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PR00913

Identifier
LVIRUSORF2  [View Relations]  [View Alignment]  
Accession
PR00913
No. of Motifs
9
Creation Date
16-APR-1998  (UPDATE 07-JUN-1999)
Title
Luteovirus ORF2 putative replicase 1 signature
Database References

INTERPRO; IPR000382
Literature References
1. MAYO, M.A., ROBINSON, D.J., JOLLY, C.A. AND HYMAN, L.
Nucleotide sequence of potato leafroll luteovirus RNA. 
J.GEN.VIROL. 70 1037-1051 (1989). 
 
2. VAN DER WILK, F., HUISMAN, M.J., CORNELISSEN, B.J., HUTTINGA, H.
AND GOLDBACH, R.
Nucleotide sequence and organization of potato leafroll virus genomic RNA.
FEBS LETT. 245 51-56 (1989). 
 
3.VEIDT, I., LOT, H., LEISER, M., SCHEIDECKER, D., GUILLEY, H., 
RICHARDS, K. AND JONARD, G.
Nucleotide sequence of beet western yellows virus RNA. 
NUCLEIC ACIDS RES. 16 9917-9932 (1988).  

Documentation
The nucleotide sequence for the RNA of potato leafroll luteovirus (PLRV) has
been determined [1,2]. The sequence contains six large open reading frames
(ORFs). The 5' coding region encodes two polypeptides of 28K and 70K, which 
overlap in different reading frames; it is suggested that the third ORF in 
the 5' block is translated by frameshift readthrough near the end of the 70K 
protein, yielding a 118K polypeptide [1]. Segments of the predicted amino
acid sequences of these ORFs resemble those of known viral RNA polymerases, 
ATP-binding proteins and viral genome-linked proteins.
 
The nucleotide sequence of the genomic RNA of beet western yellow virus
(BWYV) has been determined [3]. The sequence contains six long ORFs. A 
cluster of three of these ORFs, including the coat protein cistron, display
extensive amino acid sequence similarity to corresponding ORFs of a second
luteovirus, the PAV isolate of barley yellow dwarf virus (BYDV) [3].
 
LVIRUSORF2 is a 9-element fingerprint that provides a signature for the 
luteovirus ORF2 putative replicase 1 family. The fingerprint was derived
from an initial alignment of 7 sequences: the motifs were drawn from short
conserved regions spanning the C-terminal half of the alignment. A single
iteration on OWL30.1 was required to reach convergence, no further
sequences being identified beyond the starting set. A single partial match
was found, JQ1383, a hypothetical protein from pea enation mosaic virus
that matches motifs 2 and 5.
 
An update on SPTR37_9f identified a true set of 7 sequences.
Summary Information
7 codes involving  9 elements
0 codes involving 8 elements
0 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
9777777777
8000000000
7000000000
6000000000
5000000000
4000000000
3000000000
2000000000
123456789
True Positives
Q65968        Q83737        Q84836        Q89645        
V66K_BWYVF V70K_PLRV1 V70K_PLRVW
Sequence Titles
Q65968      HYPOTHETICAL 69.2 KD PROTEIN - CUCURBIT APHID-BORNE YELLOWS VIRUS. 
Q83737 HYPOTHETICAL 72.0 KD PROTEIN - BEET WESTERN YELLOWS VIRUS.
Q84836 ORF 2 - POTATO LEAFROLL VIRUS (PLRV).
Q89645 ORF2 - BARLEY YELLOW DWARF VIRUS.
V66K_BWYVF 66.2 KD PROTEIN (ORF 2) - BEET WESTERN YELLOWS VIRUS (ISOLATE FL-1) (BWYV).
V70K_PLRV1 69.7 KD PROTEIN (ORF 2) - POTATO LEAFROLL VIRUS (STRAIN 1) (PLRV).
V70K_PLRVW 69.7 KD PROTEIN (ORF 2) - POTATO LEAFROLL VIRUS (STRAIN WAGENINGEN) (PLRV).
Scan History
OWL30_1    1  40   NSINGLE    
SPTR37_9f 2 12 NSINGLE
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
ERAVEGYKGFSVPQKPPK V70K_PLRV1 204 204 -
EKAVEGYKGFSVPQKPPK V70K_PLRVW 204 204 -
ERAVEGYKGFSVPQKPPK PLVSQRN1 204 204 -
ERSVKGFLTFTIKQSPPR S65826 199 199 -
EKTVSGYDSYSIPSTPPK JQ1241 206 206 -
EKSVEGYLSFKIPQNPPK S41314 199 199 -
EKAIDGFKSFTIPQSPPK V66K_BWYVF 203 203 -

Motif 2 width=22
Element Seqn Id St Int Rpt
HAGYATCVTLFDGTNGLLTAQH S65826 229 12 -
HAGYASCIKLYNGENALMTATH V66K_BWYVF 233 12 -
HLGYANCIRLYSGENALVTAEH V70K_PLRV1 234 12 -
HLGYANCIRLYSGENALVTAEH PLVSQRN1 234 12 -
HAGYATCVTLYNGTNGLLTAYH S41314 229 12 -
HIGYANCIRLFDGRNAIVTVAH JQ1241 236 12 -
HLGYANCIRLYSGENALVTAEH V70K_PLRVW 234 12 -

