******************************************************************************** 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= rpa.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ RPOA_BARHE 1.0000 337 RPOA_BACSU 1.0000 314 RPOA_MYCTU 1.0000 347 RPOA_MYCS2 1.0000 350 RPOA_CORGB 1.0000 338 RPOA_POLAQ 1.0000 326 RPOA_ORITB 1.0000 342 RPOA_FERNB 1.0000 328 RPOA_CAMC1 1.0000 338 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme rpa.fasta -protein -mod oops -nmotifs 3 -minw 8 -maxw 15 -oc meme_out 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= 3020 N= 9 sample: seed= 0 hsfrac= 0 searchsize= 3020 norand= no csites= 1000 Dirichlet mixture priors file: prior30.plib Letter frequencies in dataset: A 0.0632 C 0.00629 D 0.0662 E 0.094 F 0.0255 G 0.0662 H 0.0149 I 0.0735 K 0.0626 L 0.105 M 0.0179 N 0.0427 P 0.0457 Q 0.0252 R 0.0474 S 0.0649 T 0.0579 V 0.0911 W 0.00364 Y 0.0258 Background letter frequencies (from file dataset with add-one prior applied): A 0.0632 C 0.00658 D 0.0661 E 0.0938 F 0.0257 G 0.0661 H 0.0151 I 0.0734 K 0.0625 L 0.105 M 0.0181 N 0.0428 P 0.0457 Q 0.0253 R 0.0474 S 0.0648 T 0.0579 V 0.0908 W 0.00395 Y 0.026 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF EDLDLSVRSYNCLKR MEME-1 width = 15 sites = 9 llr = 324 E-value = 3.9e-050 ******************************************************************************** -------------------------------------------------------------------------------- Motif EDLDLSVRSYNCLKR MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::::2::2::::1 pos.-specific C :::::::::::a::: probability D 46:4:::::::::1: matrix E 44:4::::::::::: F ::::1::::1::::: G ::::::::::::::: H ::::::::::::::: I ::::::::::::::: K :::::::::::::91 L ::a:9::::1::a:: M ::::::::::::::: N :::1::::::a:::2 P ::::::::::::::: Q :::::::::1::::: R :::::::a::::::6 S :::::7::a:::::: T :::::3::::::::: V ::::::8:::::::: W ::::::::::::::: Y 1::::::::4::::: bits 8.0 7.2 * 6.4 * 5.6 * Relative 4.8 * ** Entropy 4.0 ** ** (51.9 bits) 3.2 * ***** **** 2.4 *************** 1.6 *************** 0.8 *************** 0.0 --------------- Multilevel DDLDLSVRSYNCLKR consensus EE E TA A N sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif EDLDLSVRSYNCLKR MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- RPOA_BACSU 254 1.53e-18 QKEKVLEMTI EELDLSVRSYNCLKR AGINTVQELA RPOA_MYCS2 252 1.84e-18 DHIASFALPI DDLDLTVRSYNCLKR EGVHTVGELV RPOA_MYCTU 252 1.84e-18 DHIASFALPI DDLDLTVRSYNCLKR EGVHTVGELV RPOA_CORGB 251 3.29e-18 EYIAAYSMPI EDLDFSVRSYNCLKR EDIHTVGELA RPOA_BARHE 258 1.89e-16 AFNPALLKKV DELELSVRSANCLKN DNIVYIGDLI RPOA_ORITB 263 4.17e-16 TINPVLLKKV YELELSVRSQNCLKN ENIVYVGDLV RPOA_FERNB 266 1.03e-15 SPEDVMSKKV EELELSARSLNCLKR DKIETIGDLL RPOA_POLAQ 256 1.25e-15 MVDPMLMRPV DDLELTVRSANCLKA ENIYYIGDLI RPOA_CAMC1 255 4.21e-14 GEFSKLLSSV EDLNLSARSFNCLDK AEIRFIGELA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif EDLDLSVRSYNCLKR MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RPOA_BACSU 1.5e-18 253_[1]_46 RPOA_MYCS2 1.8e-18 251_[1]_84 RPOA_MYCTU 1.8e-18 251_[1]_81 RPOA_CORGB 3.3e-18 250_[1]_73 RPOA_BARHE 1.9e-16 257_[1]_65 RPOA_ORITB 4.2e-16 262_[1]_65 RPOA_FERNB 1e-15 265_[1]_48 RPOA_POLAQ 1.3e-15 255_[1]_56 