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PR00226

Identifier
GEMCOATMSV  [View Relations]  [View Alignment]  
Accession
PR00226
No. of Motifs
5
Creation Date
08-JUL-1994  (UPDATE 07-JUN-1999)
Title
Geminivirus MSV 27Kd coat protein signature
Database References
PRINTS; PR00223 GEMCOATARBR1
INTERPRO; IPR000143
Literature References
1. STANLEY, J., MARKHAM, P.G., CALLIS, R.J. AND PINNER, M.S.
The nucleotide sequence of an infectious clone of the geminivirus
beet curly top virus.
EMBO J. 5(8) 1761-1767 (1986).
 
2. MULLINEAUX, P. M., DONSON, J., MORRIS-KRSINICH, B.A., BOULTON, M. I.
AND DAVIE, J. W. 
The nucleotide sequence of maize streak virus DNA.
EMBO J. 3 3063-3068 (1984). 
 
3. LAZAROWITZ, S.G.
Infectivity and complete nucleotide sequence of the genome of a South 
African isolate of maize streak virus.
NUCLEIC ACIDS RES. 16 229-249 (1988).  
 
4. BRIDDON, R.W., LUNNESS,P., CHAMBERLIN, L.C., PINNER, M.S., BRUNDISH, H.
AND MARKHAM. P.G.
The nucleotide sequence of an infectious insect-transmissible clone of the
geminivirus Panicum streak virus. 
J.GEN.VIROL. 73(5) 1041-1047 (1992).
 
5. CHATANI, M., MATSUMOTO, Y., MIZUTA, H., IKEGAMI, M., BOULTON, M.I. AND 
DAVIES, J.W.
The nucleotide sequence and genome structure of the geminivirus miscanthus
streak virus.
J.GEN.VIROL. 72(10) 2325-2331 (1991). 

Documentation
Geminiviruses are characterised by a genome of circular single-stranded
DNA encapsidated in twinned (geminate) quasi-isometric particles, from
which the group derives its name [1]. Most geminiviruses can be divided
into 2 subgroups on the basis of host range and/or insect vector: i.e.
those that infect dicotyledenous plants and are transmitted by the same
whitefly species, and those that infect monocotyledenous plants and are
transmitted by different leafhopper vectors. The genomes of the whitefly-
transmitted cassava latent (CLV), tomato golden mosaic (TGMV) and bean
golden mosaic (BGMV) viruses possess a bipartite genome. By contrast, only
a single DNA component has been identified for the leafhopper-transmitted 
maize streak (MSV) and wheat dwarf (WDV) viruses [2,3]. Beet curly top
(BCTV), bean summer death and tobacco yellow dwarf viruses belong to a 
third possible subgroup. Like MSV and WDV, BCTV is transmitted by a 
specific leafhopper species, yet like the whitefly-transmitted gemini- 
viruses it has a host range confined to dicotyledenous plants.
 
Comparison of the MSV DNA sequence with those of CLV and TGMV shows no 
detectable similarity [2]. Amino acid sequence comparison of MSV DNA- 
encoded proteins with those of other geminiviruses infecting mono- 
cotyledonous plants, including Panicum streak virus [4] and miscanthus
streak virus [5], reveal high levels of similarity. 
 
GEMCOATMSV is a 5-element fingerprint that provides a signature for MSV
and WDV coat proteins. The fingerprint was derived from an initial 
alignment of 4 sequences: the motifs were drawn from conserved regions 
spanning the full alignment length. Two iterations on OWL23.0 were 
required to reach convergence, at which point a true set comprising 10 
sequences was identified. A single partial match was also found, COAT_BCTV,
the closely related beet curly top coat protein, matching motifs 3 and 4.
 
