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PR00912

Identifier
LVIRUSORF5  [View Relations]  [View Alignment]  
Accession
PR00912
No. of Motifs
6
Creation Date
07-APR-1998  (UPDATE 20-JUN-1999)
Title
Luteovirus ORF5 VPG protein signature
Database References

INTERPRO; IPR001964
Literature References
1. 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). 
 
2. 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). 
 
3. VINCENT, J.R., UENG, P.P., LISTER, R.M. AND LARKINS, B.A.
Nucleotide sequences of coat protein genes for three isolates of barley 
yellow dwarf virus and their relationships to other luteovirus coat protein 
sequences. 
J.GEN.VIROL. 71 2791-2799 (1990). 
 
4. 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). 
 
5. KAWCHUK, L.M., MARTIN, R.R., ROCHON, D.M. AND MCPHERSON, J.
Identification and characterization of the potato leafroll virus
putative coat protein gene. 
J.GEN.VIROL. 70 783-788 (1989). 

Documentation
The nucleotide sequence of the RNA of potato leafroll luteovirus (PLRV) has
been determined [1,2]. The sequence contains six large ORFs. The 3' coding 
region encodes three polypeptides: a 23K coat protein, a 17K polypeptide
encoded in a different frame, and a 53K polypeptide, immediately following
the coat protein sequence in the same frame. It has been suggested that the
53K polypeptide is translated by readthrough of the amber termination codon
of the coat protein gene. The amino acid sequences encoded within the 3'
region show many similarities to analogous polypeptides of barley yellow
dwarf virus, PAV strain (BYDV), and beet western yellows virus (BWYV). 
It is possible that the ORF5 protein is a VPG-precursor from which, at the
onset of RNA synthesis, the VPG molecule is released, in a similar fashion
to that proposed for cowpea mosaic virus.
 
Barley yellow dwarf virus (BYDV) can be separated into two groups based 
on serological relationships, presumably governed by the viral capsid 
structure [3]. Coding regions of coat proteins have been identified for the
MAV-PS1, P-PAV (group 1) and NY-RPV (group 2) isolates of BYDV. Group 1 
proteins show 71% sequence similarity to each other, 51% similarity to those
of group 2, and a high degree of similarity to those from other luteoviruses
(including coat proteins from beet western yellow virus (BWYV) [4] and 
potato leafroll virus (PLRV) [2,5]). 
 
LVIRUSORF5 is a 6-element fingerprint that provides a signature for the
luteovirus ORF5 VPG proteins. The fingerprint was derived from an initial
alignment of 12 sequences: the motifs were drawn from conserved regions 
spanning virtually the full alignment length. Two iterations on OWL30.1
were required to reach convergence, at which point a true set comprising 
16 sequences was identified. Two partial matches were also found: V16K_BLRV
is a bean leafroll virus ORF2 protein that matches motifs 3-6; and VPG_BYDVP
is a barley yellow dwarf VPG protein that matches motifs 1 and 4.
 