RPOA_CAMC1 4.2e-14 254_[1]_69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif EDLDLSVRSYNCLKR MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF EDLDLSVRSYNCLKR width=15 seqs=9 RPOA_BACSU ( 254) EELDLSVRSYNCLKR 1 RPOA_MYCS2 ( 252) DDLDLTVRSYNCLKR 1 RPOA_MYCTU ( 252) DDLDLTVRSYNCLKR 1 RPOA_CORGB ( 251) EDLDFSVRSYNCLKR 1 RPOA_BARHE ( 258) DELELSVRSANCLKN 1 RPOA_ORITB ( 263) YELELSVRSQNCLKN 1 RPOA_FERNB ( 266) EELELSARSLNCLKR 1 RPOA_POLAQ ( 256) DDLELTVRSANCLKA 1 RPOA_CAMC1 ( 255) EDLNLSARSFNCLDK 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif EDLDLSVRSYNCLKR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 2894 bayes= 8.32443 E= 3.9e-050 -203 -351 256 211 -412 -308 -180 -464 -194 -438 -306 -153 -315 -39 -282 -236 -274 -408 -311 155 -208 -391 284 213 -471 -334 -208 -474 -205 -450 -317 -188 -323 -40 -303 -263 -293 -414 -351 -407 -366 -197 -564 -538 -139 -501 -338 -189 -465 311 -33 -473 -440 -310 -398 -443 -376 -264 -170 -317 -216 -320 263 203 -433 -277 -162 -482 -208 -459 -329 114 -322 -58 -292 -214 -269 -429 -322 -366 -318 -150 -537 -489 136 -490 -288 -131 -417 295 28 -430 -402 -257 -350 -399 -325 -210 -110 -239 -133 -21 -345 -426 -267 -295 -232 -382 -294 -387 -226 -150 -300 -235 -264 339 176 -392 -171 -287 90 -23 -415 -417 -226 -347 -251 -53 -374 -237 -155 -355 -336 -290 -319 -268 -176 300 -214 -364 -341 -143 -478 -514 -403 -410 -144 -455 -153 -433 -342 -324 -361 -177 427 -366 -386 -528 -130 -381 -238 -154 -470 -562 -406 -368 -360 -542 -456 -530 -393 -316 -419 -377 -418 383 -113 -510 -290 -421 51 -13 -286 -288 246 -292 99 -213 -235 -78 -83 -213 -261 70 -202 -163 -208 -216 128 417 -363 -192 -267 -478 -328 -360 -57 -391 -345 -459 -318 439 -393 -221 -351 -196 -282 -446 -171 -332 -355 719 -557 -553 -408 -531 -399 -457 -546 -500 -350 -481 -527 -435 -467 -450 -393 -515 -363 -498 -366 -197 -564 -538 -139 -501 -338 -189 -465 311 -33 -473 -440 -310 -398 -443 -376 -264 -170 -317 -325 -209 -193 -433 -452 -434 -274 -433 383 -484 -336 -305 -424 -270 -33 -390 -365 -499 -226 -416 24 -180 -310 -270 -355 -321 -87 -394 97 -354 -229 168 -331 -34 353 -232 -245 -386 -149 -286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif EDLDLSVRSYNCLKR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 9 E= 3.9e-050 0.000000 0.000000 0.444444 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 0.111111 0.000000 0.000000 0.555556 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 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 0.444444 0.444444 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 0.111111 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 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 0.777778 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 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 0.222222 0.000000 0.000000 0.000000 0.111111 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 0.444444 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 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 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 0.111111 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 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.222222 0.000000 