An update on SPTR37_9f identified a true set of 29 sequences, and 3
partial matches.
Summary Information
  29 codes involving  5 elements
0 codes involving 4 elements
1 codes involving 3 elements
2 codes involving 2 elements
Composite Feature Index
52929292929
400000
310110
200220
12345
True Positives
COAT_CSMV     COAT_MISV     COAT_MSVK     COAT_MSVN     
COAT_MSVS COAT_PASVK COAT_TYDVA COAT_WDV
O36262 O39520 O40985 O56311
O56969 O72914 O73467 O73471
O73473 Q67566 Q67594 Q67595
Q67596 Q67597 Q67598 Q67599
Q83480 Q84369 Q89238 Q89551
Q89614
True Positive Partials
Codes involving 3 elements
Q68541
Codes involving 2 elements
O72689 Q65415
Sequence Titles
COAT_CSMV   COAT PROTEIN - CHLORIS STRIATE MOSAIC VIRUS (CSMV). 
COAT_MISV COAT PROTEIN - MISCANTHUS STREAK VIRUS.
COAT_MSVK COAT PROTEIN - MAIZE STREAK VIRUS (KENYAN ISOLATE) (MSV).
COAT_MSVN COAT PROTEIN - MAIZE STREAK VIRUS (NIGERIAN ISOLATE) (MSV).
COAT_MSVS COAT PROTEIN - MAIZE STREAK VIRUS (SOUTH-AFRICAN ISOLATE) (MSV).
COAT_PASVK COAT PROTEIN - PANICUM STREAK VIRUS (KENYAN ISOLATE).
COAT_TYDVA COAT PROTEIN - TOBACCO YELLOW DWARF VIRUS (STRAIN AUSTRALIA) (TYDV).
COAT_WDV COAT PROTEIN - WHEAT DWARF VIRUS (WDV).
O36262 COAT PROTEIN - MAIZE STREAK VIRUS.
O39520 COAT PROTEIN - BEAN YELLOW DWARF VIRUS.
O40985 COAT PROTEIN - MAIZE STREAK VIRUS.
O56311 COAT PROTEIN - EGYPTIAN SUGARCANE STREAK VIRUS.
O56969 27.0 KD VIRION CAPSID PROTEIN - MAIZE STREAK VIRUS.
O72914 ORF V2 - MISCANTHUS STREAK VIRUS.
O73467 27.0 KD VIRION CAPSID PROTEIN - MAIZE STREAK VIRUS.
O73471 27.0 KD VIRION CAPSID PROTEIN - MAIZE STREAK VIRUS.
O73473 27.0 KD VIRION CAPSID PROTEIN - MAIZE STREAK VIRUS.
Q67566 COMPLETE GENOME - DIGITARIA STREAK VIRUS.
Q67594 COAT PROTEIN - MAIZE STREAK VIRUS.
Q67595 COAT PROTEIN - MAIZE STREAK VIRUS.
Q67596 COAT PROTEIN - MAIZE STREAK VIRUS.
Q67597 COAT PROTEIN - MAIZE STREAK VIRUS.
Q67598 COAT PROTEIN - MAIZE STREAK VIRUS.
Q67599 COAT PROTEIN - MAIZE STREAK VIRUS.
Q83480 COAT PROTEIN - MILLET STREAK VIRUS.
Q84369 COAT PROTEIN - PANICUM STREAK VIRUS.
Q89238 CAPSID PROTEIN V2 - WHEAT DWARF VIRUS (WDV).
Q89551 27.2 KDA ORF - SUGARCANE STREAK VIRUS.
Q89614 27.0 KD VIRION CAPSID PROTEIN - MAIZE STREAK VIRUS.

Q68541 CAPSID PROTEIN - HORSERADISH CURLY TOP VIRUS.

