******************************************************************************** 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= script_results/housekeeping.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ cds-WP_045855524.1 1.0000 100 cds-WP_045855526.1 1.0000 100 cds-WP_045855542.1 1.0000 100 efp 1.0000 100 rplI 1.0000 100 rpsR 1.0000 100 rpsF 1.0000 100 cds-WP_045855573.1 1.0000 100 cds-WP_045855582.1 1.0000 100 rpoD 1.0000 100 cds-WP_045855632.1 1.0000 100 cds-WP_052691783.1 1.0000 100 cds-WP_052691784.1 1.0000 100 cds-WP_045855636.1 1.0000 100 fusA 1.0000 100 cds-WP_045855668.1 1.0000 100 pcnB 1.0000 100 cds-WP_045855789.1 1.0000 100 cds-WP_052691813.1 1.0000 100 cds-WP_045855857.1 1.0000 100 cds-WP_045855936.1 1.0000 100 gshB 1.0000 100 cds-WP_045856028.1 1.0000 100 rho 1.0000 100 slmA 1.0000 100 rpmB 1.0000 100 rpmG 1.0000 100 rpoZ 1.0000 100 cds-WP_045856103.1 1.0000 100 cds-WP_045856109.1 1.0000 100 cds-WP_045856119.1 1.0000 100 cds-WP_045856218.1 1.0000 100 cds-WP_045856238.1 1.0000 100 cds-WP_045861029.1 1.0000 100 cds-WP_045856357.1 1.0000 100 atpD 1.0000 100 atpG 1.0000 100 atpA 1.0000 100 cds-WP_045856365.1 1.0000 100 cds-WP_045856368.1 1.0000 100 atpE 1.0000 100 atpB 1.0000 100 cds-WP_045856374.1 1.0000 100 cds-WP_045856380.1 1.0000 100 rpmH 1.0000 100 dnaN 1.0000 100 cds-WP_045856454.1 1.0000 100 polA 1.0000 100 cds-WP_045856570.1 1.0000 100 cds-WP_082087156.1 1.0000 100 cds-WP_052691868.1 1.0000 100 cds-WP_045856653.1 1.0000 100 cds-WP_045856744.1 1.0000 100 rpoH 1.0000 100 hpaR 1.0000 100 cds-WP_045856936.1 1.0000 100 cds-WP_045856963.1 1.0000 100 cds-WP_121495355.1 1.0000 100 cds-WP_045857004.1 1.0000 100 rimK 1.0000 100 nrdR 1.0000 100 nusB 1.0000 100 cds-WP_045857096.1 1.0000 100 holA 1.0000 100 cds-WP_045861136.1 1.0000 100 ychF 1.0000 100 cds-WP_045857227.1 1.0000 100 cds-WP_052691908.1 1.0000 100 cds-WP_045857303.1 1.0000 100 cds-WP_045861159.1 1.0000 100 rplM 1.0000 100 rpsI 1.0000 100 rpmE 1.0000 100 cds-WP_045857501.1 1.0000 100 cds-WP_052691921.1 1.0000 100 fusA_2 1.0000 100 cds-WP_045857535.1 1.0000 100 cds-WP_162926320.1 1.0000 100 cds-WP_052691926.1 1.0000 100 cds-WP_052691927.1 1.0000 100 cds-WP_045857560.1 1.0000 100 cds-WP_045857569.1 1.0000 100 cds-WP_045857585.1 1.0000 100 cds-WP_052691930.1 1.0000 100 cds-WP_045857588.1 1.0000 100 cds-WP_045857720.1 1.0000 100 cds-WP_045857755.1 1.0000 100 cds-WP_045857797.1 1.0000 100 greA 1.0000 100 nusA 1.0000 100 infB 1.0000 100 rpsO 1.0000 100 nhaR 1.0000 100 rpsU 1.0000 100 cds-WP_045861254.1 1.0000 100 murU 1.0000 100 cds-WP_045858068.1 1.0000 100 fis 1.0000 100 prmA 1.0000 100 cds-WP_045858223.1 1.0000 100 cds-WP_045858246.1 1.0000 100 rnt 1.0000 100 cds-WP_236074861.1 1.0000 100 cds-WP_045858406.1 1.0000 100 cds-WP_045858418.1 1.0000 100 cds-WP_045858432.1 1.0000 100 cds-WP_045858470.1 1.0000 100 greB 1.0000 100 cds-WP_045858501.1 1.0000 100 rpoS 1.0000 100 cds-WP_045858535.1 1.0000 100 cds-WP_045858556.1 1.0000 100 cds-WP_045858583.1 1.0000 100 cds-WP_045858585.1 1.0000 100 cds-WP_045858741.1 1.0000 100 cds-WP_045858767.1 1.0000 100 cds-WP_045858788.1 1.0000 100 pspC 1.0000 100 dnaX 1.0000 100 cds-WP_045858963.1 1.0000 100 cds-WP_045858974.1 1.0000 100 cds-WP_045858993.1 1.0000 100 iscR 1.0000 100 cds-WP_162926391.1 1.0000 100 pspF 1.0000 100 cds-WP_045859278.1 1.0000 100 cds-WP_045859322.1 1.0000 100 scpB 1.0000 