******************************************************************************** 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 ------------- ------ ------ ------------- ------ ------ YSDC_BACSU 1.0000 361 SYH_JANSC 1.0000 505 ATPG_RHOCS 1.0000 295 FRVX_ECOLI 1.0000 356 AMP_CLOTM 1.0000 330 PEPA_LACLM 1.0000 355 SGCX_SALTY 1.0000 372 ******************************************************************************** ******************************************************************************** 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= 7 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= 2574 N= 7 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.099 C 0.012 D 0.061 E 0.068 F 0.035 G 0.094 H 0.017 I 0.068 K 0.056 L 0.080 M 0.028 N 0.034 P 0.044 Q 0.034 R 0.056 S 0.045 T 0.059 V 0.084 W 0.005 Y 0.021 Background letter frequencies (from dataset with add-one prior applied): A 0.098 C 0.012 D 0.061 E 0.068 F 0.035 G 0.093 H 0.017 I 0.068 K 0.056 L 0.080 M 0.029 N 0.034 P 0.044 Q 0.034 R 0.056 S 0.045 T 0.059 V 0.084 W 0.006 Y 0.022 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 46 sites = 5 llr = 506 E-value = 1.6e-044 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :4:::2:66:::::::::::::2:::::::2::::22::::2:::: pos.-specific C :::::::::::::::::::::::::::::::::::::::2:::::: probability D 2::::::::::a:::::::::442::::::::::::::2::::::: matrix E ::::::::::::a::::::::22::::::2:::::::::::::::: F :::::::2:::::::8:::::::::82:8:::::::::::::::2: G :6::::::4:::::a:::::::::a:::::::aa:::::::6:::: H :::::::::a:::::::::2::::::::::::::::::::::2::: I ::::6:4::::::2::::::a:::::2::::2:::::2::2::2:: K 4:26:::::::::::::::2:2:4:::::::::::::::::::::2 L ::2:2:::::2:::::::::::::::6::::2:::::2::4::::: M :::::8::::8:::::a::::::::::::::::::::::6:::::: N 4::::::::::::::::::::::::::::::::::22::::2:::: P ::6:::::::::::::::::::2:::::::2:::2:2:::2::::: Q :::::::::::::::::::2:::::::::2::::::24::::6::: R :::4::::::::::::::2::::::::a::2:::::2::::::8:: S ::::::::::::::::::22:::4:::::2:::::2::2:2:2::: T ::::::::::::::::::6::2:::2:::24:::::::2::::::8 V ::::2:62:::::8:2:a::::::::::22:6::2:::42::::8: W ::::::::::::::::::::::::::::::::::64:::::::::: Y :::::::::::::::::::2:::::::::::::::::2:::::::: bits 7.4 6.7 5.9 * 5.2 * * Relative 4.5 ** * * * Entropy 3.7 * **** **** * ** ** **** * ** * (146.0 bits) 3.0 * ** ** ************ *** ** **** * * **** 2.2 ***************************** **************** 1.5 ********************************************** 0.7 ********************************************** 0.0 ---------------------------------------------- Multilevel KGPKIMVAAHMDEVGFMVTHIDDKGFLRFETVGGWWAQVMLGQRVT consensus NAKRLAIFG L I V RK EAS TF VQAI PANIDCIAHIFK sequence D L V V SQ KED I SPL VNPLSVPNS S TP TR SQYT S Y V R -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------------------------------- YSDC_BACSU 59 7.14e-50 SLIAKKTGAE NGPKIMIAGHLDEVGFMVTQITDKGFIRFQTVGGWWAQVMLAQRVT IVTKKGEITG FRVX_ECOLI 52 5.54e-49 LGSFVARKGN KGPKVAVVGHMDEVGFMVTHIDESGFLRFTTIGGWWNQSMLNHRVT IRTHKGVKIP AMP_CLOTM 56 9.12e-45 LGNLIAVKKG KGKKIMVAAHMDEIGVMVTYIDDKGFLRFSAVGGVSRYDCIGQRVK FKNGVVGAVY PEPA_LACLM 56 7.88e-44 IFVTKASKVE NAPRIMVAAHMDEVGFMVSSIKADGTFRVVPLGGWNPLVVSGQRFT LFTRTGKKIP SGCX_SALTY 58 4.23e-43 VVARYGSDKP DALRLMIFAHMDEVGFMVRKIEPSGFLRFERVGGPAQITMPGSIVT LAGRSGDIMG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- YSDC_BACSU 7.1e-50 58_[1]_257 FRVX_ECOLI 5.5e-49 51_[1]_259 AMP_CLOTM 9.1e-45 55_[1]_229 PEPA_LACLM 7.9e-44 55_[1]_254 SGCX_SALTY 4.2e-43 57_[1]_269 