMDV---MTKCLEYHKKWG-KHMDLQGVNVAAETDLRRYQHMLKSDVKPVVTDTLHLERAVAATIT 410
Cdd:pfam00978  81 KSFLDKEKLDKLDPIINTtenVSRWLDKQSGKKaAQLKLDDLVPLHEVDLDRYKHMIKSDVKPKLDLSPQSERPALQTIT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     411 FHSKGVTSNFSPFFTACFEKLSLALKSRFIVPIGKISSLELKNVRLNN--RYFLEADLSKFDKSQGELHLEFQREILLAL 488
Cdd:pfam00978 161 YHDKGVTAYFSPIFRELFERLLYVLKPKIVFPTGMTSSLIAEHFEFLDasEDFLEIDFSKFDKSQGELHLLVQLEILKLL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     489 GFPAPLTNWWSDFHRDSYLSDPHAKVGMSVSFQRRTGDAFTYFGNTLVTMAMIAYASDLSDCDCAIFSGDDSLIISKVKP 568
Cdd:pfam00978 241 GLDPELADLWFKFHRQSYIKDRKNGVGFSVDYQRKSGDANTYLGNTLVTMAMLASVYDLEKIDCAAFSGDDSLIFSPKPI 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     569 VLDTDMFTSLFNMEIKVMDPSVPYVCSKFLVETEMGNlVSIPDPMREIQRLAKRKILRDEQMLRAHFVSFCDRMK-FINQ 647
Cdd:pfam00978 321 EDPASRFATLFNMEAKVFDPSVPYFCSKFLLEVDGGA-FFVPDPLKLLQKLGKKKIPDDEQHLDEIFTSLCDLTKsFNDD 399

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|.
gi 556694     648 LDEKMITMLCHFVYLKYGKEKPWIFEEVRAALAAFSLYSEN 688
Cdd:pfam00978 400 CVVLELLDLAVARYYKYAPEGYAALCALHKALSSFTLFFSL 440
Bromoviridae_RdRp cd23252
RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense ...
 258-620 0e+00

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: 549.52  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   258 DYSMDFDRIRLKQSDVDWYKDPDKYFQPKMNIGSAQRRVGTQKEVLTALKKRNADVPEMGDAINMKETAKAIAKRFRSTF 337
Cdd:cd23252   1 DISLDVDHCRLDQSDFNDWTKPDGYLEPVLNTGSGSKRVGTQREALLAIKKRNANVPELGDSVDLDRVSNAVANRFLTTV 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   338 LNVDGEDclrasmdvmtkcleyhkkwgkhmdlqgvnvaaetdlrRYQHMLKSDVKPVVTDTLHLERAVAATITFHSKGVT 417
Cdd:cd23252  81 IDVDRLD-------------------------------------KYMHMIKSDLKPVEDDSLHVERPVPATITYHKKGIV 123

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   418 SNFSPFFTACFEKLSLALKSRFIVPIGKISSLELKNVRLNN--RYFLEADLSKFDKSQGELHLEFQREILLALGFPAPLT 495
Cdd:cd23252 124 MQFSPLFLAAFERLLRCLRSKIVIPSGKIHQLFMIDPSVLNasKHFKEIDFSKFDKSQGELHHEIQEHILNALGCPAPFT 203

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   496 NWWSDFHRDSYLSDPHAKVGMSVSFQRRTGDAFTYFGNTLVTMAMIAYASDLSD--CDCAIFSGDDSLIISKVKPVL-DT 572
Cdd:cd23252 204 KWWFDFHRRSYISDRRAGVGFSVDFQRRTGDAFTYLGNTLVTLAELAYVYDLDDpnFDFVVASGDDSLIGSVEPLPRdDE 283

                       330       340       350       360       370
                ....*....|....*....|....*....|....*....|....*....|
gi 556694   573 DMFTSLFNMEIKVMDpSVPYVCSKFLVETEMG--NLVSIPDPMREIQRLA 620
Cdd:cd23252 284 DLFTTLFNFEAKFPH-NQPFICSKFLLSDEFGdeNVFSVPDPLKLLQRLG 332
BBMV_Gp1_N pfam04522
Broad bean mottle virus, Gp1, N-terminal; This region represents the N terminus of Broad bean ...
 1-234 2.89e-136

Broad bean mottle virus, Gp1, N-terminal; This region represents the N terminus of Broad bean mottle virus, Gp1 (2a protein), and is always found N terminal to a predicted RNA-dependent RNA polymerase region (pfam00978).


