******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.0 (Release date: Tue Mar 9 17:38:20 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** 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 ******************************************************************************** PRIMARY SEQUENCES= common/adh.s CONTROL SEQUENCES= Primary sequences shuffled preserving 2-mers ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 2BHD_STREX 1.0000 255 3BHD_COMTE 1.0000 253 ADH_DROME 1.0000 255 AP27_MOUSE 1.0000 244 BA72_EUBSP 1.0000 249 BDH_HUMAN 1.0000 343 BPHB_PSEPS 1.0000 275 BUDC_KLETE 1.0000 241 DHES_HUMAN 1.0000 327 DHGB_BACME 1.0000 262 DHII_HUMAN 1.0000 292 DHMA_FLAS1 1.0000 270 ENTA_ECOLI 1.0000 248 FIXR_BRAJA 1.0000 278 GUTD_ECOLI 1.0000 259 HDE_CANTR 1.0000 906 HDHA_ECOLI 1.0000 255 LIGD_PSEPA 1.0000 305 NODG_RHIME 1.0000 245 RIDH_KLEAE 1.0000 249 YINL_LISMO 1.0000 248 YRTP_BACSU 1.0000 238 CSGA_MYXXA 1.0000 166 DHB2_HUMAN 1.0000 387 DHB3_HUMAN 1.0000 310 DHCA_HUMAN 1.0000 276 FABI_ECOLI 1.0000 262 FVT1_HUMAN 1.0000 332 HMTR_LEIMA 1.0000 287 MAS1_AGRRA 1.0000 476 PCR_PEA 1.0000 399 RFBB_NEIGO 1.0000 346 YURA_MYXXA 1.0000 258 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -nsites 27 common/adh.s -oc results/meme45 -mod zoops -protein -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus -mpi model: mod= zoops nmotifs= 2 evt= inf objective function: em= Noise-injected mHG starts= log likelihood ratio (LLR) width: minw= 12 maxw= 12 nsites: minsites= 27 maxsites= 27 wnsites= 0.8 theta: spmap= pam spfuzz= 120 em: prior= megap b= 74865 maxiter= 50 distance= 1e-05 data: n= 9996 N= 33 sample: seed= 0 hsfrac= 0.5 searchsize= 9996 norand= no csites= -1 Dirichlet mixture priors file: prior30.plib Letter frequencies in dataset: A 0.112 C 0.0116 D 0.0518 E 0.0549 F 0.036 G 0.0888 H 0.0178 I 0.0589 K 0.0527 L 0.0912 M 0.0255 N 0.0413 P 0.0407 Q 0.0306 R 0.0484 S 0.061 T 0.0574 V 0.0821 W 0.0103 Y 0.0266 Background letter frequencies (from file dataset with add-one prior applied): A 0.111 C 0.0122 D 0.0502 E 0.0553 F 0.0359 G 0.0898 H 0.0183 I 0.0566 K 0.0518 L 0.0919 M 0.0273 N 0.0405 P 0.0405 Q 0.0295 R 0.0494 S 0.0637 T 0.0565 V 0.083 W 0.00959 Y 0.0271 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF LGRVDVLVNNAG MEME-1 width = 12 sites = 27 llr = 549 p-value = 3.1e-005 E-value = 3.1e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif LGRVDVLVNNAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::1::1:91 pos.