O72689 COAT PROTEIN V1 - BEET CURLY TOP VIRUS (BCTV).
Q65415 WORLAND STRAIN, COMPLETE GENOME - BEET CURLY TOP VIRUS (BCTV).
Scan History
OWL23_0    2  50   NSINGLE    
OWL28_0 1 100 NSINGLE
SPTR37_9f 2 35 NSINGLE
Initial Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
GANENCRHTNRTITYK COAT_TYDVA 81 81 -
GSAENQRKTAETITYK COAT_CSMV 68 68 -
GSGEGERHTNETLTYK COAT_PASV 74 74 -
GKADNNRHTNQTVLYK COAT_WDV 78 78 -

Motif 2 width=19
Element Seqn Id St Int Rpt
WLVYDAEPKQAMPDATDIF COAT_WDV 118 24 -
WLVYDAQPTGTAPTVQDIF COAT_PASV 114 24 -
WIVYDAAPTGSAVTPKDIF COAT_CSMV 108 24 -
WLVYDKNPGESNPSPSAIF COAT_TYDVA 121 24 -

Motif 3 width=18
Element Seqn Id St Int Rpt
TWTVTRNVCHRFVVKKTW COAT_TYDVA 149 9 -
TWTVQRAWSHRFVVKRKW COAT_WDV 146 9 -
TWKVGREVCHRFVVKRRW COAT_PASV 144 11 -
TWKVARAVSHRFIVKRRW COAT_CSMV 138 11 -

Motif 4 width=24
Element Seqn Id St Int Rpt
LGVKTEWKNVTDGKDGAIKKGGFY COAT_PASV 198 36 -
LGVRTEWKNAEGGDFGDIKSGALY COAT_CSMV 191 35 -
LGVSTEWKNSSTGDVADIKEGALY COAT_TYDVA 204 37 -
LRVTTEWMNTGDGKIGDIKKGALY COAT_WDV 201 37 -

Motif 5 width=12
Element Seqn Id St Int Rpt
GRFRMYFKSVGN COAT_TYDVA 242 14 -
YTHACYFKAIGI COAT_WDV 248 23 -
GNVRVYFKSVGN COAT_CSMV 229 14 -
GQCRLYFKSVGN COAT_PASV 235 13 -
Final Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
GSDEGNRHTSETLTYK COAT_MSVK 70 70 -
GSDEGNRHTSETLTYK Q89614 70 70 -
GSDEGNRHTSETLTYK Q67598 70 70 -
GSDEGNRHTSETLTYK Q67596 70 70 -
GSDEGNRHTSETLTYK Q67594 70 70 -
GSDEGNRHTSETLTYK O73473 70 70 -
GSDEGNRHTSETLTYK O73471 70 70 -
GSDEGNRHTSETLTYK O73467 70 70 -
GSDEGNRHTSETLTYK O36262 70 70 -
GSDEGNRHTSETLTYK COAT_MSVS 70 70 -
GSDEGNRHTSETLTYK COAT_MSVN 70 70 -
GSDDGNRHTSETLTYK O56969 70 70 -
GSDERNRHTSETLTYK Q67595 70 70 -
GSDEGNRHTSETLTYK O40985 70 70 -
GSDEGNRHTSETLTYK Q67599 70 70 -
GSDEGNRHTSETLTYK Q67597 70 70 -
GSDEGNRHTNETLTYK Q84369 74 74 -
GADEANRHTNETVTYK O56311 73 73 -
GSGEGERHTNETLTYK COAT_PASVK 74 74 -
GSDEGNRHTNETVIYK Q89551 74 74 -
GSDECNRHTNETVTYK Q83480 73 73 -
GSGEGDRHTNETVTYK Q67566 70 70 -
GSAENQRKTAETITYK COAT_CSMV 68 68 -
GANDNCRHTNKTVLYK O39520 70 70 -
GANENCRHTNRTITYK COAT_TYDVA 81 81 -
GTGDDQRSRHTTMLYK COAT_MISV 74 74 -
GTGDDQRSRHTTMLYK O72914 74 74 -
GKADNNRHTNQTVLYK COAT_WDV 78 78 -
GKADNNRHTNQTVLYK Q89238 78 78 -