An update on SPTR37_9f identified a true set of 16 sequences, and 1
partial match.
Summary Information
  16 codes involving  6 elements
0 codes involving 5 elements
1 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
6161616161616
5000000
4001111
3000000
2000000
123456
True Positives
O37357        Q08404        Q65866        Q65971        
Q83739 Q84828 Q84839 Q87034
Q98692 VPG_BWYVF VPG_BWYVG VPG_BYDVN
VPG_PLRV VPG_PLRV1 VPG_PLRVR VPG_PLRVW
True Positive Partials
Codes involving 4 elements
V16K_BLRV
Sequence Titles
O37357      PUTATIVE MOVEMENT PROTEIN - BARLEY YELLOW DWARF VIRUS. 
Q08404 PUTATIVE GENOME-LINKED PROTEIN PRECURSOR (VPG) (21 KD PROTEIN) - SOYBEAN DWARF VIRUS.
Q65866 MOVEMENT PROTEIN - BARLEY YELLOW DWARF VIRUS.
Q65971 HYPOTHETICAL 21.2 KD PROTEIN - CUCURBIT APHID-BORNE YELLOWS VIRUS.
Q83739 HYPOTHETICAL 19.5 KD PROTEIN - BEET WESTERN YELLOWS VIRUS.
Q84828 17 KD PROTEIN - POTATO LEAFROLL VIRUS (PLRV).
Q84839 ORF 5 - POTATO LEAFROLL VIRUS (PLRV).
Q87034 GENOME-LINKED PROTEIN - SOYBEAN DWARF VIRUS.
Q98692 GENOME-LINKED PROTEIN - SOYBEAN DWARF VIRUS.
VPG_BWYVF PUTATIVE GENOME-LINKED PROTEIN PRECURSOR (VPG) (20 KD PROTEIN) (ORF 5) - BEET WESTERN YELLOWS VIRUS (ISOLATE FL-1) (BWYV).
VPG_BWYVG PUTATIVE GENOME-LINKED PROTEIN PRECURSOR (VPG) (20 KD PROTEIN) (ORF 5) - BEET WESTERN YELLOWS VIRUS (ISOLATE GB1) (BWYV).
VPG_BYDVN PUTATIVE GENOME-LINKED PROTEIN PRECURSOR (VPG) (17 KD PROTEIN) - BARLEY YELLOW DWARF VIRUS (ISOLATE NY-RPV) (BYDV).
VPG_PLRV PUTATIVE GENOME-LINKED PROTEIN PRECURSOR (VPG) (17 KD PROTEIN) (ORF 5) - POTATO LEAFROLL VIRUS (PLRV).
VPG_PLRV1 PUTATIVE GENOME-LINKED PROTEIN PRECURSOR (VPG) (17 KD PROTEIN) (ORF 5) - POTATO LEAFROLL VIRUS (STRAIN 1) (PLRV).
VPG_PLRVR PUTATIVE GENOME-LINKED PROTEIN PRECURSOR (VPG) (17 KD PROTEIN) (ORF 5) - POTATO LEAFROLL VIRUS (STRAIN ROWHANI) (PLRV).
VPG_PLRVW PUTATIVE GENOME-LINKED PROTEIN PRECURSOR (VPG) (17 KD PROTEIN) (ORF 5) - POTATO LEAFROLL VIRUS (STRAIN WAGENINGEN) (PLRV).

V16K_BLRV 16 KD PROTEIN (ORF2) - BEAN LEAFROLL VIRUS (BLRV).
Scan History
OWL30_1       100  NSINGLE    
SPTR37_9f 2 50 NSINGLE
Initial Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
EALHEFSSWLFQRPPA SDU514481 14 14 -
DALHEFSSWLFQRPPA SDVCOATX1 14 14 -
DALQEFSSWLFQRPPA D49600 14 14 -
GLLQERSQWLWSLPTA BYDCOATP2 14 14 -
GALTEFSRWLWSRPLG PLVSQRN4 19 19 -
GALTEFSQWLWSRPLG VPG_PLRVW 19 19 -
GALTEYSQWLWSRPLG PLVCOAPRO1 19 19 -
DALSALSQWLWSKPLG VPG_BWYVG 11 11 -
GLLQERSQWLWSLPTA VPG_BYDVN 16 16 -
GALTEFSQWLWSRPLG VPG_PLRV 19 19 -
GALTEFSQWLWSRPLG VPG_PLRV1 19 19 -
GALTEFSQWLWSRPLG VPG_PLRVR 19 19 -

Motif 2 width=17
Element Seqn Id St Int Rpt
QEELFLPEEQAQARHLF VPG_BWYVG 42 15 -
QEELEFPEDEAQARHSC PLVSQRN4 49 14 -
EEEFQDQQEEAMARHSF BYDCOATP2 44 14 -
EEEALFPEDQARLTHSC D49600 45 15 -
EEEAIFPEDQARLTHSC SDVCOATX1 45 15 -
EEEAIFPEDQARLTHSS SDU514481 45 15 -
QEKLEFPEDEAQARHSC PLVCOAPRO1 49 14 -
QEELEFPEDEAQARHSC VPG_PLRVW 49 14 -
QEELEFPEDEAQARHSC VPG_PLRVR 49 14 -
QEELEFPEDEAQARHSC VPG_PLRV1 49 14 -
QEELEFPEDEAQARHSC VPG_PLRV 49 14 -
EEELQDLEEEAVARHSF VPG_BYDVN 46 14 -