-specific C :::::::::::: probability D ::::9::::::: matrix E 11:::::::::: F 2::::::::::: G 181::1:::::9 H :::::::::::: I :::2:213:::: K ::1::::::::: L 3::3:17::::: M ::::::1::::: N ::::1:::89:: P ::2::::::::: Q :::::::::::: R ::3::::::::: S :::::::::::: T 1:1::::::::: V :::4:4:6:::: W :::::::::::: Y 1::::::::::: bits 6.7 6.0 5.4 4.7 Relative 4.0 Entropy 3.4 * ** (29.3 bits) 2.7 * ***** 2.0 * ** ****** 1.3 ************ 0.7 ************ 0.0 ------------ Multilevel LGRVDVLVNNAG consensus PL I I sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif LGRVDVLVNNAG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ DHCA_HUMAN 80 4.95e-13 RALRDFLRKE YGGLDVLVNNAG IAFKVADPTP HDE_CANTR 393 5.82e-13 EAIIKNVIDK YGTIDILVNNAG ILRDRSFAKM HDHA_ECOLI 86 7.60e-13 SALADFAISK LGKVDILVNNAG GGGPKPFDMP CSGA_MYXXA 10 1.97e-12 MRAFATNVC TGPVDVLINNAG VSGLWCALGD MAS1_AGRRA 317 2.90e-12 AAWVTAAVEK FGRIDGLVNNAG YGEPVNLDKH BA72_EUBSP 83 4.39e-12 MAAVGQVAQK YGRLDVMINNAG ITSNNVFSRV DHGB_BACME 84 1.14e-11 INLVQSAIKE FGKLDVMINNAG MENPVSSHEM 2BHD_STREX 78 1.66e-11 QRVVAYAREE FGSVDGLVNNAG ISTGMFLETE HMTR_LEIMA 100 2.19e-11 AELVAACYTH WGRCDVLVNNAS SFYPTPLLRN YRTP_BACSU 81 2.63e-11 NQAVAQVKEQ LGDIDILINNAG ISKFGGFLDL 3BHD_COMTE 78 4.49e-11 TLVMAAVQRR LGTLNVLVNNAG ILLPGDMETG NODG_RHIME 78 5.36e-11 KALGQRAEAD LEGVDILVNNAG ITKDGLFLHM DHES_HUMAN 81 5.36e-11 SVAAARERVT EGRVDVLVCNAG LGLLGPLEAL FVT1_HUMAN 112 7.01e-11 ENVIKQAQEK LGPVDMLVNCAG MAVSGKFEDL AP27_MOUSE 74 2.35e-10 WDATEKALGG IGPVDLLVNNAA LVIMQPFLEV BUDC_KLETE 77 2.00e-09 FAAVEQARKA LGGFNVIVNNAG IAPSTPIESI BPHB_PSEPS 76 2.15e-09 KQAASRCVAR FGKIDTLIPNAG IWDYSTALVD PCR_PEA 162 2.69e-09 RQFVDNFRRS EMPLDVLINNAA VYFPTAKEPS GUTD_ECOLI 79 5.57e-09 LALSRGVDEI FGRVDLLVYSAG IAKAAFISDF FIXR_BRAJA 109 1.71e-08 AITEVKKRLA GAPLHALVNNAG VSPKTPTGDR ENTA_ECOLI 70 1.71e-08 AQVCQRLLAE TERLDALVNAAG ILRMGATDQL ADH_DROME 83 1.71e-08 TKLLKTIFAQ LKTVDVLINGAG ILDDHQIERT RIDH_KLEAE 86 2.10e-08 DNLLQGILQL TGRLDIFHANAG AYIGGPVAEG DHMA_FLAS1 195 2.25e-08 RHGILVNMIA PGPVDVTGNNTG YSEPRLAEQV YINL_LISMO 80 4.13e-08 KKLVELAIER YGKVDAIFLNAG IMPNSPLSAL YURA_MYXXA 87 1.32e-07 LERIRALDAE AGGLDLVVANAG VGGTTNAKRL DHB3_HUMAN 122 8.63e-07 IYEHIKEKLA GLEIGILVNNVG MLPNLLPSHF -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif LGRVDVLVNNAG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- DHCA_HUMAN 4.9e-13 79_[1]_185 HDE_CANTR 5.8e-13 392_[1]_502 HDHA_ECOLI 7.6e-13 85_[1]_158 CSGA_MYXXA 2e-12 9_[1]_145 MAS1_AGRRA 2.9e-12 316_[1]_148 BA72_EUBSP 4.4e-12 82_[1]_155 DHGB_BACME 1.1e-11 