I have a list of E. coli gene IDs with mappings between KEGG/BLATTNER and EcoCyc. I want to know which of these genes use the main sigma factor. Is there a "data-science friendly" table that I could use (e.g. tsv,csv, or excel compared to PDF)? Is this information in a database that could be downloaded?
Sigma factors in E. coli:
σ70(RpoD) - σA - the "housekeeping" sigma factor or also called as primary sigma factor, transcribes most genes in growing cells. Every cell has a "housekeeping" sigma factor that keeps essential genes and pathways operating.[1] In the case of E. coli and other gram-negative rod-shaped bacteria, the "housekeeping" sigma factor is σ70.[1] Genes recognized by σ70 all contain similar promoter consensus sequences consisting of two parts.[1] Relative to the DNA base corresponding to the start of the RNA transcript, the consensus promoter sequences are characteristically centered at 10 and 35 nucleotides before the start of transcription (–10 and –35).
I've only seen things like this which are difficult to mine: http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0090447.s002&type=supplementary