******************************************************************************** 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= syd_nd.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ SYD_ECOLI 1.0000 590 SYDND_BACSU 1.0000 592 SYDND_MYCTU 1.0000 594 SYD_STAAS 1.0000 588 SYDND_HELPY 1.0000 577 SYDND_SYNY3 1.0000 599 SYDND_CHLTR 1.0000 582 SYDND_AQUAE 1.0000 603 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme syd_nd.fasta -protein -mod oops -minw 8 -maxw 15 -nmotifs 3 -oc out_meme 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= 8 maxsites= 8 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= 4725 N= 8 sample: seed= 0 hsfrac= 0 searchsize= 4725 norand= no csites= 1000 Dirichlet mixture priors file: prior30.plib Letter frequencies in dataset: A 0.0796 C 0.00931 D 0.0684 E 0.087 F 0.0525 G 0.073 H 0.0186 I 0.0554 K 0.0599 L 0.101 M 0.0246 N 0.0286 P 0.0468 Q 0.0364 R 0.0652 S 0.0413 T 0.0468 V 0.0713 W 0.00762 Y 0.0271 Background letter frequencies (from file dataset with add-one prior applied): A 0.0795 C 0.00948 D 0.0683 E 0.0868 F 0.0525 G 0.0729 H 0.0188 I 0.0554 K 0.0599 L 0.101 M 0.0247 N 0.0287 P 0.0468 Q 0.0365 R 0.0651 S 0.0413 T 0.0468 V 0.0712 W 0.0078 Y 0.0272 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YALPQSPQLFKQLLM MEME-1 width = 15 sites = 8 llr = 345 E-value = 7.6e-072 ******************************************************************************** -------------------------------------------------------------------------------- Motif YALPQSPQLFKQLLM MEME-1 Description -------------------------------------------------------------------------------- Simplified A :a::::::::::::: pos.-specific C ::::::::::::::: probability D ::::::::::::::: matrix E ::::::::::::::: F 1::::::::a::::: G ::::::::::::::: H ::::::::::::::: I ::::::::::::3:: K ::::::::::a:::: L ::a:::::a:::8a: M ::::::::::::::a N ::::::::::::::: P :::a::a:::::::: Q ::::a::a:::a::: R ::::::::::::::: S :::::a::::::::: T ::::::::::::::: V ::::::::::::::: W ::::::::::::::: Y 9:::::::::::::: bits 7.0 6.3 5.6 * 4.9 ** * * * Relative 4.2 * ***** *** * Entropy 3.5 ************ ** (62.3 bits) 2.8 *************** 2.1 *************** 1.4 *************** 0.7 *************** 0.0 --------------- Multilevel YALPQSPQLFKQLLM consensus I sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YALPQSPQLFKQLLM MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- SYDND_SYNY3 195 7.69e-20 VPSRVNPGEW YALPQSPQLFKQLLM VAGMDRYYQI SYD_STAAS 194 7.69e-20 VPSRVHDGEF YALPQSPQLFKQLLM ISGFDKYYQI SYDND_MYCTU 190 7.69e-20 VPARLHPGSF YALPQSPQLFKQLLM VAGMERYYQI SYDND_BACSU 194 7.69e-20 VPSRVHEGEF YALPQSPQLFKQLLM VSGIERYYQI SYD_ECOLI 188 7.69e-20 VPSRVHKGKF YALPQSPQLFKQLLM MSGFDRYYQI SYDND_AQUAE 199 1.19e-19 VPSRLHPGKF YALPQSPQLFKQILM IAGFDRYFQI SYDND_CHLTR 194 1.19e-19 VPSRIYPGNF YALPQSPQLFKQILM VGGLDRYFQI SYDND_HELPY 188 2.86e-19 VPSRVHEGEF FALPQSPQLFKQLLM VGGMDRYFQI -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YALPQSPQLFKQLLM MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- SYDND_SYNY3 7.7e-20 194_[1]_390 SYD_STAAS 7.7e-20 193_[1]_380 SYDND_MYCTU 7.7e-20 189_[1]_390 SYDND_BACSU 7.7e-20 193_[1]_384 SYD_ECOLI 7.7e-20 187_[1]_388 SYDND_AQUAE 1.2e-19 198_[1]_390 SYDND_CHLTR 1.2e-19 193_[1]_374 SYDND_HELPY 2.9e-19 187_[1]_375 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YALPQSPQLFKQLLM MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YALPQSPQLFKQLLM width=15 seqs=8 SYDND_SYNY3 ( 195) YALPQSPQLFKQLLM 1 SYD_STAAS ( 194) YALPQSPQLFKQLLM 1 SYDND_MYCTU ( 190) YALPQSPQLFKQLLM 1 SYDND_BACSU ( 194) YALPQSPQLFKQLLM 1 SYD_ECOLI ( 188) YALPQSPQLFKQLLM 1 SYDND_AQUAE ( 199) YALPQSPQLFKQILM 1 SYDND_CHLTR ( 194) YALPQSPQLFKQILM 1 SYDND_HELPY ( 188) FALPQSPQLFKQLLM 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YALPQSPQLFKQLLM MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 4613 bayes= 9.16899 E= 7.6e-072 -357 -205 -459 -460 149 -452 -54 -316 -393 -294 -264 -269 -417 -322 -387 -263 -337 -334 16 479 349 -71 -466 -460 -425 -246 -360 -358 -418 -391 -307 -316 -409 -375 -430 -77 -221 -237 -320 -396 -380 -232 -553 -508 -225 -502 -352 -131 -439 315 -60 -397 -427 -344 -425 -359 -327 -211 -251 -305 -261 -284 -416 -419 -474 -395 -318 -427 -354 -422 -401 -324 430 -315 -399 -221 -296 -402 -385 -435 -311 -242 -421 -214 -471 -445 -27 -395 -308 -332 -209 -210 -348 459 -277 -251 -303 -403 -252 -383 -244 -178 -445 -518 -479 -359 -362 -469 -416 -494 -405 -223 -396 -399 -432 445 -44 -447 -362 -398 -261 -284 -416 -419 -474 -395 -318 -427 -354 -422 -401 -324 430 -315 -399 -221 -296 -402 -385 -435 -311 -242 -421 -214 -471 -445 -27 -395 -308 -332 -209 -210 -348 459 -277 -251 -303 -403 -252 -383 -380 -232 -553 -508 -225 -502 -352 -131 -439 315 -60 -397 -427 -344 -425 -359 -327 -211 -251 -305 -367 -159 -489 -503 408 -473 -332 -252 -461 -196 -219 -366 -408 -437 -494 -274 -386 -299 -113 -40 -368 -264 -503 -472 -560 -467 -324 -396 393 -485 -387 -280 -435 -349 -81 -350 -347 -471 -326 -432 -311 -242 -421 -214 -471 -445 -27 -395 -308 -332 -209 -210 -348 459 -277 -251 -303 -403 -252 -383 -349 -198 -571 -510 -180 -523 -354 165 -443 283 -21 -398 -432 -338 -430 -359 -295 -136 -225 -285 -380 -232 -553 -508 -225 -502 -352 -131 -439 315 -60 -397 -427 -344 -425 -359 -327 -211 -251 -305 -455 -261 -560 -585 -424 -527 -428 -259 -492 -228 524 -423 -497 -463 -561 -389 -399 -336 -242 -309 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YALPQSPQLFKQLLM MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 8 E= 7.6e-072 0.000000 0.000000 0.000000 0.000000 0.125000 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 0.875000 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 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 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 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 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 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 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 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 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 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 0.250000 0.000000 0.750000 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 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YALPQSPQLFKQLLM MEME-1 regular expression -------------------------------------------------------------------------------- YALPQSPQLFKQ[LI]LM -------------------------------------------------------------------------------- Time 0.93 secs. ******************************************************************************** ******************************************************************************** MOTIF CFRDEDLRADRQPEF MEME-2 width = 15 sites = 8 llr = 338 E-value = 1.9e-067 ******************************************************************************** -------------------------------------------------------------------------------- Motif CFRDEDLRADRQPEF MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::::::a:::::: pos.