83_[1]_167 2BHD_STREX 1.7e-11 77_[1]_166 HMTR_LEIMA 2.2e-11 99_[1]_176 YRTP_BACSU 2.6e-11 80_[1]_146 3BHD_COMTE 4.5e-11 77_[1]_164 NODG_RHIME 5.4e-11 77_[1]_156 DHES_HUMAN 5.4e-11 80_[1]_235 FVT1_HUMAN 7e-11 111_[1]_209 AP27_MOUSE 2.3e-10 73_[1]_159 BUDC_KLETE 2e-09 76_[1]_153 BPHB_PSEPS 2.2e-09 75_[1]_188 PCR_PEA 2.7e-09 161_[1]_226 GUTD_ECOLI 5.6e-09 78_[1]_169 FIXR_BRAJA 1.7e-08 108_[1]_158 ENTA_ECOLI 1.7e-08 69_[1]_167 ADH_DROME 1.7e-08 82_[1]_161 RIDH_KLEAE 2.1e-08 85_[1]_152 DHMA_FLAS1 2.3e-08 194_[1]_64 YINL_LISMO 4.1e-08 79_[1]_157 YURA_MYXXA 1.3e-07 86_[1]_160 DHB3_HUMAN 8.6e-07 121_[1]_177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif LGRVDVLVNNAG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF LGRVDVLVNNAG width=12 seqs=27 DHCA_HUMAN ( 80) YGGLDVLVNNAG 1 HDE_CANTR ( 393) YGTIDILVNNAG 1 HDHA_ECOLI ( 86) LGKVDILVNNAG 1 CSGA_MYXXA ( 10) TGPVDVLINNAG 1 MAS1_AGRRA ( 317) FGRIDGLVNNAG 1 BA72_EUBSP ( 83) YGRLDVMINNAG 1 DHGB_BACME ( 84) FGKLDVMINNAG 1 2BHD_STREX ( 78) FGSVDGLVNNAG 1 HMTR_LEIMA ( 100) WGRCDVLVNNAS 1 YRTP_BACSU ( 81) LGDIDILINNAG 1 3BHD_COMTE ( 78) LGTLNVLVNNAG 1 NODG_RHIME ( 78) LEGVDILVNNAG 1 DHES_HUMAN ( 81) EGRVDVLVCNAG 1 FVT1_HUMAN ( 112) LGPVDMLVNCAG 1 AP27_MOUSE ( 74) IGPVDLLVNNAA 1 BUDC_KLETE ( 77) LGGFNVIVNNAG 1 BPHB_PSEPS ( 76) FGKIDTLIPNAG 1 PCR_PEA ( 162) EMPLDVLINNAA 1 GUTD_ECOLI ( 79) FGRVDLLVYSAG 1 FIXR_BRAJA ( 109) GAPLHALVNNAG 1 ENTA_ECOLI ( 70) TERLDALVNAAG 1 ADH_DROME ( 83) LKTVDVLINGAG 1 RIDH_KLEAE ( 86) TGRLDIFHANAG 1 DHMA_FLAS1 ( 195) PGPVDVTGNNTG 1 YINL_LISMO ( 80) YGKVDAIFLNAG 1 YURA_MYXXA ( 87) AGGLDLVVANAG 1 DHB3_HUMAN ( 122) GLEIGILVNNVG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif LGRVDVLVNNAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 12 n= 14434 bayes= 8.9365 E= 3.1e-005 -134 -166 -406 15 218 -55 -152 -22 -323 127 -155 -319 -36 -270 -325 -267 77 -177 169 260 -190 -323 -302 -54 -472 320 -327 -491 -126 -227 -59 -259 -413 -360 -350 -282 -398 -478 -364 -416 -269 -316 -24 -11 -357 48 -144 -362 145 -348 -281 -152 217 -88 216 -42 84 -354 -330 -278 -487 153 -691 -631 6 -682 -546 174 -609 181 -263 -594 -604 -537 -613 -553 -417 225 -463 -458 -403 -326 409 -104 -416 -264 -47 -425 -379 -458 -414 5 -445 -307 -390 -320 -383 -440 -362 -359 -10 -172 -470 -398 -219 -51 -288 184 -369 30 50 -360 -387 -308 -363 -303 -46 222 -262 -253 -421 -266 -504 -417 -36 -550 -339 2 -395 306 95 -432 -397 -292 -364 -404 -128 -127 -291 -315 -208 -140 -389 -351 -74 -217 3 145 -353 -230 -218 -364 -340 -320 -331 -326 -193 303 -331 -348 -238 -32 -218 -399 -362 -402 -64 -331 -305 -284 -356 437 -188 -227 -345 -175 -261 -412 -285 -134 -285 -11 -224 -404 -370 -259 -72 -340 -312 -431 -364 440 -372 -234 -352 -120 -265 -418 -293 -334 295 -130 -466 -425 -400 -307 -399 -377 -427 -401 -340 -406 -448 -379 -424 -162 -72 -110 -388 -436 -113 -316 -316 -377 -482 328 -340 -500 -360 -543 -446 -271 -418 -371 -363 -120 -393 -479 -376 -428 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif LGRVDVLVNNAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 12 nsites= 27 E= 3.1e-005 0.037037 0.000000 0.000000 0.074074 0.185185 0.074074 0.000000 0.037037 0.000000 0.259259 0.000000 0.000000 0.037037 0.000000 0.000000 0.000000 0.111111 0.000000 0.037037 0.148148 0.037037 0.000000 0.000000 0.074074 0.000000 0.777778 0.000000 0.000000 0.037037 0.037037 0.037037 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.037037 0.037037 0.000000 0.148148 0.000000 0.000000 0.148148 0.000000 0.000000 0.000000 0.222222 0.000000 0.259259 0.037037 0.111111 0.000000 0.000000 0.000000 0.000000 0.037037 0.000000 0.000000 0.037037 0.000000 0.000000 0.185185 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.407407 0.000000 0.000000 0.000000 0.000000 0.851852 0.000000 0.000000 0.037037 0.037037 0.000000 0.000000 0.000000 0.000000 0.074074 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.074074 0.000000 0.222222 0.000000 0.111111 0.037037 0.000000 0.000000 0.000000 0.000000 0.000000 0.037037 0.407407 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.037037 0.000000 0.000000 0.074074 0.000000 0.740741 0.074074 0.000000 0.000000 0.000000 0.000000 0.000000 0.037037 0.037037 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.037037 0.037037 0.037037 0.259259 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.629630 0.000000 0.000000 0.074074 0.037037 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.037037 0.000000 0.777778 0.037037 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.037037 0.037037 0.037037 0.000000 0.000000 0.000000 0.037037 0.000000 0.000000 0.000000 0.000000 0.000000 0.851852 0.000000 0.000000 0.000000 0.037037 0.000000 0.000000 0.000000 0.000000 0.925926 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 0.037037 0.037037 0.000000 0.000000 0.074074 0.