5.1 PROSITE Example Flat File

Example 5-1 contains a sample pattern entry from a PROSITE flat file. This entry contains examples of the PROSITE Field Definitions, discussed later in this chapter.

Example 5-1. Sample PROSITE pattern entry

ID   PPASE; PATTERN. AC   PS00387; DT   NOV-1990 (CREATED); NOV-1995 (DATA UPDATE); NOV-1995 (INFO UPDATE). DE   Inorganic pyrophosphatase signature. PA   D-[SGN]-D-[PE]-[LIVM]-D-[LIVMGC]. NR   /RELEASE=32,49340; NR   /TOTAL=16(16); /POSITIVE=11(11); /UNKNOWN=0(0); /FALSE_POS=5(5); NR   /FALSE_NEG=0; /PARTIAL=2; CC   /TAXO-RANGE=A?EP?; /MAX-REPEAT=1; CC   /SITE=1,magnesium; /SITE=3,magnesium; /SITE=6,magnesium; DR   P21216, IPYR_ARATH, T; P37980, IPYR_BOVIN, T; P17288, IPYR_ECOLI, T; DR   P44529, IPYR_HAEIN, T; P13998, IPYR_KLULA, T; P19117, IPYR_SCHPO, T; DR   P37981, IPYR_THEAC, T; P19514, IPYR_THEP3, T; P38576, IPYR_THETH, T; DR   P00817, IPYR_YEAST, T; P28239, IPY2_YEAST, T; DR   P19371, IPYR_DESVH, P; P21616, IPYR_PHAAU, P; DR   P09167, AERA_AERHY, F; P12351, CYP1_YEAST, F; P24653, Y101_NPVOP, F; DR   P37904, YCEI_ECOLI, F; P39303, YJFU_ECOLI, F; 3D   1PYP; DO   PDOC00325; //

Example 5-2 contains a sample profile (matrix) entry from a PROSITE flat file. This entry contains further examples of the PROSITE Field Definitions described later in this chapter.

Example 5-2. Sample PROSITE profile (matrix)