Motif 2 width=19
Element Seqn Id St Int Rpt
WLVYDTTPGGQAPTPQTIF COAT_MSVK 110 24 -
WLVYDTTPGGQAPTPQTIF Q89614 110 24 -
WLVYDTTPGGQAPTPQTIF Q67598 110 24 -
WLVYDTTPGGQAPTPQTIF Q67596 110 24 -
WLVYDTTPGGQAPTPQTIF Q67594 110 24 -
WLVYDTTPGGQAPTPQTIF O73473 110 24 -
WLVYDTTPGGQAPTPQTIF O73471 110 24 -
WLVYDTTPGGQAPTPQTIF O73467 110 24 -
WLVYDTTPGGQAPTPQTIF O36262 110 24 -
WLVYDTTPGGQAPTPQTIF COAT_MSVS 110 24 -
WLVYDTTPGGQAPTPQTIF COAT_MSVN 110 24 -
WLVYDTTPGGQAPTPQTIF O56969 110 24 -
WLVYDTTPGGQAPTPQTIF Q67595 110 24 -
WLVYDTTPGGNAPTTQDIF O40985 110 24 -
WLVYHTTPGGQAPTPQTIF Q67599 110 24 -
WLVYDTTPGGQAPTPQTIF Q67597 110 24 -
WLVYDAQPTGNSPEVKDIF Q84369 114 24 -
WLVYDAQPTGNTPTTKDIF O56311 113 24 -
WLVYDAQPTGTAPTVQDIF COAT_PASVK 114 24 -
WLVYDAQPSGNPPTVKDIF Q89551 114 24 -
WLVYDAQPSGKLPAVKDIF Q83480 113 24 -
WLVYDAQPSGQVPAVTDIF Q67566 110 24 -
WIVYDAAPTGSAVTPKDIF COAT_CSMV 108 24 -
WLVYDKSPGANVPSTGDIF O39520 110 24 -
WLVYDKNPGESNPSPSAIF COAT_TYDVA 121 24 -
WLVYDAAPTGVVPKLTDIF COAT_MISV 114 24 -
WLVYDAAPTGVVPKLTDIF O72914 114 24 -
WLVYDAEPKQAMPDATDIF COAT_WDV 118 24 -
WLVYDAEPKQAMPDATDIF Q89238 118 24 -

Motif 3 width=18
Element Seqn Id St Int Rpt
TWKVSRELCHRFVVKRRW COAT_MSVK 140 11 -
TWKVSRELCHRFVVKRRW Q89614 140 11 -
TWKVSRELCHRFVVKRRW Q67598 140 11 -
TWKVSRELCHRFVVKRRW Q67596 140 11 -
TWKVSRELCHRFVVKRRW Q67594 140 11 -
TWKVSRELCHRFVVKRRW O73473 140 11 -
TWKVSRELCHRFVVKRRW O73471 140 11 -
TWKVSRELCHRFVVKRRW O73467 140 11 -
TWKVSRELCHRFVVKRRW O36262 140 11 -
TWKVSRELCHRFVVKRRW COAT_MSVS 140 11 -
TWKVSRELCHRFVVKRRW COAT_MSVN 140 11 -
TWKVSRELCHRFVVKRRW O56969 140 11 -
TWKVSRELCHRFVVKRRW Q67595 140 11 -
TWKVSRELCHRFVVKRRW O40985 140 11 -
TWKVSRELCHRFVVKRRW Q67599 140 11 -
TWKVSRELCHRFVVKRRW Q67597 140 11 -
TWKVGREVCHRFVVKRRW Q84369 144 11 -
TWKVSREVCHRFVVKRRC O56311 143 11 -
TWKVGREVCHRFVVKRRW COAT_PASVK 144 11 -
TWKVGREVCHRFVVKRRW Q89551 144 11 -
TWKVGREVCHRFVVKRRW Q83480 143 11 -
TWKVGREVCHRFVVKRRW Q67566 140 11 -
TWKVARAVSHRFIVKRRW COAT_CSMV 138 11 -
TWTVSRAACHRFVVKKTW O39520 140 11 -
TWTVTRNVCHRFVVKKTW COAT_TYDVA 149 9 -
TWQVSRSNVHRFIVKRKW COAT_MISV 142 9 -
TWQVSRSNVHRFIVKRKW O72914 142 9 -
TWTVQRAWSHRFVVKRKW COAT_WDV 146 9 -
TWTVQRAWSHRFVVKRKW Q89238 146 9 -

