Regulated Operon: ydaDEFG

Genes
Genes Synonyms Direction Genome position Function COG ID Genus clusters
ydaD
+ 471267..472127
COG1028 yhdF-BAC-2 yhdF-BAC-3  
ydaE
+ 472143..472646
COG3822  
ydaF
+ 472731..473282
COG1670  
ydaG yzzA + 473360..473782
COG3871  

Operon evidence: Northern blotting (2.8 kb and 3.3 kb transcripts)
Reference: Petersohn A, et al. (1999)
Comments: The readthrough terminator downstream of ydaE leads to a 1.6 kb transcript. Both ydaDEFG transcripts terminate before reaching ydaH. An internal promoter in front of ydaG leads to monocistronic ydaG transcripts of 0.47 kb, 0.6 kb, and 0.9 kb. A 1.6 kb ydaFG transcript was also detected.

Promoters

Binding
factor		 Regulation Location Absolute position Binding seq.(cis-element) Experimental evidence
SigB Promoter -40:+5 471197..471241 AGCCATGTTTATCCAAAGAGTGTGTGAGGTACACAACAAATAGAC Petersohn A, et al. (1999): PE NB 2D-gel
SigB Promoter -36:+4 473296..473335 TTGTTTAAATCTTCCCCGGATGTGGAAAAGTAACAGCGGA Petersohn A, et al. (1999): PE NB 2D-gel

Terminator

Terminator sequence Absolute position Position from stop codon Free energy
[kcal/mol]		 Downstream of
ACAAACCGCCCGGCGTACGCCGGACGGTTTTTTTATTGCAAA
     >>>>>>>>>    <<<<<<<<<
474178..474199
396..417
-15.3
 ydaG
TATAAGGATGGCTTAACAGCCCATCCTTTTTGTATTGAAAA
     >>>>>>>>    <<<<<<<<<
472647..472667
1..21
-11.6
 ydaE

Overview



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