-specific C a:::::::::::::: probability D :::a:a:::a::::: matrix E ::::a::::::::a: F :9::::1:::::::a G ::::::::::::::: H ::::::::::::::: I ::::::::::::::: K ::::::::::::::: L ::::::9:::::::: M ::::::::::::::: N ::::::::::::::: P ::::::::::::a:: Q :::::::::::a::: R ::a::::a::a:::: S ::::::::::::::: T ::::::::::::::: V ::::::::::::::: W ::::::::::::::: Y :1::::::::::::: bits 7.0 * 6.3 * 5.6 * 4.9 * * Relative 4.2 * ** * * **** * Entropy 3.5 ****** ******** (61.0 bits) 2.8 *************** 2.1 *************** 1.4 *************** 0.7 *************** 0.0 --------------- Multilevel CFRDEDLRADRQPEF consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CFRDEDLRADRQPEF MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- SYDND_AQUAE 226 2.37e-19 GFDRYFQIVK CFRDEDLRADRQPEF TQIDYEMSFV SYDND_CHLTR 221 2.37e-19 GLDRYFQIAT CFRDEDLRADRQPEF TQIDMEMSFG SYDND_SYNY3 222 2.37e-19 GMDRYYQIAR CFRDEDLRADRQPEF TQLDMEMSFM SYDND_HELPY 215 2.37e-19 GMDRYFQIAR CFRDEDLRADRQPEF TQIDAEMSFC SYD_STAAS 221 2.37e-19 GFDKYYQIVK CFRDEDLRADRQPEF TQVDIEMSFV SYDND_BACSU 221 2.37e-19 GIERYYQIAR CFRDEDLRADRQPEF TQIDIEMSFM SYD_ECOLI 215 2.37e-19 GFDRYYQIVK CFRDEDLRADRQPEF TQIDVETSFM SYDND_MYCTU 217 3.87e-18 GMERYYQIAR CYRDEDFRADRQPEF TQLDMEMSFV -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CFRDEDLRADRQPEF MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- SYDND_AQUAE 2.4e-19 225_[2]_363 SYDND_CHLTR 2.4e-19 220_[2]_347 SYDND_SYNY3 2.4e-19 221_[2]_363 SYDND_HELPY 2.4e-19 214_[2]_348 SYD_STAAS 2.4e-19 220_[2]_353 SYDND_BACSU 2.4e-19 220_[2]_357 SYD_ECOLI 2.4e-19 214_[2]_361 SYDND_MYCTU 3.9e-18 216_[2]_363 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CFRDEDLRADRQPEF MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CFRDEDLRADRQPEF width=15 seqs=8 SYDND_AQUAE ( 226) CFRDEDLRADRQPEF 1 SYDND_CHLTR ( 221) CFRDEDLRADRQPEF 1 SYDND_SYNY3 ( 222) CFRDEDLRADRQPEF 1 SYDND_HELPY ( 215) CFRDEDLRADRQPEF 1 SYD_STAAS ( 221) CFRDEDLRADRQPEF 1 SYDND_BACSU ( 221) CFRDEDLRADRQPEF 1 SYD_ECOLI ( 215) CFRDEDLRADRQPEF 1 SYDND_MYCTU ( 217) CYRDEDFRADRQPEF 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CFRDEDLRADRQPEF MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 4613 bayes= 9.16899 E= 1.9e-067 -386 666 -561 -541 -510 -544 -429 -415 -539 -492 -394 -422 -530 -486 -511 -384 -361 -479 -460 -503 -353 -143 -477 -486 400 -469 -272 -237 -442 -181 -203 -340 -397 -410 -472 -257 -369 -283 -71 101 -368 -190 -477 -497 -500 -419 -169 -408 -141 -421 -380 -260 -359 -223 380 -295 -349 -486 -223 -381 -349 -280 370 -165 -461 -385 -234 -416 -396 -463 -394 -32 -452 -332 -423 -255 -352 -412 -321 -352 -499 -454 -249 347 -632 -527 -414 -524 -546 -626 -547 -351 -612 -348 -578 -454 -496 -561 -483 -547 -349 -280 370 -165 -461 -385 -234 -416 -396 -463 -394 -32 -452 -332 -423 -255 -352 -412 -321 -352 -343 -195 -535 -471 41 -497 -310 -83 -404 299 -9 -364 -399 -302 -389 -326 -286 -167 -200 -235 -368 -190 -477 -497 -500 -419 -169 -408 -141 -421 -380 -260 -359 -223 380 -295 -349 -486 -223 -381 349 -71 -466 -460 -425 -246 -360 -358 -418 -391 -307 -316 -409 -375 -430 -77 -221 -237 -320 -396 -349 -280 370 -165 -461 -385 -234 -416 -396 -463 -394 -32 -452 -332 -423 -255 -352 -412 -321 -352 -368 -190 -477 -497 -500 -419 -169 -408 -141 -421 -380 -260 -359 -223 380 -295 -349 -486 -223 -381 -311 -242 -421 -214 -471 -445 -27 -395 -308 -332 -209 -210 -348 459 -277 -251 -303 -403 -252 -383 -261 -284 -416 -419 -474 -395 -318 -427 -354 -422 -401 -324 430 -315 -399 -221 -296 -402 -385 -435 -499 -454 -249 347 -632 -527 -414 -524 -546 -626 -547 -351 -612 -348 -578 -454 -496 -561 -483 -547 -367 -159 -489 -503 408 -473 -332 -252 -461 -196 -219 -366 -408 -437 -494 -274 -386 -299 -113 -40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CFRDEDLRADRQPEF MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 8 E= 1.9e-067 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 0.875000 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 0.125000 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 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 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 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 0.125000 0.000000 0.000000 0.000000 0.000000 0.875000 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 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 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 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 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 1.000000 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 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 CFRDEDLRADRQPEF MEME-2 regular expression -------------------------------------------------------------------------------- CFRDEDLRADRQPEF -------------------------------------------------------------------------------- Time 1.25 secs. ******************************************************************************** ******************************************************************************** MOTIF TPEGARDYLVPSRVH MEME-3 width = 15 sites = 8 llr = 322 E-value = 1.5e-058 ******************************************************************************** -------------------------------------------------------------------------------- Motif TPEGARDYLVPSRVH MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::a::::::1::: pos.-specific C ::::::::::::::: probability D ::::::a:::::::: matrix E ::a:::::::::::: F :::::::3::::::: G :::a::::::::::: H ::::::::::::::8 I :::::::::::::1: K ::::::::::::::: L ::::::::a::::3: M ::::::::::::::: N ::::::::::::::1 P :a::::::::a:::: Q ::::::::::::::: R :::::a::::::a:: S :::::::::::9::: T a:::::::::::::: V :::::::::a:::6: W ::::::::::::::: Y :::::::8::::::1 bits 7.0 6.3 5.6 4.9 Relative 4.2 ** *** *** * Entropy 3.5 ************* * (58.1 bits) 2.8 ************* * 2.1 *************** 1.4 *************** 0.7 *************** 0.0 --------------- Multilevel TPEGARDYLVPSRVH consensus F L sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TPEGARDYLVPSRVH MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- SYDND_HELPY 169 1.61e-19 EIETPILSKT TPEGARDYLVPSRVH EGEFFALPQS SYD_STAAS 175 1.61e-19 DIETPVLTKS TPEGARDYLVPSRVH DGEFYALPQS SYDND_BACSU 175 1.61e-19 DIETPILTGS TPEGARDYLVPSRVH EGEFYALPQS SYD_ECOLI 169 1.61e-19 DIETPMLTKA TPEGARDYLVPSRVH KGKFYALPQS SYDND_SYNY3 176 2.40e-18 EIETPILTRS TPEGARDYLVPSRVN PGEWYALPQS SYDND_AQUAE 180 3.03e-18 EIETPFLTKS TPEGARDFLVPSRLH PGKFYALPQS SYDND_CHLTR 175 8.37e-18 EVVTPILGKS TPEGARDYLVPSRIY PGNFYALPQS SYDND_MYCTU 171 5.97e-17 EIETPTITRS TPEGARDFLVPARLH PGSFYALPQS -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TPEGARDYLVPSRVH MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- SYDND_HELPY 1.6e-19 168_[3]_394 SYD_STAAS 1.6e-19 174_[3]_399 SYDND_BACSU 1.6e-19 174_[3]_403 SYD_ECOLI 1.6e-19 168_[3]_407 SYDND_SYNY3 2.4e-18 175_[3]_409 SYDND_AQUAE 3e-18 179_[3]_409 SYDND_CHLTR 8.4e-18 174_[3]_393 SYDND_MYCTU 