100 cds-WP_052692071.1 1.0000 100 cds-WP_045859382.1 1.0000 100 cds-WP_045859431.1 1.0000 100 cds-WP_052692082.1 1.0000 100 cds-WP_045859472.1 1.0000 100 cds-WP_045859486.1 1.0000 100 cds-WP_162926402.1 1.0000 100 dnaQ 1.0000 100 cds-WP_052692096.1 1.0000 100 cds-WP_045859736.1 1.0000 100 cds-WP_045859773.1 1.0000 100 cds-WP_045859830.1 1.0000 100 infA 1.0000 100 mfd 1.0000 100 cds-WP_045859916.1 1.0000 100 lexA 1.0000 100 cysB 1.0000 100 cds-WP_045859992.1 1.0000 100 rpmF 1.0000 100 cds-WP_045860159.1 1.0000 100 cds-WP_052692125.1 1.0000 100 cds-WP_045860208.1 1.0000 100 cds-WP_045860292.1 1.0000 100 cds-WP_045860338.1 1.0000 100 cds-WP_045860340.1 1.0000 100 rplT 1.0000 100 rpmI 1.0000 100 infC 1.0000 100 rpsA 1.0000 100 cds-WP_082087201.1 1.0000 100 cds-WP_045860424.1 1.0000 100 cds-WP_082087105.1 1.0000 100 cds-WP_045860457.1 1.0000 100 rpoE 1.0000 100 rplS 1.0000 100 rpsP 1.0000 100 rho_2 1.0000 100 dnaE 1.0000 100 ilvY 1.0000 100 yciH 1.0000 100 tsf 1.0000 100 rpsB 1.0000 100 cds-WP_045860654.1 1.0000 100 rpsT 1.0000 100 rpmA 1.0000 100 rplU 1.0000 100 rplQ 1.0000 100 cds-WP_045860702.1 1.0000 100 rpsD 1.0000 100 rpsK 1.0000 100 rpsM 1.0000 100 rpmJ 1.0000 100 rplO 1.0000 100 rpmD 1.0000 100 rpsE 1.0000 100 rplR 1.0000 100 rplF 1.0000 100 rpsH 1.0000 100 rpsN 1.0000 100 rplE 1.0000 100 rplX 1.0000 100 rplN 1.0000 100 rpsQ 1.0000 100 rpmC 1.0000 100 rplP 1.0000 100 rpsC 1.0000 100 rplV 1.0000 100 rpsS 1.0000 100 rplB 1.0000 100 rplW 1.0000 100 rplD 1.0000 100 rplC 1.0000 100 rpsJ 1.0000 100 tuf 1.0000 100 fusA_3 1.0000 100 rpsG 1.0000 100 rpsL 1.0000 100 rpoC 1.0000 100 rpoB 1.0000 100 rplL 1.0000 100 rplJ 1.0000 100 rplA 1.0000 100 rplK 1.0000 100 nusG 1.0000 100 cds-WP_052692230.1 1.0000 100 dinB 1.0000 100 rimK_2 1.0000 100 cds-WP_045860848.1 1.0000 100 cds-WP_045861614.1 1.0000 100 cds-WP_052692312.1 1.0000 100 cds-WP_045861829.1 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme script_results/housekeeping.fasta -dna -nmotifs 3 -minw 6 model: mod= zoops nmotifs= 3 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 6 maxw= 50 nsites: minsites= 2 maxsites= 219 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 21900 N= 219 sample: seed= 0 hsfrac= 0 searchsize= 21900 norand= no csites= 1000 Letter frequencies in dataset: A 0.285 C 0.225 G 0.204 T 0.286 Background letter frequencies (from file dataset with add-one prior applied): A 0.285 C 0.225 G 0.204 T 0.286 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GCGCMGGWAWHVBCS MEME-1 width = 15 sites = 14 llr = 169 E-value = 1.2e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGCMGGWAWHVBCS MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::1:41:3a6421:: pos.-specific C 19:75::1::24496 probability G 919319a1::122:4 matrix T :::::::6:43141: bits 2.3 * 2.1 * 1.8 * * * * 1.6 *** ** * * Relative 1.4 **** ** * * Entropy 1.1 **** ** * ** (17.5 bits) 0.9 **** ** ** ** 0.7 ******* ** ** 0.5 ********** ** 0.2 ********** **** 0.0 --------------- Multilevel GCGCCGGTAAACCCC consensus GA A TTAT G sequence CGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCMGGWAWHVBCS MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- cds-WP_045860848.1 76 6.41e-08 TAAATAAGTA GCGCCGGTAAATTCC TACGCTATAA hpaR 86 7.62e-08 CAATGTTAGG GCGCAGGTAAAATCC cds-WP_045860159.1 80 2.74e-07 GGACTTTTAA GCGCAGGTAACAGCG GCGCTT dnaX 53 2.74e-07 TTACCCCTCT GCGCAGGTATAATCG