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=46 seqs=5 YSDC_BACSU ( 59) NGPKIMIAGHLDEVGFMVTQITDKGFIRFQTVGGWWAQVMLAQRVT 1 FRVX_ECOLI ( 52) KGPKVAVVGHMDEVGFMVTHIDESGFLRFTTIGGWWNQSMLNHRVT 1 AMP_CLOTM ( 56) KGKKIMVAAHMDEIGVMVTYIDDKGFLRFSAVGGVSRYDCIGQRVK 1 PEPA_LACLM ( 56) NAPRIMVAAHMDEVGFMVSSIKADGTFRVVPLGGWNPLVVSGQRFT 1 SGCX_SALTY ( 58) DALRLMIFAHMDEVGFMVRKIEPSGFLRFERVGGPAQITMPGSIVT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 46 n= 2259 bayes= 9.06839 E= 1.6e-044 -897 -897 171 -897 -897 -897 -897 -897 285 -897 -897 354 -897 -897 -897 -897 -897 -897 -897 -897 202 -897 -897 -897 -897 268 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 185 132 -897 -897 377 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 343 -897 -897 -897 -897 -897 285 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 314 -897 132 -897 -897 -897 -897 -897 -897 -897 125 -897 -897 102 -897 -897 -897 -897 -897 -897 -897 -897 -897 481 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 256 -897 -897 -897 -897 -897 -897 -897 -897 -897 283 -897 -897 261 -897 -897 -897 249 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 125 -897 -897 261 -897 -897 -897 -897 210 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 585 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 132 481 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 403 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 388 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 156 -897 -897 -897 -897 -897 -897 -897 -897 -897 325 -897 -897 -897 -897 -897 -897 -897 342 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 449 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 125 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 513 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 357 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 185 215 335 -897 -897 -897 -897 -897 -897 -897 -897 -897 352 -897 185 -897 -897 -897 -897 256 -897 215 -897 -897 -897 321 -897 -897 -897 -897 -897 -897 -897 388 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 271 156 -897 -897 -897 -897 185 -897 -897 -897 -897 -897 -897 -897 177 -897 -897 -897 102 -897 271 156 -897 -897 -897 -897 -897 -897 -897 -897 218 -897 -897 -897 -897 -897 -897 -897 -897 -897 171 -897 -897 -897 -897 -897 285 -897 -897 -897 -897 -897 -897 315 -897 -897 -897 -897 -897 -897 -897 -897 -897 342 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 449 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 177 -897 -897 -897 -897 -897 -897 -897 249 -897 -897 156 -897 290 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 417 -897 -897 -897 -897 -897 -897 -897 -897 -897 449 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 125 -897 -897 -897 -897 -897 156 -897 -897 -897 -897 -897 -897 -897 -897 -897 256 -897 215 177 125 -897 -897 102 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 218 -897 185 -897 277 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 156 -897 132 -897 -897 -897 -897 -897 -897 -897 283 -897 -897 -897 -897 -897 -897 -897 342 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 342 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 218 -897 -897 -897 -897 125 669 -897 102 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 254 -897 -897 -897 215 -897 -897 611 -897 102 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 254 218 256 185 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 156 -897 132 -897 -897 -897 356 -897 -897 -897 -897 -897 321 -897 -897 171 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 215 177 225 -897 -897 -897 406 -897 -897 -897 -897 -897 -897 -897 -897 439 -897 -897 -897 -897 -897 -897 125 -897 -897 -897 -897 -897 -897 -897 -897 -897 156 -897 232 -897 -897 218 -897 -897 215 -897 -897 -897 -897 102 -897 -897 -897 -897 268 -897 -897 -897 -897 -897 254 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 352 -897 -897 -897 -897 -897 -897 414 -897 215 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 156 -897 -897 -897 -897 -897 -897 385 -897 -897 -897 -897 -897 -897 -897 -897 -897 249 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 325 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 185 -897 -897 -897 -897 -897 -897 -897 377 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 46 nsites= 5 E= 1.6e-044 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.600000 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 0.200000 0.200000 0.000000 0.000000 0.600000 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 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 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 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.400000 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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0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.200000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.400000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.400000 0.000000 0.000000 0.200000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 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 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [KND][GA][PKL][KR][ILV][MA][VI][AFV][AG]H[ML]DE[VI]G[FV]MV[TRS][HKQSY]I[DEKT][DAEP][KSD]G[FT][LFI]R[FV][EQSTV][TAPR][VIL]GG[WPV][WANS][ANPQR][QILY][VDST][MCV][LIPS][GAN][QHS][RI][VF][TK] -------------------------------------------------------------------------------- Time 1.17 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 50 sites = 5 llr = 491 E-value = 1.9e-022 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::2::::4::::::::::8::46:::::::6:4:::2:6:::::::: pos.-specific C ::::::::::::::::::::::::::::::::::::::2:::2::::::: probability D :2:4:::::::::::::::::::::::::::a:::::a:::::a::2242 matrix E :2:2:2:::::::2aa::::::::::2:::::::::::::::::::2::2 F :::::::22:2:::::2:::::::::2:2::::24::::::::::2:::: G ::::::::424::::::8::a::::::::::::::4:::2::6:::6::: H ::2:::::::::::::::::::::::22::::::::::::::::::::2: I ::::42222:::::::::2::22:::::6:::4:6:2:2:2::::::4:: K 42::::::::::::::::::::6::::2:4:::::::::::::::::::: L ::4:::4:2:::::::::8::::::2::::::4:::2::::::::::2:: M ::::::::::::::::::::::::::::::::::::::::2::::::::: N 22::4::::::2:::::2:::::::::::2:::::::::::::::::::4 P :224:::::::::::::::::::2::::::a:::::::::4::::8:::2 Q :::::::::::::8::::::::2::::::2::::::::::::::::::2: R :::::::::::::::::::a::::::22:2:::::::::::::::::::: S :::::::::::4::::::::::::4::2:::::::::::2:22::::22: T 4:2::4:::::4:::::::::::6:222::::::::::24:2::8::::: V ::::2:4::8::a:::8::::::22:::2:::22:26:4:2:::2::::: W :::::::::::::::::::::::::::::::::::::::::::::::::: Y :::::::6:::::::::::::::::::::::::::::::::::::::::: bits 7.4 6.7 5.9 5.2 Relative 4.5 * * Entropy 3.7 * **** ** ** * * * (141.7 bits) 3.0 * ** * * ************* * ** * * **** * 2.2 ************************************************** 1.5 ************************************************** 0.7 ************************************************** 0.0 -------------------------------------------------- Multilevel KDLDITLYGVASVQEEVGLRGAKTAAEHIKPDIAIAVDVTPAGDTPGIDN consensus TEHPNAVFFGGT