******************************************************************************** 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.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ RS2_ECOLI 1.0000 241 RS2_BACSU 1.0000 246 RS2_THET8 1.0000 256 RS2_LISW6 1.0000 249 RS2_ARTS2 1.0000 294 RS2_BURCH 1.0000 246 RS2_AERHH 1.0000 242 RS2_MAGMM 1.0000 262 RS2_SYNFM 1.0000 274 ******************************************************************************** ******************************************************************************** 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.fasta -protein -mod oops -minw 8 -maxw 15 -nmotifs 3 -oc 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= 9 maxsites= 9 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= 2310 N= 9 sample: seed= 0 hsfrac= 0 searchsize= 2310 norand= no csites= 1000 Dirichlet mixture priors file: prior30.plib Letter frequencies in dataset: A 0.097 C 0.00433 D 0.0589 E 0.0892 F 0.0355 G 0.0684 H 0.019 I 0.0697 K 0.0736 L 0.0788 M 0.0312 N 0.0411 P 0.0355 Q 0.042 R 0.0628 S 0.0333 T 0.0541 V 0.0771 W 0.00996 Y 0.0186 Background letter frequencies (from file dataset with add-one prior applied): A 0.0966 C 0.00472 D 0.0588 E 0.0888 F 0.0356 G 0.0682 H 0.0193 I 0.0695 K 0.0734 L 0.0785 M 0.0313 N 0.0412 P 0.0356 Q 0.0421 R 0.0627 S 0.0335 T 0.0541 V 0.0768 W 0.0103 Y 0.0189 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GVHFGHQTRRWNPKM MEME-1 width = 15 sites = 9 llr = 409 E-value = 1.0e-097 ******************************************************************************** -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::::::::::::: pos.-specific C ::::::::::::::: probability D ::::::::::::::: matrix E ::::::1:::::::: F :1:a:::::1::::1 G a:::a:::::::::: H ::a::a::::::::: I ::::::::::::::: K ::::::::2::::a: L ::::::::::::::: M ::::::::::::::9 N :::::::::::a::: P ::::::::::::a:: Q ::::::9:::::::: R :::::::187::::: S ::::::::::::::: T :::::::9::::::: V :9::::::::::::: W ::::::::::a:::: Y :::::::::2::::: bits 7.7 7.0 * 6.2 * 5.4 * * * Relative 4.6 ** * *** * Entropy 3.9 * ****** ***** (65.6 bits) 3.1 *************** 2.3 *************** 1.5 *************** 0.8 *************** 0.0 --------------- Multilevel GVHFGHQTRRWNPKM consensus KY sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- RS2_AERHH 13 4.44e-22 KVSMRDMLQA GVHFGHQTRYWNPKM KSYIFGARSK RS2_ECOLI 13 4.44e-22 TVSMRDMLKA GVHFGHQTRYWNPKM KPFIFGARNK RS2_SYNFM 13 1.92e-21 VISMKQLLEA GVHFGHQTRRWNPKM KTYIFGARNG RS2_ARTS2 13 1.92e-21 VVTMRQLLDS GVHFGHQTRRWNPKM KRFIFTERNG RS2_LISW6 13 1.92e-21 VISMKQLLEA GVHFGHQTRRWNPKM KKYIFTERNG RS2_BACSU 13 1.92e-21 VISMKQLLEA GVHFGHQTRRWNPKM KRYIFTERNG RS2_BURCH 12 2.75e-21 AVTMRQMLEA GVHFGHQTRFWNPKM APFIFGHRNK RS2_MAGMM 13 6.65e-20 KYSVRELLEA GFHFGHQTKRWNPKM KRHIFGARNG RS2_THET8 14 2.29e-16 EITVKELLEA GVHFGHERKRWNPKF ARYIYAERNG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RS2_AERHH 4.4e-22 12_[1]_215 RS2_ECOLI 4.4e-22 12_[1]_214 RS2_SYNFM 1.9e-21 12_[1]_247 RS2_ARTS2 1.9e-21 12_[1]_267 RS2_LISW6 1.9e-21 12_[1]_222 RS2_BACSU 1.9e-21 12_[1]_219 RS2_BURCH 2.8e-21 11_[1]_220 RS2_MAGMM 6.6e-20 12_[1]_235 RS2_THET8 2.3e-16 13_[1]_228 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GVHFGHQTRRWNPKM width=15 seqs=9 RS2_AERHH ( 13) GVHFGHQTRYWNPKM 1 RS2_ECOLI ( 13) GVHFGHQTRYWNPKM 1 RS2_SYNFM ( 13) GVHFGHQTRRWNPKM 1 RS2_ARTS2 ( 13) GVHFGHQTRRWNPKM 1 RS2_LISW6 ( 13) GVHFGHQTRRWNPKM 1 RS2_BACSU ( 13) GVHFGHQTRRWNPKM 1 RS2_BURCH ( 12) GVHFGHQTRFWNPKM 1 RS2_MAGMM ( 13) GFHFGHQTKRWNPKM 1 RS2_THET8 ( 14) GVHFGHERKRWNPKF 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 2184 bayes= 7.91687 E= 1.0e-097 -289 -173 -324 -433 -460 376 -328 -518 -397 -501 -457 -262 -380 -408 -383 -186 -384 -463 -364 -356 -185 7 -411 -422 56 -414 -284 -36 -408 -161 -209 -367 -322 -375 -371 -237 -183 332 -314 -220 -529 -228 -431 -527 -358 -471 561 -588 -538 -457 -460 -260 -431 -246 -376 -309 -430 -540 -342 -150 -404 -67 -475 -515 465 -471 -344 -294 -499 -170 -263 -426 -377 -466 -496 -253 -416 -320 -161 4 -289 -173 -324 -433 -460 376 -328 -518 -397 -501 -457 -262 -380 -408 -383 -186 -384 -463 -364 -356 -529 -228 -431 -527 -358 -471 561 -588 -538 -457 -460 -260 -431 -246 -376 -309 -430 -540 -342 -150 -291 -101 -342 -101 -381 -412 22 -380 -289 -247 -191 -213 -265 427 -223 -173 -276 -366 -251 -299 -274 -34 -362 -425 -350 -380 -275 -302 -291 -354 -265 -180 -330 -271 6 62 384 -262 -331 -306 -371 -92 -433 -418 -439 -392 -151 -420 28 -358 -376 -275 -313 -187 372 -232 -328 -452 -260 -302 -500 -170 -530 -560 180 -504 -132 -412 -388 -312 -364 -362 -445 -360 322 -322 -425 -418 -54 359 -447 -139 -431 -477 -122 -423 -325 -437 -438 -247 -332 -375 -406 -370 -390 -309 -395 -390 646 -84 -424 -144 -251 -470 -375 -364 -92 -383 -369 -417 -397 445 -357 -294 -392 -100 -272 -421 -310 -286 -315 -205 -417 -447 -441 -406 -345 -484 -408 -410 -460 -400 471 -360 -417 -216 -342 -437 -443 -403 -400 -167 -485 -480 -508 -461 -332 -432 364 -453 -426 -336 -399 -375 -79 -323 -372 -486 -369 -384 -479 -158 -543 -590 -106 -523 -417 -272 -523 -168 486 -475 -460 -478 -553 -361 -416 -332 -271 -223 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 9 E= 1.0e-097 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 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 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 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 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.222222 0.000000 0.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 0.000000 0.222222 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 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 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVHFGHQTRRWNPKM MEME-1 regular expression -------------------------------------------------------------------------------- GVHFGHQT[RK][RY]WNPKM -------------------------------------------------------------------------------- Time 0.26 secs. ******************************************************************************** ******************************************************************************** MOTIF YYVNHRWLGGMLTNF MEME-2 width = 15 sites = 9 llr = 387 E-value = 1.2e-085 ******************************************************************************** -------------------------------------------------------------------------------- Motif YYVNHRWLGGMLTNF MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::1:::::::::: pos.