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GlaR DNA-binding transcriptional repressor

Synonyms: GlaR-glutarate, GlaR
Summary:
The transcription factor CsiR, for "Carbon starvation induced Regulator," was initially identified as a repressor that controls the transcription of genes involved in the degradation and transport of 4-aminobutyrate (GABA) for utilization as a source of nitrogen [2, 4, 5]. However, CsiR does not appear to respond directly to the presence of GABA [5], and later reports suggested that it does not affect expression of gabDTP [2, 3]. CsiR represses transcription from the csiD promoter during stationary phase [2]. Currently, no DNA-binding sites for this regulator have been reported in the literature [2]. csiR expression is induced at stationary phase, but is not autoregulated and not dependent on σS [2]. A csiR mutant (gabC1) has the ability to utilize γ-aminobutyrate (GABA) as the sole source of nitrogen [5, 6, 7, 8]. In an experiment using directed cell evolution of a ΔpanD mutant (containing a damaged CoA biosynthesis pathway), a pathway for β-alanine biosynthesis via uracil degradation emerged.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
GlaR Functional   Apo nd nd nd
GlaR-glutarate Non-Functional   Holo nd nd nd
Evolutionary Family: GntR
TFBs length: 13
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: glaR
  Genome position: 2795674-2796336
  Length: 663 bp / 220 aa
Operon name: glaR
TU(s) encoding the TF:
Transcription unit        Promoter
CsiR
 