0.000000 0.555556 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif EDLDLSVRSYNCLKR MEME-1 regular expression -------------------------------------------------------------------------------- [DE][DE]L[DE]L[ST][VA]RS[YA]NCLK[RN] -------------------------------------------------------------------------------- Time 0.74 secs. ******************************************************************************** ******************************************************************************** MOTIF PLERGYGYTLGNSLR MEME-2 width = 15 sites = 9 llr = 317 E-value = 1.8e-046 ******************************************************************************** -------------------------------------------------------------------------------- Motif PLERGYGYTLGNSLR MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::1::2:::1:2:: pos.-specific C ::::::::::::::: probability D ::::::::::::::: matrix E ::a:::::::::::: F :2:::4::::::::: G ::::a:8:::9:::: H :::::::1:::1::: I ::::::::::::::: K :::1::::::::::: L :8:::1:2:9:::a: M ::::::::::::::: N :::::::::::9::: P a::3::::::::1:: Q ::::::::::::::: R :::4::::::::::a S ::::::::::::6:: T :::::::1a:::1:: V :::::::2:1::::: W ::::::::::::::: Y :::::4:3::::::: bits 8.0 7.2 6.4 5.6 Relative 4.8 * * Entropy 4.0 * ** * * * (50.8 bits) 3.2 *** *** * ** ** 2.4 *************** 1.6 *************** 0.8 *************** 0.0 --------------- Multilevel PLERGFGYTLGNSLR consensus F P YAL A sequence V -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif PLERGYGYTLGNSLR MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- RPOA_CORGB 25 1.54e-18 DNARSRFVIE PLEPGFGYTLGNSLR RTLLSSIPGA RPOA_MYCS2 25 1.54e-18 AENRSRFVIE PLEPGFGYTLGNSLR RTLLSSIPGA RPOA_MYCTU 25 1.54e-18 TDNRSQFVIE PLEPGFGYTLGNSLR RTLLSSIPGA RPOA_BACSU 27 1.79e-17 DAKFGKFVVE PLERGYGTTLGNSLR RILLSSLPGA RPOA_POLAQ 27 3.66e-17 TANQAKVVME PFERGYGHTLGNALR RVLLSSMVGY RPOA_BARHE 32 1.11e-16 NPNISSVIVE PLERGFGLTLGNALR RVLLSSLRGA RPOA_ORITB 36 4.66e-16 NPNIKTMVVE PLERGLGLTLGNSLR RVLLSSLRGA RPOA_FERNB 29 3.37e-14 DHYYARYSLS PLEKGYAVTVGNTLR RVLLSSIPSF RPOA_CAMC1 30 1.67e-12 SENVANITAY PFEAGYAVTLAHPLR RLLYTSTVGF -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif PLERGYGYTLGNSLR MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RPOA_CORGB 1.5e-18 24_[2]_299 RPOA_MYCS2 1.5e-18 24_[2]_311 RPOA_MYCTU 1.5e-18 24_[2]_308 RPOA_BACSU 1.8e-17 26_[2]_273 RPOA_POLAQ 3.7e-17 26_[2]_285 RPOA_BARHE 1.1e-16 31_[2]_291 RPOA_ORITB 4.7e-16 35_[2]_292 RPOA_FERNB 3.4e-14 28_[2]_285 RPOA_CAMC1 1.7e-12 29_[2]_294 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif PLERGYGYTLGNSLR MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF PLERGYGYTLGNSLR width=15 seqs=9 RPOA_CORGB ( 25) PLEPGFGYTLGNSLR 1 RPOA_MYCS2 ( 25) PLEPGFGYTLGNSLR 1 RPOA_MYCTU ( 25) PLEPGFGYTLGNSLR 1 RPOA_BACSU ( 27) PLERGYGTTLGNSLR 1 RPOA_POLAQ ( 27) PFERGYGHTLGNALR 1 RPOA_BARHE ( 32) PLERGFGLTLGNALR 1 RPOA_ORITB ( 36) PLERGLGLTLGNSLR 1 RPOA_FERNB ( 29) PLEKGYAVTVGNTLR 1 RPOA_CAMC1 ( 30) PFEAGYAVTLAHPLR 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif PLERGYGYTLGNSLR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 2894 bayes= 8.32443 E= 1.8e-046 -253 -253 -434 -455 -393 -402 -309 -492 -385 -452 -381 -405 435 -286 -376 -311 -351 -461 -305 -450 -349 -175 -590 -546 257 -529 -311 -139 -472 282 15 -474 -447 -300 -402 -448 -358 -227 -107 -215 -468 -402 -245 336 -530 -514 -384 -566 -556 -634 -504 -410 -611 -298 -534 -521 -529 -597 -385 -542 47 -185 -306 -246 -329 -310 -92 -375 107 -334 -210 -188 265 -26 291 -207 -221 -352 -166 -277 -228 -221 -341 -440 -413 381 -293 -526 -373 -543 -378 -267 -416 -335 -342 -281 -394 -487 -226 -402 -298 -139 -438 -450 388 -427 -19 -328 -385 -18 -191 -324 -399 -265 -332 -311 -352 -347 102 406 69 -144 -315 -410 -380 363 -267 -485 -346 -505 -334 -235 -374 -299 -314 -212 -317 -424 -203 -376 -112 14 -346 -324 85 -285 226 -95 -252 65 -6 -230 -281 -152 -221 -176 48 84 52 346 -302 -180 -485 -561 -399 -430 -352 -424 -441 -498 -311 -313 -448 -334 -413 -159 400 -399 -280 -445 -301 -136 -524 -476 -86 -478 -289 -118 -405 294 27 -418 -393 -250 -340 -384 -309 -34 -124 -270 -38 -171 -297 -395 -375 371 -254 -480 -329 -504 -330 -221 -378 -291 -299 -227 -340 -435 -190 -364 -333 -160 -231 -446 -294 -333 72 -351 -308 -424 -279 433 -364 -183 -317 -157 -245 -409 -138 -298 100 -22 -366 -427 -290 -261 -250 -403 -316 -402 -246 -183 21 -242 -287 323 111 -375 -194 -313 -366 -197 -564 -538 -139 -501 -338 -189 -465 311 -33 -473 -440 -310 -398 -443 -376 -264 -170 -317 -341 -143 -478 -514 -403 -410 -144 -455 -153 -433 -342 -324 -361 -177 427 -366 -386 -528 -130 -381 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif PLERGYGYTLGNSLR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 9 E= 1.8e-046 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 0.222222 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 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 0.111111 0.000000 0.000000 0.000000 0.333333 0.000000 0.444444 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 0.444444 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 0.444444 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 0.111111 0.000000 0.000000 0.222222 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.222222 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 0.000000 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 0.888889 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.111111 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 0.000000 0.000000 0.000000 0.888889 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 0.111111 0.000000 0.000000 0.555556 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 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif PLERGYGYTLGNSLR MEME-2 regular expression -------------------------------------------------------------------------------- P[LF]E[RP]G[FY][GA][YLV]TLGN[SA]LR -------------------------------------------------------------------------------- Time 1.03 secs. ******************************************************************************** ******************************************************************************** MOTIF GVEILNPDHHIATLN MEME-3 width = 15 sites = 9 llr = 297 E-value = 3.1e-036 ******************************************************************************** -------------------------------------------------------------------------------- Motif GVEILNPDHHIATLN MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::::::1::8::: pos.