CCTTTTTTCA fusA_2 15 6.48e-07 TCAAAGCGCC GCGCCGGAAATCACG TTCGCCAACG rpmH 1 1.15e-06 . GCGCAGGAAACCCTC ACATGACAAT cds-WP_052691927.1 20 1.37e-06 CCGAAAAGTC GCGGCGGCATTCGCC TAGCGTAAAG rpsM 26 1.63e-06 GCGATAAGAA GCGCGGGAAAGTTCC ACGAACTTAC rplC 25 1.77e-06 GAGACATTAC CCGCCGGTATCGCCC AGGTAGCGGA rpsP 26 2.64e-06 GTAATTTTAT GCGGCGGAAAGCGTC CAGGGGGTTG cds-WP_162926391.1 4 2.64e-06 GGC GGGCCGGGATTCCCG GACGTGTTAT cds-WP_045856963.1 61 2.84e-06 TGCTTGATGC GGGCAAGTAAACCCG TTACTCTCCG rpsJ 28 4.06e-06 TAATCTTAAC GCGGGAGTAAAGTCG GCTGGGTTTA rpoS 22 4.06e-06 CCGAAGGGGG GCAGCGGTATTGCCC AACCTGCTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCMGGWAWHVBCS MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-WP_045860848.1 6.4e-08 75_[+1]_10 hpaR 7.6e-08 85_[+1] cds-WP_045860159.1 2.7e-07 79_[+1]_6 dnaX 2.7e-07 52_[+1]_33 fusA_2 6.5e-07 14_[+1]_71 rpmH 1.1e-06 [+1]_85 cds-WP_052691927.1 1.4e-06 19_[+1]_66 rpsM 1.6e-06 25_[+1]_60 rplC 1.8e-06 24_[+1]_61 rpsP 2.6e-06 25_[+1]_60 cds-WP_162926391.1 2.6e-06 3_[+1]_82 cds-WP_045856963.1 2.8e-06 60_[+1]_25 rpsJ 4.1e-06 27_[+1]_58 rpoS 4.1e-06 21_[+1]_64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCMGGWAWHVBCS MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCGCMGGWAWHVBCS width=15 seqs=14 cds-WP_045860848.1 ( 76) GCGCCGGTAAATTCC 1 hpaR ( 86) GCGCAGGTAAAATCC 1 cds-WP_045860159.1 ( 80) GCGCAGGTAACAGCG 1 dnaX ( 53) GCGCAGGTATAATCG 1 fusA_2 ( 15) GCGCCGGAAATCACG 1 rpmH ( 1) GCGCAGGAAACCCTC 1 cds-WP_052691927.1 ( 20) GCGGCGGCATTCGCC 1 rpsM ( 26) GCGCGGGAAAGTTCC 1 rplC ( 25) CCGCCGGTATCGCCC 1 rpsP ( 26) GCGGCGGAAAGCGTC 1 cds-WP_162926391.1 ( 4) GGGCCGGGATTCCCG 1 cds-WP_045856963.1 ( 61) GGGCAAGTAAACCCG 1 rpsJ ( 28) GCGGGAGTAAAGTCG 1 rpoS ( 22) GCAGCGGTATTGCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCMGGWAWHVBCS MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 18834 bayes= 11.6156 E= 1.2e-001 -1045 -165 219 -1045 -1045 193 -51 -1045 -199 -1045 219 -1045 -1045 167 49 -1045 32 115 -51 -1045 -100 -1045 207 -1045 -1045 -1045 229 -1045 0 -165 -151 100 181 -1045 -1045 -1045 117 -1045 -1045 32 32 -7 -51 0 -41 93 7 -100 -199 67 7 32 -1045 193 -1045 -100 -1045 134 107 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCMGGWAWHVBCS MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 14 E= 1.2e-001 0.000000 0.071429 0.928571 0.000000 0.000000 0.857143 0.142857 0.000000 0.071429 0.000000 0.928571 0.000000 0.000000 0.714286 0.285714 0.000000 0.357143 0.500000 0.142857 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 0.000000 1.000000 0.000000 0.285714 0.071429 0.071429 0.571429 1.000000 0.000000 0.000000 0.000000 0.642857 0.000000 0.000000 0.357143 0.357143 0.214286 0.142857 0.285714 0.214286 0.428571 0.214286 0.142857 0.071429 0.357143 0.214286 0.357143 0.000000 0.857143 0.000000 0.142857 0.000000 0.571429 0.428571 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCMGGWAWHVBCS MEME-1 regular expression -------------------------------------------------------------------------------- GCG[CG][CA]GG[TA]A[AT][ATC][CAG][CTG]C[CG] -------------------------------------------------------------------------------- Time 22.39 secs. ******************************************************************************** ******************************************************************************** MOTIF GCKGCTDBNNMGYCGWSTSSAWWTTCGYC MEME-2 width = 29 sites = 17 llr = 242 E-value = 1.