******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.1.1 (Release date: Tue Apr 21 15:00:06 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= myproteins.fasta ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ NAMA_BACSU 1.0000 338 NADO_THEBR 1.0000 651 FADH_ECOLI 1.0000 672 STCD_RHIME 1.0000 678 BAICD_EUBSP 1.0000 639 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme myproteins.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= 2978 N= 5 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.101 C 0.015 D 0.054 E 0.073 F 0.036 G 0.091 H 0.028 I 0.076 K 0.048 L 0.070 M 0.031 N 0.032 P 0.046 Q 0.037 R 0.059 S 0.041 T 0.050 V 0.077 W 0.009 Y 0.025 Background letter frequencies (from dataset with add-one prior applied): A 0.101 C 0.015 D 0.054 E 0.073 F 0.036 G 0.091 H 0.028 I 0.076 K 0.048 L 0.070 M 0.031 N 0.032 P 0.046 Q 0.037 R 0.059 S 0.041 T 0.050 V 0.077 W 0.009 Y 0.025 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 40 sites = 5 llr = 453 E-value = 1.2e-044 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 8::::::::2:::::::::::::::::::::2:::::6:: pos.-specific C ::::::::::::::::::::::::::::2::4:::::::: probability D ::::::2::::::::::28::::2:2:::::::2::2::: matrix E :2:::::6:::::::2:::4:::::6:::::::8:::2:: F ::::::::a:::::::::::::::4:::::a:2::::::: G ::8:::2:::::2:::::2::aa::::::::::::::::: H :6:2::4::::::::2:::::::::::::::::::::::: I :::::8::::::::::::::::::::::::::::44::6: K :::::::::::::::2:::2::::::::::::::::2::4 L ::::a::::6:24:::2:::::::2::::::22::2:::: M :::::::::2:::2::::::::::::::6::::::::::: N ::::::2:::::::a:::::::::::8::::::::::::: P :::::2:::::8:::::::2::::2::::::2:::::::: Q :::::::4:::::::2:::2::::::::::::::::2::: R ::::::::::::4::28::::::::22a:a::2:::42:6 S 2:2:::::::8::2:::2:::::8:::::::::::::::: T ::::::::::2::6:::4:::::::::::::::::::::: V :::::::::::::::::2::::::::::::::2:64::4: W ::::::::::::::::::::2::::::::::::::::::: Y :2:8::::::::::::::::8:::2:::2:::2::::::: bits 6.8 6.1 5.4 4.8 * * * * * Relative 4.1 ** * * * * * ***** Entropy 3.4 * *** ** ** ** * * **** ***** * * (130.6 bits) 2.7 ************ ** * * ************ ** ** 2.0 **************************************** 1.4 **************************************** 0.7 **************************************** 0.0 ---------------------------------------- Multilevel AHGYLIHEFLSPLTNERTDEYGGSFENRMRFCFEVIRAIR consensus SESH PDQ ATLRM HLDGKW DLDR C ALDIVDEVK sequence Y G M GS K S P PR Y LR LKR N Q V Q Y PV Q R Y -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------------------------- BAICD_EUBSP 157 7.70e-45 AGFDAVEFHA AHSYLPHEFLSPGMNKRTDEYGGSFENRCRFCYEVVQAIR SNIPDDMPFF NAMA_BACSU 166 4.88e-42 AGFDVIEIHA AHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREIIDEVK QVWDGPLFVR NADO_THEBR 172 3.24e-41 AMFDGIELHG AHGYLIGQFMSPRTNRRVDKYGGSFERRMRFPLEIIRRIK EAVGEDYPIS FADH_ECOLI 164 2.72e-39 AGYDGVEVMG SEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVR ERVGNDFIII STCD_RHIME 169 3.09e-39 AGGMDGVELE AYGHLIDQFASPLTNELDGPYGGSLDNRMRFCFDVLKAIR ARVGDEFILG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- BAICD_EUBSP 7.7e-45 156_[1]_443 NAMA_BACSU 4.9e-42 165_[1]_133 NADO_THEBR 3.2e-41 171_[1]_440 FADH_ECOLI 2.7e-39 163_[1]_469 STCD_RHIME 3.1e-39 168_[1]_470 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=40 seqs=5 BAICD_EUBSP ( 157) AHSYLPHEFLSPGMNKRTDEYGGSFENRCRFCYEVVQAIR 1 NAMA_BACSU ( 166) AHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREIIDEVK 1 NADO_THEBR ( 172) AHGYLIGQFMSPRTNRRVDKYGGSFERRMRFPLEIIRRIK 1 FADH_ECOLI ( 164) SEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVR 1 STCD_RHIME ( 169) AYGHLIDQFASPLTNELDGPYGGSLDNRMRFCFDVLKAIR 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 40 n= 2783 bayes= 9.1179 E= 1.2e-044 299 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 227 -897 -897 -897 -897 -897 -897 -897 145 -897 -897 440 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 300 -897 -897 -897 -897 -897 314 -897 -897 -897 -897 -897 -897 -897 -897 -897 227 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 