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PR00229

Identifier
GEMCOATMSVL1  [View Relations]  [View Alignment]  
Accession
PR00229
No. of Motifs
4
Creation Date
12-JUL-1994  (UPDATE 07-JUN-1999)
Title
Geminivirus MSV AL1 coat protein signature
Database References
PRINTS; PR00227 GEMCOATAL1
INTERPRO; IPR001146
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. 
 
GEMCOATMSVL1 is a 4-element fingerprint that provides a signature for the
MSV group AL1 coat proteins. The fingerprint was derived from an initial
alignment of 3 sequences: the motifs were drawn from conserved regions
spanning the full alignment length. Two iterations on OWL23.2 were required
to reach convergence, at which point a true set comprising 9 sequences was
identified. A single partial match was also found, JQ1358, a miscanthus
streak virus C1 protein that fails to make a significant match with motif 4.
 
An update on SPTR37_9f identified a true set of 19 sequences, and 3
partial matches.
Summary Information
  19 codes involving  4 elements
3 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
419191919
33330
20000
1234
True Positives
O36264        O39521        O40987        O56313        
O56968 O73478 O73558 Q67568
Q83479 Q84370 Q89239 Q89822
VAL1_CSMV VAL1_MSVK VAL1_MSVN VAL1_MSVS
VAL1_PASVK VAL1_TYDVA VAL1_WDV
True Positive Partials
Codes involving 3 elements
O39522 O72916 Q67591
Sequence Titles
O36264      REPLICATION ASSOCIATED PROTEIN A - MAIZE STREAK VIRUS. 
O39521 PUTATIVE GENES V1, V2, C1, C1:C2 - BEAN YELLOW DWARF VIRUS.
O40987 REPLICATION-ASSOCIATED PROTEIN A - MAIZE STREAK VIRUS.
O56313 REPLICASE A - EGYPTIAN SUGARCANE STREAK VIRUS.
O56968 31.5 KD PROTEIN - MAIZE STREAK VIRUS.
O73478 31.5 KD REPA PROTEIN - MAIZE STREAK VIRUS.
O73558 31.5 KD REPA PROTEIN - MAIZE STREAK VIRUS.
Q67568 COMPLETE GENOME - DIGITARIA STREAK VIRUS.
Q83479 31.5 KD PROTEIN - MAIZE STREAK VIRUS.
Q84370 REPLICATION-ASSOCIATED PROTEIN - PANICUM STREAK VIRUS.
Q89239 REPLICATION ASSOCIATED PROTEIN - WHEAT DWARF VIRUS (WDV).
Q89822 34.9 KDA ORF - SUGARCANE STREAK VIRUS.
VAL1_CSMV AL1 PROTEIN (33.2 KD PROTEIN) - CHLORIS STRIATE MOSAIC VIRUS (CSMV).
VAL1_MSVK AL1 PROTEIN (P1A PROTEIN) - MAIZE STREAK VIRUS (KENYAN ISOLATE) (MSV).
VAL1_MSVN AL1 PROTEIN (P1A PROTEIN) - MAIZE STREAK VIRUS (NIGERIAN ISOLATE) (MSV).
VAL1_MSVS AL1 PROTEIN (P1A PROTEIN) - MAIZE STREAK VIRUS (SOUTH-AFRICAN ISOLATE) (MSV).
VAL1_PASVK AL1 PROTEIN (ORF AC1) - PANICUM STREAK VIRUS (KENYAN ISOLATE).
VAL1_TYDVA AL1 PROTEIN (C1 PROTEIN) - TOBACCO YELLOW DWARF VIRUS (STRAIN AUSTRALIA) (TYDV).
VAL1_WDV AL1 PROTEIN (PUTATIVE COMPOSITE PROTEIN) (C1 PROTEIN) - WHEAT DWARF VIRUS (WDV).