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCKGCTDBNNMGYCGWSTSSAWWTTCGYC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :12:::2132311:2311::545:::1:: pos.-specific C 181:81132241482:5155211::9157 probability G 7138::433325116222441:112:821 matrix T 21522943241242:52512164981:42 bits 2.3 2.1 1.8 * 1.6 * * Relative 1.4 *** * ** Entropy 1.1 * *** * **** (20.6 bits) 0.9 ** *** ** **** * 0.7 ** *** ** ** * **** * 0.5 ** *** * *** ** * ****** 0.2 ******** ******************* 0.0 ----------------------------- Multilevel GCTGCTGCATCGCCGTCTCCATATTCGCC consensus T GTT TGGGATT AGGGGCAT TT sequence TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKGCTDBNNMGYCGWSTSSAWWTTCGYC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------- cds-WP_045856365.1 64 1.18e-13 TGCGGTACGA GCTGTTTGAGCGTCGTCTCGATATTCGCC TCGCGTAG atpG 12 3.92e-09 CATGAATGTC GCTGCTGTAACGCTGGTTCGACTTTCGTC GTGACCTATT rnt 8 8.56e-09 TGATACC GCTGCTCGTCAATCATGGGCATTTTCGTC CGCTTTGCGA rplN 6 2.69e-08 TTTTA GCTTCTTTTTCGCTGTGTTTAAATTCGCT TAGCGGTGCC rplE 58 3.27e-08 AAAAGTTTAG GTTGCCGCTTCGCTAACTGCGTATTCGCC TGACTCACTT cds-WP_045855542.1 7 3.61e-08 CCTGAC GCGGCTTCGGGGGCATCTCCCAGTTCAGC TTTGTTCTTC rpsH 36 4.37e-08 GACGCTACGC GCCGCTGCATGGTCCGGACCATTTTCGGT CAACCATTTA nusB 37 1.31e-07 TGTTATCTTG GCTGTTAACATTCCGGAGGCATATTCGTC TCCTTACTAT greA 12 1.85e-07 GTATGGCATT GCGGTTCGGTAAGCCACTGGATGTGCGTC GTTTACAAGA rplV 62 2.38e-07 CACCGGTACA TCGTCTGTTCTTTCGATTCGCAATTCGCT CCTTATTCTC rpmE 4 2.58e-07 CGC GAAGCTGGAGACCCGAGAGTATTTGCGCC AAGCCACGAA polA 28 2.58e-07 TAATTGCCTT TCGGCCAGCTATTCCTCCGCAAATTCGCT AGAATCCCCT rpsR 38 3.04e-07 GTTGATTTTG GCTTCTTCGCGGACGTCGTCGTCTTCGCG GAAGACTTCT cds-WP_045857227.1 6 5.71e-07 TTCGG GGAGCTTTCTCCCCGAATCGCAATTTGCC GTGACAAGGA rplP 23 6.16e-07 CGCAGCTTCT TCGGCTTCGGCGAGGTTTCTTTTTTCCGC GATTTATTCG rplB 63 7.15e-07 TTCCGAGTCT CTAGCTGAAGCTTCGTCGCCTTATTCCTC GCCTAACAG cds-WP_045855632.1 46 1.47e-06 AACCACAAGC TCTTTTATGAAGCCGTCCCGCATGGCGTC ACGACTCACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKGCTDBNNMGYCGWSTSSAWWTTCGYC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-WP_045856365.1 1.2e-13 63_[+2]_8 atpG 3.9e-09 11_[+2]_60 rnt 8.6e-09 7_[+2]_64 rplN 2.7e-08 5_[+2]_66 rplE 3.3e-08 57_[+2]_14 cds-WP_045855542.1 3.6e-08 6_[+2]_65 rpsH 4.4e-08 35_[+2]_36 nusB 1.3e-07 36_[+2]_35 greA 1.9e-07 11_[+2]_60 rplV 2.4e-07 61_[+2]_10 rpmE 2.6e-07 3_[+2]_68 polA 2.6e-07 27_[+2]_44 rpsR 3e-07 37_[+2]_34 cds-WP_045857227.1 5.7e-07 5_[+2]_66 rplP 6.2e-07 22_[+2]_49 rplB 7.2e-07 62_[+2]_9 cds-WP_045855632.1 1.5e-06 45_[+2]_26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKGCTDBNNMGYCGWSTSSAWWTTCGYC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCKGCTDBNNMGYCGWSTSSAWWTTCGYC width=29 seqs=17 cds-WP_045856365.1 ( 64) GCTGTTTGAGCGTCGTCTCGATATTCGCC 1 atpG ( 12) GCTGCTGTAACGCTGGTTCGACTTTCGTC 1 rnt ( 8) GCTGCTCGTCAATCATGGGCATTTTCGTC 1 rplN ( 6) GCTTCTTTTTCGCTGTGTTTAAATTCGCT 1 rplE ( 58) GTTGCCGCTTCGCTAACTGCGTATTCGCC 1 cds-WP_045855542.1 ( 7) GCGGCTTCGGGGGCATCTCCCAGTTCAGC 1 rpsH ( 36) GCCGCTGCATGGTCCGGACCATTTTCGGT 1 nusB ( 37) GCTGTTAACATTCCGGAGGCATATTCGTC 1 greA ( 12) GCGGTTCGGTAAGCCACTGGATGTGCGTC 1 rplV ( 62) TCGTCTGTTCTTTCGATTCGCAATTCGCT 1 rpmE ( 4) GAAGCTGGAGACCCGAGAGTATTTGCGCC 1 polA ( 28) TCGGCCAGCTATTCCTCCGCAAATTCGCT 1 rpsR ( 38) GCTTCTTCGCGGACGTCGTCGTCTTCGCG 1 cds-WP_045857227.1 ( 6) GGAGCTTTCTCCCCGAATCGCAATTTGCC 1 