Regulated Operon: ctsR-mcsAB-clpC-radA-yacK

Genes
Genes Synonyms Direction Genome position Function COG ID Conserved groups
ctsR yacG + 101449..101913
COG4463K ctsR-BAC ctsR-STA ctsR-STR  
mcsA yacH + 101927..102484
COG3880S  
mcsB yacI + 102484..103575
COG3869E  
clpC mecB + 103572..106004
COG0542O clpC-BAC clpC-STA  
radA yacJ + 106096..107472
COG1066O radA-BAC  
yacK
+ 107476..108558
COG1623R  

Operon evidence: Northern blotting (7.0 kb transcript) and S1 nuclease mapping of the 3' end
Reference: Kruger E, et al. (1996)
Comments: A ctsR-mcsAB-clpC transcript and various transcripts in the radA-yacKLMN region are listed in BSORF. The 3' nuclease mapping showed two weak termination signals in the AT-rich region at the end of a proposed terminator structure eight base pairs downstream of the stop codon (i.e., in the TTAAAA region in the left arm of the indicated stem-loop). However, mfold cannot detect such a stem-loop structure. Northern blotting results in BSORF show a ctsR-mcsAB-clpC transcript.


Promoters

Binding
factor
Regulation Location Absolute position Binding seq.(cis-element) Experimental evidence
CtsR Negative +1:+29 101409..101437 AAAGTCAAATATAGTCAAAGTCAGTAAAG Derre I, et al. (1999): GS FT
SigA Promoter -43:+9 101366..101417 CGAGAAAGTTGAAAATTCTCGAGAAACGGCTTATAGTAAGATTAAAGTCAAA Kruger E, et al. (1996): NB PE
SigB Promoter -46:+6 101314..101365 ATCAGCAATCAGGTTTTGTGGACCGGGAAAATGGAAATAATGAAGGATAGAG Kruger E, et al. (1996): NB PE

Terminator

Terminator sequence Absolute position Position from stop codon Free energy
[kcal/mol]
Downstream of
TAAAACCTTATGAATACGGGTATATTAATGTTGGTTTTTGTTTATTCTG
     >>>>>>>>>>>      <<<<<<<<<<<<
108571..108599
13..41
-4.4
yacK

Overview



Upper Region






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