O39522 REPLICATION-ASSOCIATED PROTEIN - BEAN YELLOW DWARF VIRUS.
O72916 ORF C1 - MISCANTHUS STREAK VIRUS.
Q67591 ORF C1 - MISCANTHUS STREAK VIRUS.
Scan History
OWL23_2    2  100  NSINGLE    
OWL28_0 1 100 NSINGLE
SPTR37_9f 2 35 NSINGLE
Initial Motifs
Motif 1  width=21
Element Seqn Id St Int Rpt
LHLHALLQTEKPVRISDSRFF VAL1_MSVN 59 59 -
LHLHALLQTEKPVRISDSRFF VAL1_MSVS 59 59 -
LHLHALLQTEKPVRISDSRFF VAL1_MSVK 59 59 -

Motif 2 width=20
Element Seqn Id St Int Rpt
EIMRDIISHATSKEEYLSMI VAL1_MSVN 138 58 -
EIMRDIISHATSKAEYLSMI VAL1_MSVS 138 58 -
EIMRDIISHSTSKEEYLSMI VAL1_MSVK 138 58 -

Motif 3 width=19
Element Seqn Id St Int Rpt
FDWSTKLQYFEYSANKLFP VAL1_MSVN 163 5 -
FDWSTKLQYFEYSANKLFP VAL1_MSVS 163 5 -
FDWSTKLQYFEYSANKLFP VAL1_MSVK 163 5 -

Motif 4 width=22
Element Seqn Id St Int Rpt
AYMLLQPTCYTLEDAISDLQWM VAL1_MSVN 219 37 -
AYMLLQPTCYTLEDAISDLQWM VAL1_MSVS 219 37 -
AYMLLQPACYTLDDAISDLQWM VAL1_MSVK 219 37 -
Final Motifs
Motif 1  width=21
Element Seqn Id St Int Rpt
LHLHALLQTEKPVRITDSRFF O73478 59 59 -
LHLHALLQTEKPVRISDSRFF O56968 59 59 -
LHLHALLQTEKPVRISDSRFF Q83479 59 59 -
LHLHALLQTEKPVRISDSRFF O73558 59 59 -
LHLHALLQTEKPVRISDSRFF VAL1_MSVN 59 59 -
LHLHALLQTEKPVRISDSRFF VAL1_MSVS 59 59 -
LHLHALLQTEKPVRISDSRFF VAL1_MSVK 59 59 -
LHLHALLQPEKPIRISDSRFF O36264 59 59 -
QCLHALIQTEKPVRTTDSRFF O40987 59 59 -
LHSHALVQTEKQVNTTNQRFF Q67568 56 56 -
WHIHALAQSVKPVQTTNPRFF O56313 65 65 -
YHIHVLAQSAKPVYTTDSGFF Q89822 65 65 -
WHCHALLQCIKPCTTRDERYF VAL1_PASVK 66 66 -
WHCHALLQCIKPVTTRDERYF Q84370 67 67 -
PHLHCLIQLDKRSNIRDPSFF VAL1_TYDVA 60 60 -
THYHALIQLDKKPCIRDPSFF O39521 57 57 -
PHLHAFVQLEANFRTTSPKYF VAL1_CSMV 83 83 -
PHLHVLVQNKLRASITNPNAL Q89239 58 58 -
PHLHVLVQNKLRASITNPNAL VAL1_WDV 58 58 -

