this file provides the visual data that relates to the analysis of the upstream regions that were...
TRANSCRIPT
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
Fuchs et al. Nat. Struct. Mol. Biol. 2006 13:226
N(x)SMK-box(metK)
complement complement
Distance varies considerably from 50-350! nucleotides
S. agalactiaeS. agalactiaeS. dysgalactiaeS. dysgalactiaeS. equiS. equiS. gallolyticusS. gallolyticusS. gordoniS. gordoniS. mitisS. mitisS. mutansS. mutansS. oralisS. oralisS. parasanguinisS. parasanguinisS. parauberisS. parauberisS. pasteurianisS. pasteurianisS. pneumoniaeS. pneumoniaeS. pyogenesS. pyogenesS. salivariusS. salivariusS. sanguinisS. sanguinisS. suisS. suis
S thermophilus CNRZS thermophilus CNRZS thermophilusS thermophilusS. uberisS. uberis
E. faecalisE. faecalisL. acidophilusL. acidophilusL. brevis
L. caseiL. caseiL. crispatusL. crispatusL. delbrueckiiL. delbrueckiiL. fermentumL. fermentuml. gasseril. gasseriL. helveticusL. helveticusL. johnsoniiL. johnsoniiL. plantarumL. plantarumL. reuteriL. reuteriL. rhamnosusL. rhamnosusL. sakeiL. sakeiL. salivariusL. salivariusL. lactisL. lactis
L. mesenteroidesP. pentosaceusP. pentosaceusS. agalactiaeS. agalactiaeS. dysgalactiaeS. dysgalactiae
MetK upstream (streptococci)stArt
Smk boxlysR-fam
Streptococcus gordoni, sanguinis, parasanguinis, agalactiae, oralis, pneumoniae
Streptococcus
Streptococcus pasteurianis, suis, pyogenes, gallolyticus, mitis, mutans, dysgalactiae >300 bp
Streptococcus parauberis, uberis, thermophilus, equi, Lactococcus lactis
50-100
100-250
Lactobacillus crispatus, helveticus, acidophilus, delbrueckii, johnsonii, gasseri
Smk box
Rest of the upstream region highly conserved and almost palindromic
Lactobacillus
Smk box
Lactobacillus fermentum, pediococcus pentosaceus, L. salivarius, casei, rhamnosus, sakei
Smk box
Lactobacillus brevis, reuteri, acidophilus, Enterococcus faecalis, L. plantarum
CmbR
CmbR
Motif definition
Earlier analysis in Sperandio et al. 2010 J. Bacteriol. 192:3464-3473 and Kovaleva and Gelfand 2007 FEMS Microbiol Lett. 276:207-215
ATA-N9-TAT N6 ATA-N9-TAT start
>SMU.496_cysK_/106-127GTGATATGATTTCCTTATCACG>SUB1379_cysM_/97-122ATGATAAGCCTTTCCTATCACG>GALLO_0500_cysK_/98-119GTGATAGTATTTTTTTATCACC>SPs0499/86-111GTGATATGGCTTTATTATCAGA>SEQ_1768/89-114GTGATAGCGTCTCTTTATCACT>SDEG_1685_cysM_/94-119GTGATAGAACTTTATTATCAGA>SGO_0606_cysK_/105-127GATATAAAAAAAAGCTATGATA>SSA_1839_cysK_/102-124GACATAAAGAAAAGCTATGGCT>SAG0334_cysK_/100-125CCGATAAATAATAGCTATCACT>SSU0391_cysM_/106-129TCTATTAAAAAAAGCTATCGGC>str0366_cysM1_/97-121CTGATAGTCAAACATTATCACA>spr2015_cycK_/106-128GATATATAGAAATCCTATCGCT>smi_2060_cysK_/106-128GATATAAAAAAATCCTATCACT
>SMU.496_cysK_/128-148GTGATAAATAATTTATATTTT>SUB1379_cysM_/123-143CCAATAAGATTAAACTATTTT>GALLO_0500_cysK_/120-140TTGATAAGAAATATGTATTTT>SPs0499/112-132GTGATAGTAAATCTGTATTTT>SEQ_1768/115-135ACGATAGTAAATGGCTATTTT>SDEG_1685_cysM_/120-140GTGATAGTAAATCTGTATTTT>SGO_0606_cysK_/128-148GCCATAGCTTTTTTATATTTT>SSA_1839_cysK_/125-145CTCATAGCTTTTTTATATTTT>SAG0334_cysK_/126-145-TGATAAAGAATTGATATTTT>SSU0391_cysM_/130-150GAGATAGTTTTTTTATATTAT>str0366_cysM1_/122-142GTGATAAAGAAGATGTATTTT>spr2015_cycK_/129-149TCGATAGGATTTCTATATTTT>smi_2060_cysK_/129-149TCGATAGGATTTCTATATTTT
CysK upstream
cysK upstream
HomR
HomR motif
>1GTCATAAATAAAATTTATAGC>2CTTATAGTTTCTTTTTATAGC>3GATATAGTTTTTTCTTATAGC>4GTTATAGAAATAAACTATAAC>5GTTATAGTAATAAACTATATC
First palindrome of set taken from Sperandio et al. 2010 J. Bacteriol. 192:3464-3473
metBC upstream
HomR
MetR/MtaR
MetR/MtaR
metE and metH motif 2 in MEME search
>SP_0585ATAGTTTCAAACTAT>SOR_1524ATAGTTTCAAACTAT>gbs2005ATAGTTTAAAACTAT>stu0785ATAGTTTAAAACTAT>SMU.873ATAGCTTAAAACTAT>SSA_0416ATAGTTTTAGACTAT>SGGBAA2069_c13050ATAGTTAAAAACTAT>GALLO_1316ATAGCTAAAAACTAT>L0100ATAGTTTAAAACTAT>llmg_1225ATAGTTAAAAACTAT>SSU1814ATAGTTTGAAGCTAT>stu0583_1ATAGTTTCAACCTAT>GALLO_1253_1ATAGTTTTTAACTAA>SMU.951_1ATAGTCTCTAACTAA
metEmetH
Earlier definition in Rodionov et al. 2004 Nucleic Acid Res. 32:3342-3353
metE upstream
metH upstream
L.lactis
S. suis
S. agalactiae
mmuP not in Streptococcus_sanguinis_SK36
metEyitJ
metE upstream
mmuP upstream
Upstream CysK in Lactobacilli
Cbs, cblStructure forming? No additional hits found using motif: AAGGGCGCGAA
Plasmid encodedhighly conserved
Structure forming? No additional hits found using motif: AAGGGCGCGAA
Upstream Thr divergon in Lactobacilli
Thr divergon in Lactobacilli
Analyzed region