Motif 4 width=24
Element Seqn Id St Int Rpt
LGVRTQWKNVTDGGVGAIQRGALY COAT_MSVK 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY Q89614 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY Q67598 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY Q67596 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY Q67594 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY O73473 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY O73471 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY O73467 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY O36262 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY COAT_MSVS 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY COAT_MSVN 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY O56969 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY Q67595 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY O40985 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY Q67599 194 36 -
LGVRTQWKNVTDGGVGAIQRGALY Q67597 194 36 -
LGVKTEWKNVTDGKVGAIKKGALY Q84369 198 36 -
LGVKTEWKNLTDGGVGAIKKGALY O56311 197 36 -
LGVKTEWKNVTDGKDGAIKKGGFY COAT_PASVK 198 36 -
LGVKTEWKNTTGGEVGDIKKGALY Q89551 198 36 -
LGVKTEWKNTTGGDVGDIKKGALY Q83480 197 36 -
LGVKTEWKNTTDGGVGSIKKGALY Q67566 194 36 -
LGVRTEWKNAEGGDFGDIKSGALY COAT_CSMV 191 35 -
LGVSTEWKNSATGDVGDIKEGALY O39520 195 37 -
LGVSTEWKNSSTGDVADIKEGALY COAT_TYDVA 204 37 -
LRVKTEWANTSTGAIGDVKKGALY COAT_MISV 196 36 -
LRVKTEWANTSTGAIGDVKKGALY O72914 196 36 -
LRVTTEWMNTGDGKIGDIKKGALY COAT_WDV 201 37 -
LRVTTEWMNTGDGKIGDIKKGALY Q89238 201 37 -

Motif 5 width=12
Element Seqn Id St Int Rpt
GQTRLYFKSVGN COAT_MSVK 232 14 -
GQTRLYFKSVGN Q89614 232 14 -
GQTRLYFKSVGN Q67598 232 14 -
GQTRLYFKSVGN Q67596 232 14 -
GQTRLYFKSVGN Q67594 232 14 -
GQTRLYFKSVGN O73473 232 14 -
GQTRLYFKSVGN O73471 232 14 -
GQTRLYFKSVGN O73467 232 14 -
GQTRLYFKSVGN O36262 232 14 -
GQTRLYFKSVGN COAT_MSVS 232 14 -
GQTRLYFKSVGN COAT_MSVN 232 14 -
GQTRLYFKSVGN O56969 232 14 -
GQTRLYFKSVGN Q67595 232 14 -
GQTRLYFKSVGN O40985 232 14 -
GQTRLYFKSVGN Q67599 232 14 -
GQTRLYFKSVGD Q67597 232 14 -
GQCRLYFKSVGN Q84369 236 14 -
GQARLYFKSVGN O56311 235 14 -
GQCRLYFKSVGN COAT_PASVK 235 13 -
GNARLYFKSVGN Q89551 236 14 -
GNARLYFKSVGN Q83480 235 14 -
GTCRMYFKSVGN Q67566 232 14 -
GNVRVYFKSVGN COAT_CSMV 229 14 -
GYFRVYFKSVGN O39520 233 14 -
GRFRMYFKSVGN COAT_TYDVA 242 14 -
GSTRLYFKVLGN COAT_MISV 243 23 -
GSTRLYFKVLGN O72914 243 23 -
YTHACYFKAIGI COAT_WDV 248 23 -
YTHACYFKAIGI Q89238 248 23 -