Motif 2 width=20
Element Seqn Id St Int Rpt
EIMRDIISHSTSKEEYLSMI O73478 138 58 -
EIMRDIISHSTSKEEYLSMI O56968 138 58 -
EIMRDIISHSTSKEEYLSMI Q83479 138 58 -
EIMRDIISHSTSKEEYLSMI O73558 138 58 -
EIMRDIISHATSKEEYLSMI VAL1_MSVN 138 58 -
EIMRDIISHATSKAEYLSMI VAL1_MSVS 138 58 -
EIMRDIISHSTSKEEYLSMI VAL1_MSVK 138 58 -
EIMRDIISHATSKEEYLSMI O36264 138 58 -
EIMRDIISHATSKQEYLSMV O40987 138 58 -
DVMRDIIDHATSKEEYLSMV Q67568 133 56 -
DIVRDIIEHSTSKQEYLSML O56313 143 57 -
DIVRDIIEHSTNKQEYLSMI Q89822 143 57 -
EVMREIMTHATSREEYLSLV VAL1_PASVK 144 57 -
EVMKEIMTHATSRAEYLSLV Q84370 145 57 -
ERWRTIIQTATSKEEYLDMI VAL1_TYDVA 126 45 -
ARWRTIIQTATSKEEYLDMI O39521 123 45 -
KTMKQIMANATSRDEYLSMV VAL1_CSMV 155 51 -
ADMKQIIESSSSREEFLSMV Q89239 136 57 -
ADMKQIIESSSSREEFLSMV VAL1_WDV 136 57 -

Motif 3 width=19
Element Seqn Id St Int Rpt
YDWSTKLQYFEYSANKLFP O73478 163 5 -
YDWSTKLQYFEYSANKLFP O56968 163 5 -
YDWSTKLQYFEYSANKLFP Q83479 163 5 -
YDWSTKLQYFEYSANKLFP O73558 163 5 -
FDWSTKLQYFEYSANKLFP VAL1_MSVN 163 5 -
FDWSTKLQYFEYSANKLFP VAL1_MSVS 163 5 -
FDWSTKLQYFEYSANKLFP VAL1_MSVK 163 5 -
FDWSTKLQYFEYSANKLFP O36264 163 5 -
YDWSTKLQYFEYSANKLFP O40987 163 5 -
YDWATKLSYFEYSADRLFP Q67568 158 5 -
YEWATKLQYFEYSASRLFP O56313 168 5 -
YEWATKLQYFEYSANKLFP Q89822 168 5 -
YDWATKLNYFEYSASRLFP VAL1_PASVK 169 5 -
YDWATKLSYFEYSASRLFP Q84370 170 5 -
HEWATKLQWLEYSANKLFP VAL1_TYDVA 151 5 -
HEWATKLQWLEYSANKLFP O39521 148 5 -
FEWAVRLQQFQYSANALFP VAL1_CSMV 180 5 -
FEWSIRLKDFEYTARHLFP Q89239 161 5 -
FEWSIRLKDFEYTARHLFP VAL1_WDV 161 5 -

Motif 4 width=22
Element Seqn Id St Int Rpt
AYMLLQPTCYTLEDAISDLQWM O73478 219 37 -
AYMLLQPTCYTLEDAISDLQWM O56968 219 37 -
AYMLLQPTCYTLEDAISDLQWM Q83479 219 37 -
AYMLLQPTCYTLEDAISDLQWM O73558 219 37 -
AYMLLQPTCYTLEDAISDLQWM VAL1_MSVN 219 37 -
AYMLLQPTCYTLEDAISDLQWM VAL1_MSVS 219 37 -
AYMLLQPACYTLDDAISDLQWM VAL1_MSVK 219 37 -
AYMLLQPTCYTLEDAISDLQWM O36264 219 37 -
AYLLLQPNCYSIDDAISDLEWL O40987 219 37 -
AYCLLNPTCYTREEAISDLQWM Q67568 214 37 -
AYMLLTPTCLTLEEAISDLEWM O56313 224 37 -
AYMLANPSCLTLEEATSDLIWM Q89822 224 37 -
AYKLLEPSCLSLEQAIADLEWL VAL1_PASVK 225 37 -
AYMLLEPSCLSLEQAKADLEWL Q84370 226 37 -
VDAYRLVHNVTLVEAHSDLVWM VAL1_TYDVA 203 33 -
IDAYTFIHPVSYDQAQSDLEWM O39521 200 33 -
PQALSLHAGISEEQARIDLQWM VAL1_CSMV 232 33 -
LESYILCTSTPADQAQSDLEWM Q89239 213 33 -
LESYILCTSTPADQAQSDLEWM VAL1_WDV 213 33 -