Regulon       
Regulated gene(s) gabD, gabP, gabT, glaH, lhgD
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
aminobutyrate catabolism (2)
putrescine catabolism (2)
amino acids (2)
carbon compounds (1)
Porters (Uni-, Sym- and Antiporters) (1)
Regulated operon(s) glaH-lhgD-gabDTP
First gene in the operon(s) glaH
Simple and complex regulons CRP,GlaR,H-NS,Lrp,ppGpp
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[GlaR,-](1)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  GlaR repressor csiDp Sigma38 -32.0 -90.0 glaH, lhgD, gabD, gabT, gabP
tatgtcgcttTTGTGCGCATTTTTcagaaatgta
 2788889 2788902 [EXP-IEP], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2]
  GlaR repressor csiDp Sigma38 -13.0 -71.0 glaH, lhgD, gabD, gabT, gabP
tttttcagaaATGTAGATATTTTTagattatggc
 2788908 2788921 [EXP-IEP], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2], [3], [3]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  GlaR activator pliG Gene nd
acttaatttgAATATCGACGTTATATtttttagttt
1227083 1227098 1227090.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator ydfK Gene nd
aaactgttatCTATGTATACTTTTAAacccaatccg
1632674 1632689 1632681.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator ydeO Gene nd
atgttagtgcATTGTAGATATTTTTTaatggtattt
1583498 1583513 1583505.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator safA Gene nd
atgttagtgcATTGTAGATATTTTTTaatggtattt
1583498 1583513 1583505.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator ypdC Gene nd
aaccgtggttTAATAACACCTACATTctgcgactga
2501021 2501036 2501028.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator ygiW Gene nd
tgggaaatcgATAATGTTTACATCCAgtgtcaggtt
3169200 3169215 3169207.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator yehS Gene nd
cgctgcgcagAATATCGTTACTTAGCatgaggcctt
2212179 2212194 2212186.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator yehD Gene nd
atctatcaatTAATGTAGATTTATGTaaatggtatt
2192409 2192424 2192416.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator yodB Transcription-Unit nd
agcaaagcccCTAAATATATACAATTtagcgatcat
2041850 2041865 2041857.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator rfbB Gene nd
cgtacgttaaTTTATCGACATTAACAacactatcct
2112963 2112978 2112970.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator bdcA Gene nd
ggcgatcaatATCGTCGGCATTTAATtccagggcct
4473760 4473775 4473767.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator yfcV Gene nd
attaacccgcTTTTGTCGATATAATAtataaacact
2456007 2456022 2456014.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator yfbO Gene nd
atacgtatggAATTGTCACTATTTATctgctaatga
2388559 2388574 2388566.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator htrE Gene nd
cccaggcttgAGGAACGTCTATATCCagacgttgat
154968 154983 154975.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator ycgY Gene nd
attcagaaaaTAAATATTTTAGACAGtagccagtca
1245173 1245188 1245180.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator yfdV Gene nd
cgtcaccggcAGGTTATATCGACAAAtcgtttcaat
2490557 2490572 2490564.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator rpiB Gene nd
cagagcgtacTGATTATCCACATTACgccagtcaag
4313472 4313487 4313479.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator alaE Gene nd
catatcggcaTGTAAAAATCCACAATgtacaaaaaa
2798969 2798984 2798976.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator ychQ Gene nd
catctggcgaTCAAAAATATCCACATtctgcaaagc
1266566 1266581 1266573.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator cysN Gene nd
tatagcggaaCAATGTCGATATTTTCcagccagatg
2875714 2875729 2875721.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator orn Transcription-Unit nd
ccctgatgggCAAAACATCTATGATAcacgcaattg
4391540 4391555 4391547.0 nd [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ], [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator idnD Gene nd
ttcatccagcCAAAAATATAGATAAAatgtcgcagg
4494742 4494757 4494749.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator yigG Gene nd
tattttttcaGAATATATTTATTTTTtatttggacg
4003273 4003288 4003280.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator yfbU Gene nd
tgatacatctCCATAATGTCGATGATagtgcggcag
2412396 2412411 2412403.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator pdhR Gene nd
ctttcctacgTAAAGTCTACATTTGTgcatagttac
121903 121918 121910.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator murD Gene nd
gattatcaggGTAAAAATGTCGTCATtatcggcctg
97103 97118 97110.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator hinT Gene nd
gcagaaatggGAATAATGGCGATATAtacggcagca
1161728 1161743 1161735.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator bssS Gene nd
gattcctgctTCTAATATCGAAATAAattgtctggc
1120762 1120777 1120769.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator rpsF Gene nd
gctttgcacaTCGTCCATATTTCTGGcctggtggtt
4424691 4424706 4424698.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator lsrG Gene nd
ggaacccctcTTTATATCTACACTTTtccgctgaac
1607366 1607381 1607373.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator gadX Gene nd
tcaccgccatTAAAATAGCGATATTCaccattaacc
3665723 3665738 3665730.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator smg Transcription-Unit nd
tagcagggcaTTGTAGATATCTTCTCgctcaaaacc
3432340 3432355 3432347.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator gltF Gene nd
tattatccttAATTATCTATATATTTtcctattttt
3360933 3360948 3360940.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator yfbN Gene nd
atacgtatggAATTGTCACTATTTATctgctaatga