-specific C :::::::::::2::: probability D 4::::::7::::::1 matrix E ::6:::::::::::: F ::::::::::::::: G 4::::::2::::::1 H ::::3:::44::1:: I :::7::::::8::1: K ::::::::::::::: L 1:::3:::2:2::9: M :1::1:::2:::::: N :::::a::::::1:6 P ::::::a:::::::: Q :::::::1::::::: R ::::::::::::::: S ::::::::::::::2 T ::3:::::::::8:: V :9132::::3::::: W ::::::::::::::: Y :::::::::2::::: bits 8.0 7.2 6.4 5.6 Relative 4.8 ** Entropy 4.0 ** * (47.6 bits) 3.2 * ********* 2.4 *************** 1.6 *************** 0.8 *************** 0.0 --------------- Multilevel DVEIHNPDHHIATLN consensus G TVL GLVLC S sequence V MY -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVEILNPDHHIATLN MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- RPOA_MYCS2 115 3.40e-18 VTAGDIVPPA GVTVHNPDMHIATLN DKGKLEVELV RPOA_CORGB 115 4.45e-18 VTAGDIQPPA GVEIHNPDLHIATLN ETAKIEIELI RPOA_MYCTU 115 5.09e-17 VTAGDIVPPA GVTVHNPGMHIATLN DKGKLEVELV RPOA_POLAQ 117 1.24e-15 VTAKDIDLPH DVEIMNPDHVIAHLS AGGKLDMQIK RPOA_BARHE 122 1.79e-15 LRAGDISTVG DMEILNPDHVICTLD EDAEIRMEFI RPOA_BACSU 117 1.95e-15 VTAADITHDS DVEILNPDLHIATLG ENASFRVRLT RPOA_ORITB 128 2.35e-14 AGMITVTDKQ DVTILNPQHVICNLS KGFNLEMDLI RPOA_FERNB 123 6.64e-14 LTAGDIECPA GVVVVNPGHYLATLN EDADLEIELY RPOA_CAMC1 120 7.38e-13 EITGADLNND LVEIVNPDAYLATIN EDAELNFSVI -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVEILNPDHHIATLN MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RPOA_MYCS2 3.4e-18 114_[3]_221 RPOA_CORGB 4.5e-18 114_[3]_209 RPOA_MYCTU 5.1e-17 114_[3]_218 RPOA_POLAQ 1.2e-15 116_[3]_195 RPOA_BARHE 1.8e-15 121_[3]_201 RPOA_BACSU 2e-15 116_[3]_183 RPOA_ORITB 2.3e-14 127_[3]_200 RPOA_FERNB 6.6e-14 122_[3]_191 RPOA_CAMC1 7.4e-13 119_[3]_204 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVEILNPDHHIATLN MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GVEILNPDHHIATLN width=15 seqs=9 RPOA_MYCS2 ( 115) GVTVHNPDMHIATLN 1 RPOA_CORGB ( 115) GVEIHNPDLHIATLN 1 RPOA_MYCTU ( 115) GVTVHNPGMHIATLN 1 RPOA_POLAQ ( 117) DVEIMNPDHVIAHLS 1 RPOA_BARHE ( 122) DMEILNPDHVICTLD 1 RPOA_BACSU ( 117) DVEILNPDLHIATLG 1 RPOA_ORITB ( 128) DVTILNPQHVICNLS 1 RPOA_FERNB ( 123) GVVVVNPGHYLATLN 1 RPOA_CAMC1 ( 120) LVEIVNPDAYLATIN 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVEILNPDHHIATLN MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 2894 bayes= 8.32443 E= 3.1e-036 -214 -194 243 -230 -357 266 -152 -460 -257 -28 -335 -76 -351 -166 -293 -179 -259 -429 -256 -322 -125 -40 -432 -432 -201 -413 -266 -36 -387 -195 156 -378 -361 -307 -335 -336 -193 308 -212 -353 -157 -193 -108 236 -320 -304 -179 -295 -175 -337 -213 -209 -303 -41 -236 -201 213 0 -244 -323 -279 -128 -484 -508 -208 -480 -387 312 -422 -112 -64 -397 -470 -357 -432 -381 -277 144 -228 -311 -183 -45 -474 -433 -60 -368 397 -88 -348 161 243 -327 -363 -226 -310 -271 -199 109 -60 -180 -363 -192 -267 -478 -328 -360 -57 -391 -345 -459 -318 439 -393 -221 -351 -196 -282 -446 -171 -332 -253 -253 -434 -455 -393 -402 -309 -492 -385 -452 -381 -405 435 -286 -376 -311 -351 -461 -305 -450 -256 -225 333 -151 -369 90 -132 -483 -262 -476 -355 -35 -361 134 -301 -192 -273 -457 -253 -321 58 -29 -376 -349 -66 -319 447 -103 -261 95 317 -234 -324 -135 -230 -216 -170 -126 -43 -133 -355 -175 -472 -503 43 -453 471 -330 -410 -304 -217 -293 -447 -216 -329 -355 -357 156 78 310 -294 -149 -480 -503 -149 -476 -360 321 -414 55 -22 -392 -460 -331 -414 -376 -288 -1 -175 -283 352 445 -449 -452 -299 -191 -312 -371 -406 -374 -233 -342 -366 -293 -362 -99 -205 -241 -206 -373 -208 -77 -269 -371 -286 -325 189 -302 -268 -388 -178 73 -345 -175 -266 -18 360 -280 -183 -321 -310 -143 -533 -483 -81 -487 -294 12 -412 294 29 -426 -399 -254 -347 -394 -317 -192 -122 -272 -265 -211 68 -264 -365 43 -71 -493 -240 -501 -382 365 -333 -145 -288 140 -227 -496 -252 -303 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVEILNPDHHIATLN MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 9 E= 3.1e-036 0.000000 0.000000 0.444444 0.000000 0.000000 0.444444 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 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.000000 0.000000 0.000000 0.555556 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.111111 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 0.000000 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 0.333333 0.000000 0.000000 0.333333 0.111111 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 0.000000 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 0.666667 0.000000 0.000000 0.222222 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 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.444444 0.000000 0.000000 0.222222 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 0.444444 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.222222 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.222222 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.777778 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.111111 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 0.111111 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 0.000000 0.111111 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.555556 0.000000 0.000000 0.000000 0.222222 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GVEILNPDHHIATLN MEME-3 regular expression -------------------------------------------------------------------------------- [DG]V[ET][IV][HLV]NP[DG][HLM][HVY][IL][AC]TL[NS] -------------------------------------------------------------------------------- Time 1.27 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RPOA_BARHE 5.20e-36 31_[2(1.11e-16)]_75_[3(1.79e-15)]_\ 121_[1(1.89e-16)]_65 RPOA_BACSU 6.85e-39 26_[2(1.79e-17)]_75_[3(1.95e-15)]_\ 122_[1(1.53e-18)]_46 RPOA_MYCTU 2.81e-41 24_[2(1.54e-18)]_75_[3(5.09e-17)]_\ 122_[1(1.84e-18)]_81 RPOA_MYCS2 2.03e-42 24_[2(1.54e-18)]_75_[3(3.40e-18)]_\ 122_[1(1.84e-18)]_84 RPOA_CORGB 4.21e-42 24_[2(1.54e-18)]_75_[3(4.45e-18)]_\ 121_[1(3.29e-18)]_73 RPOA_POLAQ 6.99e-36 26_[2(3.66e-17)]_75_[3(1.24e-15)]_9_\ [2(5.49e-05)]_100_[1(1.25e-15)]_56 RPOA_ORITB 5.91e-34 35_[2(4.66e-16)]_77_[3(2.35e-14)]_\ 120_[1(4.17e-16)]_18_[1(6.63e-05)]_32 RPOA_FERNB 2.27e-31 28_[2(3.37e-14)]_79_[3(6.64e-14)]_\ 128_[1(1.03e-15)]_48 RPOA_CAMC1 4.26e-27 29_[2(1.67e-12)]_75_[3(7.38e-13)]_\ 120_[1(4.21e-14)]_69 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************