******************************************************************************** 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= rs2_selected.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ sp|P80371|RS2_THET8 1.0000 256 sp|A0Q4H1|RS2_FRATN 1.0000 239 sp|A0RHK0|RS2_BACAH 1.0000 233 sp|A1AQN2|RS2_PELPD 1.0000 257 sp|A1B8E9|RS2_PARDP 1.0000 261 sp|A1SLR0|RS2_NOCSJ 1.0000 307 sp|A1W0G6|RS2_CAMJJ 1.0000 263 sp|A2BW77|RS2_PROM5 1.0000 234 sp|A2CA98|RS2_PROM3 1.0000 239 sp|A2RGS9|RS2_STRPG 1.0000 255 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme rs2_selected.fasta -protein -mod oops -minw 8 -maxw 15 -nmotifs 3 -oc meme_rs2 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= 2544 N= 10 sample: seed= 0 hsfrac= 0 searchsize= 2544 norand= no csites= 1000 Dirichlet mixture priors file: prior30.plib Letter frequencies in dataset: A 0.103 C 0.00943 D 0.0609 E 0.0857 F 0.0283 G 0.0715 H 0.0161 I 0.0672 K 0.0723 L 0.0822 M 0.0366 N 0.0358 P 0.0322 Q 0.0432 R 0.0676 S 0.0334 T 0.0476 V 0.0759 W 0.011 Y 0.0204 Background letter frequencies (from file dataset with add-one prior applied): A 0.102 C 0.00975 D 0.0608 E 0.0854 F 0.0285 G 0.0714 H 0.0164 I 0.0671 K 0.0722 L 0.0819 M 0.0367 N 0.0359 P 0.0324 Q 0.0433 R 0.0675 S 0.0335 T 0.0476 V 0.0757 W 0.0113 Y 0.0207 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GVHFGHQTRRWNPKM MEME-1 width = 15 sites = 10 llr = 438 E-value = 1.1e-106 ******************************************************************************** -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 Description -------------------------------------------------------------------------------- Simplified A :2::::::1:::::: pos.-specific C ::::::::::::::: probability D ::::::::::::::: matrix E ::::::1:::::::: F :::9:::::1::::1 G a:::a:::::::::: H ::a::a::::::::: I ::::::::::::::: K ::::::112::::8: L ::::::::::::::: M ::::::::::::::9 N :::::::::::a::: P ::::::::::::a:: Q ::::::8:1::::1: R :::::::169:::1: S ::::::::::::::: T :::::::8::::::: V :8::::::::::::: W ::::::::::a:::: Y :::1::::::::::: bits 6.7 * 6.0 * * * 5.3 * * * 4.7 ** * *** Relative 4.0 * **** *** * Entropy 3.3 * ****** **** * (63.3 bits) 2.7 ******** ****** 2.0 *************** 1.3 *************** 0.7 *************** 0.0 --------------- Multilevel GVHFGHQTRRWNPKM consensus A K sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- sp|A2RGS9|RS2_STRPG 13 9.67e-22 VISMKQLLEA GVHFGHQTRRWNPKM AKYIFTERNG sp|A1W0G6|RS2_CAMJJ 11 9.67e-22 MVSMRDLLEC GVHFGHQTRRWNPKM KKFIFGERKG sp|A1SLR0|RS2_NOCSJ 13 9.67e-22 VVTMRQLLES GVHFGHQTRRWNPKM KRFIMTERNG sp|A0RHK0|RS2_BACAH 13 9.67e-22 VISMKQLLEA GVHFGHQTRRWNPKM KRYIFTERNG sp|A1AQN2|RS2_PELPD 13 2.00e-21 SISMKELLEA GVHFGHQTKRWNPKM KPYIFGARNG sp|A2CA98|RS2_PROM3 13 3.93e-21 VVTLSEMMEA GAHFGHQTRRWNPKM SRYIYCARNG sp|A2BW77|RS2_PROM5 13 3.93e-21 VVSLSEMMEA GAHFGHQTRRWNPKM SKYIYCARNG sp|A1B8E9|RS2_PARDP 17 8.44e-19 EFSMRQLLEA GVHYGHQTQRWNPRM AEFIYGERNG sp|P80371|RS2_THET8 14 5.08e-17 EITVKELLEA GVHFGHERKRWNPKF ARYIYAERNG sp|A0Q4H1|RS2_FRATN 11 1.39e-15 MSLMKEMLSA GVHFGHKKAFWNPQM KEYIFGINHG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sp|A2RGS9|RS2_STRPG 9.7e-22 12_[1]_228 sp|A1W0G6|RS2_CAMJJ 9.7e-22 10_[1]_238 sp|A1SLR0|RS2_NOCSJ 9.7e-22 12_[1]_280 sp|A0RHK0|RS2_BACAH 9.7e-22 12_[1]_206 