2388559 2388574 2388566.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator dctR Gene nd
tctggagaaaCTGAAAATATCGCTAAaaacgttcta
3655100 3655115 3655107.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator yidB Transcription-Unit nd
gttagcgccaTTAAATATCGATATTCgccgctttca
3877705 3877720 3877712.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator ygjI Transcription-Unit nd
tgaagcgattGAAAATATCGACAACAttcagcctgg
3225803 3225818 3225810.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator kdsA Gene nd
tgctgcattaATTAATCGACATTTTActcaagatta
1268129 1268144 1268136.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator yjjP Gene nd
cctaacaactTAATGTAGATATTTTAaatgtctcca
4603252 4603267 4603259.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator priC Gene nd
atggtttggcAGCTATCTACGTTTCTggcagaaaca
491053 491068 491060.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator cadC Gene nd
tcttccagacATTATCGATAAGTTCAtccctgctaa
4361767 4361782 4361774.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator yihD Gene nd
ttcaggacgaAGATCGTCGACGTTTTgtcgtcaaat
4042555 4042570 4042562.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator ppiB Gene nd
ttcgcgcgggAAATATGGGTATTATAcgcaactcaa
554555 554570 554562.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR activator yadN Transcription-Unit nd
atgattttcaGAAAATATTTATATTCgcaatataaa
157223 157238 157230.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ydcK Transcription-Unit nd
gttcttcactTAGACGATATTTGCGCatagcgtttt
1500432 1500447 1500439.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ycbV Gene nd
aaaagtgcatTACAAAATATTCATATtggtgatttt
1003037 1003052 1003044.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ycbU Gene nd
aaaagtgcatTACAAAATATTCATATtggtgatttt
1003037 1003052 1003044.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yccT Gene nd
tcatacttacTAACATATAGACATATttcccgcttt
1027840 1027855 1027847.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor mrdA Gene nd
tttgctgcacGTTATCGACTTTCTCCggcatcattt
667927 667942 667934.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yjfY Transcription-Unit nd
gctttgcacaTCGTCCATATTTCTGGcctggtggtt
4424691 4424706 4424698.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ygiV Transcription-Unit nd
tgggaaatcgATAATGTTTACATCCAgtgtcaggtt
3169200 3169215 3169207.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor mglA Gene nd
caggcattttAATAATGTCGATTTTCctgcaccgtt
2239123 2239138 2239130.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yciU Gene nd
gaatgcgggcAAAAACATCGTTGATTtcaccatctt
1306884 1306899 1306891.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor dinQ Gene nd
ggaagagaagATTGTCGGTATTCACGgcattggctt
3647502 3647517 3647509.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ydhS Transcription-Unit nd
aagtaacaatGAAAAAAATTGCTATTgtgggtgccg
1747133 1747148 1747140.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ttdA Gene nd
aagttgacagAGATTGTCGCTAACTTtaccgccatg
3206509 3206524 3206516.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor rhsD Gene nd
aagtttatgtGAAAAATATATAAATAcattagctgg
523164 523179 523171.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yehE Gene nd
atctatcaatTAATGTAGATTTATGTaaatggtatt
2192409 2192424 2192416.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor oxc Gene nd
tcgatttcagCAAAAATATCGAAAATatgtggctgt
2492327 2492342 2492334.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yhcD Gene nd
acgcgctttgATGAAAATGGCGACATttgtcttgat
3363042 3363057 3363049.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ycjP Gene nd
acgctggagcATTACGTCGACATTTTtaacccgatg
1374262 1374277 1374269.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ycgJ Gene nd
acttaatttgAATATCGACGTTATATtttttagttt
1227083 1227098 1227090.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor dgcN Gene nd
agaaaaatgaTGGATAACGATAATTCtcttaataag
2742387 2742402 2742394.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ynaE Transcription-Unit nd
gggtttaaaaGTATACATAGATAACAgtttttatct
1434613 1434628 1434620.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor zraR Gene nd
aggatgacgcACGATAATATCGATATtctggtggtg
4203327 4203342 4203334.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor baeS Gene nd
atacgcatcaAAATGTAGCTATTTCGcggcgaaaaa
2162840 2162855 2162847.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ybaN Transcription-Unit nd
atggtttggcAGCTATCTACGTTTCTggcagaaaca
491053 491068 491060.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor apt Gene nd
atggtttggcAGCTATCTACGTTTCTggcagaaaca
491053 491068 491060.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor rsgA Transcription-Unit nd
ccctgatgggCAAAACATCTATGATAcacgcaattg
4391540 4391555 4391547.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yjdP Gene nd
cagagcgtacTGATTATCCACATTACgccagtcaag
4313472 4313487 4313479.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor prmC Gene nd
catctggcgaTCAAAAATATCCACATtctgcaaagc
1266566 1266581 1266573.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ttdR Gene nd
aagttgacagAGATTGTCGCTAACTTtaccgccatg
3206509 3206524 3206516.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor sgcC Gene nd
gccagtaattGTAAATATCGACGTTCatcgttttgg
4529884 4529899 4529891.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yjjQ Gene nd
cctaacaactTAATGTAGATATTTTAaatgtctcca
4603252 4603267 4603259.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor rssB Gene nd
cctgtttgccCGCAAATATCTACGCTtgatttccat