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.037037 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif LGRVDVLVNNAG MEME-1 regular expression -------------------------------------------------------------------------------- LG[RP][VL]D[VI]L[VI]NNAG -------------------------------------------------------------------------------- Time 0.23 secs. ******************************************************************************** ******************************************************************************** MOTIF VTGASSGIGKAI MEME-2 width = 12 sites = 27 llr = 536 p-value = 3.1e-005 E-value = 3.1e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif VTGASSGIGKAI MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::531::::61 pos.-specific C :::1:::::::: probability D ::::1::::::: matrix E ::::::::::2: F :::::::::1:: G ::a3319:a::: H :::::::::1:: I 4::::::6:::3 K :::::2:::3:: L :::::::3:2:1 M :::::::::::1 N ::::1::::::: P :::::::::::: Q :::::::::::: R :::::2:::2:: S :::133::::1: T :a:::::::::3 V 5::::::1:::1 W :::::::::::: Y :::::::::::1 bits 6.7 6.0 5.4 4.7 Relative 4.0 * Entropy 3.4 ** * (28.7 bits) 2.7 *** *** 2.0 **** *** * 1.3 ************ 0.7 ************ 0.0 ------------ Multilevel VTGASSGIGKAI consensus I GA L RET sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VTGASSGIGKAI MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ YINL_LISMO 10 6.03e-14 MTIKNKVII ITGASSGIGKAT ALLLAEKGAK FVT1_HUMAN 37 6.12e-12 PLALPGAHVV VTGGSSGIGKCI AIECYKQGAF YRTP_BACSU 11 7.14e-12 MQSLQHKTAL ITGGGRGIGRAT ALALAKEGVN DHII_HUMAN 39 1.38e-11 PEMLQGKKVI VTGASKGIGREM AYHLAKMGAH BUDC_KLETE 7 1.38e-11 MQKVAL VTGAGQGIGKAI ALRLVKDGFA ENTA_ECOLI 10 5.67e-11 MDFSGKNVW VTGAGKGIGYAT ALAFVEAGAK DHCA_HUMAN 9 6.42e-11 SSGIHVAL VTGGNKGIGLAI VRDLCRLFSG DHB3_HUMAN 53 7.35e-11 FLRSMGQWAV ITGAGDGIGKAY SFELAKRGLN DHMA_FLAS1 19 7.35e-11 PGRLAGKAAI VTGAAGGIGRAT VEAYLREGAS PCR_PEA 91 8.23e-11 KKTLRKGNVV ITGASSGLGLAT AKALAESGKW RIDH_KLEAE 19 8.23e-11 NTSLSGKVAA ITGAASGIGLEC ARTLLGAGAK HDHA_ECOLI 16 9.28e-11 NLRLDGKCAI ITGAGAGIGKEI AITFATAGAS DHES_HUMAN 7 1.30e-10 ARTVVL ITGCSSGIGLHL AVRLASDPSQ AP27_MOUSE 12 1.80e-10 KLNFSGLRAL VTGAGKGIGRDT VKALHASGAK FIXR_BRAJA 41 2.22e-10 VDRGEPKVML LTGASRGIGHAT AKLFSEAGWR BPHB_PSEPS 10 2.74e-10 MKLKGEAVL ITGGASGLGRAL VDRFVAEAKV DHB2_HUMAN 87 1.01e-09 LLPVDQKAVL VTGGDCGLGHAL CKYLDELGFT HDE_CANTR 327 1.10e-09 TVSLKDKVVL ITGAGAGLGKEY AKWFAKYGAK BA72_EUBSP 11 1.81e-09 MNLVQDKVTI ITGGTRGIGFAA AKIFIDNGAK DHGB_BACME 12 3.91e-09 YKDLEGKVVV ITGSSTGLGKSM AIRFATEKAK 3BHD_COMTE 11 5.27e-09 TNRLQGKVAL VTGGASGVGLEV VKLLLGEGAK BDH_HUMAN 60 6.56e-09 AEPVGSKAVL VTGCDSGFGFSL AKHLHSKGFL HMTR_LEIMA 11 1.01e-08 MTAPTVPVAL VTGAAKRLGRSI AEGLHAEGYA 