******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.1 (Release date: Sun Jan 29 10:33:12 2023 -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= SYA_selected.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ sp|P00957|SYA_ECOLI 1.0000 876 sp|O34526|SYA_BACSU 1.0000 878 sp|P9WFW7|SYA_MYCTU 1.0000 904 sp|P74941|SYA_THET8 1.0000 882 sp|O67323|SYA_AQUAE 1.0000 867 sp|O83980|SYA_TREPA 1.0000 605 sp|O84754|SYA_CHLTR 1.0000 875 sp|P56452|SYA_HELPY 1.0000 847 sp|Q9JYG6|SYA_NEIMB 1.0000 874 sp|P74423|SYA_SYNY3 1.0000 877 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme SYA_selected.fasta -protein -mod oops -nmotifs 3 -minw 8 -maxw 15 -oc meme_SYA_output model: mod= oops nmotifs= 3 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values width: minw= 8 maxw= 15 nsites: minsites= 10 maxsites= 10 wnsites= 0.8 theta: spmap= pam spfuzz= 120 em: prior= dmix b= 0 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 8485 N= 10 sample: seed= 0 hsfrac= 0 searchsize= 8485 norand= no csites= 1000 Dirichlet mixture priors file: prior30.plib Letter frequencies in dataset: A 0.092 C 0.00872 D 0.0556 E 0.0891 F 0.0462 G 0.09 H 0.0236 I 0.0526 K 0.0581 L 0.0907 M 0.0187 N 0.0344 P 0.0346 Q 0.0369 R 0.0606 S 0.0508 T 0.0486 V 0.0754 W 0.00907 Y 0.0242 Background letter frequencies (from file dataset with add-one prior applied): A 0.0919 C 0.00882 D 0.0556 E 0.089 F 0.0462 G 0.0899 H 0.0236 I 0.0526 K 0.0581 L 0.0907 M 0.0188 N 0.0345 P 0.0347 Q 0.0369 R 0.0606 S 0.0508 T 0.0486 V 0.0754 W 0.00917 Y 0.0242 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TFFEMLGNFSFGDYF MEME-1 width = 15 sites = 10 llr = 427 E-value = 1.4e-094 ******************************************************************************** -------------------------------------------------------------------------------- Motif TFFEMLGNFSFGDYF MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::1::::::::: pos.-specific C ::::::::::::::: probability D ::::::::::::a:: matrix E :::9::::::::::: F :8a:::::9:8:::a G ::::::a::::a::: H ::::::::::::::: I ::::::::::1:::: K ::::::::::::::: L :1:::8::::1:::: M ::::a1::::::::: N :::::::a::::::: P ::::::::::::::: Q :::1::::::::::: R ::::::::::::::: S :::::::::a::::: T a:::::::::::::: V ::::::::::::::: W ::::::::1:::::: Y :1:::::::::::a: bits 6.8 6.1 5.5 * * 4.8 * * * Relative 4.1 * * * *** *** Entropy 3.4 ***** ********* (61.6 bits) 2.7 *************** 2.0 *************** 1.4 *************** 0.7 *************** 0.0 --------------- Multilevel TFFEMLGNFSFGDYF consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TFFEMLGNFSFGDYF MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- sp|P74423|SYA_SYNY3 89 2.96e-20 ENVGRTARHH TFFEMLGNFSFGDYF KSQAIAWAWE sp|O84754|SYA_CHLTR 87 2.96e-20 ENVGHTSRHL TFFEMLGNFSFGDYF KQDAISFAWE sp|O67323|SYA_AQUAE 89 2.96e-20 EQVGYTSRHH TFFEMLGNFSFGDYF KKEAIEYAWE sp|P00957|SYA_ECOLI 89 2.96e-20 ENVGYTARHH TFFEMLGNFSFGDYF KHDAIQFAWE sp|Q9JYG6|SYA_NEIMB 87 3.57e-20 ENVGYTARHH TFFEMMGNFSFGDYF KRDAIHFAWE sp|P74941|SYA_THET8 87 5.71e-20 ENVGRTSRHN TYFEMLGNFSFGDYF KKEAILWAWE sp|O34526|SYA_BACSU 86 3.20e-19 ENVGKTARHH TFFEMLGNFSIGDYF KEEAITWAWE sp|P56452|SYA_HELPY 84 3.94e-19 ENVGYTARHH TLFEMLGNFSFGDYF KEEAILFAWE