1290038 1290053 1290045.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yfdC Transcription-Unit nd
cctttggtttTATTATCGTCATTATGgcccgccagc
2465606 2465621 2465613.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor chaBC Transcription-Unit nd
cgtctcatgcCCAGGATATCTATAAAgaagcgttca
1272181 1272196 1272188.0 nd [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ], [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yfjD Transcription-Unit nd
cgtggcgtggTTTGTCTATATTGTGCtgctgtgggg
2748613 2748628 2748620.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yihM Gene nd
cgtttttctcTTGGTAATATGGACGAtaaagaactc
4061355 4061370 4061362.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor hxpA Gene nd
tgatacatctCCATAATGTCGATGATagtgcggcag
2412396 2412411 2412403.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ldcC Gene nd
ctggggcaggCGGAAGATATCGCCATtcgtatgcgt
210007 210022 210014.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor nlpA Gene nd
gcggcccctgTCCGTAGATGATGTGTtgtcagtttc
3839966 3839981 3839973.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ycgV Transcription-Unit nd
agaaaaagcaAAAAACATCGATATTCatttttggtc
1256356 1256371 1256363.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor inaA Gene nd
acattactctTTATTAAGAAATTTTActgccttatc
2349942 2349957 2349949.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor gcvA Gene nd
gccccgaccaTAAAATATCGCCACATcaacatcatc
2942128 2942143 2942135.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor casA Gene nd
ccgttattggTCTTATTATCGTCATTgataacaatc
2884517 2884532 2884524.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor elfC Gene nd
gcgagatgtaTAGAACTCATCGACAAcacagcctgt
999221 999236 999228.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor pdxA Gene nd
gcagcgtcggTTTTATCGACATTACGggtatccagc
53538 53553 53545.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor tam Gene nd
ggaacccctcTTTATATCTACACTTTtccgctgaac
1607366 1607381 1607373.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor bdcR Transcription-Unit nd
ggcgatcaatATCGTCGGCATTTAATtccagggcct
4473760 4473775 4473767.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yeaE Gene nd
tggaaagatgCATTATCAGAATTTGTaggtgatccc
1865721 1865736 1865728.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ppx Gene nd
gggtactggaCATCATCGACATATTGttcagcgata
2624960 2624975 2624967.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yqhC Transcription-Unit nd
ctgtaactgcAAAATATCGACATTGAgacgcaaccc
3154845 3154860 3154852.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor aroP Gene nd
ctttcctacgTAAAGTCTACATTTGTgcatagttac
121903 121918 121910.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ynjH Gene nd
ttgaacaaaaTCCAAAATATCGCCAGatgtcattac
1842496 1842511 1842503.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor tehA Gene nd
gttcttcactTAGACGATATTTGCGCatagcgtttt
1500432 1500447 1500439.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor gadW Gene nd
tttcttatgaGAAAACATCGATAAACaggaaaggta
3664257 3664272 3664264.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor kdgT Transcription-Unit nd
tattgattaaATGAATGTCTATCTTCgtttccatca
4101601 4101616 4101608.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yccU Transcription-Unit nd
tcatacttacTAACATATAGACATATttcccgcttt
1027840 1027855 1027847.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor chaA Transcription-Unit nd
cgtctcatgcCCAGGATATCTATAAAgaagcgttca
1272181 1272196 1272188.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor tar Gene nd
ccagtattgcCATAATCTAGATAATCaatcagttca
1972262 1972277 1972269.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yfiR Gene nd
tgagcattctGAAAAAATATCGATGCatttcgagcg
2741829 2741844 2741836.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yfiL Gene nd
tgagcattctGAAAAAATATCGATGCatttcgagcg
2741829 2741844 2741836.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor phoH Gene nd
tgcgcgtagcCGTTTTTCGGCATTTTatccaaaagc
1085142 1085157 1085149.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor fhuE Gene nd
gcagaaatggGAATAATGGCGATATAtacggcagca
1161728 1161743 1161735.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ydfI Transcription-Unit nd
tcggggcataGCTTTTATCTACAATGatagaaagca
1631374 1631389 1631381.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor pdeG Transcription-Unit nd
tgtttattacCGGTGTCGCTATTTTGaacatccagc
1217378 1217393 1217385.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yobD Gene nd
ttaatccgcgTTCGAAATATCGACGAtctggaaaaa
1905204 1905219 1905211.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor aroB Gene nd
tacgttccccGAGAGTAACGACAATCctctccataa
3518463 3518478 3518470.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor idnK Gene nd
ttcatccagcCAAAAATATAGATAAAatgtcgcagg
4494742 4494757 4494749.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor ypjA Transcription-Unit nd
agtgtggttgGATAAAAAAGTCAATCcattcaggaa
2782942 2782957 2782949.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor cysS Gene nd
ttcgcgcgggAAATATGGGTATTATAcgcaactcaa
554555 554570 554562.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor gdhA Gene nd
ttgaacaaaaTCCAAAATATCGCCAGatgtcattac
1842496 1842511 1842503.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]
  GlaR repressor yfcO Gene nd
gacaacttgcTTTGTTGATATTTTGAtggtagccaa
2449768 2449783 2449775.0 nd [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ] S [3]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [EXP-IEP] Inferred from expression pattern

