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Synonyms: RcsB, RcsB-Pasp56 |
Summary:
RcsB protein for "Regulator capsule synthesis B," is a response regulator that belongs to the multicomponent RcsF/RcsC/RcsD/RcsA-RcsB phosphorelay system [5, 14, 15, 16, 17] and is involved in the regulation of the synthesis of colanic acid capsule, cell division, periplasmic proteins, motility, biofilm formation, and a small RNA [3, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26]. The response regulator RcsB is the principal regulator of this system and is capable of forming complexes with the RcsA [15, 17, 20, 24, 25, 27, 28] and MatA, DctR, and BglJ proteins (forming a heterodimer) [], while RcsB activates the others genes independently (in the form of a homodimer) [2, 3, 9, 10, 12, 15]. RcsC is a sensor histidine kinase and is known to be a transmembrane protein composed of three domains: the external sensory domain (amino terminal), a cytoplasmic transmitter domain (carboxyl terminal), and a transmembrane hydrophobic central domain (unknown function). Read more > |
Transcription factor | ![]() ![]() |
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TF conformation(s): |
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Evolutionary Family: | LuxR/UhpA | ||||||||||||||||||
Sensing class: | External-Two-component systems | ||||||||||||||||||
Connectivity class: | Local Regulator | ||||||||||||||||||
Gene name: | rcsB | ||||||||||||||||||
Genome position: | 2316177-2316827 | ||||||||||||||||||
Length: | 651 bp / 216 aa | ||||||||||||||||||
Operon name: | rcsDB | ||||||||||||||||||
TU(s) encoding the TF: |
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Regulon |
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Regulated gene(s) | bdm, ftsA, ftsZ, gadA, gadB, gadC, gadX, gadY, hdeA, hdeB, hdeD, lolA, osmB, osmC, rarA, rpoE, rprA, rseA, rseB, rseC, rseD, safA, sra, ydeO, ydeP, yhiD | ||||||
Multifun term(s) of regulated gene(s) |
MultiFun Term (List of genes associated to the multifun term)
pH (6)
Transcription related (6)
membrane (4)
sigma factors, anti-sigmafactors (4)
other (mechanical, nutritional, oxidative stress) (4)
Read more >
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Regulated operon(s) | bdm-sra, gadAXW, gadBC, gadY, hdeAB-yhiD, hdeD, lolA-rarA, mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC, osmB, osmC, rprA, rseD-rpoE-rseABC, safA-ydeO, ydeP | ||||||
First gene in the operon(s) | bdm, ftsA, gadA, gadB, gadY, hdeA, hdeD, lolA, osmB, osmC, rseD, rprA, safA, ydeP | ||||||
Simple and complex regulons | AdiY,ArcA,CRP,FNR,Fis,GadE-RcsB,GadW,GadX,H-NS,RcsB,TorR,ppGpp AdiY,CRP,Fis,FliZ,GadE,GadW,GadX,RcsB CRP,GlrR,NtrC,RcsB CpxR,RcsB EvgA,H-NS,NagC,NarL,NarP,PhoP,RcsB,UvrY 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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RcsB-Pasp56 | activator | bdmp | nd | -41.5 | -101.5 | bdm, sra |
aatcatcaacCAGGACTAATCTTAacaacgaagc
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1556375 | 1556388 | [BPP], [GEA] | [2] | |
RcsB-Pasp56 | activator | ftsAp1 | Sigma70 | -43.5 | -464.5 | ftsA, ftsZ |
ctgatgaattGAAGATTCATCTGGttgaatatgt
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103511 | 103524 | [APIORCISFBSCS], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] | [3] | |
RcsB-Pasp56 | repressor | gadAp | Sigma38, Sigma70, Sigma38, Sigma70 | -18.5 | -45.5 | gadA, gadX |
tgcttccattGCGGATAAATCCTActtttttatt
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3667619 | 3667632 | [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [IHBCE], [SM] | [4], [5], [6] | |