rplP ( 23) TCGGCTTCGGCGAGGTTTCTTTTTTCCGC 1 rplB ( 63) CTAGCTGAAGCTTCGTCGCCTTATTCCTC 1 cds-WP_045855632.1 ( 46) TCTTTTATGAAGCCGTCCCGCATGGCGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKGCTDBNNMGYCGWSTSSAWWTTCGYC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 15768 bayes= 9.92531 E= 1.4e+001 -1073 -193 179 -28 -227 176 -179 -128 -69 -193 53 72 -1073 -1073 191 -28 -1073 176 -1073 -28 -1073 -93 -1073 163 -69 -93 79 30 -128 39 53 4 4 -35 53 -28 -69 -35 53 30 4 87 -21 -128 -128 -93 138 -28 -128 87 -79 30 -1073 176 -179 -70 -69 -35 167 -1073 4 -1073 -21 89 -128 106 21 -70 -128 -93 21 89 -1073 123 79 -128 -1073 106 79 -70 89 6 -79 -128 31 -193 -1073 104 72 -193 -79 30 -1073 -1073 -179 172 -1073 -1073 -21 153 -1073 206 -1073 -228 -227 -93 201 -1073 -1073 106 -21 30 -1073 165 -179 -28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKGCTDBNNMGYCGWSTSSAWWTTCGYC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 17 E= 1.4e+001 0.000000 0.058824 0.705882 0.235294 0.058824 0.764706 0.058824 0.117647 0.176471 0.058824 0.294118 0.470588 0.000000 0.000000 0.764706 0.235294 0.000000 0.764706 0.000000 0.235294 0.000000 0.117647 0.000000 0.882353 0.176471 0.117647 0.352941 0.352941 0.117647 0.294118 0.294118 0.294118 0.294118 0.176471 0.294118 0.235294 0.176471 0.176471 0.294118 0.352941 0.294118 0.411765 0.176471 0.117647 0.117647 0.117647 0.529412 0.235294 0.117647 0.411765 0.117647 0.352941 0.000000 0.764706 0.058824 0.176471 0.176471 0.176471 0.647059 0.000000 0.294118 0.000000 0.176471 0.529412 0.117647 0.470588 0.235294 0.176471 0.117647 0.117647 0.235294 0.529412 0.000000 0.529412 0.352941 0.117647 0.000000 0.470588 0.352941 0.176471 0.529412 0.235294 0.117647 0.117647 0.352941 0.058824 0.000000 0.588235 0.470588 0.058824 0.117647 0.352941 0.000000 0.000000 0.058824 0.941176 0.000000 0.000000 0.176471 0.823529 0.000000 0.941176 0.000000 0.058824 0.058824 0.117647 0.823529 0.000000 0.000000 0.470588 0.176471 0.352941 0.000000 0.705882 0.058824 0.235294 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKGCTDBNNMGYCGWSTSSAWWTTCGYC MEME-2 regular expression -------------------------------------------------------------------------------- [GT]C[TG][GT][CT]T[GT][CGT][AGT][TG][CA][GT][CT]CG[TA][CG][TG][CG][CG][AC][TA][AT]TTCG[CT][CT] -------------------------------------------------------------------------------- Time 43.76 secs. ******************************************************************************** ******************************************************************************** MOTIF CGVSCACBGCDVDAACGAGHVBGWCGDCGBTTNRACGCAGTCTTNCS MEME-3 width = 47 sites = 4 llr = 155 E-value = 9.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGVSCACBGCDVDAACGAGHVBGWCGDCGBTTNRACGCAGTCTTNCS MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::3::8::::333aa:3a:35:35::5:3::335a:::8:3:::3:: pos.-specific C 83358:83:a:3:::a:::535::8::8:53:3::8:8:::8::385 probability G 38553:338:553:::8:a:338::83:83::35::a3:8:3::3:5 matrix T :::::3:53:3:5::::::3:3:53333:3883::3::338:aa33: bits 2.3 * * 2.1 * * * * 1.8 * *** ** * * ** 1.6 * *** ** * * ** Relative 1.4 ** * * ** ****** * * * * ** * *** Entropy 1.1 ** ** * ** ****** * ** ** * ***** * *** ** (56.1 bits) 0.9 ** **** ** ****** **** ** ** *********** ** 0.7 ******* ** * ****** ***** ***** *********** ** 0.5 ******************************** *********** ** 0.2 ******************************** *********** ** 0.0 ----------------------------------------------- Multilevel CGGCCACTGCGGTAACGAGCACGACGACGCTTAAACGCAGTCTTACC consensus GCAGGTGCT AAA A ACGATTTGTAGCACG T GTTAG CTG sequence C G TCG TGT T T G G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGVSCACBGCDVDAACGAGHVBGWCGDCGBTTNRACGCAGTCTTNCS MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------------------------- cds-WP_045861136.1 47 1.24e-20 GTAAAACCCC GGGCGACGGCGGGAACGAGTCCGTCGGCGTTTGGATGCAGTCTTCCC CTTATGG rplD 30 2.31e-18 ACCACGAGGG CCACCACTGCACTAACAAGCAGGACGACAGTTCGACGCATTGTTGCC AATTCATAGG rpmC 27 5.66e-18 GCTTCTCAAC CGCGCTCTTCGAAAACGAGAACGACGACGCTTTAACGGTGACTTATG TTGAAAACAA rpsQ 14 1.84e-17 CTACTTCGTT CGGGCAGCGCTGTAACGAGCGTATTTTTGCCAAAACGCAGTCTTTCG CAGGTGGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGVSCACBGCDVDAACGAGHVBGWCGDCGBTTNRACGCAGTCTTNCS MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-WP_045861136.1 1.2e-20 46_[+3]_7 rplD 2.3e-18 29_[+3]_24 rpmC 5.7e-18 26_[+3]_27 rpsQ 1.8e-17 13_[+3]_40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGVSCACBGCDVDAACGAGHVBGWCGDCGBTTNRACGCAGTCTTNCS MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGVSCACBGCDVDAACGAGHVBGWCGDCGBTTNRACGCAGTCTTNCS width=47 seqs=4 cds-WP_045861136.1 ( 47) GGGCGACGGCGGGAACGAGTCCGTCGGCGTTTGGATGCAGTCTTCCC 1 rplD ( 30) CCACCACTGCACTAACAAGCAGGACGACAGTTCGACGCATTGTTGCC 1 rpmC ( 27) CGCGCTCTTCGAAAACGAGAACGACGACGCTTTAACGGTGACTTATG 1 rpsQ ( 14) CGGGCAGCGCTGTAACGAGCGTATTTTTGCCAAAACGCAGTCTTTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGVSCACBGCDVDAACGAGHVBGWCGDCGBTTNRACGCAGTCTTNCS MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 47 n= 11826 bayes= 11.5292 E= 9.6e+001 -865 173 29 -865 -865 15 188 -865 -19 15 129 -865 -865 115 129 -865 -865 173 29 -865 139 -865 -865 -19 -865 173 29 -865 -865 15 29 80 -865 -865 188 -19 -865 215 -865 -865 -19 -865 129 -19 -19 15 129 -865 -19 -865 29 80 181 -865 -865 -865 181 -865 -865 -865 -865 215 -865 -865 -19 -865 188 -865 181 -865 -865 -865 -865 -865 229 -865 -19 115 -865 -19 81 15 29 -865 -865 115 29 -19 -19 -865 188 -865 81 -865 -865 80 -865 173 -865 -19 -865 -865 188 -19 81 -865 29 -19 -865 173 -865 -19 -19 -865 188 -865 -865 115 29 -19 -865 15 -865 139 -19 -865 -865 139 -19 15 29 -19 81 -865 129 -865 181 -865 -865 -865 -865 173 -865 -19 -865 -865 229 -865 -865 173 29 -865 139 -865 -865 -19 -865 -865 188 -19 -19 -865 -865 139 -865 173 29 -865 -865 -865 -865 180 -865 -865 -865 180 -19 15 29 -19 -865 173 -865 -19 -865 115 129 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGVSCACBGCDVDAACGAGHVBGWCGDCGBTTNRACGCAGTCTTNCS MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 47 nsites= 4 E= 9.6e+001 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.500000 0.250000 0.250000 0.250000 0.500000 0.000000 0.250000 0.000000 0.250000 0.500000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.500000 0.000000 0.250000 0.500000 0.250000 0.250000 0.000000 0.000000 0.500000 0.250000 0.250000 0.250000 0.000000 0.750000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 0.500000 0.000000 0.250000 0.250000 0.000000 0.750000 0.000000 0.250000 0.250000 0.000000 0.750000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.250000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.250000 0.250000 0.250000 0.250000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 0.250000 0.000000 