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence

 [COMP-HINF-PATTERN-DISCOVERY] Manually curated inference based on sequence pattern discovery


Reference(s)    

 [1] Knorr S., Sinn M., Galetskiy D., Williams RM., Wang C., Muller N., Mayans O., Schleheck D., Hartig JS., 2018, Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate., Nat Commun 9(1):5071

 [2] Metzner M., Germer J., Hengge R., 2004, Multiple stress signal integration in the regulation of the complex sigma S-dependent csiD-ygaF-gabDTP operon in Escherichia coli., Mol Microbiol 51(3):799-811

 [3] Aquino P., Honda B., Jaini S., Lyubetskaya A., Hosur K., Chiu JG., Ekladious I., Hu D., Jin L., Sayeg MK., Stettner AI., Wang J., Wong BG., Wong WS., Alexander SL., Ba C., Bensussen SI., Bernstein DB., Braff D., Cha S., Cheng DI., Cho JH., Chou K., Chuang J., Gastler DE., Grasso DJ., Greifenberger JS., Guo C., Hawes AK., Israni DV., Jain SR., Kim J., Lei J., Li H., Li D., Li Q., Mancuso CP., Mao N., Masud SF., Meisel CL., Mi J., Nykyforchyn CS., Park M., Peterson HM., Ramirez AK., Reynolds DS., Rim NG., Saffie JC., Su H., Su WR., Su Y., Sun M., Thommes MM., Tu T., Varongchayakul N., Wagner TE., Weinberg BH., Yang R., Yaroslavsky A., Yoon C., Zhao Y., Zollinger AJ., Stringer AM., Foster JW., Wade J., Raman S., Broude N., Wong WW., Galagan JE., 2017, Coordinated regulation of acid resistance in Escherichia coli., BMC Syst Biol 11(1):1

 [4] Metzer E, Levitz R, Halpern YS, 1979, Isolation and properties of Escherichia coli K-12 mutants impaired in the utilization of gamma-aminobutyrate., J Bacteriol, 137(3):1111 10.1128/jb.137.3.1111-1118.1979

 [5] Schneider BL., Ruback S., Kiupakis AK., Kasbarian H., Pybus C., Reitzer L., 2002, The Escherichia coli gabDTPC operon: specific gamma-aminobutyrate catabolism and nonspecific induction., J Bacteriol 184(24):6976-86

 [6] Dover S, Halpern YS, 1972, Utilization of -aminobutyric acid as the sole carbon and nitrogen source by Escherichia coli K-12 mutants., J Bacteriol, 109(2):835 10.1128/jb.109.2.835-843.1972

 [7] Dover S, Halpern YS, 1972, Control of the pathway of -aminobutyrate breakdown in Escherichia coli K-12., J Bacteriol, 110(1):165 10.1128/jb.110.1.165-170.1972

 [8] Dover S, Halpern YS, 1974, Genetic analysis of the gamma-aminobutyrate utilization pathway in Escherichia coli K-12., J Bacteriol, 117(2):494 10.1128/jb.117.2.494-501.1974

 [9] Pontrelli S., Fricke RCB., Teoh ST., Lavina WA., Putri SP., Fitz-Gibbon S., Chung M., Pellegrini M., Fukusaki E., Liao JC., 2018, Metabolic repair through emergence of new pathways in Escherichia coli., Nat Chem Biol 14(11):1005-1009


RegulonDB