!!AA_SCORING_MATRIX_RECT 1.0 This scoring matrix was generated by MEME version 2.1 (Release date: 1997/03/25 22:39:11). For further information or to get a copy of the MEME software please access http://www.sdsc.edu/MEME. MEME reference: 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 ******************************************************************************** DATAFILE= lysr_frags.seq (deleted by web version of MEME) ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Length Sequence name Length ------------- ------ ------------- ------ ALSR_BACSU 20 AMPR_CITDI 20 AMPR_CITFR 20 AMPR_ENTCL 20 AMPR_PSEAE 20 AMPR_RHOCA 20 AMPR_YEREN 20 ARAB_STRAT 20 BLAA_PROVU 20 BLAA_STRCI 20 BUDR_ENTAE 20 BUDR_KLETE 20 CATM_ACICA 20 CATR_PSEPU 20 CBBR_RHORU 20 CBBR_RHOSH 20 CBBR_XANFL 20 CFXR_ALCEU 20 CITR_BACSU 20 CLCR_PSEPU 20 CYNR_ECOLI 20 CYSB_ECOLI 20 CYSB_HAEIN 20 CYSB_KLEAE 20 CYSB_SALTY 20 CYSB_THIRO 20 DGDR_BURCE 20 DSDC_ECOLI 20 ESTR_ACICA 20 GBPR_AGRTU 20 GBPR_AZOBR 20 GCVA_ECOLI 20 GCVA_HAEIN 20 GLTC_BACSU 20 HLYT_VIBCH 20 HVRB_RHOCA 20 ICIA_ECOLI 20 ILVR_CAUCR 20 ILVY_ECOLI 20 ILVY_HAEIN 20 IRGB_VIBCH 20 LEUO_ECOLI 20 LRHA_ECOLI 20 LRRA_SYNP7 20 LTRA_KLEPN 20 LYSR_ECOLI 20 MAUR_KLEPN 20 MAUR_PARDE 20 METR_ECOLI 20 METR_HAEIN 20 METR_SALTY 20 MLER_LACLA 20 MPRR_STRCO 20 NAC_KLEAE 20 NAHR_PSEPU 20 NHAR_ECOLI 20 NMCR_ENTCL 20 NOCR_AGRT5 20 NOCR_AGRT7 20 NOD1_BRAEL 20 NOD1_BRAJA 20 NOD1_BRASN 20 NOD1_RHIGA 20 NOD1_RHILP 20 NOD1_RHIME 20 NOD1_RHITR 20 NOD2_BRAEL 20 NOD2_BRAJA 20 NOD2_BRASN 20 NOD2_RHILP 20 NOD2_RHIME 20 NOD2_RHITR 20 NOD3_RHILP 20 NOD3_RHIME 20 NODD_AZOCA 20 NODD_BRASP 20 NODD_RHILE 20 NODD_RHILT 20 NODD_RHILV 20 NTCB_SYNP7 20 OCCR_AGRT6 20 OPRR_PSEAE 20 OXYR_ECOLI 20 OXYR_HAEIN 20 OXYR_MYCAV 20 OXYR_MYCLE 20 PCAQ_AGRTU 20 PCPR_FLAS3 20 PECT_ERWCH 20 PHCA_BURSO 20 PSSR_ECOLI 20 RBCR_CHRVI 20 RBCR_THIFE 20 SDSB_PSESP 20 SINR_SALTY 20 SMER_SERMA 20 SNPR_STRLI 20 SYRM_RHILP 20 SYRM_RHIME 20 TCBR_PSESP 20 TDCA_ECOLI 20 TFDR_ALCEU 20 TFDT_ALCEU 20 TRPI_PSEAE 20 TRPI_PSESY 20 TTUA_AGRVI 20 VRPR_SALDU 20 VRPR_SALTY 20 XAPR_ECOLI 20 Y775_HAEIN 20 YAFC_ECOLI 20 YBEF_ECOLI 20 YC30_CYAPA 20 YC30_ODOSI 20 YC30_PORPU 20 YDHB_ECOLI 20 YEIE_ECOLI 20 YFIE_ECOLI 20 YGFI_ECOLI 20 YGIP_ECOLI 20 YHAJ_ECOLI 20 YHCS_ECOLI 20 YHCS_HAEIN 20 YHJC_ECOLI 20 YIAU_ECOLI 20 YIDZ_ECOLI 20 YJIE_ECOLI 20 YNA2_KLEAE 20 YW34_MYCTU 20 YWBI_BACSU 20 YWFK_BACSU 20 YXJO_BACSU 20 YYBE_BACSU 20 ******************************************************************************** MOTIF 1 width = 20 sites = 133.0 ******************************************************************************** Simplified A :139911:::::16::22:2 motif letter- C ::::::::1::::::::::: probability D :::::1:::::::::::::: matrix E ::1::22::::::::::::: F 5::::::::::::::::::: G :1::::::2::::::::::1 H ::::::::2:::::::11:: I 1::::::1:2::::2:::5: K ::1::11:::::::::1::2 L 2::::::7:3::::3:::2: M :::::::1:1::::2:::1: N ::::::::2::::::::::: P :::::::::::161:::::: Q :::::11::::8::::24:1 R ::3::21::1::::::31:2 S :21:::2:::5:3::8:1:1 T :5:1::::::3::1:1:::: V 