Pssm-ID: 461342  Cd Length: 234  Bit Score: 403.74  E-value: 2.89e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694       1 MSSKTWDDDFVRQVPSFQWIIDQSLEDEVEAASLQVPEPADGVAIDGSLASFKLAIAPLEIGGVFDPPFDRVRWGSICDT 80
Cdd:pfam04522   1 MKSKDDDDDFQRPSFQFIIDIDLEDEDEAAAAQLQEPADADAIAGDGALAKFAIAIAEIEGGFDFDFDFDRVGSGCDCDQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694      81 VQQMVQQFTDRPLIPQAEMARMLYLDIPGSFVLEDEIDDWYPEDTSDGYGVTFAPDEDHASDLKLASDSSNCEIEEVRVT 160
Cdd:pfam04522  81 QMQMQFQDRDLILIAEAAMALMLDIDGPFSFEDEDDDDDPEDEDDGDGVGFAAAADEAHALDLALASDNCECEEEEVRGD 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556694     161 GDTPKELTLGDRYMGIDEEFQTTNTDYDITLQIMNPIEHRVSRVIDTHCHPDNPDISTGPIYVERVSLARTEAT 234
Cdd:pfam04522 161 GDKEKELGDGDMGIDEDEEFQNTDTDIDIQIMIMIEHEHRRSIDIDCHCDNDDIDIGPGPIEMERLALAEAEAH 234
 
Name Accession Description Interval E-value
RdRP_2 pfam00978
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...
 256-688 0e+00

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: 573.82  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     256 NGDYSMDFDRIRLKQSDVDWY-KDPDKYFQPKMNIGSAQRRVGTQKEVLTALKKRNADVPEMGDAINMKETAKAIAKRFR 334
Cdd:pfam00978   1 TSDISLDLDDCRLDPSKSKPKpKDKEPYLVPVLRTAAPSPRQNTLKEVLLALKKRNFNVPELQESVDLDDTAERVAERFK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     335 STFLNVDGEDCLRASMDV---MTKCLEYHKKWG-KHMDLQGVNVAAETDLRRYQHMLKSDVKPVVTDTLHLERAVAATIT 410
Cdd:pfam00978  81 KSFLDKEKLDKLDPIINTtenVSRWLDKQSGKKaAQLKLDDLVPLHEVDLDRYKHMIKSDVKPKLDLSPQSERPALQTIT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     411 FHSKGVTSNFSPFFTACFEKLSLALKSRFIVPIGKISSLELKNVRLNN--RYFLEADLSKFDKSQGELHLEFQREILLAL 488
Cdd:pfam00978 161 YHDKGVTAYFSPIFRELFERLLYVLKPKIVFPTGMTSSLIAEHFEFLDasEDFLEIDFSKFDKSQGELHLLVQLEILKLL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     489 GFPAPLTNWWSDFHRDSYLSDPHAKVGMSVSFQRRTGDAFTYFGNTLVTMAMIAYASDLSDCDCAIFSGDDSLIISKVKP 568
Cdd:pfam00978 241 GLDPELADLWFKFHRQSYIKDRKNGVGFSVDYQRKSGDANTYLGNTLVTMAMLASVYDLEKIDCAAFSGDDSLIFSPKPI 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694     569 VLDTDMFTSLFNMEIKVMDPSVPYVCSKFLVETEMGNlVSIPDPMREIQRLAKRKILRDEQMLRAHFVSFCDRMK-FINQ 647
Cdd:pfam00978 321 EDPASRFATLFNMEAKVFDPSVPYFCSKFLLEVDGGA-FFVPDPLKLLQKLGKKKIPDDEQHLDEIFTSLCDLTKsFNDD 399

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|.
gi 556694     648 LDEKMITMLCHFVYLKYGKEKPWIFEEVRAALAAFSLYSEN 688
Cdd:pfam00978 400 CVVLELLDLAVARYYKYAPEGYAALCALHKALSSFTLFFSL 440
Bromoviridae_RdRp cd23252
RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense ...
 258-620 0e+00

