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| Synonyms: CaiF-L-carnitine, CaiF |
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Summary:
Under anaerobiosis and in the presence of "carnitine," CaiF activates the transcription of genes involved in carnitine metabolism [2]. This protein recognizes and binds to two 11-bp inverted repeat half-sites separated by 13 bp in the intergenic region of two operons located divergently in the genome (caiTABCDE and fixABCX). CaiF possibly binds as a dimer, with each monomer of the complex recognizing one half of the site. A genome-wide computerized scan demonstrated that there are no more sites in the genome for CaiF [1]. A complex composed of two CRP dimers and two CaiF dimers needs to be bound in order for the RNA polymerase to bind to the promoter. CRP, which makes contact with the RNA polymerase, seems to be the main protein of the complex. CaiF was suggested to counteract the repression effect of HNS. It has been proposed that CRP and CaiF bind to opposite DNA strands [1]. Carnitine and crotonobetaine, the putative inducers of carnitine metabolism, seem to be of no help in CaiF binding [1]. Read more > |
| Transcription factor |  |
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| TF conformation(s): |
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| Evolutionary Family: | CaiF | |||||||||||||||||||||
| TFBs length: | 16 | |||||||||||||||||||||
| Sensing class: | External sensing using transported metabolites | |||||||||||||||||||||
| Connectivity class: | Local Regulator | |||||||||||||||||||||
| Gene name: | caiF | |||||||||||||||||||||
| Genome position: | 34300-34695 | |||||||||||||||||||||
| Length: | 396 bp / 131 aa | |||||||||||||||||||||
| Operon name: | caiF | |||||||||||||||||||||
| TU(s) encoding the TF: |
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| Regulon |
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| Regulated gene(s) | caiA, caiB, caiC, caiD, caiE, caiT, fixA, fixB, fixC, fixX | ||||||
| Multifun term(s) of regulated gene(s) |
MultiFun Term (List of genes associated to the multifun term)
carnitine metabolism (6)
amines (2)
energy production/transport (2)
electron acceptors (1)
carbon compounds (1)
Read more >
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| Regulated operon(s) | caiTABCDE, fixABCX | ||||||
| First gene in the operon(s) | caiT, fixA | ||||||
| Simple and complex regulons | ArcA,CRP,CaiF,FNR,H-NS CRP,CaiF,FNR | ||||||
| Simple and complex regulatory phrases | Regulatory phrase (List of promoters regulated by the phrase) | ||||||
| Transcription factor regulation |
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Transcription factor binding sites (TFBSs) arrangements
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| Alignment and PSSM for CaiF TFBSs | |
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| Aligned TFBS of CaiF |
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| Sequence | |
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| CACCAATATTGAAAGTCAG | |
| TAACAATATTGAAAGTTGG | |
| CACCAATATTGAAAACACG | |
| AAACAATATTGAAAATTTC |
| Position weight matrix (PWM). CaiF matrix-quality result |
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A 1 4 2 0 4 4 0 4 0 0 0 4 4 4 2 0 1 1 0 C 2 0 2 4 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 G 0 0 0 0 0 0 0 0 0 0 4 0 0 0 2 0 0 1 3 T 1 0 0 0 0 0 4 0 4 4 0 0 0 0 0 3 2 1 0 |
| Consensus |
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; consensus.strict cAcCAATATTGAAAgttgG ; consensus.strict.rc CCAACTTTCAATATTGGTG ; consensus.IUPAC cAmCAATATTGAAAryysS ; consensus.IUPAC.rc SSRRYTTTCAATATTGKTG ; consensus.regexp cA[ac]CAATATTGAAA[ag][ct][ct][cg][CG] ; consensus.regexp.rc [CG][CG][AG][AG][CT]TTTCAATATTG[GT]TG |
| PWM logo |
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| Evolutionary conservation of regulatory elements | |
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| TF-target gene evolutionary conservation |
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| Promoter-target gene evolutionary conservation |
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| Reference(s) |
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[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis