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Synonyms: RcdA |
Summary:
RcdA, also known as YbjK, belongs to the TetR family and is involved in the regulation of a number of stress response genes, biofilm formation, and transcription regulator genes [1] Genomic SELEX analysis showed that RcdA can bind to the upstream regions of 27 genes. Among these predicted targets of RcdA, six genes correspond to transcription regulators (AppY, CsgD, FimB, RcdA, Sxy, and YcgF). This indicates that a large number of genes must be regulated indirectly by these regulators. Another group of target genes includes membrane-associated stress response proteins (CsgB, NanC, OmpA, PgaA, YbjJ, YehA, and YoeA) and stress response cytoplasmic proteins (Asr and YdeI), among others [1] RcdA exhibits strong cooperative DNA binding and produces aggregates of RcdA-DNA complexes. In a specific way and with high binding affinity, this regulator recognizes and binds to sites that have closely related sequences. Furthermore, a consensus sequence has been proposed for RcdA sites. This consensus sequence shows a core binding site of 9 bp, TTGTgtACA, with inverted repeat symmetry [1] According to the analysis performed by the curator, the consensus sequence has a length of 10 bp (TTGTgtACAa). The X-ray structure of RcdA was determined at 2.55 A resolution [3] Atomic force microscopic observations of several aggregates of RcdA-DNA-forming filaments showed that the T46 residue of RcdA is apparently involved in this oligomerization mode [3] The R32 residue of RcdA plays an important role in the recognition of and binding to DNA [3] Read more > |
Transcription factor | ![]() ![]() |
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TF conformation(s): |
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Evolutionary Family: | TetR/AcrR | ||||||||||||
Connectivity class: | Local Regulator | ||||||||||||
Gene name: | rcdA | ||||||||||||
Genome position: | 887423-887959 | ||||||||||||
Length: | 537 bp / 178 aa | ||||||||||||
Operon name: | rcdA | ||||||||||||
TU(s) encoding the TF: |
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Regulon |
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Regulated gene(s) | asr, bluF, csgD, csgE, csgF, csgG, rmf, rsd, sulA, yagK, ydeI | ||||||
Multifun term(s) of regulated gene(s) |
MultiFun Term (List of genes associated to the multifun term)
posttranscriptional (2)
Transcription related (2)
pH (1)
activator (1)
repressor (1)
Read more >
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Regulated operon(s) | asr, bluF, csgDEFG, rmf, rsd, sulA, yagK, ydeI | ||||||
First gene in the operon(s) | asr, bluF, csgD, rmf, rsd, sulA, yagK, ydeI | ||||||
Simple and complex regulons | ArcA,CRP,McbR,RcdA,SdiA,SlyA,ppGpp ArcA,McbR,RcdA,SdiA,SlyA BasR,BolA,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA,ppGpp BasR,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA H-NS,PhoB,RcdA,RstA 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 (Confirmed, Strong, Weak) | References | |
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RcdA | activator | asrp | Sigma70 | -68.5 | -117.5 | asr |
tttattcagcGTTTGTACATAtcgttacacg
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1671254 | 1671264 | [GEA], [IC], [BPP], [IC] | [1] | |
RcdA | activator | asrp | Sigma70 | -58.5 | -107.5 | asr |
gtttgtacatATCGTTACACGctgaaaccaa
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1671264 | 1671274 | [GEA], [IC], [BPP], [IC] | [1] | |
RcdA | activator | asrp2 | Sigma38 | -68.5 | -117.5 | asr |
tttattcagcGTTTGTACATAtcgttacacg
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1671254 | 1671264 | [GEA], [IC], [BPP], [IC] | [1] | |
RcdA | activator | asrp2 | Sigma38 | -58.5 | -107.5 | asr |
gtttgtacatATCGTTACACGctgaaaccaa
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1671264 | 1671274 | [GEA], [IC], [BPP], [IC] | [1] | |
