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