Motif 3 width=16
Element Seqn Id St Int Rpt
RTTSWATPKEVSPSGR VPG_PLRVW 68 2 -
KTISREVPADESRSGR VPG_BWYVG 61 2 -
RIHSRATPLEVSPSGR VPG_BYDVN 65 2 -
RTTSWATPKEVSPSGR VPG_PLRV 68 2 -
RTTSWATPKEVSPSGR VPG_PLRV1 68 2 -
RTTSWATPKEVSPSGR VPG_PLRVR 68 2 -
RTASMAVPKELSLSGR SDU514481 64 2 -
RTASMVVPREVSLSGR SDVCOATX1 64 2 -
RTASMVVPREVSLSGR D49600 64 2 -
RIHSRATPLEVSPSGR BYDCOATP2 63 2 -
RTTSWATPKEVSPSGR PLVSQRN4 68 2 -
RTTSWATPKEVSPSGR PLVCOAPRO1 68 2 -

Motif 4 width=17
Element Seqn Id St Int Rpt
RLYQNASHSLMEYSRPT SDVCOATX1 79 -1 -
RVYQTVRHSRMEYSRPT VPG_PLRVW 83 -1 -
RVYQTAQHSLMEYSRPT VPG_BWYVG 76 -1 -
RLYQSIRHSRMEYSRPT VPG_BYDVN 80 -1 -
RVYQTVRLSRMEYSRPT VPG_PLRV 83 -1 -
RVYQTVRHSRMEYSRPT VPG_PLRV1 83 -1 -
RVYQTVRHSRMEYSRPT VPG_PLRVR 83 -1 -
RVYQTVRHSRMEYSRPT PLVCOAPRO1 83 -1 -
RVYQTVRHSRMEYSRPT PLVSQRN4 83 -1 -
RLYQSIRHSKMEYSRPT BYDCOATP2 78 -1 -
RLYQNASHSLMEYSRPT D49600 79 -1 -
RLYQSASHSLMEYSRPT SDU514481 79 -1 -

Motif 5 width=16
Element Seqn Id St Int Rpt
TMSIRSQASYFSSSAR VPG_PLRV1 99 -1 -
TMSIRSQVSYFSSSAR PLVCOAPRO1 99 -1 -
TMSIRSQASYFSSSAR PLVSQRN4 99 -1 -
TMNIRSQIVSYSSSPR BYDCOATP2 94 -1 -
TMNIRSRVSYYSSSPR D49600 95 -1 -
TMNIRSRVSYYSSSPR SDVCOATX1 95 -1 -
TMNIRSRVSYYSSSPR SDU514481 95 -1 -
TMSIRSQASYFSSSAR VPG_PLRVW 99 -1 -
TMSIRSQASYFSSSAR VPG_PLRVR 99 -1 -
TMSIRSQASYFSSSAR VPG_PLRV 99 -1 -
TMNIRSQIVSYSSSAR VPG_BYDVN 96 -1 -
TMSIKSRWSFWSSSPK VPG_BWYVG 92 -1 -