Motif 3 width=17
Element Seqn Id St Int Rpt
SIPITEFRVIFESKTMD JQ1241 273 15 -
RIPMSTFFPIFKSARND V70K_PLRV1 270 14 -
RIPLAEFKTIAKSDKGD V66K_BWYVF 273 18 -
RIPMSTFFPIFKSARND PLVSQRN1 270 14 -
KVPLSEFRSIMESEKRD S41314 266 15 -
RIPMSTFFPIFKSARND V70K_PLRVW 270 14 -
KIPLDEFRVTYTSEKRD S65826 274 23 -

Motif 4 width=18
Element Seqn Id St Int Rpt
DVTLLRGPPNWEGLLGCK V66K_BWYVF 289 -1 -
DQLLMHGPPNWEGVLACK S65826 290 -1 -
DIAILVGPINWESILGCK JQ1241 289 -1 -
DLVLLAGPPNWEGTLACK S41314 282 -1 -
DISILVGPPNWEGLLSVK PLVSQRN1 286 -1 -
DISILVGPPNWEGLLSVK V70K_PLRV1 286 -1 -
DISILVGPPNWEGLLSVK V70K_PLRVW 286 -1 -

Motif 5 width=23
Element Seqn Id St Int Rpt
VLCNTGPGYSGTGFWSSKNLLGV PLVSQRN1 345 41 -
VLSDTKSGHSGTPYFNGKSVLGV S65826 351 43 -
VLSNTKVGHSGAGYFYGKTLVGL JQ1241 349 42 -
VLSNTDAGHSGTPYFNGRTVLGV S41314 343 43 -
VLSHTEGGHSGSPYFNGKTILGV V66K_BWYVF 348 41 -
VLCNTGPGYSGTGFWSSKNLLGV V70K_PLRV1 345 41 -
VLCNTGPGYSGTGFWSSKNLLGV V70K_PLRVW 345 41 -

Motif 6 width=17
Element Seqn Id St Int Rpt
NVMSVIPSIPGITSPNY V70K_PLRVW 380 12 -
NLMAPLPGIPGLTSPQY JQ1241 383 11 -
NYMSPIPRFPGLTSPNY S65826 387 13 -
NVMSVIPSIPGITSPNY PLVSQRN1 380 12 -
NLMAPIPSLPGLTSPTY V66K_BWYVF 381 10 -
NVMSVIPSIPGITSPNY V70K_PLRV1 380 12 -
NYMAPIPPVYGLTSPSY S41314 376 10 -

Motif 7 width=16
Element Seqn Id St Int Rpt
YVFESTAVKGRVFSDE V70K_PLRV1 396 -1 -
YVFESTAVKGRVFSDE PLVSQRN1 396 -1 -
YEFETTAPQGRLFTQE S41314 392 -1 -
YVVESDPPQGLVFPEE JQ1241 399 -1 -
YIFETTALAGKFFSQE S65826 403 -1 -
YVFESTAVKGRVFSDE V70K_PLRVW 396 -1 -
YVFETTAPQGRVFAQE V66K_BWYVF 397 -1 -

Motif 8 width=19
Element Seqn Id St Int Rpt
IMNLLVQRIDMSKIEKSIV JQ1241 541 126 -
IITAMVGRINLSEIEEKIV V70K_PLRVW 521 109 -
IITAMVGRINLSEIEEKIV V70K_PLRV1 521 109 -
IISSLVGKINLENIERKVI V66K_BWYVF 493 80 -
IKQVIMDKIDVHSIEKQVV S41314 516 108 -
IKKALIDKMDLKSIERQVV S65826 544 125 -
IITAMVGRINLSEIEEKIV PLVSQRN1 521 109 -

Motif 9 width=21
Element Seqn Id St Int Rpt
GGENSVPNTLSWVRKLPVSGG JQ1241 625 65 -
GGKNSAKFIPSWRRKQQDSAG PLVSQRN1 608 68 -
GGKNSAKFTPSWRIKQQDSAG V70K_PLRV1 608 68 -
GGRPSSGTIPRWVRKQAASAG V66K_BWYVF 579 67 -
GGKNSAKFIPSWRIKQQDSAG V70K_PLRVW 608 68 -
GARSSPASTQNWRRKPEASGG S65826 628 65 -
GETKSANSTQKWVISQRASGG S41314 602 67 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
EKAVEGYKGFSVPQKPPK V70K_PLRVW 204 204 -
ERAVEGYKGFSVPQKPPK Q84836 204 204 -
ERAVEGYKGFSVPQKPPK V70K_PLRV1 204 204 -
EKAIDGFKSFTIPQSPPK V66K_BWYVF 203 203 -
EKSVEGYLSFKIPQNPPK Q65968 199 199 -
ERSVKGFLTFTIKQSPPR Q83737 199 199 -
EKTVSGYDSYSIPSTPPK Q89645 207 207 -