-specific C ::::::::::::::: probability D ::::::::::::::: matrix E ::::::::::::::: F 32::::::::::::7 G ::::::::aa::::: H ::::4:::::::::: I ::1:::::::::::: K ::::::::::::::: L :::::::a:::9::: M ::::::::::71::: N :::a:::::::::a: P 3:::::::::::::: Q ::::4:::::::::: R :::::a::::::::: S ::::::::::::::: T ::::::::::3:a:: V ::9:::::::::::: W ::::::a:::::::3 Y 38::::::::::::: bits 7.7 7.0 * 6.2 * 5.4 * Relative 4.6 * * * ** Entropy 3.9 ** ******** *** (62.1 bits) 3.1 *************** 2.3 *************** 1.5 *************** 0.8 *************** 0.0 --------------- Multilevel FYVNHRWLGGMLTNF consensus PF Q T W sequence Y -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYVNHRWLGGMLTNF MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- RS2_AERHH 90 1.84e-21 VKEAAERCDQ FYVNHRWLGGMLTNW KTVRQSIKRL RS2_MAGMM 90 2.00e-20 VSAEARRTGQ FYVNHRWLGGTLTNW RTIQGSIRRL RS2_ARTS2 90 2.62e-20 IAEQATRVGQ PYVNQRWLGGMLTNF QTVSKRIQRM RS2_THET8 91 2.62e-20 VRMEAERAGM PYVNQRWLGGMLTNF KTISQRVHRL RS2_BACSU 90 4.15e-20 VKEEAQRSGM YYVNQRWLGGTLTNF ETIQKRIKRL RS2_ECOLI 90 4.15e-20 VKDAALSCDQ FFVNHRWLGGMLTNW KTVRQSIKRL RS2_SYNFM 90 7.44e-20 IAEEAQRCGM YYINQRWLGGMLTNF KTIKLRVDRL RS2_LISW6 90 1.03e-19 VRDEAIRSGQ YFVNHRWLGGTLTNF ETIQKRIQHL RS2_BURCH 89 1.99e-18 IAQEAQRAGM PYVNARWLGGMMTNF KTLKVSIKRL -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYVNHRWLGGMLTNF MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RS2_AERHH 1.8e-21 89_[2]_138 RS2_MAGMM 2e-20 89_[2]_158 RS2_ARTS2 2.6e-20 89_[2]_190 RS2_THET8 2.6e-20 90_[2]_151 RS2_BACSU 4.2e-20 89_[2]_142 RS2_ECOLI 4.2e-20 89_[2]_137 RS2_SYNFM 7.4e-20 89_[2]_170 RS2_LISW6 1e-19 89_[2]_145 RS2_BURCH 2e-18 88_[2]_143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYVNHRWLGGMLTNF MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YYVNHRWLGGMLTNF width=15 seqs=9 RS2_AERHH ( 90) FYVNHRWLGGMLTNW 1 RS2_MAGMM ( 90) FYVNHRWLGGTLTNW 1 RS2_ARTS2 ( 90) PYVNQRWLGGMLTNF 1 RS2_THET8 ( 91) PYVNQRWLGGMLTNF 1 RS2_BACSU ( 90) YYVNQRWLGGTLTNF 1 RS2_ECOLI ( 90) FFVNHRWLGGMLTNW 1 RS2_SYNFM ( 90) YYINQRWLGGMLTNF 1 RS2_LISW6 ( 90) YFVNHRWLGGTLTNF 1 RS2_BURCH ( 89) PYVNARWLGGMMTNF 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYVNHRWLGGMLTNF MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 2184 bayes= 7.91687 E= 1.2e-085 -452 -148 -497 -529 313 -488 -102 -387 -476 -290 -338 -356 292 -377 -426 -288 -404 -386 -41 419 -396 -116 -449 -474 261 -454 -70 -361 -434 -271 -311 -333 -389 -354 -393 -244 -370 -357 -36 519 -188 9 -417 -428 -270 -426 -309 60 -415 -175 -223 -377 -329 -390 -381 -250 -184 333 -374 -329 -424 -144 -251 -470 -375 -364 -92 -383 -369 -417 -397 445 -357 -294 -392 -100 -272 -421 -310 -286 -46 -85 -221 -206 -275 -296 430 -382 -168 -287 -262 -107 -273 309 -158 -93 -217 -336 -247 -83 -402 -95 -461 -507 -450 -415 -180 -447 -177 -392 -421 -319 -325 -250 387 -271 -376 -503 -269 -335 -447 -139 -431 -477 -122 -423 -325 -437 -438 -247 -332 -375 -406 -370 -390 -309 -395 -390 646 -84 -427 -149 -547 -530 -186 -506 -373 -182 -488 353 -112 -468 -404 -383 -438 -348 -366 -240 -308 -270 -289 -173 -324 -433 -460 376 -328 -518 -397 -501 -457 -262 -380 -408 -383 -186 -384 -463 -364 -356 -289 -173 -324 -433 -460 376 -328 -518 -397 -501 -457 -262 -380 -408 -383 -186 -384 -463 -364 -356 -249 -64 -483 -500 -240 -350 -361 -197 -424 -150 421 -371 -383 -387 -420 -153 240 -203 -326 -253 -370 -94 -509 -468 -125 -486 -321 -119 -427 337 111 -414 -355 -319 -378 -292 -305 -179 -255 -221 -364 -132 -468 -553 -446 -435 -388 -416 -464 -456 -390 -307 -412 -407 -453 -64 410 -375 -418 -399 -424 -144 -251 -470 -375 -364 -92 -383 -369 -417 -397 445 -357 -294 -392 -100 -272 -421 -310 -286 -520 -175 -555 -602 413 -524 -157 -393 -535 -278 -345 -397 -465 -418 -475 -342 -453 -410 475 130 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYVNHRWLGGMLTNF MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 9 E= 1.2e-085 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.222222 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.444444 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.444444 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 0.666667 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 0.666667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYVNHRWLGGMLTNF MEME-2 regular expression -------------------------------------------------------------------------------- [FPY][YF]VN[HQ]RWLGG[MT]LTN[FW] -------------------------------------------------------------------------------- Time 0.43 secs. ******************************************************************************** ******************************************************************************** MOTIF CDPDEVDYVIPGNDD MEME-3 width = 15 sites = 9 llr = 348 E-value = 2.8e-065 ******************************************************************************** -------------------------------------------------------------------------------- Motif CDPDEVDYVIPGNDD MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::::::::2::: pos.-specific C 6:::::::::::::: probability D :8:9::9::::::aa matrix E :::13:::::::::: F :::::::2::::::: G ::::3::::::8::: H 1:::::::::::::: I :::::4::19::::: K ::::::::::::::: L ::::2:::::::::: M ::::::::::::::: N :1::::1:::::a:: P ::a:1:::3:a:::: Q ::::::::::::::: R ::::::::::::::: S 31::::::::::::: T ::::::::::::::: V :::::6:161::::: W ::::::::::::::: Y :::::::7::::::: bits 7.7 7.0 6.2 5.4 * Relative 4.6 * * * * Entropy 3.9 * ** ** * *** (55.8 bits) 3.1 **** ********** 2.3 **** ********** 1.5 *************** 0.8 *************** 0.0 --------------- Multilevel CDPDEVDYVIPGNDD consensus S GI FP A sequence L -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDPDEVDYVIPGNDD MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- RS2_ARTS2 192 2.02e-19 IPVVAILDTN CDPDEVDFPIPGNDD AIRSVNLLTR RS2_MAGMM 191 3.50e-19 IPVVALVDSN CDPDPIDYPVPGNDD AIRALTLFIS RS2_LISW6 191 7.66e-19 IPIIGIVDTN CDPDEIDYVIPANDD AIRAVKLLTA RS2_SYNFM 191 1.74e-18 IPVVAIVDTN CDPDLINYPIPGNDD AIRAIRLITS RS2_ECOLI 191 4.17e-18 IPVFAIVDTN SDPDGVDFVIPGNDD AIRAVTLYLG RS2_THET8 192 4.96e-18 IPVIALADTD SDPDLVDYIIPGNDD AIRSIQLILS RS2_AERHH 191 1.13e-17 IPVVSIVDTN SNPDGVDYVIPGNDD AIRAVQLYLN RS2_BACSU 191 4.59e-17 IPIIGIVDTN CDPDEIDVVIPANDD AIRAVKLLTS RS2_BURCH 190 1.24e-15 VPVIAVVDTN HSPEGVDYVIPGNDD SSKAVALYAE -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDPDEVDYVIPGNDD MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RS2_ARTS2 2e-19 191_[3]_88 RS2_MAGMM 3.5e-19 190_[3]_57 RS2_LISW6 7.7e-19 190_[3]_44 RS2_SYNFM 1.7e-18 190_[3]_69 RS2_ECOLI 4.2e-18 190_[3]_36 RS2_THET8 5e-18 191_[3]_50 RS2_AERHH 1.1e-17 190_[3]_37 RS2_BACSU 4.6e-17 190_[3]_41 RS2_BURCH 1.2e-15 189_[3]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDPDEVDYVIPGNDD MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CDPDEVDYVIPGNDD width=15 seqs=9 RS2_ARTS2 ( 192) CDPDEVDFPIPGNDD 1 RS2_MAGMM ( 191) CDPDPIDYPVPGNDD 1 RS2_LISW6 ( 191) CDPDEIDYVIPANDD 1 RS2_SYNFM ( 191) CDPDLINYPIPGNDD 1 RS2_ECOLI ( 191) SDPDGVDFVIPGNDD 1 RS2_THET8 ( 192) SDPDLVDYIIPGNDD 1 RS2_AERHH ( 191) SNPDGVDYVIPGNDD 1 RS2_BACSU ( 191) CDPDEIDVVIPANDD 1 RS2_BURCH ( 190) HSPEGVDYVIPGNDD 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDPDEVDYVIPGNDD MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 2184 bayes= 