******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.3.0 (Release date: Sat Sep 26 01:51:56 PDT 2009) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= temp.fasta ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ SPSE_BACSU 1.0000 373 RIMO_SPHAL 1.0000 455 SIAS_HUMAN 1.0000 359 Y1065_METJA 1.0000 337 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme temp.fasta -mod zoops -nmotifs 3 -prior dirichlet -nostatus -protein -text model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 4 wnsites= 0.8 theta: prob= 1 spmap= pam spfuzz= 120 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 1524 N= 4 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.091 C 0.014 D 0.062 E 0.085 F 0.037 G 0.070 H 0.026 I 0.072 K 0.072 L 0.087 M 0.025 N 0.029 P 0.056 Q 0.026 R 0.045 S 0.055 T 0.041 V 0.070 W 0.008 Y 0.030 Background letter frequencies (from dataset with add-one prior applied): A 0.090 C 0.014 D 0.062 E 0.084 F 0.038 G 0.070 H 0.026 I 0.071 K 0.071 L 0.087 M 0.025 N 0.029 P 0.056 Q 0.027 R 0.045 S 0.055 T 0.041 V 0.070 W 0.008 Y 0.030 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 44 sites = 3 llr = 315 E-value = 9.8e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::3:::::a:3::::::::::7:3:::3a3:3:a:73::: pos.-specific C ::::::::3::::::::::::::::::::::::::7:::3:::: probability D :::::3:::::::::::::3:7:a::::::3:::::::a::::: matrix E ::::::3::::::a:::::::::::::3:::3::7::::::::: F :::::::::a::::::::::::::::3:::::::::::::::a: G :::a33::::::::3a::::a::::3::::::::::a::::::: H ::::::3:::::::::::a::::::::::::::::::::::::: I ::::::::::aa::3:3:::::3:3::::7::::::::::3::: K 3:::7::::::::::::::::3::::7:::3::73::::::a:: L ::::::::::::::::3:::::7:::::7::::::::::::::: M ::::::::::::::::::::::::::::3::3:::::::::::: N :::::::::::::::::a:3:::::::::::::::::::::::: P :::::::a:::::::::::::::::::::::::::::::::::: Q :::::3::::::::::3::3::::3::::::::::::::::::a R 7::::::::::::::::::::::::::3::3::::::::::::: S :::::::::::::::::::::::::::::::::::::::::::: T :3::::::3::::::::::::::::::::::::::::::::::: V ::a:::::3:::::::::::::::3::::3::::::::::3::: W :3:::::::::::::::::::::::::::::::::::::::::: Y :3:::::::::::::::::::::::::::::::::::::::::: bits 6.9 6.2 5.5 * * 4.8 * ** ** Relative 4.1 *** * *** * ** * * ** * *** Entropy 3.4 **** ******* * **** * * * * ***** *** (151.6 bits) 2.8 ************** ************ ************ *** 2.1 ******************************************** 1.4 ******************************************** 0.7 ******************************************** 0.0 -------------------------------------------- Multilevel RTVGKDAPCFIIAEAGINHDGDLDIAKALIDAAKECGADAAKFQ consensus KW GGE T G L N KI QGFEMVKE AKA CI sequence Y QH V I Q Q V R RM V -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------- SIAS_HUMAN 11 5.55e-55 MPLELELCPG RWVGGQHPCFIIAEIGQNHQGDLDVAKRMIRMAKECGADCAKFQ KSELEFKFNR Y1065_METJA 9 2.79e-46 MEKIKIGD RYVGKGEPTFIIAEGGLNHNGDIDIGKELVKEAKKCGADAIKFQ SYHTEDFISK SPSE_BACSU 9 4.32e-45 MAAFQIAN KTVGKDAPVFIIAEAGINHDGKLDQAFALIDAAAEAGADAVKFQ MFQADRMYQK -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- SIAS_HUMAN 5.6e-55 10_[1]_305 Y1065_METJA 2.8e-46 8_[1]_285 SPSE_BACSU 4.3e-45 8_[1]_321 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=44 seqs=3 SIAS_HUMAN ( 11) RWVGGQHPCFIIAEIGQNHQGDLDVAKRMIRMAKECGADCAKFQ 1 Y1065_METJA ( 9) RYVGKGEPTFIIAEGGLNHNGDIDIGKELVKEAKKCGADAIKFQ 1 SPSE_BACSU ( 9) KTVGKDAPVFIIAEAGINHDGKLDQAFALIDAAAEAGADAVKFQ 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 44 n= 1352 bayes= 9.26103 E= 9.8e-014 -823 -823 -823 -823 -823 -823 -823 -823 222 -823 -823 -823 -823 -823 389 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 300 -823 530 345 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 383 -823 -823 -823 -823 -823 -823 -823 383 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 225 -823 -823 322 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 242 -823 -823 225 -823 -823 -823 -823 -823 -823 -823 365 -823 -823 -823 -823 -823 -823 189 -823 -823 198 -823 -823 368 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 416 -823 -823 -823 -823 -823 -823 -823 -823 454 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 300 225 -823 -823 -823 -823 -823 -823 473 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 381 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 381 