Motif 2 width=22
Element Seqn Id St Int Rpt
HLGYANCIRLYSGENALVTAEH V70K_PLRVW 234 12 -
HLGYANCIRLYSGENALVTAEH Q84836 234 12 -
HLGYANCIRLYSGENALVTAEH V70K_PLRV1 234 12 -
HAGYASCIKLYNGENALMTATH V66K_BWYVF 233 12 -
HAGYATCVTLYNGTNGLLTAYH Q65968 229 12 -
HAGYATCVTLFDGTNGLLTAQH Q83737 229 12 -
HIGYANCIRLFDGRNAIVTVAH Q89645 237 12 -

Motif 3 width=17
Element Seqn Id St Int Rpt
RIPMSTFFPIFKSARND V70K_PLRVW 270 14 -
RIPMSTFFPIFKSARND Q84836 270 14 -
RIPMSTFFPIFKSARND V70K_PLRV1 270 14 -
RIPLAEFKTIAKSDKGD V66K_BWYVF 273 18 -
KVPLSEFRSIMESEKRD Q65968 266 15 -
KIPLDEFRVTYTSEKRD Q83737 274 23 -
SIPITEFRVIFESKTMD Q89645 274 15 -

Motif 4 width=18
Element Seqn Id St Int Rpt
DISILVGPPNWEGLLSVK V70K_PLRVW 286 -1 -
DISILVGPPNWEGLLSVK Q84836 286 -1 -
DISILVGPPNWEGLLSVK V70K_PLRV1 286 -1 -
DVTLLRGPPNWEGLLGCK V66K_BWYVF 289 -1 -
DLVLLAGPPNWEGTLACK Q65968 282 -1 -
DQLLMHGPPNWEGVLACK Q83737 290 -1 -
DIAILVGPINWESILGCK Q89645 290 -1 -

Motif 5 width=23
Element Seqn Id St Int Rpt
VLCNTGPGYSGTGFWSSKNLLGV V70K_PLRVW 345 41 -
VLCNTGPGYSGTGFWSSKNLLGV Q84836 345 41 -
VLCNTGPGYSGTGFWSSKNLLGV V70K_PLRV1 345 41 -
VLSHTEGGHSGSPYFNGKTILGV V66K_BWYVF 348 41 -
VLSNTDAGHSGTPYFNGRTVLGV Q65968 343 43 -
VLSDTKSGHSGTPYFNGKSVLGV Q83737 351 43 -
VLSNTKVGHSGAGYFYGKTLVGL Q89645 350 42 -

Motif 6 width=17
Element Seqn Id St Int Rpt
NVMSVIPSIPGITSPNY V70K_PLRVW 380 12 -
NVMSVIPSIPGITSPNY Q84836 380 12 -
NVMSVIPSIPGITSPNY V70K_PLRV1 380 12 -
NLMAPIPSLPGLTSPTY V66K_BWYVF 381 10 -
NYMAPIPPVYGLTSPSY Q65968 376 10 -
NYMSPIPRFPGLTSPNY Q83737 387 13 -
NLMAPLPGIPGLTSPQY Q89645 384 11 -

Motif 7 width=16
Element Seqn Id St Int Rpt
YVFESTAVKGRVFSDE V70K_PLRVW 396 -1 -
YVFESTAVKGRVFSDE Q84836 396 -1 -
YVFESTAVKGRVFSDE V70K_PLRV1 396 -1 -
YVFETTAPQGRVFAQE V66K_BWYVF 397 -1 -
YEFETTAPQGRLFTQE Q65968 392 -1 -
YIFETTALAGKFFSQE Q83737 403 -1 -
YVVESDPPQGLVFPEE Q89645 400 -1 -

Motif 8 width=19
Element Seqn Id St Int Rpt
IITAMVGRINLSEIEEKIV V70K_PLRVW 521 109 -
IITAMVGRINLSEIEEKIV Q84836 521 109 -
IITAMVGRINLSEIEEKIV V70K_PLRV1 521 109 -
IISSLVGKINLENIERKVI V66K_BWYVF 493 80 -
IKQVIMDKIDVHSIEKQVV Q65968 516 108 -
IKKALIDKMDLKSIERQVV Q83737 544 125 -
IMNLLVQRIDMSKIEKSIV Q89645 542 126 -

Motif 9 width=21
Element Seqn Id St Int Rpt
GGKNSAKFIPSWRIKQQDSAG V70K_PLRVW 608 68 -
GGKNSAKFIPSWRRKQQDSAG Q84836 608 68 -
GGKNSAKFTPSWRIKQQDSAG V70K_PLRV1 608 68 -
GGRPSSGTIPRWVRKQAASAG V66K_BWYVF 579 67 -
GETKSANSTQKWVISQRASGG Q65968 602 67 -
GARSSPASTQNWRRKPEASGG Q83737 628 65 -
GGENSVPNTLSWVRKLPVSGG Q89645 626 65 -