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: 549.52  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   258 DYSMDFDRIRLKQSDVDWYKDPDKYFQPKMNIGSAQRRVGTQKEVLTALKKRNADVPEMGDAINMKETAKAIAKRFRSTF 337
Cdd:cd23252   1 DISLDVDHCRLDQSDFNDWTKPDGYLEPVLNTGSGSKRVGTQREALLAIKKRNANVPELGDSVDLDRVSNAVANRFLTTV 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   338 LNVDGEDclrasmdvmtkcleyhkkwgkhmdlqgvnvaaetdlrRYQHMLKSDVKPVVTDTLHLERAVAATITFHSKGVT 417
Cdd:cd23252  81 IDVDRLD-------------------------------------KYMHMIKSDLKPVEDDSLHVERPVPATITYHKKGIV 123

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   418 SNFSPFFTACFEKLSLALKSRFIVPIGKISSLELKNVRLNN--RYFLEADLSKFDKSQGELHLEFQREILLALGFPAPLT 495
Cdd:cd23252 124 MQFSPLFLAAFERLLRCLRSKIVIPSGKIHQLFMIDPSVLNasKHFKEIDFSKFDKSQGELHHEIQEHILNALGCPAPFT 203

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   496 NWWSDFHRDSYLSDPHAKVGMSVSFQRRTGDAFTYFGNTLVTMAMIAYASDLSD--CDCAIFSGDDSLIISKVKPVL-DT 572
Cdd:cd23252 204 KWWFDFHRRSYISDRRAGVGFSVDFQRRTGDAFTYLGNTLVTLAELAYVYDLDDpnFDFVVASGDDSLIGSVEPLPRdDE 283

                       330       340       350       360       370
                ....*....|....*....|....*....|....*....|....*....|
gi 556694   573 DMFTSLFNMEIKVMDpSVPYVCSKFLVETEMG--NLVSIPDPMREIQRLA 620
Cdd:cd23252 284 DLFTTLFNFEAKFPH-NQPFICSKFLLSDEFGdeNVFSVPDPLKLLQRLG 332
BBMV_Gp1_N pfam04522
Broad bean mottle virus, Gp1, N-terminal; This region represents the N terminus of Broad bean ...
 1-234 2.89e-136

Broad bean mottle virus, Gp1, N-terminal; This region represents the N terminus of Broad bean mottle virus, Gp1 (2a protein), and is always found N terminal to a predicted RNA-dependent RNA polymerase region (pfam00978).


Pssm-ID: 461342  Cd Length: 234  Bit Score: 403.74  E-value: 2.89e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694       1 MSSKTWDDDFVRQVPSFQWIIDQSLEDEVEAASLQVPEPADGVAIDGSLASFKLAIAPLEIGGVFDPPFDRVRWGSICDT 80
Cdd:pfam04522   1 MKSKDDDDDFQRPSFQFIIDIDLEDEDEAAAAQLQEPADADAIAGDGALAKFAIAIAEIEGGFDFDFDFDRVGSGCDCDQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694      81 VQQMVQQFTDRPLIPQAEMARMLYLDIPGSFVLEDEIDDWYPEDTSDGYGVTFAPDEDHASDLKLASDSSNCEIEEVRVT 160
Cdd:pfam04522  81 QMQMQFQDRDLILIAEAAMALMLDIDGPFSFEDEDDDDDPEDEDDGDGVGFAAAADEAHALDLALASDNCECEEEEVRGD 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556694     161 GDTPKELTLGDRYMGIDEEFQTTNTDYDITLQIMNPIEHRVSRVIDTHCHPDNPDISTGPIYVERVSLARTEAT 234
Cdd:pfam04522 161 GDKEKELGDGDMGIDEDEEFQNTDTDIDIQIMIMIEHEHRRSIDIDCHCDNDDIDIGPGPIEMERLALAEAEAH 234
Mayoviridae_RdRp cd23256
RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense ...
 354-672 1.14e-67