0.000000 0.750000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.250000 0.250000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGVSCACBGCDVDAACGAGHVBGWCGDCGBTTNRACGCAGTCTTNCS MEME-3 regular expression -------------------------------------------------------------------------------- [CG][GC][GAC][CG][CG][AT][CG][TCG][GT]C[GAT][GAC][TAG]AAC[GA]AG[CAT][ACG][CGT][GA][AT][CT][GT][AGT][CT][GA][CGT][TC][TA][ACGT][AG]A[CT]G[CG][AT][GT][TA][CG]TT[ACGT][CT][CG] -------------------------------------------------------------------------------- Time 64.47 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-WP_045855524.1 9.10e-01 100 cds-WP_045855526.1 2.29e-01 100 cds-WP_045855542.1 6.91e-06 6_[+2(3.61e-08)]_65 efp 2.43e-01 100 rplI 3.83e-01 100 rpsR 2.07e-05 37_[+2(3.04e-07)]_34 rpsF 3.53e-01 100 cds-WP_045855573.1 6.46e-01 100 cds-WP_045855582.1 2.23e-01 100 rpoD 6.36e-01 100 cds-WP_045855632.1 2.00e-04 45_[+2(1.47e-06)]_26 cds-WP_052691783.1 8.61e-01 100 cds-WP_052691784.1 3.79e-02 100 cds-WP_045855636.1 7.32e-01 100 fusA 8.86e-01 100 cds-WP_045855668.1 8.99e-01 100 pcnB 1.24e-01 100 cds-WP_045855789.1 5.45e-01 100 cds-WP_052691813.1 1.18e-01 100 cds-WP_045855857.1 9.52e-01 100 cds-WP_045855936.1 5.14e-01 100 gshB 8.13e-01 100 cds-WP_045856028.1 5.32e-01 100 rho 9.64e-01 100 slmA 8.12e-01 100 rpmB 8.83e-02 100 rpmG 1.93e-01 100 rpoZ 5.58e-01 100 cds-WP_045856103.1 9.84e-01 100 cds-WP_045856109.1 6.60e-01 100 cds-WP_045856119.1 6.55e-01 100 cds-WP_045856218.1 8.44e-02 100 cds-WP_045856238.1 4.57e-01 100 cds-WP_045861029.1 7.20e-01 100 cds-WP_045856357.1 3.54e-01 100 atpD 6.28e-01 100 atpG 5.98e-06 11_[+2(3.92e-09)]_60 atpA 1.35e-01 100 cds-WP_045856365.1 5.35e-10 63_[+2(1.18e-13)]_8 cds-WP_045856368.1 2.23e-01 100 atpE 5.75e-01 100 atpB 6.45e-01 100 cds-WP_045856374.1 4.93e-02 100 cds-WP_045856380.1 5.53e-01 100 rpmH 1.26e-03 [+1(1.15e-06)]_85 dnaN 5.68e-01 100 cds-WP_045856454.1 7.44e-02 100 polA 3.51e-04 27_[+2(2.58e-07)]_44 cds-WP_045856570.1 9.87e-01 100 cds-WP_082087156.1 9.37e-01 100 cds-WP_052691868.1 5.46e-01 100 cds-WP_045856653.1 6.47e-01 100 cds-WP_045856744.1 7.29e-01 100 rpoH 5.86e-01 100 hpaR 2.21e-04 85_[+1(7.62e-08)] cds-WP_045856936.1 3.99e-01 100 cds-WP_045856963.1 5.27e-03 60_[+1(2.84e-06)]_25 cds-WP_121495355.1 9.67e-01 100 cds-WP_045857004.1 2.84e-01 100 rimK 3.35e-01 100 nrdR 7.91e-02 100 nusB 9.91e-09 36_[+2(1.31e-07)]_35 cds-WP_045857096.1 5.48e-01 100 holA 2.26e-01 100 cds-WP_045861136.1 1.42e-18 46_[+3(1.24e-20)]_7 ychF 4.00e-01 100 cds-WP_045857227.1 2.43e-04 5_[+2(5.71e-07)]_66 cds-WP_052691908.1 7.26e-01 100 cds-WP_045857303.1 4.00e-01 100 cds-WP_045861159.1 3.76e-01 100 rplM 9.72e-03 100 rpsI 4.82e-01 100 rpmE 9.58e-06 3_[+2(2.58e-07)]_68 cds-WP_045857501.1 4.53e-02 [+1(2.25e-05)]_85 cds-WP_052691921.1 8.37e-01 100 fusA_2 3.05e-04 14_[+1(6.48e-07)]_71 cds-WP_045857535.1 8.12e-01 100 cds-WP_162926320.1 8.82e-01 100 cds-WP_052691926.1 1.02e-01 100 cds-WP_052691927.1 1.46e-04 19_[+1(1.37e-06)]_66 cds-WP_045857560.1 2.09e-01 100 cds-WP_045857569.1 2.39e-01 100 cds-WP_045857585.1 4.80e-01 100 cds-WP_052691930.1 9.15e-01 100 cds-WP_045857588.1 5.76e-01 100 cds-WP_045857720.1 2.68e-01 100 cds-WP_045857755.1 1.99e-01 100 cds-WP_045857797.1 5.98e-01 100 greA 1.96e-04 11_[+2(1.85e-07)]_60 nusA 3.95e-01 100 infB 7.30e-01 100 rpsO 1.01e-01 100 nhaR 1.19e-01 100 rpsU 3.23e-01 100 