Regulated Operon: comFABC-yvyF-flgM-yvyG-flgKL

Genes
Genes Synonyms Direction Genome position Function COG ID Genus clusters
comFA
- 3641197..3642588 late competence protein COG4098  
comFB
- 3640841..3641137

 
comFC
- 3640155..3640844
COG1040  
yvyF yviB - 3639662..3640081

 
flgM
- 3639315..3639581 anti-sigma factor repressor of sigma-D-dependent transcription COG2747  
yvyG yviC - 3638817..3639299

 
flgK
- 3637275..3638798 flagellar hook-associated protein 1 (HAP1) COG1256 x1601-BAC  
flgL yviD - 3636368..3637264 flagellar hook-associated protein 3 (HAP3) COG1344  

Operon evidence: Genome analysis
Reference: Londono-Vallejo JA & Dubnau D (1993), Soldo B, et al. (1996), Mirel DB, et al. (1994), Liu J & Zuber P (1998), Serizawa M, et al. (2004)
Comments: Insertion mutations and RT-PCR by Liu & Zuber showed the presence of a comF-flgM transcript, suggesting that the stem-loop downstream of comFC functions as a readthrough terminator. Soldo et al. suggest that the stem-loop structure downstream of flgL may be an mRNA stabilizer rather than a terminator. In that case, the operon would also contain the genes yviE, yviF, and csrA. Serizawa et al. show that yviE-yviF, like the operon containing yvyF, are SigD-dependent.


Promoters

Binding
factor
Regulation Location Absolute position Binding seq.(cis-element) Experimental evidence
ComK Positive -92:-63 3642668..3642697 ATAAGGCCAAATCTCCGTTTTTAGAGCGGA Londono-Vallejo JA, et al. (1993): DB RG
Van Sinderen D, et al. (1995): GS RG OV
Hamoen LW, et al. (1998): FT
Liu J & Zuber P (1998): DB
Ogura M, et al. (2002): AR RG DB
ComK Positive -63:-33 3642638..3642668 AGATTTTTTTATATTCTTATTTTAATAGTTG Londono-Vallejo JA, et al. (1993): DB RG
Van Sinderen D, et al. (1995): GS RG OV
Hamoen LW, et al. (1998): FT
Liu J & Zuber P (1998): DB
Ogura M, et al. (2002): AR RG DB
SigA Promoter -46:+19 3642587..3642651 TATTTTAATAGTTGGACAGAAAATATTCATTCAGGCATACTGTTTCGAAAGGAGGCGTGCTATGT Londono-Vallejo JA, et al. (1993): PE S1
SigD Promoter -40:+5 3640119..3640163 AGAAGCTAAATGATTCTGTTTTTATGCCGATATAATCACTAGAAA Gilman MZ, et al. (1981): S1 RO, in-vitro transcription
Gilman MZ & Chamberlin ML (1982): S1
Mirel DB, et al. (1994): RO

Terminator

Terminator sequence Absolute position Position from stop codon Free energy
[kcal/mol]
Downstream of
TTGATCAGAAGCTAAATGATTCTGTTTTTATGCCGATAT
     >>>>>         <<<<<
3640146..3640164
-9..9
-4.6
comFC
AGTAAGCGGCTCTTAGGAGTTCGCTTTTTTTATAGTTCA
     >>>>>>>    <<<<<<<<
3636349..3636367
1..19
-8.1
flgL

Overview



Upper Region






Copyright: Human Genome Center, Inst. Med. Sci., Univ. Tokyo; 1999-2006
Contact: Kenta Nakai