Motif 6 width=17
Element Seqn Id St Int Rpt
RPLPPPPVPSLMSWTPI VPG_PLRVR 114 -1 -
RPLPPPPVPSLMSWTPI VPG_PLRV1 114 -1 -
RPLPPPPAPSLMSWTPI PLVCOAPRO1 114 -1 -
RPLPPPPAPSLMSWTPI VPG_PLRV 114 -1 -
RPLPQQPAPSLTSWTPI VPG_BYDVN 111 -1 -
KPLPKTPVPSLTSWTHT VPG_BWYVG 107 -1 -
RPLPPPPVPSLMSWTPI VPG_PLRVW 114 -1 -
RPLPPRQAPSLMSLTHT SDU514481 110 -1 -
RPLPPRQVPSLMNLTHT SDVCOATX1 110 -1 -
RPLPPRQVPSLMNLTHT D49600 110 -1 -
RPLQPQPAPSLMSWAPI BYDCOATP2 109 -1 -
RPLPPPPVPSLMSWTPI PLVSQRN4 114 -1 -
Final Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
GALTEFSQWLWSRPLG VPG_PLRVW 19 19 -
GALTEFSQWLWSRPLG VPG_PLRVR 19 19 -
GALTEFSQWLWSRPLG VPG_PLRV1 19 19 -
GALTEFSRWLWSRPLG Q84839 19 19 -
GALTEFSQWLWSRPLG VPG_PLRV 19 19 -
GALTEYSQWLWSRPLG Q84828 19 19 -
GLLSERSQWLWSLPTA O37357 16 16 -
GLLQERSQWLWSLPTA VPG_BYDVN 16 16 -
DALSALSQWLWSKPLG Q83739 11 11 -
DALHEFSSWLFQRPPA Q08404 14 14 -
DALQEFSSWLFQRPPA Q87034 14 14 -
EALHEFSSWLFQRPPA Q98692 14 14 -
GLLQERSQWLWSLPTA Q65866 14 14 -
DALSALSQWLWSKPLG VPG_BWYVF 11 11 -
DALSALSQWLWSKPLG VPG_BWYVG 11 11 -
SALRGATAWLWSTPLG Q65971 10 10 -

Motif 2 width=17
Element Seqn Id St Int Rpt
QEELEFPEDEAQARHSC VPG_PLRVW 49 14 -
QEELEFPEDEAQARHSC VPG_PLRVR 49 14 -
QEELEFPEDEAQARHSC VPG_PLRV1 49 14 -
QEELEFPEDEAQARHSC Q84839 49 14 -
QEELEFPEDEAQARHSC VPG_PLRV 49 14 -
QEKLEFPEDEAQARHSC Q84828 49 14 -
EEELQDSEEQAVGRHLF O37357 46 14 -
EEELQDLEEEAVARHSF VPG_BYDVN 46 14 -
QEELFLPEEQVRARHSF Q83739 42 15 -
EEEAIFPEDQARLTHSC Q08404 45 15 -
EEEALFPEDQARLTHSC Q87034 45 15 -
EEEAIFPEDQARLTHSS Q98692 45 15 -
EEEFQDQQEEAMARHSF Q65866 44 14 -
QEELFLPEEQVRARHLF VPG_BWYVF 42 15 -
QEELFLPEEQAQARHLF VPG_BWYVG 42 15 -
LIEEAELEEEAQAKHLY Q65971 40 14 -

Motif 3 width=16
Element Seqn Id St Int Rpt
RTTSWATPKEVSPSGR VPG_PLRVW 68 2 -
RTTSWATPKEVSPSGR VPG_PLRVR 68 2 -
RTTSWATPKEVSPSGR VPG_PLRV1 68 2 -
RTTSWATPKEVSPSGR Q84839 68 2 -
RTTSWATPKEVSPSGR VPG_PLRV 68 2 -
RTTSWATPKEVSPSGR Q84828 68 2 -
RTHSLATPLEVSPSGR O37357 65 2 -
RIHSRATPLEVSPSGR VPG_BYDVN 65 2 -
KTISREVPAEQSRSGR Q83739 61 2 -
RTASMVVPREVSLSGR Q08404 64 2 -
RTASMVVPREVSLSGR Q87034 64 2 -
RTASMAVPKELSLSGR Q98692 64 2 -
RIHSRATPLEVSPSGR Q65866 63 2 -
KTISREVPAEQSRSGR VPG_BWYVF 61 2 -
KTISREVPADESRSGR VPG_BWYVG 61 2 -
RTISRAVPQEVSPSGR Q65971 59 2 -

