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Synonyms: YdcI |
Summary:
Based on results with purified YdcI protein with a DNA probe in a gel shift assay, YdcI was shown to be a DNA-binding transcriptional repressor which negatively regulates its own expression in Salmonella enterica serovar Typhimurium [2]. YdcI was confirmed as a TF through an integrated workflow comprised of computational prediction, knowledge-based classification, and experimental validation of candidate TFs at the genome scale [3]. YdcI is involved in pH homeostasis and acetate metabolism [3]. YdcI belongs to the LysR family of transcriptional regulators, which is found in a wide range of Gram-negative bacteria and is involved in a number of Salmonella enterica serovar Typhimurium phenotypes [2]. YdcI regulates a number of genes involved in aspects of bacterial biology related to survival, stress responses, and cell interactions [2]. Read more > |
Transcription factor | ![]() ![]() |
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TF conformation(s): |
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TFBs symmetry: | inverted-repeat | ||||||||||||||
Connectivity class: | Local Regulator | ||||||||||||||
Gene name: | ydcI | ||||||||||||||
Genome position: | 1494148-1495071 | ||||||||||||||
Length: | 924 bp / 307 aa | ||||||||||||||
Operon name: | ydcI | ||||||||||||||
TU(s) encoding the TF: |
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Regulon |
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Regulated gene(s) | flu, isrC | ||||||
Multifun term(s) of regulated gene(s) |
MultiFun Term (List of genes associated to the multifun term)
prophage genes and phage related functions (1)
RNA related (1)
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Regulated operon(s) | isrC-flu | ||||||
First gene in the operon(s) | isrC | ||||||
Simple and complex regulons | DksA,OxyR,YdcI,ppGpp | ||||||
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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YdcI | activator | flup | Sigma70 | nd | nd | isrC, flu | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ] | 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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YdcI | activator | smrB | Transcription-Unit | nd | nd | nd | nd | nd | [EXP-IEP-RNA-SEQ] | W | [1] | ||
YdcI | activator | iraP | Gene | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ] | W | [1] |
Evolutionary conservation of regulatory elements | ![]() |
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Reference(s) |
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