cds-WP_045861254.1 5.79e-01 100 murU 1.77e-01 100 cds-WP_045858068.1 5.84e-01 100 fis 8.72e-02 100 prmA 2.72e-01 100 cds-WP_045858223.1 7.64e-01 100 cds-WP_045858246.1 5.36e-01 100 rnt 1.93e-06 7_[+2(8.56e-09)]_64 cds-WP_236074861.1 2.37e-01 100 cds-WP_045858406.1 8.91e-01 100 cds-WP_045858418.1 4.09e-01 100 cds-WP_045858432.1 4.46e-01 100 cds-WP_045858470.1 7.91e-01 100 greB 8.59e-01 100 cds-WP_045858501.1 2.09e-01 100 rpoS 3.03e-03 21_[+1(4.06e-06)]_64 cds-WP_045858535.1 7.53e-01 100 cds-WP_045858556.1 4.59e-01 100 cds-WP_045858583.1 9.83e-01 100 cds-WP_045858585.1 9.99e-01 100 cds-WP_045858741.1 5.28e-01 100 cds-WP_045858767.1 5.39e-01 100 cds-WP_045858788.1 9.18e-01 100 pspC 7.63e-01 100 dnaX 1.48e-04 52_[+1(2.74e-07)]_33 cds-WP_045858963.1 2.50e-01 100 cds-WP_045858974.1 4.30e-01 100 cds-WP_045858993.1 2.28e-02 100 iscR 9.89e-01 100 cds-WP_162926391.1 3.35e-03 3_[+1(2.64e-06)]_82 pspF 1.85e-02 100 cds-WP_045859278.1 9.87e-01 100 cds-WP_045859322.1 3.92e-02 100 scpB 1.74e-01 100 cds-WP_052692071.1 1.06e-01 100 cds-WP_045859382.1 1.65e-01 100 cds-WP_045859431.1 7.62e-01 100 cds-WP_052692082.1 9.77e-01 100 cds-WP_045859472.1 5.80e-01 100 cds-WP_045859486.1 6.75e-01 100 cds-WP_162926402.1 2.24e-01 100 dnaQ 1.28e-01 100 cds-WP_052692096.1 4.79e-01 100 cds-WP_045859736.1 3.93e-01 100 cds-WP_045859773.1 2.34e-01 100 cds-WP_045859830.1 6.52e-01 100 infA 4.58e-01 100 mfd 9.20e-01 100 cds-WP_045859916.1 8.18e-01 100 lexA 9.08e-01 100 cysB 2.27e-02 100 cds-WP_045859992.1 7.61e-01 100 rpmF 4.06e-01 100 cds-WP_045860159.1 8.82e-04 79_[+1(2.74e-07)]_6 cds-WP_052692125.1 8.79e-01 100 cds-WP_045860208.1 9.17e-01 100 cds-WP_045860292.1 3.20e-01 100 cds-WP_045860338.1 9.53e-01 100 cds-WP_045860340.1 9.74e-01 100 rplT 8.99e-01 100 rpmI 8.25e-01 100 infC 3.27e-02 100 rpsA 4.87e-01 100 cds-WP_082087201.1 4.44e-01 100 cds-WP_045860424.1 1.28e-01 100 cds-WP_082087105.1 3.23e-01 100 cds-WP_045860457.1 8.62e-01 100 rpoE 7.86e-01 100 rplS 5.09e-01 100 rpsP 4.22e-03 25_[+1(2.64e-06)]_60 rho_2 4.99e-01 100 dnaE 5.84e-01 100 ilvY 8.59e-01 100 yciH 8.04e-01 100 tsf 3.54e-01 100 rpsB 7.87e-01 100 cds-WP_045860654.1 6.77e-01 100 rpsT 8.00e-02 100 rpmA 1.64e-01 100 rplU 8.93e-01 100 rplQ 7.51e-01 100 cds-WP_045860702.1 7.48e-01 100 rpsD 3.22e-01 100 rpsK 1.24e-01 100 rpsM 2.28e-03 25_[+1(1.63e-06)]_60 rpmJ 7.71e-01 100 rplO 6.44e-01 100 rpmD 2.00e-01 100 rpsE 7.80e-01 100 rplR 5.09e-02 100 rplF 7.54e-01 100 rpsH 1.92e-06 35_[+2(4.37e-08)]_36 rpsN 5.89e-01 100 rplE 4.89e-05 57_[+2(3.27e-08)]_14 rplX 8.68e-01 100 rplN 3.31e-05 5_[+2(2.69e-08)]_66 rpsQ 6.09e-14 13_[+3(1.84e-17)]_40 rpmC 1.47e-13 26_[+3(5.66e-18)]_27 rplP 3.82e-04 22_[+2(6.16e-07)]_49 rpsC 2.68e-01 100 rplV 8.32e-05 61_[+2(2.38e-07)]_10 rpsS 1.76e-01 100 rplB 3.36e-04 62_[+2(7.15e-07)]_9 rplW 7.78e-01 100 rplD 1.86e-14 29_[+3(2.31e-18)]_24 rplC 3.04e-03 24_[+1(1.77e-06)]_61 rpsJ 7.58e-03 27_[+1(4.06e-06)]_58 tuf 1.48e-01 100 fusA_3 9.58e-01 100 rpsG 8.49e-01 100 rpsL 2.63e-01 100 rpoC 5.92e-01 100 rpoB 3.25e-02 100 rplL 9.22e-01 100 rplJ 6.78e-01 100 rplA 1.87e-01 100 rplK 3.10e-01 100 nusG 9.13e-01 100 cds-WP_052692230.1 2.39e-01 100 dinB 5.44e-01 100 rimK_2 5.27e-01 100 cds-WP_045860848.1 1.74e-04 75_[+1(6.41e-08)]_10 cds-WP_045861614.1 8.44e-02 100 cds-WP_052692312.1 8.38e-01 100 cds-WP_045861829.1 7.98e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************