sp|O83980|SYA_TREPA 86 2.59e-18 IDAVGDNSHL TFFEMLGNWSLGDYF KEEAIAFSFE sp|P9WFW7|SYA_MYCTU 82 8.09e-18 DEVGITTRHN TFFQMAGNFSFGDYF KRGAIELAWA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TFFEMLGNFSFGDYF MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sp|P74423|SYA_SYNY3 3e-20 88_[1]_774 sp|O84754|SYA_CHLTR 3e-20 86_[1]_774 sp|O67323|SYA_AQUAE 3e-20 88_[1]_764 sp|P00957|SYA_ECOLI 3e-20 88_[1]_773 sp|Q9JYG6|SYA_NEIMB 3.6e-20 86_[1]_773 sp|P74941|SYA_THET8 5.7e-20 86_[1]_781 sp|O34526|SYA_BACSU 3.2e-19 85_[1]_778 sp|P56452|SYA_HELPY 3.9e-19 83_[1]_749 sp|O83980|SYA_TREPA 2.6e-18 85_[1]_505 sp|P9WFW7|SYA_MYCTU 8.1e-18 81_[1]_808 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TFFEMLGNFSFGDYF MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TFFEMLGNFSFGDYF width=15 seqs=10 sp|P74423|SYA_SYNY3 ( 89) TFFEMLGNFSFGDYF 1 sp|O84754|SYA_CHLTR ( 87) TFFEMLGNFSFGDYF 1 sp|O67323|SYA_AQUAE ( 89) TFFEMLGNFSFGDYF 1 sp|P00957|SYA_ECOLI ( 89) TFFEMLGNFSFGDYF 1 sp|Q9JYG6|SYA_NEIMB ( 87) TFFEMMGNFSFGDYF 1 sp|P74941|SYA_THET8 ( 87) TYFEMLGNFSFGDYF 1 sp|O34526|SYA_BACSU ( 86) TFFEMLGNFSIGDYF 1 sp|P56452|SYA_HELPY ( 84) TLFEMLGNFSFGDYF 1 sp|O83980|SYA_TREPA ( 86) TFFEMLGNWSLGDYF 1 sp|P9WFW7|SYA_MYCTU ( 82) TFFQMAGNFSFGDYF 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TFFEMLGNFSFGDYF MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 8345 bayes= 9.70304 E= 1.4e-094 -383 -249 -485 -581 -509 -495 -441 -406 -459 -504 -347 -311 -430 -416 -475 -154 427 -402 -424 -459 -367 -126 -443 -485 418 -497 -354 -222 -438 -100 -157 -375 -349 -422 -468 -282 -373 -285 -115 68 -407 -167 -476 -524 428 -518 -382 -264 -475 -201 -199 -410 -382 -456 -500 -323 -409 -327 -154 -41 -483 -448 -201 341 -613 -543 -432 -510 -471 -592 -487 -361 -526 -165 -536 -453 -473 -549 -508 -522 -481 -255 -534 -593 -412 -561 -465 -256 -492 -219 563 -454 -458 -469 -555 -423 -409 -350 -270 -297 -112 -173 -481 -448 -168 -506 -335 -80 -374 311 160 -369 -335 -286 -355 -329 -275 -171 -237 -252 -294 -275 -328 -445 -508 337 -369 -490 -375 -533 -396 -248 -387 -401 -390 -258 -381 -472 -358 -403 -427 -244 -253 -482 -422 -414 -131 -353 -345 -447 -334 472 -362 -286 -397 -171 -267 -429 -302 -332 -377 -136 -451 -494 420 -503 -331 -232 -444 -168 -167 -376 -357 -422 -470 -291 -380 -295 150 8 -320 -226 -475 -586 -520 -436 -452 -527 -480 -539 -433 -320 -405 -462 -485 421 -127 -510 -436 -440 -368 -129 -450 -490 417 -503 -380 -77 -444 -79 -134 -384 -353 -426 -474 -289 -371 -270 -128 -20 -294 -275 -328 -445 -508 337 -369 -490 -375 -533 -396 -248 -387 -401 -390 -258 -381 -472 -358 -403 -387 -284 402 -185 -458 -430 -283 -425 -408 -463 -371 -75 -422 -351 -428 -302 -373 -436 -359 -351 -606 -375 -594 -688 -192 -585 -312 -521 -592 -477 -444 -478 -512 -509 -561 -506 -538 -557 -193 531 -407 -167 -476 -524 428 -518 -382 -264 -475 -201 -199 -410 -382 -456 -500 -323 -409 -327 -154 -41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TFFEMLGNFSFGDYF MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 10 E= 1.4e-094 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 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 0.900000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 0.900000 