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: 227.70  E-value: 1.14e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   354 TKCLEYHKKWGKHMDlQGVNVAAeTDLRRYQHMLKSDVKPVVTDTLHLERAVAATITFHSKGVTSNFSPFFTACFEKLSL 433
Cdd:cd23256   8 DQIQLYQNKVGNKVN-DPVVLAL-TSLNKYSHMIKRDRKPVLTTAVQSEYTKAATITYHDKDITQVATPIFRQFKTRLLA 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   434 ALKSRFIVPIGKISSLE--LKNVRL--NNRYFLEADLSKFDKSQGELHLEFQREILLALGFPAPLTNWWSDFHRDSYLSD 509
Cdd:cd23256  86 CKKSNLCIPLDHDHDISgwLTNRHLgsENGTFTEIDFSKFDKSQGELHQLIQDLILLRFGCDPEFVSLWSTAHRSSSIKD 165

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   510 PHAKVGMSVSFQRRTGDAFTYFGNTLVTMAMIAYAsdLSDCDCAIF-----SGDDSLIISKVKPVLDTDMFTSLFNMEIK 584
Cdd:cd23256 166 QNVGISFKTDFQRRTGDAFTFLGNSLVTAVMLAYV--LSFEDEKKIrymlvGGDDSLICSYGPISVPLEPLSTIFNMSCK 243

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   585 VMDPSVPYVCSKFLVETEmGNLVSIPDPMREIQRLAKRKILRDEQMLRAHFVSFCDRMKFInqLDEKMITMLCHFVYLKY 664
Cdd:cd23256 244 LIQPSCPYFASRYIIRVG-DEILCVPDPYKLLVKMGRKDIPDNEASLEEVRTGLADSAKPL--FDDEVKQKLSILVQIRY 320


                ....*...
gi 556694   665 GKEKPWIF 672
Cdd:cd23256 321 NKSAPSLY 328
Kitaviridae_RdRp cd23254
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of ...
 381-640 1.05e-62

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: 212.01  E-value: 1.05e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   381 RRYQHMLKSDVKPVVTDTLHLERAVAATITFHSKGVTSNFSPFFTACFEKLSLALKSRFIVpIGKISSLELKNvRLNNR- 459
Cdd:cd23254   1 NVYSFMIKRNPKPNLTVDAAYKYPALQTIAYHDKDINAIFCPIFRELKKRLLAVLKPNFVI-FTDMSPEDFEE-LLNRRf 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   460 ---------YFLEADLSKFDKSQGELHLEFQREILLALGFPAPLTNWWSDFHRDSYLSDPHAKVGMSVSFQRRTGDAFTY 530
Cdd:cd23254  79 ppevlskllHKLEIDISKYDKSQGELALLFECKLMRRFGVPEELVELWFNAHVLTTLYDRTNKLKALVEYQRKSGDASTF 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   531 FGNTLVTMAMIAYASDLSDCDCAIFSGDDSLIISKVKPVL-DTDMFTSLFNMEIKVMDPSVPYVCSKFLVETEmGNLVSI 609
Cdd:cd23254 159 FGNTLFLMAVLADLFDLSDLELALFSGDDSLLFGRNLLDYdDSQHFALKFNLESKFLNYKYPYFCSKFLLPVG-GRWYFV 237

                       250       260       270
                ....*....|....*....|....*....|.
gi 556694   610 PDPMREIQRLAkRKILRDEQMLRAHFVSFCD 640
Cdd:cd23254 238 PDPVKLLTKLG-RHDLVNWEHVEEYRISLKD 267
ps-ssRNAv_Martellivirales_RdRp cd23208
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of ...
 382-565 1.96e-60

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: 202.98  E-value: 1.96e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   382 RYQHMLKSDVKPVVTDTLHLERAVAATITFHSKGVTSNFSPFFTACFEKLSLALKSRFIVPIGKISSLELKNV-----RL 456
Cdd:cd23208   2 KYEMMIKSDVKPKLDLTAQQEYPKLQTIVYHDKNITAIFCPIFKELFERLLSCLKKKVVIYTGMMTSAELNDFisalhLE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   457 NNRYFLEADLSKFDKSQGELHLEFQREILLALGFPAPLTNWWSDFHRDSYLSDPHAKVGMSVSFQRRTGDAFTYFGNTLV 536
Cdd:cd23208  82 SGYYVLEIDFSKFDKSQGALHLLTELLILRRLGVDEPLLVLWEFAHTQSTTRDINNGISFETAYQRKSGDAFTYFGNTLV 161