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 347 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 357 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 189 -823 -823 -823 -823 225 -823 222 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 383 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 222 -823 194 -823 -823 -823 365 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 510 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 527 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 242 -823 -823 -823 -823 -823 -823 -823 -823 351 -823 365 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 383 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 342 -823 -823 -823 -823 -823 222 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 222 -823 294 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 400 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 222 -823 -823 -823 -823 -823 365 -823 -823 -823 225 -823 -823 288 -823 -823 -823 -823 225 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 315 -823 -823 -823 322 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 189 -823 -823 198 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 289 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 294 372 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 322 -823 -823 -823 -823 -823 -823 -823 -823 -823 225 -823 -823 -823 -823 242 -823 -823 -823 -823 -823 222 -823 -823 -823 -823 -823 289 -823 -823 -823 -823 -823 189 -823 -823 198 -823 -823 -823 -823 -823 -823 372 -823 -823 -823 -823 -823 -823 -823 -823 -823 347 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 189 -823 -823 -823 -823 -823 -823 -823 322 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 298 -823 -823 -823 -823 222 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 189 554 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 383 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 347 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 400 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 288 454 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 189 -823 -823 -823 -823 -823 -823 222 -823 -823 -823 -823 -823 -823 -823 -823 -823 225 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 381 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 473 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 523 -823 -823 -823 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 44 nsites= 3 E= 9.8e-014 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [RK][TWY]VG[KG][DGQ][AEH]P[CTV]FIIAE[AGI]G[ILQ]NH[DNQ]G[DK][LI]D[IQV][AG][KF][AER][LM][IV][DKR][AEM]A[KA][EK][CA]GAD[AC][AIV]KFQ -------------------------------------------------------------------------------- Time 0.48 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 29 sites = 4 llr = 251 E-value = 1.2e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :5::8:::::::::::::::3::3353:: pos.-specific C ::::::::::::::::::::3:::3::3: probability D :::::3::::::::8::::::8:::::3: matrix E :3::::::8:::::::::5::::::::3: F :::::::::::5::::::::::::3:3:: G ::3a:::::::::::::::a::::::::: H ::::::::::a:::::::::::a:::::: I :::::::5:::3:3::3:::::::::::3 K :::::8:::5:::::a::3:::::::::: L ::8:3:53:::::53::3::::::3:5:: M :::::::::::::::::3::::::::::: N ::::::::::::::::5::::3:::::3: P 3:::::::3:::::::::3:3:::::::8 Q ::::::::::::::::::::::::::::: R :3:::::::5::::::::::::::::::: S ::::::::::::3::::3::3::8:5::: T :::::::3::::8:::3:::::::::::: V 8:::::5:::::::::::::::::::::: W :::::::::::::::::3::::::::::: Y :::::::::::3:3::::::::::::::: bits 6.9 6.2 5.5 * * 4.8 * * Relative 4.1 * * * * * Entropy 3.4 * * ** * ** * *** * (90.5 bits) 2.8 * **************** ******* ** 2.1 ***************************** 1.4 ***************************** 0.7 ***************************** 0.0 ----------------------------- Multilevel VALGAKLIEKHFTLDKNLEGADHSAALCP consensus PEG LDVLPR ISIL IMK CN ACSADI sequence R T Y Y TSP P F FE W S L N -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------- SPSE_BACSU 226 7.94e-30 EHPTEAPCAA VRLGAKLIEKHFTIDKNLPGADHSFALNP DELKEMVDGI SIAS_HUMAN 228 3.24e-29 ETGIAISVAA VALGAKVLERHITLDKTWKGSDHSASLEP GELAELVRSV Y1065_METJA 213 5.17e-29 TLGILAPVVS VALGADVIEKHFTLDKNMEGPDHALSADP EEFKEMVNNI RIMO_SPHAL 131 1.41e-27 PTQGPFVDLV PEGGLKLTPRHYSYLKISEGCNHSCAFCI IPDLRGKLVS -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- SPSE_BACSU 