7.91687 E= 2.8e-065 -150 666 -313 -418 -348 -230 230 -430 -376 -397 -385 -215 -310 -331 -384 317 -209 -329 -365 -250 -353 -163 383 -149 -390 -338 -207 -433 -387 -412 -410 12 -390 -320 -392 -39 -337 -406 -349 -278 -315 -205 -417 -447 -441 -406 -345 -484 -408 -410 -460 -400 471 -360 -417 -216 -342 -437 -443 -403 -355 -164 387 -97 -388 -361 -218 -427 -401 -407 -405 -62 -399 -326 -398 -204 -352 -401 -346 -281 -189 -110 -94 173 -306 181 -138 -302 -145 102 -249 -124 122 -90 -204 -57 -168 -260 -310 -201 -334 -62 -562 -578 -295 -544 -507 261 -546 -151 -218 -482 -482 -527 -563 -369 -283 270 -465 -351 -356 -163 387 -145 -387 -357 -216 -428 -402 -409 -407 -7 -399 -331 -398 -200 -350 -402 -346 -280 -268 -26 -336 -352 247 -360 13 -271 -328 -199 -224 -261 -288 -282 -303 -135 -269 -13 -21 492 -274 -31 -510 -509 -261 -466 -394 95 -479 -155 -207 -426 278 -441 -471 -283 -241 278 -385 -297 -337 -86 -436 -472 -240 -461 -390 337 -414 -45 -119 -362 -412 -399 -441 -258 -258 91 -335 -238 -315 -205 -417 -447 -441 -406 -345 -484 -408 -410 -460 -400 471 -360 -417 -216 -342 -437 -443 -403 8 -96 -298 -402 -428 358 -303 -477 -369 -463 -414 -230 -338 -372 -355 -117 -307 -400 -341 -330 -424 -144 -251 -470 -375 -364 -92 -383 -369 -417 -397 445 -357 -294 -392 -100 -272 -421 -310 -286 -385 -187 393 -176 -413 -383 -246 -457 -433 -435 -436 -93 -419 -361 -425 -233 -380 -431 -368 -307 -385 -187 393 -176 -413 -383 -246 -457 -433 -435 -436 -93 -419 -361 -425 -233 -380 -431 -368 -307 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDPDEVDYVIPGNDD MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 9 E= 2.8e-065 0.000000 0.555556 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 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 0.888889 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.333333 0.000000 0.000000 0.000000 0.222222 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.444444 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.555556 0.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.222222 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.666667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.555556 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 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 0.222222 0.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 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 CDPDEVDYVIPGNDD MEME-3 regular expression -------------------------------------------------------------------------------- [CS]DPD[EGL][VI]D[YF][VP]IP[GA]NDD -------------------------------------------------------------------------------- Time 0.63 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RS2_ECOLI 6.31e-48 12_[1(4.44e-22)]_62_[2(4.15e-20)]_\ 86_[3(4.17e-18)]_36 RS2_BACSU 3.00e-46 12_[1(1.92e-21)]_62_[2(4.15e-20)]_\ 86_[3(4.59e-17)]_41 RS2_THET8 2.34e-42 13_[1(2.29e-16)]_62_[2(2.62e-20)]_\ 86_[3(4.96e-18)]_50 RS2_LISW6 1.36e-47 12_[1(1.92e-21)]_62_[2(1.03e-19)]_\ 86_[3(7.66e-19)]_44 RS2_ARTS2 1.60e-48 12_[1(1.92e-21)]_62_[2(2.62e-20)]_\ 87_[3(2.02e-19)]_88 RS2_BURCH 4.86e-43 11_[1(2.75e-21)]_62_[2(1.99e-18)]_\ 86_[3(1.24e-15)]_42 RS2_AERHH 7.98e-49 12_[1(4.44e-22)]_62_[2(1.84e-21)]_\ 86_[3(1.13e-17)]_37 RS2_MAGMM 4.81e-47 12_[1(6.65e-20)]_62_[2(2.00e-20)]_\ 86_[3(3.50e-19)]_57 RS2_SYNFM 2.99e-47 12_[1(1.92e-21)]_62_[2(7.44e-20)]_\ 86_[3(1.74e-18)]_69 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************