2:::::11:3::::3:::3: W :::::::::::::::::::: Y ::::::::1::::::::::: bits 11.4 10.2 9.1 8.0 Information 6.8 content 5.7 (32.5 bits) 4.6 3.4 2.3 1.1 ** ** ********* * 0.0 -------------------- Multilevel FTAAAExLNLSQPAVSRQIR consensus L R R HVT S L AVK sequence log-odds matrix: alength= 20 w= 20 n= 133 bayes= -664.386 .. Width 20 Threshold 10.0 -1.606 -4.971 -7.553 -6.909 3.540 -6.791 -5.855 0.457 -6.585 1.197 0.432 -6.488 -6.897 -6.162 -6.413 -5.936 -2.712 1.294 -5.561 -1.085 0.275 -5.290 -2.394 -2.389 -5.627 0.188 -0.527 -2.735 -1.599 -2.506 -4.389 -2.162 -5.278 -1.926 -0.434 1.407 2.978 -1.471 -5.692 -5.098 1.906 -5.536 -3.888 -0.159 -5.495 -1.564 0.045 -1.316 1.271 -1.577 -4.331 -0.889 -5.052 -0.027 2.358 -0.256 -2.438 -2.809 -5.565 -1.990 3.600 -5.125 -8.235 -8.180 -7.862 -2.103 -7.711 -7.755 -8.296 -7.892 -6.944 -7.287 -7.165 -7.500 -7.827 -2.911 -0.169 -1.082 -7.968 -8.229 3.661 -5.377 -8.582 -8.636 -8.284 -1.561 -8.021 -8.268 -8.799 -8.397 -7.406 -7.476 -7.225 -7.748 -8.171 -1.214 -1.899 -6.653 -8.357 -8.605 0.181 -5.536 0.037 1.857 -5.495 -4.977 0.430 -0.614 0.647 -1.278 -4.331 -0.239 -5.051 1.017 2.107 -1.140 -0.883 -1.463 -5.565 -4.836 0.694 -1.281 -1.551 1.378 -1.420 -1.564 0.734 -2.737 0.647 -1.030 -0.043 -1.372 -5.051 0.745 1.262 1.060 -1.242 -0.132 -5.564 -4.835 -3.123 -0.487 -6.512 -5.775 -1.347 -6.522 -5.101 1.338 -5.554 2.833 1.251 -1.825 -5.732 -2.432 -2.774 -3.280 -4.887 0.064 -4.839 -4.851 -1.928 1.651 -1.551 -2.224 -0.150 1.370 3.158 -5.368 -1.493 -3.270 -1.487 2.321 -5.052 -1.120 -0.678 -1.483 -2.438 -4.934 -5.565 1.808 -4.497 -0.247 -6.947 -6.299 -4.366 -6.177 -5.261 1.480 -5.969 1.788 1.948 -5.869 -6.330 -0.140 -0.011 -5.302 -0.368 2.088 -5.104 -4.802 -0.641 -3.462 -4.857 -3.114 -5.036 -4.959 -4.615 -5.079 -4.546 -3.529 -4.278 -2.149 -1.422 -4.748 -2.683 2.879 2.439 -1.756 -5.178 -4.925 -2.309 -4.189 -4.700 -1.899 -5.233 -5.443 0.757 -3.044 -2.125 -3.931 -2.694 -2.418 0.619 4.236 -1.790 -3.052 -4.161 -2.426 -4.114 -5.037 0.409 -5.491 -6.658 -6.543 -7.116 -1.211 -6.315 -6.959 -6.383 -6.856 -6.438 -6.505 3.467 -1.444 -6.474 1.822 -1.374 -2.992 -7.515 -7.472 3.147 -3.282 -6.054 -5.743 -2.424 -0.906 -5.653 -5.195 -5.761 -5.350 -1.593 -2.616 0.880 -5.660 -5.672 -0.639 1.115 -2.492 -5.694 -5.978 -1.281 -6.605 -9.876 -9.375 -1.354 -9.358 -8.419 1.684 -9.178 1.525 2.829 -9.082 -8.995 -8.278 -8.908 -8.819 -7.080 2.416 -7.157 -7.222 -1.989 -4.139 -5.774 -6.322 -5.943 -2.208 -0.709 -6.099 -5.534 -6.284 -5.246 -4.276 -5.663 -5.665 -5.419 3.490 0.876 -5.890 -6.084 -5.844 1.072 -5.490 -3.919 -3.347 -1.416 -0.883 1.549 -1.848 0.947 -1.572 -0.040 -1.377 -5.072 2.211 2.280 -1.487 -1.721 -2.792 -5.548 -0.545 1.578 -4.919 -4.526 -2.480 -4.879 -2.969 1.832 -2.471 -3.761 -1.211 -0.001 -4.208 -5.427 3.226 0.370 0.028 -0.893 -1.349 -0.836 -1.973 -7.429 -6.836 -10.226 -9.774 -1.351 -9.810 -8.785 3.149 -9.610 0.874 1.201 -9.539 -9.251 -8.484 -9.260 -9.436 -7.392 2.024 -7.221 -7.380 1.432 -6.023 -4.538 -3.902 -6.105 -0.420 -0.507 -5.868 1.830 -5.706 -1.528 -1.447 -5.618 1.782 2.037 0.496 -0.920 -5.455 -6.001 -5.356