******************************************************************************** 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 ------------- ------ ------ ------------- ------ ------ DACC_BACSU 1.0000 491 DAC_ACTSP 1.0000 538 DACB_ECOLI 1.0000 477 DACB_HAEIN 1.0000 479 Y4IL_RHISN 1.0000 432 ******************************************************************************** ******************************************************************************** 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= 5 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= 2417 N= 5 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.110 C 0.007 D 0.059 E 0.051 F 0.034 G 0.085 H 0.016 I 0.045 K 0.047 L 0.100 M 0.021 N 0.041 P 0.053 Q 0.041 R 0.049 S 0.074 T 0.058 V 0.073 W 0.011 Y 0.026 Background letter frequencies (from dataset with add-one prior applied): A 0.109 C 0.007 D 0.059 E 0.051 F 0.034 G 0.085 H 0.016 I 0.045 K 0.047 L 0.099 M 0.021 N 0.041 P 0.053 Q 0.041 R 0.049 S 0.073 T 0.058 V 0.073 W 0.011 Y 0.026 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 27 sites = 4 llr = 248 E-value = 7.6e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::5:::::::::::::::::a::::: pos.-specific C ::::::::::::::::::::::::::: probability D :::::::5:::::::::5::::5:::: matrix E ::::3::3::::::::::::::5:::: F :::::::::3::5::3:::::::::5: G :::::::::::::::::::5::::::: H 8:::::3:::::::::::::5:::::: I ::::::::3::3::::::::5:::::: K 3::3:::3::53::a5::::::::::5 L :3:::a::88:::3:3::::::::8:: M :::3::::::::58:::::3:::3::: N :::::::::::::::::5a:::::::: P ::::8:3::::5::::::::::::::: Q :3:::::::::::::::::3::::::: R :3::::::::::::::::::::::::5 S ::a:::5:::::::::a::::::3::: T :3:::::::::::::::::::::3::: V ::::::::::5::::::::::::335: W ::::::::::::::::::::::::::: Y ::::::::::::::::::::::::::: bits 7.2 6.4 5.7 5.0 * Relative 4.3 * *** * * Entropy 3.6 * * ** *** *** * ** (89.5 bits) 2.9 * ********************* *** 2.1 *************************** 1.4 *************************** 0.7 *************************** 0.0 --------------------------- Multilevel HLSAPLSDLLKPFMKKSDNGHADMLFK consensus KQ KE HEIFVIML F N MI ESVVR sequence R M PK K L Q T T V -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------------- DACC_BACSU 312 7.24e-29 APSSSDVLLS HRSMPLSKLFVPFMKLSNNGHAEVLVK EMGKVKKGEG DAC_ACTSP 331 9.25e-29 DWQDAEVLAD HTSAELSEILVPFMKFSNNGHAEMLVK SIGQETAGAG DACB_HAEIN 294 1.04e-28 KPQQGQLLAK HLSKPLPDLLKKMMKKSDNQIADSLFR AVAFNYYKRP DACB_ECOLI 290 1.30e-27 VNEPGTVVAS KQSAPLHDLLKIMLKKSDNMIADTVFR MIGHARFNVP -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- DACC_BACSU 7.2e-29 311_[1]_153 DAC_ACTSP 9.3e-29 330_[1]_181 DACB_HAEIN 1e-28 293_[1]_159 DACB_ECOLI 1.3e-27 289_[1]_161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=27 seqs=4 DACC_BACSU ( 312) HRSMPLSKLFVPFMKLSNNGHAEVLVK 1 DAC_ACTSP ( 331) HTSAELSEILVPFMKFSNNGHAEMLVK 1 DACB_HAEIN ( 294) HLSKPLPDLLKKMMKKSDNQIADSLFR 1 DACB_ECOLI ( 290) KQSAPLHDLLKIMLKKSDNMIADTVFR 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 27 n= 2287 bayes= 9.15672 E= 7.6e-013 -865 -865 -865 -865 -865 -865 551 -865 240 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 133 -865 -865 -865 260 235 -865 210 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 376 -865 -865 -865 -865 219 -865 -865 -865 -865 -865 -865 -865 240 -865 355 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 228 -865 -865 -865 -865 -865 -865 -865 -865 383 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 333 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 393 -865 -865 -865 -865 -865 225 -865 -865 276 -865 -865 -865 -865 -865 -865 309 228 -865 -865 -865 -865 240 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 248 -865 291 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 286 -865 -865 -865 -865 291 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 340 -865 -865 -865 -865 -865 -865 -865 -865 277 -865 -865 -865 -865 -865 -865 -865 -865 -865 248 240 -865 -865 -865 325 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 386 -865 -865 -865 -865 -865 455 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 133 513 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 440 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 286 -865 -865 -865 340 133 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 376 -865 -865 -865 -865 -865 -865 309 -865 -865 -865 -865 -865 -865 -865 -865 359 