2BHD_STREX 11 1.33e-08 MNDLSGKTVI ITGGARGLGAEA ARQAVAAGAR MAS1_AGRRA 250 1.64e-08 VEIHQSPVIL VSGSNRGVGKAI AEDLIAHGYR NODG_RHIME 11 1.64e-08 MFELTGRKAL VTGASGAIGGAI ARVLHAQGAI RFBB_NEIGO 11 4.21e-08 MQTEGKKNIL VTGGAGFIGSAV VRHIIQNTRD -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VTGASSGIGKAI MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- YINL_LISMO 6e-14 9_[2]_227 FVT1_HUMAN 6.1e-12 36_[2]_284 YRTP_BACSU 7.1e-12 10_[2]_216 DHII_HUMAN 1.4e-11 38_[2]_242 BUDC_KLETE 1.4e-11 6_[2]_223 ENTA_ECOLI 5.7e-11 9_[2]_227 DHCA_HUMAN 6.4e-11 8_[2]_256 DHB3_HUMAN 7.3e-11 52_[2]_246 DHMA_FLAS1 7.3e-11 18_[2]_240 PCR_PEA 8.2e-11 90_[2]_297 RIDH_KLEAE 8.2e-11 18_[2]_219 HDHA_ECOLI 9.3e-11 15_[2]_228 DHES_HUMAN 1.3e-10 6_[2]_309 AP27_MOUSE 1.8e-10 11_[2]_221 FIXR_BRAJA 2.2e-10 40_[2]_226 BPHB_PSEPS 2.7e-10 9_[2]_254 DHB2_HUMAN 1e-09 86_[2]_289 HDE_CANTR 1.1e-09 326_[2]_568 BA72_EUBSP 1.8e-09 10_[2]_227 DHGB_BACME 3.9e-09 11_[2]_239 3BHD_COMTE 5.3e-09 10_[2]_231 BDH_HUMAN 6.6e-09 59_[2]_272 HMTR_LEIMA 1e-08 10_[2]_265 2BHD_STREX 1.3e-08 10_[2]_233 MAS1_AGRRA 1.6e-08 249_[2]_215 NODG_RHIME 1.6e-08 10_[2]_223 RFBB_NEIGO 4.2e-08 10_[2]_324 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VTGASSGIGKAI MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF VTGASSGIGKAI width=12 seqs=27 YINL_LISMO ( 10) ITGASSGIGKAT 1 FVT1_HUMAN ( 37) VTGGSSGIGKCI 1 YRTP_BACSU ( 11) ITGGGRGIGRAT 1 DHII_HUMAN ( 39) VTGASKGIGREM 1 BUDC_KLETE ( 7) VTGAGQGIGKAI 1 ENTA_ECOLI ( 10) VTGAGKGIGYAT 1 DHCA_HUMAN ( 9) VTGGNKGIGLAI 1 DHB3_HUMAN ( 53) ITGAGDGIGKAY 1 DHMA_FLAS1 ( 19) VTGAAGGIGRAT 1 PCR_PEA ( 91) ITGASSGLGLAT 1 RIDH_KLEAE ( 19) ITGAASGIGLEC 1 HDHA_ECOLI ( 16) ITGAGAGIGKEI 1 DHES_HUMAN ( 7) ITGCSSGIGLHL 1 AP27_MOUSE ( 12) VTGAGKGIGRDT 1 FIXR_BRAJA ( 41) LTGASRGIGHAT 1 BPHB_PSEPS ( 10) ITGGASGLGRAL 1 DHB2_HUMAN ( 87) VTGGDCGLGHAL 1 HDE_CANTR ( 327) ITGAGAGLGKEY 1 BA72_EUBSP ( 11) ITGGTRGIGFAA 1 DHGB_BACME ( 12) ITGSSTGLGKSM 1 3BHD_COMTE ( 11) VTGGASGVGLEV 1 BDH_HUMAN ( 60) VTGCDSGFGFSL 1 HMTR_LEIMA ( 11) VTGAAKRLGRSI 1 2BHD_STREX ( 11) ITGGARGLGAEA 1 MAS1_AGRRA ( 250) VSGSNRGVGKAI 1 NODG_RHIME ( 11) VTGASGAIGGAI 1 RFBB_NEIGO ( 11) VTGGAGFIGSAV 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VTGASSGIGKAI MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 12 n= 14434 bayes= 8.9365 E= 3.1e-005 -517 -345 -738 -704 -447 -767 -730 294 -698 -107 -356 -670 -682 -680 -749 -657 -447 261 -649 -579 -369 -263 -460 -490 -463 -501 -394 -384 -411 -493 -356 -292 -450 -350 -422 -24 398 -379 -434 -481 -543 -516 -527 -593 -662 345 -530 -712 -574 -725 -665 -492 -593 -574 -569 -510 -610 -699 -553 -615 220 256 -629 -624 -590 184 -549 -606 -640 -618 -543 -505 -467 -505 -587 33 -349 -480 -566 -611 114 -392 67 -324 -570 145 -271 -640 -356 -631 -590 104 -446 -312 -437 215 -54 -597 -556 -461 -53 131 -25 -118 -337 7 -130 -341 171 -328 -261 -150 -277 66 169 197 -37 -334 -312 -260 -190 -323 -303 -365 -98 329 -328 -492 -347 -536 -438 -259 -413 -362 -122 -282 -399 -478 -364 -417 -485 -340 -566 -549 -15 -640 -503 345 -511 129 -181 -508 -557 -468 -541 -498 -397 19 -405 -400 -543 -516 -527 -593 -662 345 -530 -712 -574 -725 -665 -492 -593 -574 -569 -510 -610 -699 -553 -615 -125 -295 -214 -142 79 -129 183 -320 232 77 -259 -172 -296 -88 196 -45 -205 -322 -315 31 234 130 -52 161 -392 -309 66 -386 -279 -393 -332 -220 -401 -236 -331 63 -268 -295 -378 -379 -55 150 -473 -395 -206 -437 -279 207 -362 69 139 -351 -383 -297 -357 -291 201 9 -246 130 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VTGASSGIGKAI MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 12 nsites= 27 E= 3.1e-005 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.444444 0.000000 0.037037 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.518519 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 0.037037 0.962963 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 0.518519 0.074074 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 0.074074 0.000000 0.000000 0.000000 0.000000 0.259259 0.000000 0.074074 0.000000 0.000000 0.259259 0.000000 0.000000 0.000000 0.000000 0.000000 0.074074 0.000000 0.000000 0.000000 0.296296 0.037037 0.000000 0.000000 0.000000 0.074074 0.037037 0.037037 0.000000 0.000000 0.111111 0.000000 0.000000 0.185185 0.000000 0.000000 0.000000 0.000000 0.037037 0.185185 0.296296 0.037037 0.000000 0.000000 0.000000 0.037037 0.000000 0.000000 0.000000 0.037037 0.888889 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.037037 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.037037 0.000000 0.000000 0.629630 0.000000 0.259259 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.074074 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 0.037037 0.000000 0.000000 0.000000 0.074074 0.037037 0.074074 0.000000 0.296296 0.185185 0.000000 0.000000 0.000000 0.000000 0.222222 0.037037 0.000000 0.000000 0.000000 0.037037 0.555556 0.037037 0.037037 0.222222 0.000000 0.000000 0.037037 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.074074 