6e-17 170_[3]_409 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TPEGARDYLVPSRVH MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TPEGARDYLVPSRVH width=15 seqs=8 SYDND_HELPY ( 169) TPEGARDYLVPSRVH 1 SYD_STAAS ( 175) TPEGARDYLVPSRVH 1 SYDND_BACSU ( 175) TPEGARDYLVPSRVH 1 SYD_ECOLI ( 169) TPEGARDYLVPSRVH 1 SYDND_SYNY3 ( 176) TPEGARDYLVPSRVN 1 SYDND_AQUAE ( 180) TPEGARDFLVPSRLH 1 SYDND_CHLTR ( 175) TPEGARDYLVPSRIY 1 SYDND_MYCTU ( 171) TPEGARDFLVPARLH 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TPEGARDYLVPSRVH MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 4613 bayes= 9.16899 E= 1.5e-058 -308 -206 -463 -521 -475 -423 -358 -353 -405 -464 -325 -225 -428 -358 -431 -63 428 -334 -355 -426 -261 -284 -416 -419 -474 -395 -318 -427 -354 -422 -401 -324 430 -315 -399 -221 -296 -402 -385 -435 -499 -454 -249 347 -632 -527 -414 -524 -546 -626 -547 -351 -612 -348 -578 -454 -496 -561 -483 -547 -249 -263 -334 -418 -505 366 -313 -474 -356 -526 -411 -197 -409 -376 -377 -205 -352 -440 -313 -397 349 -71 -466 -460 -425 -246 -360 -358 -418 -391 -307 -316 -409 -375 -430 -77 -221 -237 -320 -396 -368 -190 -477 -497 -500 -419 -169 -408 -141 -421 -380 -260 -359 -223 380 -295 -349 -486 -223 -381 -349 -280 370 -165 -461 -385 -234 -416 -396 -463 -394 -32 -452 -332 -423 -255 -352 -412 -321 -352 -338 -194 -444 -442 216 -440 -43 -306 -379 -286 -254 -260 -403 -313 -375 -248 -324 -323 18 459 -380 -232 -553 -508 -225 -502 -352 -131 -439 315 -60 -397 -427 -344 -425 -359 -327 -211 -251 -305 -192 -125 -464 -457 -354 -437 -330 -32 -416 -246 -225 -351 -391 -396 -415 -295 -199 359 -347 -391 -261 -284 -416 -419 -474 -395 -318 -427 -354 -422 -401 -324 430 -315 -399 -221 -296 -402 -385 -435 36 -71 -393 -446 -413 -253 -305 -383 -347 -417 -312 -150 -314 -319 -361 418 40 -332 -311 -345 -368 -190 -477 -497 -500 -419 -169 -408 -141 -421 -380 -260 -359 -223 380 -295 -349 -486 -223 -381 -238 -127 -525 -504 -286 -491 -383 138 -454 98 -140 -379 -443 -420 -470 -335 -215 304 -328 -352 -329 -161 -267 -329 -232 -359 527 -371 -340 -305 -219 93 -321 -8 -179 -145 -217 -339 -126 94 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TPEGARDYLVPSRVH MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 8 E= 1.5e-058 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 1.000000 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 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 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-------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TPEGARDYLVPSRVH MEME-3 regular expression -------------------------------------------------------------------------------- TPEGARD[YF]LVPSR[VL]H -------------------------------------------------------------------------------- Time 1.57 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- SYD_ECOLI 3.54e-45 168_[3(1.61e-19)]_4_[1(7.69e-20)]_\ 12_[2(2.37e-19)]_361 SYDND_BACSU 3.57e-45 174_[3(1.61e-19)]_4_[1(7.69e-20)]_\ 12_[2(2.37e-19)]_357 SYDND_MYCTU 1.85e-41 170_[3(5.97e-17)]_4_[1(7.69e-20)]_\ 12_[2(3.87e-18)]_363 SYD_STAAS 3.50e-45 174_[3(1.61e-19)]_4_[1(7.69e-20)]_\ 12_[2(2.37e-19)]_353 SYDND_HELPY 1.20e-44 168_[3(1.61e-19)]_4_[1(2.86e-19)]_\ 12_[2(2.37e-19)]_348 SYDND_SYNY3 5.24e-44 175_[3(2.40e-18)]_4_[1(7.69e-20)]_\ 12_[2(2.37e-19)]_363 SYDND_CHLTR 2.52e-43 174_[3(8.37e-18)]_4_[1(1.19e-19)]_\ 12_[2(2.37e-19)]_347 SYDND_AQUAE 1.03e-43 179_[3(3.03e-18)]_4_[1(1.19e-19)]_\ 12_[2(2.37e-19)]_363 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************