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 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.100000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TFFEMLGNFSFGDYF MEME-1 regular expression -------------------------------------------------------------------------------- TFFEMLGNFSFGDYF -------------------------------------------------------------------------------- Time 1.17 secs. ******************************************************************************** ******************************************************************************** MOTIF RYJEIWNLVFMQYNR MEME-2 width = 15 sites = 10 llr = 386 E-value = 4.5e-072 ******************************************************************************** -------------------------------------------------------------------------------- Motif RYJEIWNLVFMQYNR MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::::::::::::: pos.-specific C :::::::1::::::: probability D :::::::1:::::1: matrix E :::a:::::::2:2: F :4::1::::a::4:: G ::::::::::::::: H ::::::::::::::1 I ::3:6::1::::::: K 1:::::::::::::1 L ::5::::7::::::: M ::::::::::8:::: N ::::::a:::::16: P ::::::::::::::: Q :::::::::::8::: R 9::::::::::::18 S ::::::::::1:::: T ::::::::::1:::: V ::2:2:::a:::::: W :1:::9::::::::: Y :5::11::::::5:: bits 6.8 6.1 * 5.5 * 4.8 ** * Relative 4.1 * ** *** Entropy 3.4 ** * ** ***** * (55.6 bits) 2.7 ** ************ 2.0 *************** 1.4 *************** 0.7 *************** 0.0 --------------- Multilevel RYLEIWNLVFMQYNR consensus FI V EFE sequence V -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYJEIWNLVFMQYNR MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- sp|O67323|SYA_AQUAE 189 3.45e-21 DRGEEYEGDE RYLEIWNLVFMQYNR DENGVLTPLP sp|Q9JYG6|SYA_NEIMB 205 7.68e-20 IPGSPEEDGD RWIEIWNCVFMQFNR DEQGNMNPLP sp|P00957|SYA_ECOLI 207 1.59e-19 PPGSPEEDGD RYIEIWNIVFMQFNR QADGTMEPLP sp|P56452|SYA_HELPY 191 1.88e-19 SEDYFGGEGD RFLEIWNLVFMQYER SNDGVLSPLP sp|P9WFW7|SYA_MYCTU 194 7.30e-18 PAGGPIVSED RYLEVWNLVFMQNER GEGTTKEDYQ sp|O84754|SYA_CHLTR 194 3.53e-17 ASPLEDVDGE RFLEYWNLVFMEFNR TSDGTLLALQ sp|P74941|SYA_THET8 202 8.10e-17 ETGPNTGSGD RFVEIWNLVFTQYDR QGPIPGPGIL sp|P74423|SYA_SYNY3 196 8.85e-17 DEKLDLEDDS RFIEFYNLVFMQYNR DNAGNLTPLE sp|O83980|SYA_TREPA 202 2.26e-15 VSCRPGCSCG KYVEIWNDVFMQYRK DADGRYRPLE sp|O34526|SYA_BACSU 197 1.22e-14 PELYPGGEND RYLEVWNLVFSEFNH NPDGTYTPLP -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYJEIWNLVFMQYNR MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sp|O67323|SYA_AQUAE 3.5e-21 188_[2]_664 sp|Q9JYG6|SYA_NEIMB 7.7e-20 204_[2]_655 sp|P00957|SYA_ECOLI 1.6e-19 206_[2]_655 sp|P56452|SYA_HELPY 1.9e-19 190_[2]_642 sp|P9WFW7|SYA_MYCTU 7.3e-18 193_[2]_696 sp|O84754|SYA_CHLTR 3.5e-17 193_[2]_667 sp|P74941|SYA_THET8 8.1e-17 201_[2]_666 sp|P74423|SYA_SYNY3 8.8e-17 195_[2]_667 sp|O83980|SYA_TREPA 2.3e-15 201_[2]_389 sp|O34526|SYA_BACSU 1.2e-14 196_[2]_667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYJEIWNLVFMQYNR MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RYJEIWNLVFMQYNR width=15 seqs=10 sp|O67323|SYA_AQUAE ( 189) RYLEIWNLVFMQYNR 1 sp|Q9JYG6|SYA_NEIMB ( 205) RWIEIWNCVFMQFNR 1 sp|P00957|SYA_ECOLI ( 207) RYIEIWNIVFMQFNR 1 sp|P56452|SYA_HELPY ( 191) RFLEIWNLVFMQYER 1 