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

Genes
Genes Synonyms Direction Genome position Function COG ID Conserved groups
comFA
- 3642167..3643558
COG4098L  
comFB
- 3641811..3642107

 
comFC
- 3641125..3641814
COG1040R  
yvyF yviB - 3640632..3641051

 
flgM
- 3640285..3640551
COG2747KNU  
yvyG yviC - 3639787..3640269

 
flgK
- 3638245..3639768
COG1256N x1601-BAC  
flgL yviD - 3637338..3638234
COG1344N  

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 3643638..3643667 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 3643608..3643638 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 3643557..3643621 TATTTTAATAGTTGGACAGAAAATATTCATTCAGGCATACTGTTTCGAAAGGAGGCGTGCTATGT Londono-Vallejo JA, et al. (1993): PE S1
SigD Promoter -40:+5 3641089..3641133 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
     >>>>>         <<<<<
3641116..3641134
-9..9
-4.6
comFC
AGTAAGCGGCTCTTAGGAGTTCGCTTTTTTTATAGTTCA
     >>>>>>>    <<<<<<<<
3637319..3637337
1..19
-8.1
flgL

Overview



Upper Region






Copyright: Human Genome Center, Inst. Med. Sci., Univ. Tokyo; 1999-2008
Contact: Kenta Nakai