ID   GLOBIN; MATRIX. AC   PS01033; DT   JUN-1994 (CREATED); DEC-2001 (DATA UPDATE); DEC-2001 (INFO UPDATE). DE   Globins profile. MA   /GENERAL_SPEC: ALPHABET='ABCDEFGHIKLMNPQRSTVWYZ'; LENGTH=154; MA   /DISJOINT: DEFINITION=PROTECT; N1=1; N2=154; MA   /NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=-0.8705306; R2=0.0209303; TEXT='-LogE'; MA   /CUT_OFF: LEVEL=0; SCORE=424; N_SCORE=8.0; MODE=1; TEXT='!'; MA   /CUT_OFF: LEVEL=-1; SCORE=353; N_SCORE=6.5; MODE=1; TEXT='?'; MA   /DEFAULT: D=-20; I=-20; MI=-210; MD=-210; IM=0; DM=0; MA   /I: I=-6; MA   /M: SY='A'; M=7,-7,-8,-10,-10,-8,3,-12,-4,-8,-6,-4,-6,-10,-10,-10,3,4,3, -14,-10,-10; D=-6; MA   /I: I=-6; MI=-59; MD=-59; MA   /M: SY='H'; M=1,-3,-21,0,-6,-20,0,2,-16,-10,-16,-10,-4,0,-8,-12,-2,-9,-11, -23,-13,-8; D=-6;     <deleted for brevity>     MA   /M: SY='H'; M=-1,4,-18,5,3,-19,-10,9,-20,8,-16,-9,3,-10,2,8,-2,-7,-14,-19,-6,1; D=-5; MA   /I: I=0; MI=*; NR   /RELEASE=40.7,103373; NR   /TOTAL=797(796); /POSITIVE=796(795); /UNKNOWN=0(0); /FALSE_POS=1(1); NR   /FALSE_NEG=0; /PARTIAL=3; CC   /MATRIX_TYPE=protein_domain; CC   /SCALING_DB=reversed; CC   /AUTHOR=P_Bucher; CC   /TAXO-RANGE=??EP?; /MAX-REPEAT=9; CC   /FT_KEY=DOMAIN; /FT_DESC=GLOBIN; DR   P04252, BAHG_VITST, T; Q03331, FHP_CANNO , T; P39676, FHP_YEAST , T; DR   P02212, GLB1_ANABR, T; P19363, GLB1_ARTSX, T; P14805, GLB1_CALSO, T; DR   P02221, GLB1_CHITH, T; P02216, GLB1_GLYDI, T; P20412, GLB1_LAMSP, T; DR   P41260, GLB1_LUCPE, T; P08924, GLB1_LUMTE, T; P21197, GLB1_MORMR, T;     <deleted for brevity>     DR   P42430, YKYB_BACSU, F; 3D   1VHB; 2VHB; 3VHB; 1HBG; 2HBG; 1B0B; 1EBT; 1FLP; 1MOH; 1HBI; 2HBI; 3HBI; 3D   3SDH; 4HBI; 4SDH; 5HBI; 6HBI; 7HBI; 1ECA; 1ECD; 1ECN; 1ECO; 1VRE; 1VRF; 3D   2LHB; 3LHB; 1DM1; 1MBA; 2FAL; 2FAM; 3MBA; 4MBA; 5MBA; 1SCT; 1HLB; 1HLM; 3D   1OUT; 1OUU; 1A4F; 1FSX; 1HDA; 1CG5; 1CG8; 1IBE; 2DHB; 2MHB; 1A00; 1A01; 3D   1A0U; 1A0V; 1A0W; 1A0X; 1A0Y; 1A0Z; 1A3N; 1A3O; 1A9W; 1ABW; 1ABY; 1AJ9; 3D   1AXF; 1B86; 1BAB; 1BBB; 1BIJ; 1BUW; 1BZ0; 1BZ1; 1BZZ; 1CLS; 1CMY; 1COH; 3D   1DSH; 1DXT; 1DXU; 1DXV; 1FDH; 1GBU; 1GBV; 1GLI; 1HAB; 1HAC; 1HBA; 1HBB; 3D   1HBS; 1HCO; 1HDB; 1HGA; 1HGB; 1HGC; 1HHO; 1NIH; 1QI8; 1QSH; 1QSI; 1RVW; 3D   1SDK; 1SDL; 1THB; 1VWT; 2HBC; 2HBD; 2HBE; 2HBF; 2HBS; 2HCO; 2HHB; 2HHD; 3D   2HHE; 3HHB; 4HHB; 6HBW; 1SPG; 1HDS; 1HBH; 1PBX; 1QPW; 2PGH; 1HBR; 1CBL; 3D   1CBM; 1ITH; 1D8U; 1CQX; 1GDI; 1GDJ; 1GDK; 1GDL; 1LH1; 1LH2; 1LH3; 1LH5; 3D   1LH6; 1LH7; 2GDM; 2LH1; 2LH2; 2LH3; 2LH5; 2LH6; 2LH7; 1BIN; 1FSL; 1LHS; 3D   1LHT; 1EMY; 1MBS; 1AZI; 1BJE; 1DWR; 1DWS; 1DWT; 1HRM; 1HSY; 1RSE; 1WLA; 3D   1XCH; 1YMA; 1YMB; 1YMC; 2MM1; 101M; 102M; 103M; 104M; 105M; 106M; 107M; 3D   108M; 109M; 110M; 111M; 112M; 1A6G; 1A6K; 1A6M; 1A6N; 1ABS; 1AJG; 1AJH; 3D   1BVC; 1BVD; 1BZ6; 1BZP; 1BZR; 1CH1; 1CH2; 1CH3; 1CH5; 1CH7; 1CH9; 1CIK; 3D   1CIO; 1CO8; 1CO9; 1CP0; 1CP5; 1CPW; 1CQ2; 1DO1; 1DO3; 1DO4; 1DO7; 1DTI; 3D   1DTM; 1DUK; 1DUO; 1DXC; 1DXD; 1EBC; 1F63; 1F65; 1F6H; 1FCS; 1HJT; 1IOP; 3D   1IRC; 1JDO; 1LTW; 1MBC; 1MBD; 1MBI; 1MBN; 1MBO; 1MCY; 1MGN; 1MLF; 1MLG; 3D   1MLH; 1MLJ; 1MLK; 1MLL; 1MLM; 1MLN; 1MLO; 1MLQ; 1MLR; 1MLS; 1MLU; 1MOA; 3D   1MOB; 1MOC; 1MOD; 1MTI; 1MTJ; 1MTK; 1MYF; 1MYM; 1OBM; 1OFJ; 1OFK; 1SPE; 3D   1SWM; 1TES; 1VXA; 1VXB; 1VXC; 1VXD; 1VXE; 1VXF; 1VXG; 1VXH; 1YOG; 1YOH; 3D   1YOI; 2CMM; 2MB5; 2MBW; 2MGA; 2MGB; 2MGC; 2MGD; 2MGE; 2MGF; 2MGG; 2MGH; 3D   2MGI; 2MGJ; 2MGK; 2MGL; 2MGM; 2MYA; 2MYB; 2MYC; 2MYD; 2MYE; 2SPL; 2SPM; 3D   2SPN; 2SPO; 4MBN; 5MBN; 1M6C; 1M6M; 1MDN; 1MNH; 1MNI; 1MNJ; 1MNK; 1MNO; 3D   1MWC; 1MWD; 1MYG; 1MYH; 1MYI; 1MYJ; 1PMB; 1YCA; 1YCB; 1MYT; 1ASH; DO   PDOC00793; //