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 - | downstream |
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 PF1934 PF1935 PF1936 PF1937 PF1938 | putative sugar transport ATP-hydrolyzing hypothetical protein amylopullulanase 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 | Â | Â |
singleton | PF2016 | preprotein translocase subunit SecG | - | downstream |
singleton | PF2047 | l-asparaginase | - | upstream |