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 459 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 255 -865 -865 -865 -865 355 -865 -865 260 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 493 348 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 319 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 309 328 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 355 -865 -865 -865 -865 176 210 177 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 291 -865 -865 -865 -865 -865 -865 -865 177 -865 -865 -865 -865 -865 -865 386 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 277 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 340 -865 -865 -865 -865 -865 335 -865 -865 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 27 nsites= 4 E= 7.6e-013 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.750000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.250000 0.250000 0.000000 0.250000 0.000000 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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 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [HK][LQRT]S[AKM][PE]L[SHP][DEK][LI][LF][KV][PIK][FM][ML]K[KFL]S[DN]N[GMQ][HI]A[DE][MSTV][LV][FV][KR] -------------------------------------------------------------------------------- Time 1.10 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 29 sites = 3 llr = 211 E-value = 1.0e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::3:::::::::::::7::7a7:3:::: pos.-specific C ::::::::::::::7:::::::::::::7 probability D :7:::3::::a::::::::::::::7::: matrix E :::::::::::3::::::::::::::::3 F :::::::::::::::7::::::::::::: G :::3:7::::::::::3:::::::::::: H 7:::::::::::::::::::::::::::: I :::::::3:::::::::::3:::33:::: K ::3:::::::::::::::::::::::::: L ::3:3::::::3::::::::::3:::::: M 3:::::3::::3:3::::::::::::::: N :::::::::7::::::3::::::3::3a: P ::::7::7::::::::::a7::::::3:: Q :::::::::::::3::::::::::::::: R :33:::::::::::::::::::::::3:: S :::3:::::3::::::33::3::::3::: T ::::::::::::73:::::::::3::::: V ::::::::::::::::::::::::3:::: W ::::::7:a:::::::::::::::::::: Y ::::::::::::3:33::::::::::::: bits 7.2 6.4 * 5.7 * * 5.0 * * * * * Relative 4.3 * * * * ** * ** Entropy 3.6 ** ***** * ** ** ** (101.6 bits) 2.9 ** ************ ** * * **** 2.1 ***************************** 1.4 ***************************** 0.7 ***************************** 0.0 ----------------------------- Multilevel HDKAPGWPWNDETMCFGAPPAAAIADNNC consensus MRLGLDMI S LYQYYNS IS LNISP E sequence RS M T S TV R -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------- DACB_ECOLI 145 6.62e-36 VLIDTSIFAS HDKAPGWPWNDMTQCFSAPPAAAIVDRNC FSVSLYSAPK DACB_HAEIN 152 1.80e-34 LVLDTSVFSS HDRGLGWIWNDLTMCFNSPPAAANIDNNC FYAELDANKN DACC_BACSU 164 3.44e-29 LIGDDTWHDD MRLSPDMPWSDEYTYYGAPISALTASPNE DYDAGTVIVE -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- DACB_ECOLI 6.6e-36 144_[2]_304 DACB_HAEIN 1.8e-34 151_[2]_299 DACC_BACSU 3.4e-29 163_[2]_299 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=29 seqs=3 DACB_ECOLI ( 145) HDKAPGWPWNDMTQCFSAPPAAAIVDRNC 1 DACB_HAEIN ( 152) HDRGLGWIWNDLTMCFNSPPAAANIDNNC 1 DACC_BACSU ( 164) MRLSPDMPWSDEYTYYGAPISALTASPNE 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 29 n= 2277 bayes= 10.014 E= 1.0e-008 -823 -823 -823 -823 -823 -823 534 -823 -823 -823 396 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 350 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 277 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 282 174 -823 -823 -823 -823 277 -823 -823 -823 -823 -823 161 -823 -823 -823 -823 197 -823 -823 -823 -823 -823 -823 -823 -823 -823 218 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 174 -823 -823 366 -823 -823 -823 -823 -823 -823 -823 -823 -823 250 -823 -823 297 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 396 -823 -823 -823 -823 -823 -823 -823 591 -823 -823 -823 -823 -823 -823 -823 -823 289 -823 -823 -823 -823 366 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 649 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 400 -823 -823 -823 218 -823 -823 -823 -823 -823 -823 409 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 270 -823 -823 -823 -823 -823 174 396 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 351 -823 -823 368 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 396 -823 -823 302 -823 -823 251 -823 -823 -823 -823 657 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 368 -823 -823 -823 -823 427 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 368 -823 -823 -823 -823 -823 197 -823 -823 -823 -823 -823 300 -823 -823 -823 218 -823 -823 -823 -823 261 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 218 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 425 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 289 -823 -823 -823 -823 366 -823 -823 -823 -823 -823 -823 -823 261 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 218 -823 -823 -823 -823 319 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 261 -823 -823 -823 -823 -823 -823 -823 -823 174 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 289 -823 -823 -823 300 -823 -823 -823 -823 251 -823 -823 -823 161 -823 -823 -823 -823 -823 -823 289 -823 -823 -823 -823 -823 -823 -823 -823 -823 219 -823 -823 -823 -823 350 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 218 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 300 266 -823 277 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 459 -823 -823 -823 -823 -823 -823 -823 -823 -823 657 -823 270 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 29 nsites= 3 E= 1.0e-008 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.666667 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 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 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 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-------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [HM][DR][KLR][AGS][PL][GD][WM][PI]W[NS]D[ELM][TY][MQT][CY][FY][GNS][AS]P[PI][AS]A[AL][INT][AIV][DS][NPR]N[CE] -------------------------------------------------------------------------------- Time 2.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 41 sites = 4 llr = 336 E-value = 3.8e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :3:::3:::::3::::3:58::33:::::::::::3::::: pos.-specific C ::::::::::::::::::::::::::::::::::::::::: probability D ::::::a:3::::8:5::::::::::::::3:5:::a5::: matrix E ::::::::::::3::::::35:::::::::::::::::::: F :::5::::::::::3:::::::::::::::::::::::::8 G :::538::::::3::::::::::::a:::::a:::3::::: H :::::::::::::::::::::::3::::::::::::::::3 I 3:::::::::::::3:::::3:::::3::8::::33:::3: K ::3:3:::::3:::::3:::::85:::53:3:::::::::: L :5:::::::a3:::5::33::8:::::::::::833::::: M :::::::::::::::::8::::::::::::::::::::::: N ::::::::::::::::3::::::::::3::3:5:::::::: P :::::::a:::3::::::::::::::::::::::::::::: Q ::::::::::::33::::::::::3:::3:::::::::::: R ::5:3::::::5:::3:::::::::::3::3:::::::::: S ::::::::::3:3:::3:::::::8:::::::::::::5:: T ::::3:::8:3:::::::::3:::::::3::::::::55:: V 333:::::::::::::::3::3::::8:33:::33::::3: W :::::::::::::::::::::::::::::::::::::::5: Y 5::::::::::::::3::::::::::::::::::3:::::: bits 7.2 6.4 5.7 5.0 Relative 4.3 ** * * * Entropy 3.6 **** * * * * * ** * ** (121.0 bits) 2.9 * ** ***** * * * * ********* * *** ***** 2.1 *********************************** ***** 1.4 ***************************************** 0.7 ***************************************** 0.0 ----------------------------------------- Multilevel YLRFGGDPTLKREDLDAMAAELKKSGVKKIDGDLIADDSWF consensus IAKGKA D LAGQFRKLLEIVAAQ INQVK NVLG TTIH sequence VVV R SPQ IYN V T H RT N VI V T T S S V R YL -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------------------- DACC_BACSU 121 4.04e-41 LKGKKLNGNL YLKGKGDPTLLPSDFDKMAEILKHSGVKVIKGNLIGDDTWH DDMRLSPDMP DACB_ECOLI 102 4.17e-38 VENGVLKGDL VARFGADPTLKRQDIRNMVATLKKSGVNQIDGNVLIDTSIF ASHDKAPGWP DAC_ACTSP 138 3.56e-37 PGRRGEVQDL YLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWF DSERLVDDWW DACB_HAEIN 109 8.76e-37 IQNGNLDGNL IVRFTGDPDLTRGQLYSLLAELKKQGIKKINGDLVLDTSVF SSHDRGLGWI -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- DACC_BACSU 4e-41 120_[3]_330 DACB_ECOLI 4.2e-38 101_[3]_335 DAC_ACTSP 3.6e-37 137_[3]_360 DACB_HAEIN 8.8e-37 108_[3]_330 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=41 seqs=4 DACC_BACSU ( 121) YLKGKGDPTLLPSDFDKMAEILKHSGVKVIKGNLIGDDTWH 1 DACB_ECOLI ( 102) VARFGADPTLKRQDIRNMVATLKKSGVNQIDGNVLIDTSIF 1 DAC_ACTSP ( 138) YLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWF 1 DACB_HAEIN ( 109) IVRFTGDPDLTRGQLYSLLAELKKQGIKKINGDLVLDTSVF 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 41 n= 2217 bayes= 9.11179 E= 3.8e-008 -865 -865 -865 -865 -865 -865 -865 248 -865 -865 -865 -865 -865 -865 -865 -865 -865 177 -865 427 119 -865 -865 -865 -865 -865 -865 -865 -865 233 -865 -865 -865 -865 -865 -865 -865 177 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 240 -865 -865 -865 -865 -865 335 -865 -865 177 -865 -865 -865 -865 -865 -865 386 255 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 156 -865 -865 240 -865 -865 -865 -865 -865 235 -865 210 -865 -865 -865 119 -865 -865 -865 -865 314 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 409 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 425 -865 -865 -865 -865 -865 -865 -865 -865 -865 209 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 368 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 333 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 240 133 -865 -865 -865 -865 -865 176 210 -865 -865 -865 119 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 225 -865 335 -865 -865 -865 -865 -865 -865 -865 -865 228 -865 156 -865 -865 -865 -865 -865 -865 -865 260 -865 176 -865 -865 -865 -865 -865 -865 367 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 260 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 286 -865 -865 248 -865 233 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 309 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 235 -865 -865 -865 -865 327 119 -865 -865 -865 -865 -865 -865 -865 240 -865 -865 259 -865 -865 -865 176 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 133 513 -865 -865 -865 -865 -865 -865 -865 -865 -865 219 -865 -865 -865 -865 -865 -865 -865 -865 133 -865 -865 -865 -865 -865 -865 -865 177 -865 -865 278 -865 -865 228 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 328 -865 -865 -865 248 -865 -865 -865 -865 -865 -865 -865 -865 210 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 291 -865 -865 -865 -865 -865 -865 -865 177 -865 -865 119 -865 -865 -865 -865 -865 -865 -865 399 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 119 -865 -865 -865 -865 -865 393 -865 340 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 260 -865 335 -865 -865 -865 -865 -865 -865 -865 -865 -865 355 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 248 -865 -865 -865 -865 -865 -865 -865 -865 -865 336 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 340 -865 -865 259 -865 -865 235 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 240 -865 -865 -865 -865 260 -865 -865 210 177 -865 -865 -865 -865 -865 -865 -865 -865 -865 406 -865 -865 -865 -865 -865 -865 -865 -865 -865 177 -865 -865 -865 -865 209 -865 -865 -865 -865 -865 240 -865 -865 259 -865 -865 235 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 355 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 309 -865 -865 -865 -865 -865 -865 -865 -865 359 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 291 -865 -865 -865 -865 -865 -865 -865 177 -865 -865 -865 -865 -865 -865 -865 -865 -865 248 -865 133 -865 -865 -865 -865 -865 -865 -865 177 -865 327 119 -865 -865 -865 -865 156 -865 248 -865 133 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 409 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 309 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 310 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 276 310 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 248 -865 -865 -865 -865 -865 -865 -865 -865 -865 177 549 -865 -865 -865 -865 -865 444 -865 393 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 41 nsites= 4 E= 3.8e-008 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 0.250000 0.000000 0.500000 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0.250000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.750000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [YIV][LAV][RKV][FG][GKRT][GA]DP[TD]L[KLST][RAP][EGQS][DQ][LFI][DRY][AKNS][ML][ALV][AE][EIT][LV][KA][KAH][SQ]G[VI][KNR][KQTV][IV][DKNR]G[DN][LV][ILVY][AGIL]D[DT][ST][WIV][FH] -------------------------------------------------------------------------------- Time 2.96 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- DACC_BACSU 2.07e-85 120_[3(4.04e-41)]_2_[2(3.44e-29)]_119_[1(7.24e-29)]_153 DAC_ACTSP 2.40e-61 137_[3(3.56e-37)]_2_[2(4.97e-09)]_121_[1(9.25e-29)]_181 DACB_ECOLI 7.11e-88 101_[3(4.17e-38)]_2_[2(6.62e-36)]_116_[1(1.30e-27)]_161 DACB_HAEIN 3.19e-86 108_[3(8.76e-37)]_2_[2(1.80e-34)]_113_[1(1.04e-28)]_159 Y4IL_RHISN 2.12e-01 432 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo.fbb.msu.ru ********************************************************************************