                       170       180
                ....*....|....*....|....*....
gi 556694   537 TMAMIAYASDLSDCDCAIFSGDDSLIISK 565
Cdd:cd23208 162 TMAALLDVLDLEKIVCIAFGGDDSLIFSK 190
Closteroviridae_RdRp cd23253
RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense ...
 382-640 3.55e-59

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: 202.02  E-value: 3.55e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   382 RYQHMLKSDVKPVVTDTLHLERAVAATITFHSKGVTSNFSPFFTACFEKLSLALKSRFIV-------PIGKISSLELKNv 454
Cdd:cd23253   2 SFKLMVKGDMKPKLDSSSLSKYPPGQNIVYHERAINAFFSPIFLEVFDRIKYCLSDKIILysgmnleELASLIRSKLGD- 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   455 RLNNRYFLEADLSKFDKSQGELHLEFQREILLALGFPAPLTNWW--SDFHRDSYLSDphAKVGMSVSFQRRTGDAFTYFG 532
Cdd:cd23253  81 PLDEYKTVEIDFSKFDKSQGVLFKVYEELVYKFFGFSEELYDNWkcSEYFSCRATSD--SGVSLELGAQRRTGSPNTWLG 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   533 NTLVTMAMIAYASDLSDCDCAIFSGDDSLIISKVKPVLDTDMFTSLFNMEIKVMDPSVPYVCSKFLVETEmGNLVSIPDP 612
Cdd:cd23253 159 NTLVTLGILSSSYDLDDIDLLLVSGDDSLIFSKKPLPNKANEINLDFGFEAKFIENSVPYFCSKFIIEDR-GKIKVVPDP 237

                       250       260
                ....*....|....*....|....*...
gi 556694   613 MREIQRLAKRKILRDEQMLRAHFVSFCD 640
Cdd:cd23253 238 VKLFEKLSVPIRLEDETLLKERFTSFKD 265
Virgaviridae_RdRp cd23251
RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense ...
 247-653 2.25e-48

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: 177.43  E-value: 2.25e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   247 DSYHqalVENGDYSMDFDRIRLKQS-DVDWYKDPdKYFQPKMNIGSAQRRVGTQKEVLTALKKRNADVPEMGDAINMKET 325
Cdd:cd23251  12 DGYT---VATSDINLNVEDCTLDPSkSVKVWQEK-EGLKPVLRTAMPEKRQNGLLESLLALIKRNMAAPKLQGAVNEFET 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   326 AKAIAKRFRSTFLNVDGEDCLRASmdvmtkCLEYHKKWgkhMDLQGVNVAA----------ETDLRRYQHMLKSDVKPVV 395
Cdd:cd23251  88 IERVIKKAKDVFFDEDLIDRSPLS------TRESFLRW---WDKQSTTARAqlladdrvldEIDVCTYNFMIKNDVKPKL 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   396 TDTLHLERAVAATITFHSKGVTSNFSPFFTACFEKLSLALKSRFIVpigkisslelkNVRLN----NRYF---------- 461
Cdd:cd23251 159 DLSPQSEYAALQTVVYPDKIVNALFGPIFKEINERILSALDPHVVF-----------NTRMTaeelNETVefldpdeeyd 227

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   462 -LEADLSKFDKSQGELHLEFQREILLALGFPAPLTNWWSDFHRDSYLSDPHAKVGMSVSFQRRTGDAFTYFGNTLVTMAM 540
Cdd:cd23251 228 aLEIDFSKFDKSKTSLHIRAVIELYKLFGLDGMLAFLWEKSQCQTTVKDRQNGIKAYLLYQQKSGNCDTYGSNTWSAALA 307

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   541 IAYASDLSDCDCAIFSGDDSLI-ISKVKPVLD-TDMFTSLFNMEIKVMDPSVPYVCSKFLVETEMGNLVSiPDPMREIQR 618
Cdd:cd23251 308 LLSMLPLEKAIFMIFGGDDSLIlFPKGLVIPDpCRRLASLWNFECKLFKFKYGYFCGKFLLKHGDGYIFY-PDPLKLITK 386

