Curation Information

Publication
Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species.;Ueki T, Lovley DR;Nucleic acids research 2010 Jan; 38(3):810-21 [19939938]
TF
HgtR [Q747A3, view regulon]
Reported TF sp.
Geobacter sulfurreducens strain DL1
Reported site sp.
Geobacter sulfurreducens strain DL1
Created by
Erill Lab
Curation notes
-

Experimental Process

Electron source-dependent expression verified by primer extension. Sites identified through MSA with other known HgtR sites.

Transcription Factor Binding Sites


AAATTGTATACAGTATCCATTT
CTTTTGTATACTGTATACAAAC
AAGTTGTATACAGTATGTGCTA
ATGCAGTATACTGTATGCGAAA
GTTTAGTATACAGTATACAGTA
CCGCCGTATACTGTATACACTT
AGATTGTATACAGTATGCGATC
ATAGTGCATACTGTATACACTT
TTATTGTATACAGTATACAGGG
AAATTGTATACAGTATCCATTT
CTTTTGTATACTGTATACAAAC
AAGTTGTATACAGTATGTGCTA
ATGCAGTATACTGTATGCGAAA
GTTTAGTATACAGTATACAGTA
CCGCCGTATACTGTATACACTT
AGATTGTATACAGTATGCGATC
ATAGTGCATACTGTATACACTT
TTATTGTATACAGTATACAGGG

Gene Regulation

Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence Regulated genes Gene diagram Experimental techniques TF function TF type
AAATTGTATACAGTATCCATTT acnB,
... ... acnB hisS GSU1658 GSU1657 GSU1661 GSU1662
Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) - repressor not specified
CTTTTGTATACTGTATACAAAC icd,
... ... icd GSU1464 aspS mdh
Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) - repressor not specified
AAGTTGTATACAGTATGTGCTA korD, korA, korB, korC,
... ... korD korA korB korC mdh icd
Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) - repressor not specified
ATGCAGTATACTGTATGCGAAA ato-1,
... ... ato-1 comM trxB rhlE-1
Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) - repressor not specified
GTTTAGTATACAGTATACAGTA frdC, frdA, frdB,
... ... frdC frdA frdB tgt-1 mazG
Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) - repressor not specified
CCGCCGTATACTGTATACACTT fumB,
... ... fumB GSU0993 GSU0992 GSU0991 GSU0990 GSU0989 GSU0988 GSU0987 GSU0986 GSU0985 GSU0996 mutM dnaB lpxA-2 GSU1000
Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) - repressor not specified
AGATTGTATACAGTATGCGATC GSU0385,
... ... GSU0385 GSU0384 GSU0383 GSU0382 GSU0381 lipA lplA gcvP2 gcvP1 gcvH-1 gcvT hypA GSU0386 uppP
Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) - repressor not specified
ATAGTGCATACTGTATACACTT sfrB, sfrA,
... ... sfrB sfrA yceG plsY GSU0506 GSU0505 GSU0504 crcB GSU0502 yfiO typA GSU0511 GSU0512 GSU0513 GSU0514
Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) - repressor not specified
TTATTGTATACAGTATACAGGG GSU3370,
... ... GSU3370 GSU3371 cls-2
Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) - repressor not specified