sp|P9WFW7|SYA_MYCTU ( 194) RYLEVWNLVFMQNER 1 sp|O84754|SYA_CHLTR ( 194) RFLEYWNLVFMEFNR 1 sp|P74941|SYA_THET8 ( 202) RFVEIWNLVFTQYDR 1 sp|P74423|SYA_SYNY3 ( 196) RFIEFYNLVFMQYNR 1 sp|O83980|SYA_TREPA ( 202) KYVEIWNDVFMQYRK 1 sp|O34526|SYA_BACSU ( 197) RYLEVWNLVFSEFNH 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYJEIWNLVFMQYNR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 8345 bayes= 9.70304 E= 4.5e-072 -374 -167 -436 -478 -473 -440 -186 -384 -57 -391 -323 -269 -304 -204 387 -309 -337 -478 -233 -352 -424 -231 -472 -507 296 -520 -121 -346 -429 -313 -262 -327 -412 -356 -412 -333 -381 -380 323 432 -363 -180 -597 -598 -254 -595 -498 247 -526 232 -82 -476 -478 -465 -543 -439 -297 145 -353 -344 -524 -445 -222 344 -616 -560 -450 -519 -548 -614 -511 -380 -573 -354 -571 -488 -505 -572 -508 -533 -315 -171 -404 -445 -71 -470 -365 362 -351 -48 -24 -307 -380 -344 -400 -285 -225 104 -265 6 -427 -216 -411 -463 -139 -454 -334 -380 -391 -252 -242 -335 -393 -336 -371 -356 -366 -371 659 -18 -427 -244 -253 -482 -422 -414 -131 -353 -345 -447 -334 472 -362 -286 -397 -171 -267 -429 -302 -332 -323 191 -78 -430 -169 -483 -317 24 -355 304 30 -346 -321 -272 -340 -304 -251 -151 -228 -238 -260 -157 -477 -508 -376 -502 -409 -62 -458 -269 -226 -421 -390 -443 -452 -368 -249 356 -409 -412 -407 -167 -476 -524 428 -518 -382 -264 -475 -201 -199 -410 -382 -456 -500 -323 -409 -327 -154 -41 -357 -212 -505 -556 -402 -477 -440 -252 -460 -223 556 -408 -423 -434 -512 -127 -127 -327 -270 -294 -286 -205 -282 -24 -430 -448 -21 -349 -248 -280 -130 -191 -266 441 -226 -237 -265 -369 -248 -342 -347 -183 -404 -435 287 -467 -78 -301 -368 -279 -218 111 -356 -319 -364 -271 -326 -331 -23 432 -288 -282 90 101 -456 -266 -160 -430 -186 -439 -336 390 -282 -151 39 -119 -204 -425 -385 -298 -373 -168 -435 -471 -473 -440 -26 -384 -52 -389 -321 -267 -304 -200 384 -307 -335 -475 -234 -351 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYJEIWNLVFMQYNR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 10 E= 4.5e-072 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.900000 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 0.000000 0.000000 0.000000 0.100000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.300000 0.000000 0.500000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.100000 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 0.900000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.100000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.700000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.100000 0.100000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.100000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYJEIWNLVFMQYNR MEME-2 regular expression -------------------------------------------------------------------------------- R[YF][LIV]E[IV]WNLVFM[QE][YF][NE]R -------------------------------------------------------------------------------- Time 1.97 secs. ******************************************************************************** ******************************************************************************** MOTIF GPCGPCSEIFYDRGE MEME-3 width = 15 sites = 10 llr = 385 E-value = 1.1e-071 ******************************************************************************** -------------------------------------------------------------------------------- Motif GPCGPCSEIFYDRGE MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::::::::::::: pos.