                       410       420       430       440
                ....*....|....*....|....*....|....*....|.
gi 556694   619 LAkRKILRDEQMLRAHFVSFCD------RMKFINQLDEKMI 653
Cdd:cd23251 387 LG-RKDIKDGEHLSEIFVSICDnyksyrDYRVLEALDVAVV 426
ps-ssRNAv_Alsuviricetes_RdRp cd23182
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of ...
 381-562 2.52e-18

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: 83.80  E-value: 2.52e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   381 RRYQHMLKSDVKPVvTDTLHLERAVAATITFHSKGVTSNFSPFFTACFEKLSLALKSRFIVPIG----KISSLELKNVRL 456
Cdd:cd23182   1 TDIDFLIKTQQKVS-PKTPFNTGKAGQTIAAHSKSINFVLGPWIRYLEERLRDGSRTHRYSNGLmdeeEAMLSQWKINHV 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   457 NNRYFLEADLSKFDKSQGELHLEFQREILLALGFPAPLTNWWSDFHRDSYLSDPHAKVGMSVSFQRRTGDAFTYFGNTLV 536
Cdd:cd23182  80 PHATFVSNDYTAFDKSHNGESLLLEAAIMRRIGTPAAAPNLFIELHGKRTLRAKVLGGSGELDGMRDSGAAWTYCRNTDY 159

                       170       180
                ....*....|....*....|....*.
gi 556694   537 TMAMIaYASDLSDCDCAIFSGDDSLI 562
Cdd:cd23182 160 NLAVM-LSLYRLKVKPAAFSGDDSLL 184
ps-ssRNAv_Hepelivirales_RdRp cd23209
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of ...
 409-562 2.48e-15

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: 74.83  E-value: 2.48e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   409 ITFHSKGVTSNFSPFFTACFEKLSLALKSRFIVPIGKISSLELKNV-RLNNRYFLEADLSKFDKSQGELHLEFQREILLA 487
Cdd:cd23209  28 ISAWSKELCFVFGPWFRALEKILRRALKPNVLYANGHEAEPFVDKInQAHSAVFIENDFTEFDSTQNLFSLLVELEILEA 107

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 556694   488 LGFPAPLTNWWSDFHRDSYLSDPHAKVGMsvSFQRRTGDAFTYFGNTLVTMAMIAYASDLSDCDCAIFSGDDSLI 562
Cdd:cd23209 108 CGMPPALAELYRALRAKWTLQAREGSLEG--TCKKTSGEPGTLLHNTIWNMAVMMHMVRGGVRKAAAFKGDDSVV 180
Endornaviridae_RdRp cd23255
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Endornaviridae of ...
 409-581 4.86e-12

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: 66.40  E-value: 4.86e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   409 ITFHSKGVTSNFSPFFTACFEKLSLALKSRFIVPIGK----ISSLeLKNVRlNNRYFLEADLSKFDKsQGELH-LEFQRE 483
Cdd:cd23255  61 IVWQRKGICAIFSPIFNEAKKRLKSLLKPKVVYADGLtpdeLSAR-LRLVK-NVKYFFEDDLSKQDR-QTDKPiIDVEME 137

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   484 ILLALGFPAPLTNWWSDFHRDSYLSDPHAKvGMSvSFQRRTGDAFTYFGNTLVTMAMIA--YASDLSDCDCAIFSGDDSL 561
Cdd:cd23255 138 LYKLLGVDPNVIELWREVHENWRFKGKGVR-GVG-DAMRLTGQATTALGNVITNLLVHSrlVKRNGSNLKLMLVLGDDNL 215

                       170       180
                ....*....|....*....|....
gi 556694   562 IISKVKPvlDTDMFT----SLFNM 581
Cdd:cd23255 216 ILTDTKI--DLENLRkeiaEYHNM 237
Togaviridae_RdRp cd23250
RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense ...
 462-629 8.46e-10

