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Table 1 Selected known, predicted and novel TrmBL1 binding sites identified by ChIP-seq and corresponding genes

From: Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus

Known and predicted TrmBL1 binding sites found by ChIP-Seq
Transcript organisation Gene Gene product (Refseq) Additional information Position TGM relative to the promoter elements
operon PF0132PF0133 hypothetical protein
hypothetical protein
putative isomaltase
singleton PF0196 glucose-6-phosphate isomerase - downstream
singleton PF0272 alpha-amylase - downstream
singleton PF0464 glyceraldehyde-3-phosphate: ferredoxin oxidoreductase - downstream
singleton PF0477 alpha-amylase cytoplasmatic upstream
singleton PF0478 alpha-amylase - downstream
singleton PF0588 phospho-sugar mutase - downstream
operon PF1109 hypothetical protein one gene product: extracellular starch-binding protein downstream
operon PF1110 hypothetical protein
singleton PF1784 ADP-specific phosphofructokinase - downstream
singleton PF1874 glyceraldehyde-3-phosphate dehydrogenase - upstream
singleton PF1920 triosephosphate isomerase - downstream
operon PF1933
putative sugar transport ATP-hydrolyzing
hypothetical protein
malG-like sugar transport
inner membrane protein
malF-like sugar transport
inner membrane protein
malE-like sugar binding protein
MD system downstream
singleton PF1956 fructose-bisphosphate aldolase - downstream
singleton PF1959 cofactor-independent phosphoglycerate mutase - downstream
Novel TrmBL1 binding sites found by ChIP-Seq
singleton PF0287 pyrolysin - upstream
singleton PF0505 hypothetical protein predicted DNA binding protein upstream
operon PF0735 hypothetical protein - upstream
PF0736 hypothetical protein
singleton PF0853 5'-methylthioadenosine phosphorylase - downstream
operon PF0874 membrane dipeptidase - downstream
PF0875 hypothetical protein -
operon PF0965 pyruvate-ferredoxin oxidoreductase subunit beta operon PF0971 to PF0965 downstream
PF0966 pyruvate-ferredoxin oxidoreductase subunit alpha
PF0967 pyruvate-ferredoxin oxidoreductase subunit delta
singleton PF1025 hypothetical protein conserved downstream
singleton PF1062 hypothetical protein - upstream
singleton PF1085.1n hypothetical protein - downstream
singleton PF1350 major facilitator superfamily protein transporter downstream
singleton PF1476 hypothetical protein predicted transcriptional regulator: PadR family downstream
operon PF1535 alpha-glucan phosphorylase same promoter region downstream
PF1536 hypothetical protein
PF1537 hypothetical protein
PF1538 N-ethylammeline chlorohydrolase
singleton PF1539 dihydroorotate dehydrogenase 1B   
singleton PF2016 preprotein translocase subunit SecG - downstream
singleton PF2047 l-asparaginase - upstream
  1. Genes containing a TrmBL1 binding site in their promoter region are depicted in bold