0.037037 0.000000 0.000000 0.000000 0.000000 0.000000 0.259259 0.000000 0.148148 0.074074 0.000000 0.000000 0.000000 0.000000 0.000000 0.259259 0.074074 0.000000 0.074074 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VTGASSGIGKAI MEME-2 regular expression -------------------------------------------------------------------------------- [VI]TG[AG][SAG]SG[IL]G[KR][AE][IT] -------------------------------------------------------------------------------- Time 0.39 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2BHD_STREX 4.35e-13 10_[2(1.33e-08)]_55_[1(1.66e-11)]_\ 166 3BHD_COMTE 4.56e-13 10_[2(5.27e-09)]_55_[1(4.49e-11)]_\ 164 ADH_DROME 2.09e-05 82_[1(1.71e-08)]_161 AP27_MOUSE 7.98e-14 11_[2(1.80e-10)]_50_[1(2.35e-10)]_\ 159 BA72_EUBSP 1.63e-14 10_[2(1.81e-09)]_60_[1(4.39e-12)]_\ 69_[2(1.71e-05)]_74 BDH_HUMAN 2.53e-08 59_[2(6.56e-09)]_63_[1(1.62e-06)]_\ 197 BPHB_PSEPS 1.31e-12 9_[2(2.74e-10)]_54_[1(2.15e-09)]_\ 188 BUDC_KLETE 5.11e-14 6_[2(1.38e-11)]_58_[1(2.00e-09)]_\ 153 DHES_HUMAN 2.51e-14 6_[2(1.30e-10)]_62_[1(5.36e-11)]_\ 235 DHGB_BACME 9.73e-14 11_[2(3.91e-09)]_60_[1(1.14e-11)]_\ 167 DHII_HUMAN 1.77e-09 38_[2(1.38e-11)]_59_[1(6.74e-05)]_\ 171 DHMA_FLAS1 3.42e-12 18_[2(7.35e-11)]_53_[1(1.26e-05)]_\ 99_[1(2.25e-08)]_64 ENTA_ECOLI 1.72e-12 9_[2(5.67e-11)]_48_[1(1.71e-08)]_\ 167 FIXR_BRAJA 8.11e-12 40_[2(2.22e-10)]_56_[1(1.71e-08)]_\ 158 GUTD_ECOLI 7.67e-07 78_[1(5.57e-09)]_169 HDE_CANTR 1.85e-14 12_[2(2.47e-08)]_64_[1(7.97e-10)]_\ 226_[2(1.10e-09)]_54_[1(5.82e-13)]_502 HDHA_ECOLI 1.72e-16 15_[2(9.28e-11)]_58_[1(7.60e-13)]_\ 158 LIGD_PSEPA 4.03e-03 10_[2(3.36e-06)]_283 NODG_RHIME 1.53e-12 10_[2(1.64e-08)]_55_[1(5.36e-11)]_\ 156 RIDH_KLEAE 3.04e-12 18_[2(8.23e-11)]_55_[1(2.10e-08)]_\ 152 YINL_LISMO 5.24e-15 9_[2(6.03e-14)]_58_[1(4.13e-08)]_\ 157 YRTP_BACSU 3.89e-16 10_[2(7.14e-12)]_58_[1(2.63e-11)]_\ 146 CSGA_MYXXA 5.01e-09 9_[1(1.97e-12)]_145 DHB2_HUMAN 1.48e-07 86_[2(1.01e-09)]_59_[1(5.32e-05)]_\ 218 DHB3_HUMAN 1.52e-10 52_[2(7.35e-11)]_57_[1(8.63e-07)]_\ 177 DHCA_HUMAN 9.28e-17 8_[2(6.42e-11)]_59_[1(4.95e-13)]_\ 185 FABI_ECOLI 1.40e-02 262 FVT1_HUMAN 1.71e-15 36_[2(6.12e-12)]_63_[1(7.01e-11)]_\ 209 HMTR_LEIMA 5.49e-13 10_[2(1.01e-08)]_77_[1(2.19e-11)]_\ 99_[1(7.41e-05)]_65 MAS1_AGRRA 3.41e-13 249_[2(1.64e-08)]_55_[1(2.90e-12)]_\ 148 PCR_PEA 1.07e-12 90_[2(8.23e-11)]_59_[1(2.69e-09)]_\ 226 RFBB_NEIGO 7.61e-05 10_[2(4.21e-08)]_324 YURA_MYXXA 1.92e-05 86_[1(1.32e-07)]_160 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************