Motif 4 width=17
Element Seqn Id St Int Rpt
RVYQTVRHSRMEYSRPT VPG_PLRVW 83 -1 -
RVYQTVRHSRMEYSRPT VPG_PLRVR 83 -1 -
RVYQTVRHSRMEYSRPT VPG_PLRV1 83 -1 -
RVYQTVRHSRMEYSRPT Q84839 83 -1 -
RVYQTVRLSRMEYSRPT VPG_PLRV 83 -1 -
RVYQTVRHSRMEYSRPT Q84828 83 -1 -
RLYQTIRHSRMEYSRPT O37357 80 -1 -
RLYQSIRHSRMEYSRPT VPG_BYDVN 80 -1 -
RVYQTARHSLMECSRPT Q83739 76 -1 -
RLYQNASHSLMEYSRPT Q08404 79 -1 -
RLYQNASHSLMEYSRPT Q87034 79 -1 -
RLYQSASHSLMEYSRPT Q98692 79 -1 -
RLYQSIRHSKMEYSRPT Q65866 78 -1 -
RVYQTARHSLMECSRPT VPG_BWYVF 76 -1 -
RVYQTAQHSLMEYSRPT VPG_BWYVG 76 -1 -
RLFQRAQHSALEYSRPT Q65971 74 -1 -

Motif 5 width=16
Element Seqn Id St Int Rpt
TMSIRSQASYFSSSAR VPG_PLRVW 99 -1 -
TMSIRSQASYFSSSAR VPG_PLRVR 99 -1 -
TMSIRSQASYFSSSAR VPG_PLRV1 99 -1 -
TMSIRSQASYFSSSAR Q84839 99 -1 -
TMSIRSQASYFSSSAR VPG_PLRV 99 -1 -
TMSIRSQVSYFSSSAR Q84828 99 -1 -
TMNIRSQIVSYSSSAR O37357 96 -1 -
TMNIRSQIVSYSSSAR VPG_BYDVN 96 -1 -
TMSIKSQWSFWSSSPR Q83739 92 -1 -
TMNIRSRVSYYSSSPR Q08404 95 -1 -
TMNIRSRVSYYSSSPR Q87034 95 -1 -
TMNIRSRVSYYSSSPR Q98692 95 -1 -
TMNIRSQIVSYSSSPR Q65866 94 -1 -
TMSIKSQWSFWSSSPK VPG_BWYVF 92 -1 -
TMSIKSRWSFWSSSPK VPG_BWYVG 92 -1 -
TMNIRSSWSSWSSSPR Q65971 90 -1 -

Motif 6 width=17
Element Seqn Id St Int Rpt
RPLPPPPVPSLMSWTPI VPG_PLRVW 114 -1 -
RPLPPPPVPSLMSWTPI VPG_PLRVR 114 -1 -
RPLPPPPVPSLMSWTPI VPG_PLRV1 114 -1 -
RPLPPPPVPSLMSWTPI Q84839 114 -1 -
RPLPPPPAPSLMSWTPI VPG_PLRV 114 -1 -
RPLPPPPAPSLMSWTPI Q84828 114 -1 -
RPLPQQPVPSLMSWTPI O37357 111 -1 -
RPLPQQPAPSLTSWTPI VPG_BYDVN 111 -1 -
RPLPKIPVPSLTSWTHT Q83739 107 -1 -
RPLPPRQVPSLMNLTHT Q08404 110 -1 -
RPLPPRQVPSLMNLTHT Q87034 110 -1 -
RPLPPRQAPSLMSLTHT Q98692 110 -1 -
RPLQPQPAPSLMSWAPI Q65866 109 -1 -
KPLPKIPVPSLTSWTHT VPG_BWYVF 107 -1 -
KPLPKTPVPSLTSWTHT VPG_BWYVG 107 -1 -
RPLPPPRVPSLMSWTPT Q65971 105 -1 -