-specific C ::8::6::::::::: probability D :::::1:::::a::1 matrix E :::::::a::::::5 F ::::1::::52:1:: G a::a:::::::::9: H ::::::::::::21: I ::::::::9:1:::: K ::::::::::::::: L ::::::::11::::: M ::::::::::::::: N :::::1::::::::: P :a::9:::::::::3 Q ::::::::::::1:: R ::::::::::::5:: S ::2::27:::::::: T ::::::3:::::1:: V ::::::::::1:::1 W ::::::::::::::: Y :::::::::46:::: bits 6.8 6.1 5.5 * 4.8 ** Relative 4.1 ** ** * Entropy 3.4 ************ * (55.5 bits) 2.7 ************** 2.0 *************** 1.4 *************** 0.7 *************** 0.0 --------------- Multilevel GPCGPCSEIFYDRGE consensus S ST YF H P sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GPCGPCSEIFYDRGE MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- sp|Q9JYG6|SYA_NEIMB 175 1.77e-20 SDNFWQMGDT GPCGPCSEIFYDHGE EIWGGIPGSP sp|P9WFW7|SYA_MYCTU 166 1.42e-19 ADNYWSMGIP GPCGPSSEIYYDRGP EFGPAGGPIV sp|P00957|SYA_ECOLI 177 3.67e-19 SDNFWQMGDT GPCGPCTEIFYDHGD HIWGGPPGSP sp|P74423|SYA_SYNY3 168 6.35e-19 DDNFWVSGPT GPCGPCSEIYYDFHP ELGDEKLDLE sp|P74941|SYA_THET8 171 1.61e-18 PGGAITHGPN GPSGPCSEIFYDRGP AYGTPDETGP sp|P56452|SYA_HELPY 161 1.83e-18 KDNFWQMGDS GPCGPCSEIYIDQGE KHFKGSEDYF sp|O67323|SYA_AQUAE 168 1.38e-17 EDNFWQMGDV GPCGPSSEIYVDRGE EYEGDERYLE sp|O34526|SYA_BACSU 164 2.29e-16 LEGNFWDIGE GPSGPNTEIFYDRGE AYGNDPEDPE sp|O84754|SYA_CHLTR 164 9.68e-16 KDNFWSMADT GPCGFCSELLFDRGE KFGKAASPLE sp|O83980|SYA_TREPA 173 1.27e-15 DNWWGPTGET GPCGPDTEIFFDTGV PPCSVSCRPG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GPCGPCSEIFYDRGE MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sp|Q9JYG6|SYA_NEIMB 1.8e-20 174_[3]_685 sp|P9WFW7|SYA_MYCTU 1.4e-19 165_[3]_724 sp|P00957|SYA_ECOLI 3.7e-19 176_[3]_685 sp|P74423|SYA_SYNY3 6.3e-19 167_[3]_695 sp|P74941|SYA_THET8 1.6e-18 170_[3]_697 sp|P56452|SYA_HELPY 1.8e-18 160_[3]_672 sp|O67323|SYA_AQUAE 1.4e-17 167_[3]_685 sp|O34526|SYA_BACSU 2.3e-16 163_[3]_700 sp|O84754|SYA_CHLTR 9.7e-16 163_[3]_697 sp|O83980|SYA_TREPA 1.3e-15 172_[3]_418 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GPCGPCSEIFYDRGE MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GPCGPCSEIFYDRGE width=15 seqs=10 sp|Q9JYG6|SYA_NEIMB ( 175) GPCGPCSEIFYDHGE 1 sp|P9WFW7|SYA_MYCTU ( 166) GPCGPSSEIYYDRGP 1 sp|P00957|SYA_ECOLI ( 177) GPCGPCTEIFYDHGD 1 sp|P74423|SYA_SYNY3 ( 168) GPCGPCSEIYYDFHP 1 sp|P74941|SYA_THET8 ( 171) GPSGPCSEIFYDRGP 1 sp|P56452|SYA_HELPY ( 161) GPCGPCSEIYIDQGE 1 sp|O67323|SYA_AQUAE ( 168) GPCGPSSEIYVDRGE 1 sp|O34526|SYA_BACSU ( 164) GPSGPNTEIFYDRGE 1 sp|O84754|SYA_CHLTR ( 164) GPCGFCSELLFDRGE 1 sp|O83980|SYA_TREPA ( 173) GPCGPDTEIFFDTGV 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GPCGPCSEIFYDRGE MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 8345 bayes= 9.70304 E= 1.1e-071 -294 -275 -328 -445 -508 337 -369 -490 -375 -533 -396 -248 -387 -401 -390 -258 -381 -472 -358 -403 -333 -317 -432 -472 -500 -467 -396 -469 -399 -455 -411 -397 477 -365 -435 -300 -350 -459 -445 -460 -260 661 -518 -556 -497 -410 -462 -431 -531 -488 -368 -405 -414 -463 -502 75 -301 -430 -465 -471 -294 -275 -328 -445 -508 337 -369 -490 -375 -533 -396 -248 -387 -401 -390 -258 -381 -472 -358 -403 -215 -223 -329 -357 24 -381 -290 -347 -283 -337 -289 -290 457 -250 -327 -185 -236 -340 -351 -312 -279 582 93 -263 -473 -246 -180 -483 -241 -490 -399 172 -302 -216 -334 180 -209 -460 -420 -314 -191 -66 -323 -422 -355 -344 -300 -339 -286 -369 -236 -121 -263 -294 -302 377 192 -374 -295 -279 -524 -445 -222 344 -616 -560 -450 -519 -548 -614 -511 -380 -573 -354 -571 -488 -505 -572 -508 -533 -344 -192 -439 -482 -254 -510 -419 379 -389 8 -35 -347 -414 -381 -441 -329 -256 40 -304 -271 -409 -218 -464 -499 328 -514 -124 -311 -423 -3 -229 -328 -403 -355 -410 -325 -372 -357 -36 401 -212 -77 -286 -308 191 -361 16 2 -253 -181 -108 -205 -245 -233 -262 -153 -210 -42 -4 444 -387 -284 402 -185 -458 -430 -283 -425 -408 -463 -371 -75 -422 -351 -428 -302 -373 -436 -359 -351 -229 -188 -227 -207 32 -332 239 -287 -23 -288 -183 -121 -246 102 299 -143 49 -296 -234 -194 -246 -237 -277 -394 -467 328 48 -444 -324 -494 -348 -195 -350 -354 -342 -210 -336 -427 -319 -357 -249 -448 98 242 -549 -388 -275 -411 -178 -411 -304 -205 270 -82 -319 -225 -256 3 -477 -396 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GPCGPCSEIFYDRGE MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 10 E= 1.1e-071 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.900000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.700000 0.300000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.900000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.100000 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 0.200000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.500000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.900000 0.100000 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 0.100000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.300000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GPCGPCSEIFYDRGE MEME-3 regular expression -------------------------------------------------------------------------------- GP[CS]GP[CS][ST]EI[FY][YF]D[RH]G[EP] -------------------------------------------------------------------------------- Time 2.70 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sp|P00957|SYA_ECOLI 6.87e-45 88_[1(2.96e-20)]_73_[3(3.67e-19)]_\ 15_[2(1.59e-19)]_655 sp|O34526|SYA_BACSU 2.41e-36 85_[1(3.20e-19)]_63_[3(2.29e-16)]_\ 18_[2(1.22e-14)]_667 sp|P9WFW7|SYA_MYCTU 3.12e-41 81_[1(8.09e-18)]_69_[3(1.42e-19)]_\ 13_[2(7.30e-18)]_696 sp|P74941|SYA_THET8 2.59e-41 86_[1(5.71e-20)]_69_[3(1.61e-18)]_\ 16_[2(8.10e-17)]_666 sp|O67323|SYA_AQUAE 5.44e-45 88_[1(2.96e-20)]_64_[3(1.38e-17)]_6_\ [2(3.45e-21)]_664 sp|O83980|SYA_TREPA 6.26e-36 85_[1(2.59e-18)]_72_[3(1.27e-15)]_\ 14_[2(2.26e-15)]_389 sp|O84754|SYA_CHLTR 3.10e-39 86_[1(2.96e-20)]_62_[3(9.68e-16)]_\ 15_[2(3.53e-17)]_291_[3(8.16e-06)]_245_[1(6.77e-05)]_101 sp|P56452|SYA_HELPY 4.49e-43 83_[1(3.94e-19)]_62_[3(1.83e-18)]_\ 15_[2(1.88e-19)]_642 sp|Q9JYG6|SYA_NEIMB 2.05e-46 86_[1(3.57e-20)]_73_[3(1.77e-20)]_\ 15_[2(7.68e-20)]_655 sp|P74423|SYA_SYNY3 5.84e-42 88_[1(2.96e-20)]_64_[3(6.35e-19)]_\ 13_[2(8.85e-17)]_667 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************