282 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 500 -897 -897 -897 -897 -897 -897 -897 -897 -897 383 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 340 -897 -897 -897 -897 211 -897 -897 -897 -897 -897 -897 -897 -897 -897 188 -897 -897 114 382 -897 -897 -897 -897 263 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 304 -897 -897 -897 -897 -897 -897 -897 -897 -897 343 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 479 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 99 -897 -897 -897 -897 -897 -897 -897 -897 310 269 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 427 201 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 151 -897 -897 411 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 114 -897 -897 -897 251 -897 -897 -897 -897 276 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 269 -897 -897 -897 -897 227 359 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 495 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 145 -897 -897 282 -897 205 -897 -897 -897 -897 243 176 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 151 -897 -897 -897 -897 376 -897 -897 -897 -897 -897 -897 -897 188 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 227 301 138 -897 -897 -897 -897 388 -897 -897 114 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 245 -897 -897 -897 -897 205 -897 -897 -897 211 243 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 447 500 -897 -897 -897 -897 -897 346 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 346 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 188 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 427 -897 -897 -897 -897 -897 -897 -897 -897 347 -897 -897 -897 -897 151 -897 -897 211 -897 -897 -897 -897 -897 -897 300 -897 -897 188 304 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 176 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 463 -897 -897 176 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 408 -897 -897 -897 -897 -897 -897 373 -897 -897 -897 -897 -897 -897 -897 -897 427 -897 -897 -897 -897 -897 -897 -897 -897 300 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 408 -897 -897 -897 -897 -897 -897 -897 -897 -897 479 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 99 473 -897 -897 -897 -897 -897 -897 -897 151 -897 -897 211 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 247 -897 -897 -897 -897 151 -897 -897 -897 -897 176 -897 -897 138 -897 300 -897 -897 188 345 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 240 -897 -897 -897 -897 -897 -897 -897 -897 -897 296 -897 -897 -897 -897 -897 -897 -897 -897 -897 240 -897 151 -897 -897 -897 -897 -897 -897 -897 238 -897 -897 -897 -897 188 -897 -897 -897 -897 -897 205 -897 -897 -897 -897 243 276 -897 -897 -897 -897 -897 257 -897 -897 145 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 176 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 298 -897 -897 -897 -897 -897 -897 -897 -897 -897 238 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 305 -897 -897 -897 -897 -897 334 -897 -897 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 40 nsites= 5 E= 1.2e-044 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 0.200000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 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 0.400000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 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 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 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 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AS][HEY][GS][YH]L[IP][HDGN][EQ]F[LAM][ST][PL][LRG][TMS]N[EHKQR][RL][TDSV][DG][EKPQ][YW]GG[SD][FLPY][EDR][NR]R[MCY]RF[CALP][FLRVY][ED][VI][IVL][RDKQ][AER][IV][RK] -------------------------------------------------------------------------------- Time 2.83 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 48 sites = 5 llr = 466 E-value = 3.2e-020 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :a::2:4:::6:::2:2:4::6:2::2::62:::2::::2:::2::2: pos.