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: 61.71  E-value: 8.46e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   462 LEADLSKFDKSQGELHLEFQREILLALGFPAPLTNWWSDFHRDsyLSDPHAKVGMSVSF--QRRTGDAFTYFGNTL--VT 537
Cdd:cd23250 218 LETDIASFDKSQDDAMALTALMILEDLGVDQELLDLIEAAFGE--ITSVHLPTGTRFKFgaMMKSGMFLTLFVNTVlnIV 295

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   538 MAMIAYASDLSDCDCAIFSGDDSLIISKVKPVLDTDMFTSLFNMEIKVMDPSV----PYVCSKF-LVETEMGNLVSIPDP 612
Cdd:cd23250 296 IASRVLRERLTNSRCAAFIGDDNIVHGVVSDKLMADRCATWLNMEVKIIDAVIgekpPYFCGGFiLYDSVTGTACRVADP 375

                       170
                ....*....|....*..
gi 556694   613 MREIQRLAKRKILRDEQ 629
Cdd:cd23250 376 LKRLFKLGKPLPADDEQ 392
Gammaflexiviridae_RdRp cd23249
RNA-dependent RNA polymerase (RdRp) in the family Gammaflexiviridae of positive-sense ...
 463-567 8.38e-08

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: 8.38e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   463 EADLSKFDKSQGELHLEFQREILLALGFPAPLTNWWSDFHRDSYlsdphAKVGmSVSFQRRTGDAFTYFGNTLVTMAMIA 542
Cdd:cd23249 155 EGDYTAFDASQDADFLNFETLLMRALGVPLDLIEAYLEMKASIT-----SHLG-PLAIMRFSGEVWTYLFNTLGNMAYTA 228

                        90       100
                ....*....|....*....|....*
gi 556694   543 YASDLSDCDCAIFSGDDSLIISKVK 567
Cdd:cd23249 229 AKYEVPPPVPRVYGGDDKSINSRIT 253
ps-ssRNA_RdRp_Tymovirales cd23207
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Tymovirales of ...
 456-562 1.36e-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: 46.63  E-value: 1.36e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   456 LNNRYFLEADLSKFDKSQGELHLEFQREILLALGFPAPLTNWWSDF--HRDSYLSdPHakvgmsvSFQRRTGDAFTYFGN 533
Cdd:cd23207  85 WQHGPSTANDYTAFDQSQDGEFVVFEVLLMRHLHIPDDLIELYVDIktNAYSHLG-PL-------SIMRLTGEPGTFDFN 156

                        90       100
                ....*....|....*....|....*....
gi 556694   534 TLVTMAMIAYASDLSDCDCAIFSGDDSLI 562
Cdd:cd23207 157 TDYNLALTYAKYDLPPGTPICFSGDDSVA 185
Hepeviridae_RdRp cd23259
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of ...
 463-562 6.97e-05

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: 45.51  E-value: 6.97e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   463 EADLSKFDKSQGELHLEFQREILLALGFPapltNW-WSDFH--RDSY-LSDPhaKVGMSVSFQRRTGDAFTYFGNTLVTM 538
Cdd:cd23259 147 ENDFSEFDSTQNNFSLGLECEIMEECGMP----QWlVRLYHlvRSAWvLQAP--KESLRGFWKKHSGEPGTLLWNTVWNM 220

                        90       100
                ....*....|....*....|....
gi 556694   539 AMIAYASDLSDCDCAIFSGDDSLI 562
Cdd:cd23259 221 AVIAHCYEFRDLAVAAFKGDDSVV 244
Tymoviridae_RdRp cd23247
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tymoviridae of ...
 465-562 9.11e-03

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: 39.10  E-value: 9.11e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556694   465 DLSKFDKSQGELHLEFQREILLALGFPAPLTnwwsDFHRdsylsdpHAKVGMSVSF-----QRRTGDAFTYFGNTLVTMA 539
Cdd:cd23247 173 DYTAFDQSQHGEAVVFERLKMERLSIPQHLI----DLHV-------HLKTNVSTQFgpltcMRLTGEPGTYDDNTDYNLA 241

                        90       100
                ....*....|....*....|...
gi 556694   540 MIAYASDLSDCDCAIfSGDDSLI 562
Cdd:cd23247 242 VIYSQYDISSTPIMV-SGDDSVI 263
 
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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