RcdA | activator | bluFp | Sigma70 | -222.5 | -253.5 | bluF |
caatagcaaaCTTGTACGAAAtatgtgtaca
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1215724 | 1215734 | [GEA], [APIORCISFBSCS], [BPP] | [1] | |
RcdA | activator | bluFp | Sigma70 | -211.5 | -242.5 | bluF |
ttgtacgaaaTATGTGTACAGaatgataaat
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1215713 | 1215723 | [GEA], [APIORCISFBSCS], [BPP] | [1] | |
RcdA | activator | csgDp1 | Sigma70 | -298.5 | -446.5 | csgD, csgE, csgF, csgG |
tgcgatatgtCTTGCGCACAAgccgtgacaa
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1103638 | 1103648 | [GEA], [IC], [BPP], [IC] | [1] | |
RcdA | activator | csgDp3 | Sigma38 | -298.5 | -446.5 | csgD, csgE, csgF, csgG |
tgcgatatgtCTTGCGCACAAgccgtgacaa
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1103638 | 1103648 | [GEA], [IC], [BPP], [IC] | [1] | |
RcdA | activator | rmfp | nd | nd | nd | rmf | nd | nd | [GEA], [BPP] | [2] | ||
RcdA | activator | rsdp2 | Sigma70 | nd | nd | rsd | nd | nd | [GEA], [BPP] | [2] | ||
RcdA | repressor | sulAp | Sigma70 | 33.5 | 5.5 | sulA |
ctggattgatTATGTACACTTcaggctatgc
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1020910 | 1020920 | [GEA], [APIORCISFBSCS], [BPP] | [1] | |
RcdA | repressor | sulAp | Sigma70 | 47.5 | 19.5 | sulA |
tacacttcagGCTATGCACATcgttcttcgt
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1020896 | 1020906 | [GEA], [APIORCISFBSCS], [BPP] | [1] | |
RcdA | repressor | yagKp6 | Sigma70 | 3.5 | -167.5 | yagK |
atataatggcATTGTGTACTCttactacctg
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293111 | 293121 | [BPP] | [1] | |
RcdA | activator | ydeIp5 | Sigma70 | nd | nd | ydeI | nd | nd | [GEA], [BPP] | [1] |
Functional conformation | Function | Object name | Object type | Distance to first Gene | Sequence | LeftPos | RightPos | Center Position | Growth Condition | Evidence (Confirmed, Strong, Weak) | References | |
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RcdA | activator | ybjK | Transcription-Unit | -35.5 |
ttgtgtacaaATGTACACAAccttgctaat
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887383 | 887393 | 887387.5 | nd | [GEA], [APIORCISFBSCS], [BPP] | [1] | |
RcdA | activator | ybjK | Transcription-Unit | -25.5 |
ctctctgcaaTTGTGTACAAatgtacacaa
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887393 | 887403 | 887397.5 | nd | [GEA], [APIORCISFBSCS], [BPP] | [1] | |
RcdA | repressor | ybjJI | Transcription-Unit | -58.5 |
ctctctgcaaTTGTGTACAAatgtacacaa
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887393 | 887403 | 887397.5 | nd | [GEA], [APIORCISFBSCS], [BPP] | [1] | |
RcdA | repressor | ybjJI | Transcription-Unit | -48.5 |
ttgtgtacaaATGTACACAAccttgctaat
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887383 | 887393 | 887387.5 | nd | [GEA], [APIORCISFBSCS], [BPP] | [1] |
Alignment and PSSM for RcdA TFBSs | ![]() |
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Aligned TFBS of RcdA |
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Sequence | |
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ATGTGTACAGAATG | |
ATGTACAAACGCTG | |
ATGTGCATAGCCTG | |
AAGAGTACACAATG | |
TTGCGCACAAGCCG | |
ATCGTTACACGCTG | |
AAGTGTACATAATC | |
TTGTACGAAATATG |
Position weight matrix (PWM). RcdA matrix-quality result |
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A 6 2 0 1 2 0 7 2 8 2 3 4 0 0 C 0 0 1 1 0 4 0 5 0 3 1 4 1 1 G 0 0 7 1 5 0 1 0 0 2 3 0 0 7 T 2 6 0 5 1 4 0 1 0 1 1 0 7 0 |
Consensus |
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; consensus.strict atGtGcACAcgcTG ; consensus.strict.rc CAGCGTGTGCACAT ; consensus.IUPAC atGtGyACAsrmTG ; consensus.IUPAC.rc CAKYSTGTRCACAT ; consensus.regexp atGtG[ct]ACA[cg][ag][ac]TG ; consensus.regexp.rc CA[GT][CT][CG]TGT[AG]CACAT |
Evolutionary conservation of regulatory elements | ![]() |
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Reference(s) |
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