7.9e-30 225_[2]_119 SIAS_HUMAN 3.2e-29 227_[2]_103 Y1065_METJA 5.2e-29 212_[2]_96 RIMO_SPHAL 1.4e-27 130_[2]_296 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=29 seqs=4 SPSE_BACSU ( 226) VRLGAKLIEKHFTIDKNLPGADHSFALNP 1 SIAS_HUMAN ( 228) VALGAKVLERHITLDKTWKGSDHSASLEP 1 Y1065_METJA ( 213) VALGADVIEKHFTLDKNMEGPDHALSADP 1 RIMO_SPHAL ( 131) PEGGLKLTPRHYSYLKISEGCNHSCAFCI 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 29 n= 1412 bayes= 8.45943 E= 1.2e-008 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 216 -865 -865 -865 -865 342 -865 -865 247 -865 -865 157 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 248 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 183 -865 -865 -865 311 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 383 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 306 -865 -865 -865 -865 -865 -865 -865 -865 152 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 200 -865 -865 -865 -865 -865 339 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 252 -865 -865 -865 -865 -865 -865 -865 283 -865 -865 -865 -865 -865 -865 -865 -865 -865 281 -865 152 -865 -865 -865 -865 -865 -865 259 -865 -865 -865 -865 -865 -865 315 -865 -865 -865 -865 -865 -865 -865 -865 216 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 281 -865 -865 -865 -865 -865 348 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 527 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 373 -865 -865 181 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 303 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 218 417 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 181 -865 252 -865 -865 -865 -865 -865 -865 -865 -865 -865 303 -865 -865 359 -865 -865 -865 -865 -865 -865 152 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 381 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 181 -865 -865 -865 410 -865 -865 -865 -865 259 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 152 330 -865 -865 -865 -865 218 -865 -865 489 -865 -865 -865 -865 257 -865 -865 -865 -865 181 -865 -865 -865 216 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 383 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 147 413 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 216 -865 -865 218 -865 -865 -865 -865 -865 -865 359 -865 -865 -865 -865 -865 -865 -865 -865 310 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 527 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 147 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 376 -865 -865 -865 -865 147 413 -865 -865 273 -865 -865 -865 -865 152 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 247 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 318 -865 -865 -865 -865 147 -865 -865 -865 273 -865 -865 -865 -865 252 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 413 200 157 -865 -865 -865 -865 -865 -865 -865 310 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 181 -865 -865 -865 -865 375 -865 -865 -865 -865 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 29 nsites= 4 E= 1.2e-008 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.500000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 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0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [VP][AER][LG]G[AL][KD][LV][ILT][EP][KR]H[FIY][TS][LIY][DL]K[NIT][LMSW][EKP]G[ACPS][DN]H[SA][ACFL][AS][LAF][CDEN][PI] -------------------------------------------------------------------------------- Time 0.87 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 26 sites = 4 llr = 222 E-value = 1.1e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::3::3:::::33::3::3:::::5: pos.-specific C :3:::3:::8:::::::::::::::: probability D :::3:::::::::::::3:5:::::: matrix E ::::::::::::::::::8::::::3 F ::::3:3::::::::::::::::::: G 8::::::::::::::::::::::::: H ::::::::8::::::3:::::::::: I ::::533:::3:::::::::3::::8 K ::::::::::::3::::::::::::: L 3:::::38:::::::3::::::a::: M :::::::3:::::::::::::::3:: N :533:::::::::::::::::8:3:: P ::33::::::::3:a:55:::3:::: Q :::3::::3:::::::3::::::::: R :33:::3::::::::::::::::3:: S :::::::::::53:::::::3::3:: T ::::::::::3::::3:::::::::: V :::::3::::5:::::3::35:::5: W ::::3::::::::::::::::::::: Y :::::::::3:3:a:::3:3:::::: bits 6.9 6.2 5.5 4.8 * * Relative 4.1 ** ** * Entropy 3.4 * * *** ** ** (80.1 bits) 2.8 ** ** ***** ** ********** 2.1 ************************** 1.4 ************************** 0.7 ************************** 0.0 -------------------------- Multilevel GNADIAFLHCVSAYPAPPEDVNLMAI consensus LCNNFCIMQYIAK HQDAVIP NVE sequence RPPWIL TYP LVY YS R RQ VR S T S -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------- Y1065_METJA 161 6.65e-27 WEAVKVLENN GCRDIILLHCISSYPTPYEDVNLNAI KTLKSIFNIP SIAS_HUMAN 175 8.99e-27 MKQVYQIVKP LNPNFCFLQCTSAYPLQPEDVNLRVI SEYQKLFPDI SPSE_BACSU 172 2.77e-26 HEAWRTIRAE GNNQIAIMHCVAKYPAPPEYSNLSVI PMLAAAFPEA RIMO_SPHAL 235 6.64e-24 RELGQLRTSE GRAPWVRLHYVYPYPHVDAVIPLMAE GLLTPYLDIP -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Y1065_METJA 6.7e-27 160_[3]_151 SIAS_HUMAN 9e-27 174_[3]_159 SPSE_BACSU 2.8e-26 171_[3]_176 RIMO_SPHAL 6.6e-24 234_[3]_195 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=26 seqs=4 Y1065_METJA ( 161) GCRDIILLHCISSYPTPYEDVNLNAI 1 SIAS_HUMAN ( 175) LNPNFCFLQCTSAYPLQPEDVNLRVI 1 SPSE_BACSU ( 172) GNNQIAIMHCVAKYPAPPEYSNLSVI 1 RIMO_SPHAL ( 235) GRAPWVRLHYVYPYPHVDAVIPLMAE 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 26 n= 1424 bayes= 9.21027 E= 1.1e-006 -865 -865 -865 -865 -865 342 -865 -865 -865 152 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 413 -865 -865 -865 -865 -865 -865 -865 -865 -865 410 -865 -865 248 -865 -865 -865 -865 -865 147 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 310 216 -865 248 -865 -865 -865 -865 -865 -865 -865 200 -865 -865 -865 -865 -865 -865 -865 -865 310 216 323 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 273 -865 -865 281 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 489 -865 147 413 -865 -865 -865 -865 -865 181 -865 -865 -865 -865 -865 -865 -865 -865 -865 183 -865 -865 -865 -865 -865 -865 273 -865 -865 181 -865 152 -865 -865 -865 -865 248 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 311 330 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 485 -865 -865 -865 -865 -865 -865 323 -865 -865 -865 -865 -865 -865 -865 571 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 303 -865 -865 -865 -865 -865 -865 -865 181 -865 -865 -865 -865 -865 -865 -865 -865 259 283 -865 -865 147 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 318 -865 -865 -865 303 147 -865 -865 -865 -865 -865 -865 -865 181 -865 -865 -865 216 -865 -865 218 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 503 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 416 -865 -865 -865 -865 -865 -865 -865 147 -865 -865 -865 -865 -865 327 -865 -865 152 -865 -865 -865 -865 -865 -865 259 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 316 323 -865 -865 -865 183 -865 -865 -865 -865 200 -865 -865 -865 -865 -865 -865 -865 -865 -865 316 -865 -865 -865 -865 -865 -865 303 147 -865 -865 315 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 300 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 183 -865 303 -865 -865 -865 -865 -865 -865 -865 181 -865 -865 -865 -865 -865 -865 -865 218 -865 283 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 468 216 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 352 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 330 310 -865 -865 248 218 -865 -865 -865 -865 247 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 283 -865 -865 -865 -865 -865 157 -865 -865 -865 339 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 26 nsites= 4 E= 1.1e-006 0.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 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0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.000000 0.000000 0.250000 0.250000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GL][NCR][ANPR][DNPQ][IFW][ACIV][FILR][LM][HQ][CY][VIT][SAY][AKPS]YP[AHLT][PQV][PDY][EA][DVY][VIS][NP]L[MNRS][AV][IE] -------------------------------------------------------------------------------- Time 1.20 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- SPSE_BACSU 8.42e-88 8_[1(4.32e-45)]_119_[3(2.77e-26)]_28_[2(7.94e-30)]_119 RIMO_SPHAL 5.22e-42 130_[2(1.41e-27)]_75_[3(6.64e-24)]_24_[2(2.86e-05)]_142 SIAS_HUMAN 1.55e-97 10_[1(5.55e-55)]_120_[3(8.99e-27)]_27_[2(3.24e-29)]_103 Y1065_METJA 6.24e-89 8_[1(2.79e-46)]_108_[3(6.65e-27)]_26_[2(5.17e-29)]_96 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo.fbb.msu.ru ********************************************************************************