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SMS_searchinput_motifs.xls

This file provides the visual data that relates to the analysis of the upstream regions that were used to define the regulator specific motifs given in file:. SMS_searchinput_motifs.xls. Smk-box. Smk analysis. S MK -box ( metK ). N(x). complement. complement.

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SMS_searchinput_motifs.xls

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  1. This file provides the visual data that relates to the analysis of the upstream regions that were used to define the regulator specific motifs given in file: SMS_searchinput_motifs.xls

  2. Smk-box

  3. Smk analysis SMK-box (metK) N(x) complement complement Distance varies considerably from 50-350! nucleotides Fuchs et al. Nat. Struct. Mol. Biol. 2006 13:226

  4. stArt MetK upstream (streptococci)

  5. Streptococcus Streptococcus gordoni, sanguinis, parasanguinis, agalactiae, oralis, pneumoniae lysR-fam Smk box 50-100 Streptococcus parauberis, uberis, thermophilus, equi, Lactococcus lactis 100-250 Streptococcus pasteurianis, suis, pyogenes, gallolyticus, mitis, mutans, dysgalactiae >300 bp

  6. Lactobacillus Lactobacillus crispatus, helveticus, acidophilus, delbrueckii, johnsonii, gasseri Smk box Rest of the upstream region highly conserved and almost palindromic

  7. Lactobacillus fermentum, pediococcus pentosaceus, L. salivarius, casei, rhamnosus, sakei Smk box Lactobacillus brevis, reuteri, acidophilus, Enterococcus faecalis, L. plantarum Smk box

  8. CmbR

  9. CmbR Earlier analysis in Sperandio et al. 2010 J. Bacteriol. 192:3464-3473 and Kovaleva and Gelfand 2007 FEMS Microbiol Lett. 276:207-215 Motif definition

  10. CysK upstream ATA-N9-TAT N6 ATA-N9-TAT start >SMU.496_cysK_/106-127 GTGATATGATTTCCTTATCACG >SUB1379_cysM_/97-122 ATGATAAGCCTTTCCTATCACG >GALLO_0500_cysK_/98-119 GTGATAGTATTTTTTTATCACC >SPs0499/86-111 GTGATATGGCTTTATTATCAGA >SEQ_1768/89-114 GTGATAGCGTCTCTTTATCACT >SDEG_1685_cysM_/94-119 GTGATAGAACTTTATTATCAGA >SGO_0606_cysK_/105-127 GATATAAAAAAAAGCTATGATA >SSA_1839_cysK_/102-124 GACATAAAGAAAAGCTATGGCT >SAG0334_cysK_/100-125 CCGATAAATAATAGCTATCACT >SSU0391_cysM_/106-129 TCTATTAAAAAAAGCTATCGGC >str0366_cysM1_/97-121 CTGATAGTCAAACATTATCACA >spr2015_cycK_/106-128 GATATATAGAAATCCTATCGCT >smi_2060_cysK_/106-128 GATATAAAAAAATCCTATCACT >SMU.496_cysK_/128-148 GTGATAAATAATTTATATTTT >SUB1379_cysM_/123-143 CCAATAAGATTAAACTATTTT >GALLO_0500_cysK_/120-140 TTGATAAGAAATATGTATTTT >SPs0499/112-132 GTGATAGTAAATCTGTATTTT >SEQ_1768/115-135 ACGATAGTAAATGGCTATTTT >SDEG_1685_cysM_/120-140 GTGATAGTAAATCTGTATTTT >SGO_0606_cysK_/128-148 GCCATAGCTTTTTTATATTTT >SSA_1839_cysK_/125-145 CTCATAGCTTTTTTATATTTT >SAG0334_cysK_/126-145 -TGATAAAGAATTGATATTTT >SSU0391_cysM_/130-150 GAGATAGTTTTTTTATATTAT >str0366_cysM1_/122-142 GTGATAAAGAAGATGTATTTT >spr2015_cycK_/129-149 TCGATAGGATTTCTATATTTT >smi_2060_cysK_/129-149 TCGATAGGATTTCTATATTTT

  11. cysK upstream

  12. HomR

  13. HomR motif First palindrome of set taken from Sperandio et al. 2010 J. Bacteriol. 192:3464-3473 >1 GTCATAAATAAAATTTATAGC >2 CTTATAGTTTCTTTTTATAGC >3 GATATAGTTTTTTCTTATAGC >4 GTTATAGAAATAAACTATAAC >5 GTTATAGTAATAAACTATATC

  14. metBC upstream HomR

  15. MetR/MtaR

  16. MetR/MtaR Earlier definition in Rodionov et al. 2004 Nucleic Acid Res. 32:3342-3353 metE and metH motif 2 in MEME search >SP_0585 ATAGTTTCAAACTAT >SOR_1524 ATAGTTTCAAACTAT >gbs2005 ATAGTTTAAAACTAT >stu0785 ATAGTTTAAAACTAT >SMU.873 ATAGCTTAAAACTAT >SSA_0416 ATAGTTTTAGACTAT >SGGBAA2069_c13050 ATAGTTAAAAACTAT >GALLO_1316 ATAGCTAAAAACTAT >L0100 ATAGTTTAAAACTAT >llmg_1225 ATAGTTAAAAACTAT >SSU1814 ATAGTTTGAAGCTAT >stu0583_1 ATAGTTTCAACCTAT >GALLO_1253_1 ATAGTTTTTAACTAA >SMU.951_1 ATAGTCTCTAACTAA metE metH

  17. metE upstream L.lactis S. agalactiae yitJ metE metH upstream S. suis mmuP not in Streptococcus_sanguinis_SK36

  18. metE upstream

  19. mmuP upstream

  20. Upstream CysK in Lactobacilli

  21. Cbs, cbl Structure forming? No additional hits found using motif: AAGGGCGCGAA Plasmid encoded highly conserved

  22. Structure forming? No additional hits found using motif: AAGGGCGCGAA

  23. Upstream Thr divergon in Lactobacilli

  24. Thr divergon in Lactobacilli Analyzed region

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