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Synonyms: YdeO |
Summary:
YdeO belongs to the AraC/XylS family of transcriptional regulators and shows more similarity to YhiW, AppY, AdiY, and GadX than the other AraC/XylS regulators [5, 6]. The members of this family exhibit two domains, an amino-terminal domain involved in coinducer recognition and dimerization and a carboxy-terminal domain that contains a potential helix-turn-helix DNA-binding motif [5, 7]. YdeO activates genes involved in the cellular response to acid resistance [2, 8, 9]. This protein, together with the proteins HNS, EvgA, and GadE, pertains to a specific regulatory circuit that is functional in exponential-phase cells growing in minimal medium [2, 8, 9]. Several of the genes directly regulated by YdeO are also directly regulated by GadX [9]. The YdeO regulon has been determined [1]. Read more > |
Transcription factor | ![]() ![]() |
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TF conformation(s): |
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Evolutionary Family: | AraC/XylS | ||||||||||||||
TFBs symmetry: | inverted-repeat | ||||||||||||||
Connectivity class: | Local Regulator | ||||||||||||||
Gene name: | ydeO | ||||||||||||||
Genome position: | 1582926-1583687 | ||||||||||||||
Length: | 762 bp / 253 aa | ||||||||||||||
Operon name: | safA-ydeO | ||||||||||||||
TU(s) encoding the TF: |
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Regulon |
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Regulated gene(s) | appA, appB, appC, appX, dctR, gadE, gadF, gadW, hyaA, hyaB, hyaC, hyaD, hyaE, hyaF, mdtE, mdtF, safA, slp, uspD, ydeO, yiiS | ||||||
Multifun term(s) of regulated gene(s) |
MultiFun Term (List of genes associated to the multifun term)
aerobic respiration (6)
anaerobic respiration (6)
membrane (5)
Transcription related (3)
electron donors (3)
Read more >
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Regulated operon(s) | appCBXA, gadAXW, gadEF-mdtEF, hyaABCDEF, safA-ydeO, slp-dctR, yiiS-uspD | ||||||
First gene in the operon(s) | appC, gadE, gadW, hyaA, safA, slp, yiiS | ||||||
Simple and complex regulons | AppY,ArcA,Fis,IscR,NarL,NarP,YdeO AppY,ArcA,YdeO ArcA,GadX,YdeO CRP,EvgA,FliZ,GadE,GadW,GadX,H-NS,YdeO EvgA,PhoP,RcsB,YdeO Read more > | ||||||
Simple and complex regulatory phrases | Regulatory phrase (List of promoters regulated by the phrase) |
Transcription factor regulation |
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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 | |
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YdeO | activator | appCp | Sigma70 | -27.5 | -57.5 | appC, appB, appX, appA |
tggtcgtagaGTTTCAGGATAAAGAGGGAGATCtaccattatc
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1037672 | 1037694 | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1] | |
YdeO | activator | appCp2 | Sigma38 | -27.5 | -57.5 | appC, appB, appX, appA |
tggtcgtagaGTTTCAGGATAAAGAGGGAGATCtaccattatc
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1037672 | 1037694 | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1] | |
YdeO | activator | gadEp2 | Sigma38 | nd | nd | gadE, gadF, mdtE, mdtF | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2] | ||
YdeO | activator | gadEp3 | Sigma70 | -41.0 | -607.0 | gadE, gadF |
caaattagccATTTCAAACATTATCATGGCTGATATTttccgtagtc
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3657746 | 3657772 | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1], [3] | |
YdeO | activator | gadWp1 | nd | -13.0 | -46.0 | gadW |
agtctggcatCATTTCATTAGTATACTGAAATtgaaataatc
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3664654 | 3664675 | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1] | |
YdeO | activator | hyaAp | Sigma70 | -61.0 | -216.0 | hyaA, hyaB, hyaC, hyaD, hyaE, hyaF |
aaataggtccATTTTTATCGCTAAAAGATAAATCcacacagttt
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1031912 | 1031935 | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1] | |
YdeO | activator | hyaAp2 | Sigma38 | -61.0 | -216.0 | hyaA, hyaB, hyaC, hyaD, hyaE, hyaF |
aaataggtccATTTTTATCGCTAAAAGATAAATCcacacagttt
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1031912 | 1031935 | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1] | |
YdeO | repressor | safAp | Sigma70 | nd | nd | safA, ydeO | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [4] | ||
YdeO | activator | slpp | Sigma70 | -40.0 | -65.0 | slp, dctR |
actatcaggcATATCACCTCAGAATCAGATGAAAACtataaagaaa
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3653884 | 3653909 | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1] | |
YdeO | activator | yiiSp | Sigma24 | -55.0 | -153.0 | yiiS, uspD |
cgggattgttATTTCCACGATGCAAATGACAATACCCGGAAAATccttctgaac
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4112798 | 4112831 | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1] |
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 | |
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YdeO | activator | nhaR | Transcription-Unit | nd |
tgacattgctTTTGCACTTGGTGTACTGGCGCTGTTGGGAAGTCgtgttccgtt
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17894 | 17927 | 17910.5 | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1] |
Alignment and PSSM for YdeO TFBSs | ![]() |
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Aligned TFBS of YdeO |
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Sequence | |
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TGTTATTTCCACGATGCAAATGACAATACCC | |
GTAGAGTTTCAGGATAAAGAGGGAGATCTAC | |
TTTCAATTTCAGTATACTAATGAAATGATGC | |
GTCCATTTTTATCGCTAAAAGATAAATCCAC | |
TAGTTTTCATCTGATTCTGAGGTGATATGCC | |
AGCCATTTCAAACATTATCATGGCTGATATT |
Position weight matrix (PWM). YdeO matrix-quality result |
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A 1 1 1 0 5 1 0 0 1 1 5 1 0 5 0 2 3 3 3 6 0 1 2 3 4 3 2 2 1 2 0 C 0 0 2 3 0 0 0 1 2 3 1 1 2 0 1 0 3 0 1 0 0 0 0 2 0 0 0 2 2 2 5 G 2 2 1 1 0 1 0 0 0 0 0 2 3 1 0 1 0 0 2 0 3 5 2 1 1 1 1 0 1 1 0 T 3 3 2 2 1 4 6 5 3 2 0 2 1 0 5 3 0 3 0 0 3 0 2 0 1 2 3 2 2 1 1 |
Consensus |
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; consensus.strict ttccatTttcaggattcaaAgGgaaatcccC ; consensus.strict.rc GGGGATTTCCCTTTGAATCCTGAAAATGGAA ; consensus.IUPAC kkyyatTtyyaksatwmwrAkGdmawwhymC ; consensus.IUPAC.rc GKRDWWTKHCMTYWKWATSMTRRAAATRRMM ; consensus.regexp [gt][gt][ct][ct]atTt[ct][ct]a[gt][cg]at[at][ac][at][ag]A[gt]G[agt][ac]a[at][at][act][ct][ac]C ; consensus.regexp.rc G[GT][AG][AGT][AT][AT]T[GT][ACT]C[AC]T[CT][AT][GT][AT]AT[CG][AC]T[AG][AG]AAAT[AG][AG][AC][AC] |
Evolutionary conservation of regulatory elements | ![]() |
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Reference(s) |
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