E FNI IIPSLFKFN LFFGI CAISC VFDDHD sequence NKPEVEIII FN QVVTHRVQ VV VL IGMTS ELQE NT I L RS R TSV SSP P TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- YSDC_BACSU 200 1.30e-47 AIDVLRNLQN TDHPNIVYGVGTVQEEVGLRGAKTAAHTIQPDIAFGVDVGIAGDTPGISE KEAQSKMGKG AMP_CLOTM 184 1.54e-47 AVVVKAIKEL KKTDNEIYFVFTVQEEVGLRGAKTAAFSIKPDIAIAVDVTMTGDTPESHP MEVKCGGGPA PEPA_LACLM 199 8.55e-44 ILELLEFLAD KELPVTLIIGANVQEEVGLRGAKVSTTKFNPDLFFAVDCSPASDTFGDDN GRLGEGTTLR FRVX_ECOLI 191 2.07e-43 AMMAELLQTV NNPEITLYGVGSVEEEVGLRGAQTSAEHIKPDVVIVLDTAVAGDVPGIDN IKYPLKLGQG SGCX_SALTY 198 1.28e-41 LLGVAEALAS TPLDIAVFLVASVQEEFNIRGIIPVLRRVRPDLAIGIDITPSCDTPDLQD YSDVRVNHGV -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- YSDC_BACSU 1.3e-47 199_[2]_112 AMP_CLOTM 1.5e-47 183_[2]_97 PEPA_LACLM 8.6e-44 198_[2]_107 FRVX_ECOLI 2.1e-43 190_[2]_116 SGCX_SALTY 1.3e-41 197_[2]_125 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=50 seqs=5 YSDC_BACSU ( 200) TDHPNIVYGVGTVQEEVGLRGAKTAAHTIQPDIAFGVDVGIAGDTPGISE 1 AMP_CLOTM ( 184) KKTDNEIYFVFTVQEEVGLRGAKTAAFSIKPDIAIAVDVTMTGDTPESHP 1 PEPA_LACLM ( 199) KELPVTLIIGANVQEEVGLRGAKVSTTKFNPDLFFAVDCSPASDTFGDDN 1 FRVX_ECOLI ( 191) NNPEITLYGVGSVEEEVGLRGAQTSAEHIKPDVVIVLDTAVAGDVPGIDN 1 SGCX_SALTY ( 198) TPLDIAVFLVASVQEEFNIRGIIPVLRRVRPDLAIGIDITPSCDTPDLQD 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 50 n= 2231 bayes= 9.05037 E= 1.9e-022 -897 -897 -897 -897 -897 -897 -897 -897 285 -897 -897 254 -897 -897 -897 -897 277 -897 -897 -897 -897 -897 171 156 -897 -897 -897 -897 185 -897 -897 254 218 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 352 -897 -897 232 -897 -897 218 -897 -897 -897 177 -897 -897 -897 -897 -897 271 156 -897 -897 -897 -897 -897 -897 -897 -897 318 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 256 -897 -897 -897 354 -897 -897 -897 -897 -897 125 -897 -897 102 -897 -897 156 -897 -897 -897 156 -897 -897 -897 -897 -897 -897 -897 -897 277 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 156 -897 232 -897 -897 -897 -897 -897 -897 -897 225 -897 -897 -897 -897 -897 -897 249 -897 -897 156 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 479 -897 -897 -897 -897 249 210 -897 156 -897 132 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 110 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 325 -897 -897 202 -897 -897 -897 249 210 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 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0.200000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [KTN][DEKNP][LHPT][DPE][INV][TAEI][LVI][YFI][GFIL][VG][AGF][STN]V[QE]EE[VF][GN][LI]RG[AI][KIQ][TPV][ASV][ALT][EFHRT][HKRST][IFV][KNQR]PD[ILV][AFV][IF][AGV][VIL]D[VCIT][TAGS][PIMV][AST][GCS]D[TV][PF][GDE][IDLS][DHQS][NDEP] -------------------------------------------------------------------------------- Time 2.17 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 36 sites = 5 llr = 356 E-value = 2.1e-017 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::2:42::24::::224:::22::::2:42:4::2: pos.-specific C ::::::::::::::2:::2::2:::::::::::::: probability D :8::::::::2:::::::::::::::::::::::4a matrix E :2::::::2::::::::::::::::::::4:::::: F :::::::::::::::::::::::::::::::2:::: G ::2a:::::26a:::2::2::::::::::2:::::: H ::::::6::::::::::::::::::a:4::::2::: I :::::6::::::4::::6:6::::4:::::22:2:: K :::::::::::::::::::::::::::::::::2:: L :::::::6:2:::::2:4:2::::2::::::2:2:: M ::::::::2:::::::::::::::::::::4::2:: N ::::::2::22::::::::::::::::2::::2::: P ::2::::::::::a::::::6::::::4:::::::: Q ::::::2:::::::::::::::::::::2::::::: R ::::2:::::::2:::::::::a::::::::::22: S 2:2:2:::::::::4:4:4:::::::6:2:::6:2: T 8:2:::::4::::::22:2::4::2:2::22::::: V :::::::4::::4:22:::222::2:::2:2::::: W :::::::::::::::::::::::::::::::::::: Y ::::22:::::::::::::::::a:::::::::::: bits 7.4 6.7 5.9 * 5.2 * * Relative 4.5 * ** * Entropy 3.7 * * * * * ** * * * * (102.8 bits) 3.0 ** * *** * * ** * ** *** * * 2.2 ** ****** ***** ************* ****** 1.5 ************************************ 0.7 ************************************ 0.0 ------------------------------------ Multilevel TDAGAIHLTAGGIPSAAISIPTRYIHSHAEMASIDD consensus SEG RANVAGD V AGSLCLAA L APQAIFHKA sequence P SYQ ELN R CLT GVVC T TNSGTINLR S Y MN VT T V V VTVL MS T V R -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------ AMP_CLOTM 282 1.93e-34 YQLEILEAGG SDPGSIHLTAGGIPSGAISIPVRYVHSPVETASMSD INNAVKLLVE YSDC_BACSU 300 1.59e-33 YQFDAIAGGG TDSGAIHLTANGVPALSITIATRYIHTHAAMLHRDD YENAVKLITE SGCX_SALTY 304 3.86e-33 VQREVAPGVI TETGYIQVELDGIPCASLSIPCRYTHSPAEVASLRD LADCIRLLTA PEPA_LACLM 294 1.31e-31 KTQVYMAKGG TDAGAAHLANGGVPSTTIGVVARYIHSHQTIFNIDD FLQAQTFLRA FRVX_ECOLI 291 5.70e-31 LQFSTMKTGA TDGGRYNVMGGGRPVVALCLPTRYLHANSGMISKAD YEALLTLIRG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- AMP_CLOTM 1.9e-34 281_[3]_13 YSDC_BACSU 1.6e-33 299_[3]_26 SGCX_SALTY 3.9e-33 303_[3]_33 PEPA_LACLM 1.3e-31 293_[3]_26 FRVX_ECOLI 5.7e-31 290_[3]_30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=36 seqs=5 AMP_CLOTM ( 282) SDPGSIHLTAGGIPSGAISIPVRYVHSPVETASMSD 1 YSDC_BACSU ( 300) TDSGAIHLTANGVPALSITIATRYIHTHAAMLHRDD 1 SGCX_SALTY ( 304) TETGYIQVELDGIPCASLSIPCRYTHSPAEVASLRD 1 PEPA_LACLM ( 294) TDAGAAHLANGGVPSTTIGVVARYIHSHQTIFNIDD 1 FRVX_ECOLI ( 291) TDGGRYNVMGGGRPVVALCLPTRYLHANSGMISKAD 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 36 n= 2329 bayes= 9.80537 E= 2.1e-017 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 215 377 -897 -897 -897 -897 -897 371 156 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 102 -897 -897 -897 -897 110 -897 -897 -897 -897 -897 -897 218 -897 -897 215 177 -897 -897 -897 -897 -897 -897 -897 -897 342 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 202 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 185 215 -897 -897 -897 321 102 -897 -897 -897 -897 -897 -897 314 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 321 -897 -897 -897 -897 -897 -897 511 -897 -897 -897 -897 254 -897 256 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 290 -897 -897 -897 -897 -897 -897 -897 225 -897 -897 102 -897 -897 156 -897 -897 -897 -897 -897 -897 281 -897 -897 -897 -897 -897 277 -897 -897 -897 202 -897 -897 -897 -897 110 -897 -897 -897 132 -897 254 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 171 -897 -897 268 -897 -897 -897 -897 -897 254 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 342 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 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-------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- YSDC_BACSU 1.86e-117 58_[1(7.14e-50)]_95_[2(1.30e-47)]_50_[3(1.59e-33)]_26 SYH_JANSC 8.46e-01 505 ATPG_RHOCS 3.71e-02 143_[1(1.27e-05)]_106 FRVX_ECOLI 6.91e-110 51_[1(5.54e-49)]_93_[2(2.07e-43)]_50_[3(5.70e-31)]_30 AMP_CLOTM 2.35e-113 55_[1(9.12e-45)]_82_[2(1.54e-47)]_48_[3(1.93e-34)]_13 PEPA_LACLM 8.62e-106 55_[1(7.88e-44)]_97_[2(8.55e-44)]_45_[3(1.31e-31)]_26 SGCX_SALTY 2.33e-104 57_[1(4.23e-43)]_94_[2(1.28e-41)]_56_[3(3.86e-33)]_33 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo.fbb.msu.ru ********************************************************************************