-specific C ::::::::::::::::::::::::::::::::::::::::8::6::26 probability D ::22:::::2:a::::::::::a::::::::::::42:::::::2::: matrix E ::42::24::::::::::2:::::4::::::6::426:::::::2::: F 2:::::::::2:2:2::::2::::22:::::::::::::::::::::: G ::::::::a:::::4:6:2:::::::::::::6:::::::::6:::6: H :::2:::::::::::::::2::::2::::::::::::::2:::::::: I ::::66:::::::2:4::::2::::22::22::::::a:::6:::2:: K :::4:::::4:::::::::::::::::28:2222:::::2:::::::: L :::::4::::::4::::::46::::22::::::2::2::::::::::2 M 4:::::::::::4::4::::2::::::::::::::::::::::::::: N ::2::::2::::::::::::::::2:::::::::22::2:::::6::: P ::::::::::::::::::2::::8::2:::::::::::222::::::: Q ::::::2::::::::::::2::::::::::2:2:2:::::::2::4:: R ::2::::2:4:::::::a:::2:::::4::2::6::::6::::::2:: S ::::::22::::::2::::::::::::2:::2::::::::::2::::: T 2:::::::::::::::2::::2:::::22::::::2:::2:::::::: V 2:::2:::::2::8:2::::::::::2::2:::::::::::4:::::: W :::::::::::::::::::::::::4:::::::::::::::::::::2 Y :::::::::::::::::::::::::::::::::::::::::::2:2:: bits 6.8 6.1 5.4 4.8 * Relative 4.1 * * * * * * Entropy 3.4 * * * * ** * * * * ** * (134.6 bits) 2.7 ** * * ** *** * * ** **** * *** *** ******** 2.0 ************************** ********************* 1.4 ************************************************ 0.7 ************************************************ 0.0 ------------------------------------------------ Multilevel MAEKIIAEGKADLVGIGRALLADPEWARKAAEGREDEIRACIGCNQGC consensus F DDALEN RF MIAMA EFIR AFFIKTIIKKKAED NHPVQADIAL sequence T NEV QR DV F FVT GHMT HILS VKSQLNNL PK SYERCW V RH SS S PQ NLPT Q QT P Y V R T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------------------ BAICD_EUBSP 292 1.48e-45 MGVGRINTGE MANKVIEEGKFDLVGIGRAQLADPNWITKVREGKEDLIRHCIGCDQGC YDAVINPKMK NADO_THEBR 304 1.75e-45 ITVGVIREPE FAEKIIAEGRADFVAVGRGLIADPEWPKKAKEGRQNEIRKCISCNIGC IGGRVFQNLR FADH_ECOLI 295 3.70e-42 VTTNRINDPQ VADDILSRGDADMVSMARPFLADAELLSKAQSGRADEINTCIGCNQAC LDQIFVGKVT STCD_RHIME 305 7.78e-41 FHAAKIPDVA TARHAIASGKVDMVGMTRAHMTDPHIVRKIIEKREEDIRPCVGANYCL DRIYQGGAAY NAMA_BACSU 291 3.59e-39 GAVGMITDGS MAEEILQNGRADLIFIGRELLRDPFFARTAAKQLNTEIPAPVQYERGW -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- BAICD_EUBSP 1.5e-45 291_[2]_300 NADO_THEBR 1.7e-45 303_[2]_300 FADH_ECOLI 3.7e-42 294_[2]_330 STCD_RHIME 7.8e-41 304_[2]_326 NAMA_BACSU 3.6e-39 290_[2] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=48 seqs=5 BAICD_EUBSP ( 292) MANKVIEEGKFDLVGIGRAQLADPNWITKVREGKEDLIRHCIGCDQGC 1 NADO_THEBR ( 304) FAEKIIAEGRADFVAVGRGLIADPEWPKKAKEGRQNEIRKCISCNIGC 1 FADH_ECOLI ( 295) VADDILSRGDADMVSMARPFLADAELLSKAQSGRADEINTCIGCNQAC 1 STCD_RHIME ( 305) TARHAIASGKVDMVGMTRAHMTDPHIVRKIIEKREEDIRPCVGANYCL 1 NAMA_BACSU ( 291) MAEEILQNGRADLIFIGRELLRDPFFARTAAKQLNTEIPAPVQYERGW 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 48 n= 2743 bayes= 9.34894 E= 3.2e-020 -897 -897 -897 -897 247 -897 -897 -897 -897 -897 369 -897 -897 -897 -897 -897 201 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[MFTV]A[EDNR][KDEH][IAV][IL][AEQS][ENRS]G[KRD][AFV]D[LMF][VI][GAFS][IMV][GAT]R[AEGP][LFHQ][LIM][ART]D[PA][EFHN][WFIL][AILPV][RKST][KT][AIV][AIKQR][EKS][GKQ][RKL][EANQ][DENT][EDL]I[RNP][AHKPT][CP][IV][GQS][CAY][NDE][QIRY][GAC][CLW] -------------------------------------------------------------------------------- Time 5.34 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 32 sites = 5 llr = 330 E-value = 3.2e-017 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::2:::2::2::2:8:::2:4::2:::2:4:: pos.