sp|A1AQN2|RS2_PELPD 2e-21 12_[1]_230 sp|A2CA98|RS2_PROM3 3.9e-21 12_[1]_212 sp|A2BW77|RS2_PROM5 3.9e-21 12_[1]_207 sp|A1B8E9|RS2_PARDP 8.4e-19 16_[1]_230 sp|P80371|RS2_THET8 5.1e-17 13_[1]_228 sp|A0Q4H1|RS2_FRATN 1.4e-15 10_[1]_214 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GVHFGHQTRRWNPKM width=15 seqs=10 sp|A2RGS9|RS2_STRPG ( 13) GVHFGHQTRRWNPKM 1 sp|A1W0G6|RS2_CAMJJ ( 11) GVHFGHQTRRWNPKM 1 sp|A1SLR0|RS2_NOCSJ ( 13) GVHFGHQTRRWNPKM 1 sp|A0RHK0|RS2_BACAH ( 13) GVHFGHQTRRWNPKM 1 sp|A1AQN2|RS2_PELPD ( 13) GVHFGHQTKRWNPKM 1 sp|A2CA98|RS2_PROM3 ( 13) GAHFGHQTRRWNPKM 1 sp|A2BW77|RS2_PROM5 ( 13) GAHFGHQTRRWNPKM 1 sp|A1B8E9|RS2_PARDP ( 17) GVHYGHQTQRWNPRM 1 sp|P80371|RS2_THET8 ( 14) GVHFGHERKRWNPKF 1 sp|A0Q4H1|RS2_FRATN ( 11) GVHFGHKKAFWNPQM 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 2404 bayes= 7.90328 E= 1.1e-106 -309 -289 -341 -439 -439 371 -316 -525 -406 -519 -492 -254 -377 -424 -405 -199 -378 -473 -389 -380 11 -85 -406 -408 -247 -366 -267 -44 -400 -207 -262 -335 -291 -372 -374 -181 -152 328 -372 -339 -569 -362 -469 -557 -360 -501 586 -617 -568 -497 -519 -278 -443 -288 -423 -344 -445 -572 -386 -200 -394 -152 -465 -489 490 -471 -267 -269 -475 -156 -265 -380 -349 -443 -484 -232 -377 -297 -135 126 -309 -289 -341 -439 -439 371 -316 -525 -406 -519 -492 -254 -377 -424 -405 -199 -378 -473 -389 -380 -569 -362 -469 -557 -360 -501 586 -617 -568 -497 -519 -278 -443 -288 -423 -344 -445 -572 -386 -200 -300 -211 -335 -87 -353 -416 40 -377 -137 -257 -218 -193 -254 419 -222 -173 -257 -365 -269 -311 -299 -168 -356 -345 -335 -383 -183 -311 26 -340 -290 -155 -313 -186 22 33 385 -276 -336 -296 -78 -240 -401 -322 -411 -382 -120 -407 111 -344 -363 -219 -311 64 324 -197 -265 -401 -304 -290 -397 -187 -456 -489 -62 -413 -140 -423 -160 -379 -425 -285 -300 -240 372 -257 -344 -484 -261 -289 -460 -248 -440 -476 -95 -433 -306 -436 -441 -258 -360 -360 -397 -379 -405 -314 -381 -392 633 -102 -442 -258 -266 -476 -353 -380 -79 -388 -377 -432 -430 466 -352 -309 -412 -111 -264 -429 -333 -309 -348 -331 -445 -466 -430 -433 -343 -504 -430 -440 -507 -403 486 -388 -451 -241 -347 -460 -475 -437 -388 -269 -468 -413 -464 -444 -245 -414 357 -420 -415 -281 -370 -70 -13 -282 -320 -451 -369 -362 -490 -264 -549 -585 -90 -531 -398 -272 -522 -180 464 -457 -447 -485 -567 -362 -400 -335 -287 -242 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 10 E= 1.1e-106 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 0.200000 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 0.800000 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 0.900000 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 0.000000 0.100000 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 0.100000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.800000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.100000 0.600000 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 0.900000 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 0.000000 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 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 0.800000 0.000000 0.000000 0.000000 0.000000 0.100000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 regular expression -------------------------------------------------------------------------------- G[VA]HFGHQT[RK]RWNPKM -------------------------------------------------------------------------------- Time 0.72 secs. ******************************************************************************** ******************************************************************************** MOTIF PYVNQRWLGGMLTNF MEME-2 width = 15 sites = 10 llr = 422 E-value = 6.0e-097 ******************************************************************************** -------------------------------------------------------------------------------- Motif PYVNQRWLGGMLTNF MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1:::::::::::::: pos.-specific C ::::::::::::::: probability D ::::::::::::::: matrix E ::::::::::::::: F 13::::::::::::5 G ::::::::aa::::: H 1:::4:::::::::: I ::1:::::::::::: K ::::::::::::::: L :::::::a:::9::: M ::1:::::::71::: N :::9:::::::::a: P 4:::::::::::::: Q ::::6:::::::::: R :::::a::::::::: S 1::1::::::::::: T ::::::::::3:a:: V ::8:::::::::::: W ::::::a:::::::4 Y 27::::::::::::1 bits 6.7 * 6.0 * 5.3 * 4.7 * * *** Relative 4.0 * **** *** *** Entropy 3.3 * ************ (60.8 bits) 2.7 *************** 2.0 *************** 1.3 *************** 0.7 *************** 0.0 --------------- Multilevel PYVNQRWLGGMLTNF consensus YF H T W sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif PYVNQRWLGGMLTNF MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- sp|A1SLR0|RS2_NOCSJ 90 1.16e-20 IAEQATRVGM PYVNQRWLGGMLTNF STVHQRINRL sp|P80371|RS2_THET8 91 1.16e-20 VRMEAERAGM PYVNQRWLGGMLTNF KTISQRVHRL sp|A1AQN2|RS2_PELPD 90 4.73e-20 VCEEAQRCGM HYVNQRWLGGMLTNF TTVKQSIDRL sp|A2CA98|RS2_PROM3 90 5.29e-20 VALEATRCGA SYVNQRWLGGMLTNW TTMKARIDRL sp|A1W0G6|RS2_CAMJJ 88 8.21e-20 IKEYAEKCGM PYVNHRWLGGMMTNF GTIRQSIRKL sp|A0RHK0|RS2_BACAH 90 1.32e-19 IKEEATRAGM YFVNQRWLGGTLTNF QTIQKRIKRL sp|A2BW77|RS2_PROM5 90 1.53e-19 VAQEAVRCGA AYVNQRWLGGMLTNW STMKARIERL sp|A2RGS9|RS2_STRPG 90 4.08e-19 VADEATRAGQ YFINHRWLGGTLTNW GTIQKRIARL sp|A1B8E9|RS2_PARDP 94 5.38e-19 VADAAERSAQ FYMNHRWLGGTLTNW KTVSQSIQRL sp|A0Q4H1|RS2_FRATN 88 4.20e-18 VEAEAKRCGM PFVSHRWLGGMLTNY KTVRQSIKRL -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif PYVNQRWLGGMLTNF MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sp|A1SLR0|RS2_NOCSJ 1.2e-20 89_[2]_203 sp|P80371|RS2_THET8 1.2e-20 90_[2]_151 sp|A1AQN2|RS2_PELPD 4.7e-20 89_[2]_153 sp|A2CA98|RS2_PROM3 5.3e-20 89_[2]_135 sp|A1W0G6|RS2_CAMJJ 8.2e-20 87_[2]_161 sp|A0RHK0|RS2_BACAH 1.3e-19 89_[2]_129 sp|A2BW77|RS2_PROM5 1.5e-19 89_[2]_130 sp|A2RGS9|RS2_STRPG 4.1e-19 89_[2]_151 sp|A1B8E9|RS2_PARDP 5.4e-19 93_[2]_153 sp|A0Q4H1|RS2_FRATN 4.2e-18 87_[2]_137 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif PYVNQRWLGGMLTNF MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF PYVNQRWLGGMLTNF width=15 seqs=10 sp|A1SLR0|RS2_NOCSJ ( 90) PYVNQRWLGGMLTNF 1 sp|P80371|RS2_THET8 ( 91) PYVNQRWLGGMLTNF 1 sp|A1AQN2|RS2_PELPD ( 90) HYVNQRWLGGMLTNF 1 sp|A2CA98|RS2_PROM3 ( 90) SYVNQRWLGGMLTNW 1 sp|A1W0G6|RS2_CAMJJ ( 88) PYVNHRWLGGMMTNF 1 sp|A0RHK0|RS2_BACAH ( 90) YFVNQRWLGGTLTNF 1 sp|A2BW77|RS2_PROM5 ( 90) AYVNQRWLGGMLTNW 1 sp|A2RGS9|RS2_STRPG ( 90) YFINHRWLGGTLTNW 1 sp|A1B8E9|RS2_PARDP ( 94) FYMNHRWLGGTLTNW 1 sp|A0Q4H1|RS2_FRATN ( 88) PFVSHRWLGGMLTNY 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif PYVNQRWLGGMLTNF MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 2404 bayes= 7.90328 E= 6.0e-097 -62 -120 -266 -258 175 -301 184 -239 -230 -197 -228 -185 327 -201 -254 88 -172 -220 -106 356 -437 -245 -484 -500 330 -486 -69 -379 -460 -297 -357 -334 -401 -379 -428 -273 -377 -380 -63 495 -194 -97 -418 -418 -230 -429 -278 54 -408 -176 36 -353 -311 -387 -386 -245 -164 328 -374 -334 -396 -218 -218 -429 -313 -340 -32 -342 -331 -391 -385 458 -315 -263 -370 4 -217 -385 -294 -270 -390 -294 -358 -275 -314 -419 413 -472 -262 -365 -347 -225 -345 382 -267 -230 -327 -452 -322 -221 -417 -206 -472 -508 -424 -427 -162 -448 -181 -404 -450 -305 -317 -261 376 -277 -364 -508 -288 -354 -460 -248 -440 -476 -95 -433 -306 -436 -441 -258 -360 -360 -397 -379 -405 -314 -381 -392 633 -102 -454 -272 -568 -544 -171 -526 -367 -195 -505 348 -153 -466 -407 -406 -468 -367 -367 -257 -338 -301 -309 -289 -341 -439 -439 371 -316 -525 -406 -519 -492 -254 -377 -424 -405 -199 -378 -473 -389 -380 -309 -289 -341 -439 -439 371 -316 -525 -406 -519 -492 -254 -377 -424 -405 -199 -378 -473 -389 -380 -278 -192 -519 -529 -230 -375 -367 -215 -458 -175 411 -385 -392 -424 -464 -184 242 -227 -360 -288 -385 -205 -520 -468 -99 -499 -304 -120 -431 332 82 -401 -348 -329 -395 -299 -293 -183 -275 -241 -399 -263 -498 -575 -439 -462 -389 -442 -490 -490 -443 -317 -420 -439 -491 -94 430 -403 -454 -436 -442 -258 -266 -476 -353 -380 -79 -388 -377 -432 -430 466 -352 -309 -412 -111 -264 -429 -333 -309 -562 -301 -576 -611 403 -550 -119 -430 -540 -333 -407 -373 -473 -419 -485 -358 -446 -438 495 273 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif PYVNQRWLGGMLTNF MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 10 E= 6.0e-097 0.100000 0.000000 0.000000 0.000000 0.100000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.300000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.700000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.100000 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 0.900000 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 0.400000 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 0.000000 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 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 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 0.700000 0.000000 0.000000 0.000000 0.000000 0.000000 0.300000 0.000000 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 0.000000 0.000000 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 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.100000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif PYVNQRWLGGMLTNF MEME-2 regular expression -------------------------------------------------------------------------------- [PY][YF]VN[QH]RWLGG[MT]LTN[FW] -------------------------------------------------------------------------------- Time 0.90 secs. ******************************************************************************** ******************************************************************************** MOTIF NCDPDLVDYPIPGND MEME-3 width = 15 sites = 10 llr = 376 E-value = 6.2e-073 ******************************************************************************** -------------------------------------------------------------------------------- Motif NCDPDLVDYPIPGND MEME-3 Description -------------------------------------------------------------------------------- Simplified A :1::::::::::2:: pos.