RcsB-Pasp56 | activator | gadBp | Sigma38, Sigma70, Sigma38, Sigma70 | -64.5 | -91.5 | gadB, gadC |
ataaataacaTTAGGATTTTGTTATttaaacacga
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1572130 | 1572144 | [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] | [5], [7] | |
RcsB-Pasp56 | activator | gadYp | Sigma38 | nd | nd | gadY | nd | nd | [GEA] | [7] | ||
RcsB-Pasp56 | activator | hdeAp | Sigma38, Sigma70, Sigma70, Sigma38 | nd | nd | hdeA, hdeB, yhiD | nd | nd | [GEA] | [7] | ||
RcsB-Pasp56 | activator | hdeDp | Sigma38, Sigma70 | nd | nd | hdeD | nd | nd | [GEA] | [7] | ||
RcsB-Pasp56 | activator | lolAp | Sigma70 | -43.5 | -87.5 | lolA, rarA |
aactgaaaatTCAGTATTTTCTTCtttcctcaag
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937278 | 937291 | [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] | [8] | |
RcsB-Pasp56 | activator | osmBp1 | Sigma38 | -41.5 | -189.5 | osmB |
ggttgataatTAAGACTATTTACCtgttattaac
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1343511 | 1343524 | [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] | [9] | |
RcsB-Pasp56 | activator | osmCp1 | Sigma70 | -41.5 | -70.5 | osmC |
cggattttatTCGGAATATCCTGCttatcctcgt
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1556548 | 1556561 | [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] | [2], [10] | |
RcsB-Pasp56 | activator | rpoEp2b | Sigma70, Sigma54 | -52.5 | -227.5 | rseD, rpoE, rseA, rseB, rseC |
aatttactaaACATGGTTTGGTCAgcatagcatc
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2710385 | 2710398 | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/SM)], [SM] | [11] | |
RcsB-Pasp56 | activator | rprAp | nd | -42.5 | -42.5 | rprA |
tttaaactaaTGAGACGAATCTGAtcgacgcaaa
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1770323 | 1770336 | [APIORCISFBSCS], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] | [12] | |
RcsB-Pasp56 | activator | safAp | Sigma70 | nd | nd | safA, ydeO | nd | nd | [GEA] | [7] | ||
RcsB-Pasp56 | activator | ydePp | Sigma70 | nd | nd | ydeP | nd | nd | [BPP], [GEA] | [7], [13] |
Alignment and PSSM for RcsB TFBSs | ![]() |
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Aligned TFBS of RcsB |
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Sequence | |
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CTAAATGTATTCTGAAA | |
CTTGATATATTCTGAAT | |
ATAAATATTTTCTGAAA | |
CTTTATATATTCTGAAT | |
CTAAGGATTATCCGAAA | |
CTAAGATTTTTCCTAAA | |
CTTTATAAATTCCTAAA | |
CTTTATAAATTCCTAAA | |
ATAAATGATTTCTGAAA | |
CTTTATGTTTTCCGAAT | |
AGCAGGATATTCCGAAT | |
CTAAAGAAACTCCTAAA | |
CGAGTCATATTCTGAAA | |
GTGAGGTTAATCCTAAA | |
AGAAGAAAATACTGAAT | |
GTAGGATTTATCCGCAA | |
AATAACAAAATCCTAAT | |
CCAGGACTAATCTTAAC | |
AAAGGATATTTCAGAAA | |
AGGTAAATAGTCTTAAT | |
GCAGTCAGATTCTTAAA | |
ACCAGATGAATCTTCAA | |
ATTGAATGACACTTAAT | |
ATGAGACGAATCTGATC | |
CATGGTTTGGTCAGCAT | |
ATTAGTGAATTGCCATT |
Position weight matrix (PWM). RcsB matrix-quality result |
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A 11 3 12 13 12 9 13 8 18 7 2 0 2 0 23 24 14 C 12 3 2 0 0 3 2 0 0 2 0 25 11 1 3 0 2 G 3 4 3 8 12 4 4 4 1 2 0 1 0 14 0 0 0 T 0 16 9 5 2 10 7 14 7 15 24 0 13 11 0 2 10 |
Consensus |
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; consensus.strict ctaagtatatTCcgAAa ; consensus.strict.rc TTTCGGAATATACTTAG ; consensus.IUPAC mtwrrwawatTCykAAw ; consensus.IUPAC.rc WTTMRGAATWTWYYWAK ; consensus.regexp [ac]t[at][ag][ag][at]a[at]atTC[ct][gt]AA[at] ; consensus.regexp.rc [AT]TT[AC][AG]GAAT[AT]T[AT][CT][CT][AT]A[GT] |
Evolutionary conservation of regulatory elements | ![]() |
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Reference(s) |
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