-specific C :::::::::::::::::::::::::::::::: probability D 248::::::::::4:::::::::::::::::: matrix E :::4::4:::4::6:::64::::::::::::: F ::::::::42:::::::::::::2:::::::2 G :::::::4:::::::::::a4::4:::::2a: H :::24::22:::::::8::::::::::2a::: I ::::24::2::2::::::::::8:6:4::::: K :::2:::::24:::::2::::8:::::::::: L ::::::::2::6::::::::::::2:62:2:: M :::::2:::::2::::::::::222::::::: N 2::::::::::::::::::::::::::::::: P ::::::4::::::::::::::::::::::::: Q ::::2::2::::::2::22::::::a:::::: R :2:::::::4:::::::::::::::::::::8 S :2:2:::::::::::::2::2::::::::::: T :2::::::::2:8::::::::::::::2:2:: V :::::4:::::::::a:::::2:::::::::: W 2::::::2:::::::::::::::::::2:::: Y 4:::2:::::::::::::2::::::::::::: bits 6.8 6.1 5.4 * 4.8 * * Relative 4.1 * * * Entropy 3.4 * * * ** * ** * * ** (95.1 bits) 2.7 * ******* ******** * ** *** * ** 2.0 ******************************** 1.4 ******************************** 0.7 ******************************** 0.0 -------------------------------- Multilevel YDDEHIEGFRELTEAVHEEGAKIGIQLAHAGR consensus DRAHIVPHHAKIADQ KQA GVMAL IH G F sequence NS KQMAQIFTM SQ S FM L L WT SY WLK Y M T T W -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------- BAICD_EUBSP 76 3.21e-31 APHAYMYMGL YTDHHVEQLKKLTDAVHEAGGKMGIQLWHGGF SPQMFFDETN NAMA_BACSU 77 8.98e-31 GRITDQDLGI WSDEHIEGFAKLTEQVKEQGSKIGIQLAHAGR KAELEGDIFA STCD_RHIME 77 1.82e-30 SPPVFNNLLA YRDEIVPWIREMTDAVHEEGAVIMIQLTHLGR RTRWDKGDWL NADO_THEBR 79 5.86e-30 GKNVACQLRL DDDKYMAGFFELAEAVHSYGAKIFMQIHHAGR QTTPGITEGL FADH_ECOLI 76 5.56e-29 GVGMEGGAML NDASQIPHHRTITEAVHQEGGKIALQILHTGR YSYQPHLVAP -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- BAICD_EUBSP 3.2e-31 75_[3]_532 NAMA_BACSU 9e-31 76_[3]_230 STCD_RHIME 1.8e-30 76_[3]_570 NADO_THEBR 5.9e-30 78_[3]_541 FADH_ECOLI 5.6e-29 75_[3]_565 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=32 seqs=5 BAICD_EUBSP ( 76) YTDHHVEQLKKLTDAVHEAGGKMGIQLWHGGF 1 NAMA_BACSU ( 77) WSDEHIEGFAKLTEQVKEQGSKIGIQLAHAGR 1 STCD_RHIME ( 77) YRDEIVPWIREMTDAVHEEGAVIMIQLTHLGR 1 NADO_THEBR ( 79) DDDKYMAGFFELAEAVHSYGAKIFMQIHHAGR 1 FADH_ECOLI ( 76) NDASQIPHHRTITEAVHQEGGKIALQILHTGR 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 32 n= 2823 bayes= 9.13853 E= 3.2e-017 -897 -897 188 -897 -897 -897 -897 -897 -897 -897 -897 263 -897 -897 -897 -897 -897 -897 447 400 -897 -897 288 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 176 227 201 -897 -897 -897 99 -897 388 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 245 -897 -897 282 -897 205 -897 -897 -897 -897 -897 -897 227 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 382 140 -897 -897 -897 -897 -897 243 -897 -897 -897 -897 -897 300 -897 -897 -897 -897 -897 -897 -897 240 -897 -897 269 -897 -897 -897 -897 -897 -897 238 -897 -897 99 -897 -897 245 -897 -897 -897 -897 -897 -897 -897 -897 311 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 214 282 -897 -897 -897 -897 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-897 -897 -897 514 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 199 -897 -897 -897 -897 114 -897 -897 -897 151 -897 -897 -897 -897 -897 -897 201 -897 -897 -897 -897 -897 -897 -897 -897 346 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 247 -897 -897 -897 -897 -897 -897 -897 -897 -897 376 -897 -897 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 32 nsites= 5 E= 3.2e-017 0.000000 0.000000 0.200000 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 0.200000 0.400000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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0.000000 0.200000 0.000000 0.000000 0.000000 0.200000 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 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 0.200000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [YDNW][DRST][DA][EHKS][HIQY][IVM][EPA][GHQW][FHIL][RAFK][EKT][LIM][TA][ED][AQ]V[HK][EQS][EAQY]G[AGS][KV][IM][GAFM][ILM]Q[LI][AHLTW]H[AGLT]G[RF] -------------------------------------------------------------------------------- Time 7.52 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NAMA_BACSU 1.18e-98 76_[3(8.98e-31)]_57_[1(4.88e-42)]_85_[2(3.59e-39)] NADO_THEBR 2.29e-102 78_[3(5.86e-30)]_61_[1(3.24e-41)]_92_[2(1.75e-45)]_300 FADH_ECOLI 3.78e-96 75_[3(5.56e-29)]_56_[1(2.72e-39)]_91_[2(3.70e-42)]_46_[2(5.96e-05)]_236 STCD_RHIME 3.06e-96 76_[3(1.82e-30)]_60_[1(3.09e-39)]_96_[2(7.78e-41)]_326 BAICD_EUBSP 2.61e-107 75_[3(3.21e-31)]_49_[1(7.70e-45)]_95_[2(1.48e-45)]_300 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo-count ********************************************************************************