-specific C :7::::2:::::2:: probability D 1:8:81:7::::::a matrix E ::::11:2::::::: F ::::::::1:::::: G :::::2::::::6:: H ::::::::1:::::: I ::::::4:13a:::: K ::::1:::::::::: L :::::5::::::::: M ::::::::::::::: N 9:1::::::::::a: P :::a:1:::4:a::: Q ::::::::::::::: R ::::::::::::::: S :21:::::::::::: T :::::::1::::::: V ::::::4:23::::: W ::::::::::::::: Y ::::::::5:::::: bits 6.7 6.0 5.3 4.7 * * * * Relative 4.0 ** * ** ** Entropy 3.3 ***** * ** ** (54.3 bits) 2.7 ***** ********* 2.0 *************** 1.3 *************** 0.7 *************** 0.0 --------------- Multilevel NCDPDLIDYPIPGND consensus S GVEVI A sequence C V C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NCDPDLVDYPIPGND MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- sp|A1SLR0|RS2_NOCSJ 191 1.40e-19 RIPIIGILDS NCDPDLVDFPIPGND DAIRAVGLLT sp|A1AQN2|RS2_PELPD 190 1.40e-19 GIPVVAIVDT NCDPDPIDYVIPGND DAIRAIRLLS sp|A1W0G6|RS2_CAMJJ 188 9.73e-19 RIPVVAPLDT NCDPDLVTYPIPGND DAIRSVQLFC sp|A2CA98|RS2_PROM3 190 2.41e-18 DIPLVSMLDT NCDPDLCEVPIPCND DAVRSVQLVL sp|A2BW77|RS2_PROM5 190 2.41e-18 DISLVSMLDT NCDPDLCEVPIPCND DAVRSVQLIL sp|A0RHK0|RS2_BACAH 190 1.64e-17 HIPIIGIVDT NCDPDEIDHVIPAND DAIRAVKLLT sp|P80371|RS2_THET8 191 1.23e-16 FIPVIALADT DSDPDLVDYIIPGND DAIRSIQLIL sp|A1B8E9|RS2_PARDP 193 5.84e-16 GIPVVAVVDT NCSPKGVDYVIPGND DAARAIALYC sp|A0Q4H1|RS2_FRATN 188 1.73e-15 GIKVVAIVDT NSNPEGIDYIIPGND DAVKSISFYM sp|A2RGS9|RS2_STRPG 190 5.39e-15 GIPVVAMVDT NADPDDIDIIIPAND DAIRAVKLIT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NCDPDLVDYPIPGND MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sp|A1SLR0|RS2_NOCSJ 1.4e-19 190_[3]_102 sp|A1AQN2|RS2_PELPD 1.4e-19 189_[3]_53 sp|A1W0G6|RS2_CAMJJ 9.7e-19 187_[3]_61 sp|A2CA98|RS2_PROM3 2.4e-18 189_[3]_35 sp|A2BW77|RS2_PROM5 2.4e-18 189_[3]_30 sp|A0RHK0|RS2_BACAH 1.6e-17 189_[3]_29 sp|P80371|RS2_THET8 1.2e-16 190_[3]_51 sp|A1B8E9|RS2_PARDP 5.8e-16 192_[3]_54 sp|A0Q4H1|RS2_FRATN 1.7e-15 187_[3]_37 sp|A2RGS9|RS2_STRPG 5.4e-15 189_[3]_51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NCDPDLVDYPIPGND MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF NCDPDLVDYPIPGND width=15 seqs=10 sp|A1SLR0|RS2_NOCSJ ( 191) NCDPDLVDFPIPGND 1 sp|A1AQN2|RS2_PELPD ( 190) NCDPDPIDYVIPGND 1 sp|A1W0G6|RS2_CAMJJ ( 188) NCDPDLVTYPIPGND 1 sp|A2CA98|RS2_PROM3 ( 190) NCDPDLCEVPIPCND 1 sp|A2BW77|RS2_PROM5 ( 190) NCDPDLCEVPIPCND 1 sp|A0RHK0|RS2_BACAH ( 190) NCDPDEIDHVIPAND 1 sp|P80371|RS2_THET8 ( 191) DSDPDLVDYIIPGND 1 sp|A1B8E9|RS2_PARDP ( 193) NCSPKGVDYVIPGND 1 sp|A0Q4H1|RS2_FRATN ( 188) NSNPEGIDYIIPGND 1 sp|A2RGS9|RS2_STRPG ( 190) NADPDDIDIIIPAND 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NCDPDLVDYPIPGND MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 2404 bayes= 7.90328 E= 6.2e-073 -400 -224 -97 -409 -318 -331 -35 -349 -327 -397 -391 457 -315 -261 -370 -64 -219 -391 -300 -271 10 609 -521 -550 -423 -257 -400 -483 -552 -467 -453 -362 -320 -437 -502 234 -210 -353 -466 -440 -364 -270 379 -144 -359 -352 -188 -428 -391 -419 -434 24 -381 -330 -406 -51 -324 -405 -364 -294 -348 -331 -445 -466 -430 -433 -343 -504 -430 -440 -507 -403 486 -388 -451 -241 -347 -460 -475 -437 -359 -274 379 -75 -361 -366 -195 -425 -191 -415 -429 -46 -378 -311 -403 -202 -329 -400 -365 -297 -217 -234 66 58 -268 101 -101 -301 -147 216 -264 -67 119 -101 -218 -52 -151 -273 -326 -211 -355 405 -601 -597 -274 -560 -500 252 -569 -182 -261 -482 -486 -550 -600 -379 -276 237 -490 -373 -348 -285 370 2 -371 -358 -195 -430 -353 -416 -429 -53 -361 -273 -397 -192 -85 -400 -376 -304 -212 -79 -284 -286 228 -313 190 -49 -269 -163 -197 -198 -220 -242 -263 -78 -193 14 -27 456 -333 -165 -569 -556 -250 -511 -432 212 -522 -174 -246 -446 336 -488 -543 -321 -260 200 -434 -334 -426 -260 -537 -573 -281 -522 -442 371 -521 -155 -245 -447 -465 -502 -547 -358 -334 -56 -424 -336 -348 -331 -445 -466 -430 -433 -343 -504 -430 -440 -507 -403 486 -388 -451 -241 -347 -460 -475 -437 85 397 -429 -497 -418 305 -360 -490 -480 -471 -451 -301 -310 -414 -454 -64 -215 -353 -427 -409 -442 -258 -266 -476 -353 -380 -79 -388 -377 -432 -430 466 -352 -309 -412 -111 -264 -429 -333 -309 -402 -299 389 -179 -388 -397 -230 -460 -439 -449 -467 -81 -412 -374 -444 -242 -370 -437 -389 -328 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NCDPDLVDYPIPGND MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 10 E= 6.2e-073 0.000000 0.000000 0.100000 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 0.100000 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 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 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 0.800000 0.100000 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 0.100000 0.100000 0.000000 0.200000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.100000 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 0.400000 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 0.700000 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 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.100000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.300000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.300000 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 0.200000 0.200000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NCDPDLVDYPIPGND MEME-3 regular expression -------------------------------------------------------------------------------- N[CS]DPD[LG][IVC][DE][YV][PIV]IP[GAC]ND -------------------------------------------------------------------------------- Time 1.09 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sp|P80371|RS2_THET8 5.63e-42 13_[1(5.08e-17)]_62_[2(1.16e-20)]_\ 85_[3(1.23e-16)]_51 sp|A0Q4H1|RS2_FRATN 5.00e-37 10_[1(1.39e-15)]_62_[2(4.20e-18)]_\ 85_[3(1.73e-15)]_37 sp|A0RHK0|RS2_BACAH 1.46e-46 12_[1(9.67e-22)]_62_[2(1.32e-19)]_\ 85_[3(1.64e-17)]_29 sp|A1AQN2|RS2_PELPD 1.37e-48 12_[1(2.00e-21)]_62_[2(4.73e-20)]_\ 85_[3(1.40e-19)]_53 sp|A1B8E9|RS2_PARDP 2.13e-41 16_[1(8.44e-19)]_62_[2(5.38e-19)]_\ 84_[3(5.84e-16)]_54 sp|A1SLR0|RS2_NOCSJ 2.93e-49 12_[1(9.67e-22)]_62_[2(1.16e-20)]_\ 86_[3(1.40e-19)]_102 sp|A1W0G6|RS2_CAMJJ 8.34e-48 10_[1(9.67e-22)]_62_[2(8.21e-20)]_\ 85_[3(9.73e-19)]_61 sp|A2BW77|RS2_PROM5 1.03e-46 12_[1(3.93e-21)]_62_[2(1.53e-19)]_\ 85_[3(2.41e-18)]_30 sp|A2CA98|RS2_PROM3 3.88e-47 12_[1(3.93e-21)]_62_[2(5.29e-20)]_\ 85_[3(2.41e-18)]_35 sp|A2RGS9|RS2_STRPG 1.74e-43 12_[1(9.67e-22)]_62_[2(4.08e-19)]_\ 85_[3(5.39e-15)]_51 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************