[Q]Prosite pattern

Pierre Lindenbaum lindenb at biotec.jouy.inra.fr
Thu Sep 23 03:54:47 EST 1999


Hello,

how can I define a consensus from a PROSITE protein matrix ?. I found a
protein matching a pattern using the ISREC server but no motif (such as
[RW]-X-G-X-[ALVI] ) is described ...

Thank you !

----------------

For example, here is the entry found at
http://www.expasy.ch/cgi-bin/get-prosite-entry?PS01031


PROSITE: PS01031

ID   HSP20; MATRIX.
AC   PS01031;
DT   JUN-1994 (CREATED); JUN-1994 (DATA UPDATE); JUL-1998 (INFO UPDATE).
DE   Heat shock hsp20 proteins family profile.
MA   /GENERAL_SPEC: ALPHABET='ACDEFGHIKLMNPQRSTVWY'; LENGTH=97;
MA   /DISJOINT: DEFINITION=PROTECT; N1=2; N2=96;
MA   /NORMALIZATION: MODE=1; FUNCTION=GLE_ZSCORE;
MA    R1=239.0; R2=-0.0036; R3=0.8341; R4=1.016; R5=0.169;
MA   /CUT_OFF: LEVEL=0; SCORE=400; N_SCORE=10.0; MODE=1;
MA   /DEFAULT: MI=-210; MD=-210; IM=0; DM=0; I=-20; D=-20;
MA   /M: SY='R';
M=-12,-44,-11,-13,-13,-22,-2,-7,18,-12,5,-3,-11,0,21,-6,-5,-11,-16,-34;
MA   /M: SY='D';
M=1,-41,17,16,-41,-3,3,-11,-1,-22,-12,8,-7,12,-7,0,-2,-19,-53,-36;
MA   /M: SY='D';
M=2,-37,15,13,-36,2,5,-15,-3,-26,-17,10,-6,7,-10,3,2,-17,-53,-28;
MA   /M: SY='P';
<...)
MA   /M: SY='G';
M=3,-35,6,3,-38,18,7,-20,-10,-29,-21,6,-4,4,-11,3,-4,-13,-56,-36;
MA   /M: SY='F';
M=-22,-45,-40,-39,43,-38,-18,17,-9,28,18,-26,-31,-28,-30,-25,-18,6,-17,19;
MA   /M: SY='K';
M=3,-28,2,0,-19,2,-7,-14,14,-27,-7,6,0,-1,8,7,7,-13,-39,-37;
MA   /M: SY='P';
(...)
MA   /M: SY='V';
M=5,-20,-14,-24,-18,-3,-21,20,-21,4,6,-11,-8,-16,-23,-4,3,24,-58,-32;
MA   /M: SY='P';
M=9,-30,-6,-2,-45,-5,2,-20,-9,-25,-20,-2,50,5,-1,8,2,-14,-55,-46;
MA   /M: SY='K';
M=-11,-52,1,-1,-1,-17,2,-18,43,-28,3,9,-10,8,33,-2,-1,-23,-33,-43;
MA   /I: MI=*; MD=*; I=0;
NR   /RELEASE=38,80000;
NR   /TOTAL=160(159); /POSITIVE=160(159); /UNKNOWN=0(0); /FALSE_POS=0(0);
NR   /FALSE_NEG=0; /PARTIAL=3;
CC   /TAXO-RANGE=A?EP?; /MAX-REPEAT=2;
DR   P30223, 14KD_MYCTU, T; P46729, 18K1_MYCAV, T; P46730, 18K1_MYCIT, T; 
DR   P46731, 18K2_MYCAV, T; P46732, 18K2_MYCIT, T; P12809, 18KD_MYCLE, T; 
(..)
DR   Q57733, Y285_METJA, T; P34328, YKZ1_CAEEL, T; P12812, P40_SCHMA , T; 
DR   P81083, HS11_PINPS, P; P81161, HS2M_LYCES, P; P30220, HS3E_XENLA, P; 
DO   PDOC00791;
//





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