Search and comparison of genetic clusters containing HP0310 and homologous gene were conducted using the Microbesonline web server (http://microbesonline.org).org
We thank Andrew Spiers, Rob Edwards, Dave Ussery, Chris Taylor, Peter Sterk, Mike Allen, Anil Wipat, Alice MorningStar, Lisa Crossman, Jack Gilbert and Sarah Turner for critical reading of the manuscript and Keith Keller for mapping of unique identifiers for use in the MicrobesOnline database [27].
We used the 1752 bacterial genomes available in the Microbesonline database (October 2013) and searched for protein sequences from cog0613, cog1218, and cog0618.
The MicrobesOnline database [27] was queried for the E.coli orphan genes using their unique VIMSS ID.
Of these 100 orphans, 17 had identifiers not found in the MicrobesOnline database and were excluded.
To test whether we could validate the expression of orphans with low QIPP scores in a well-studied model organism, we searched the MicrobesOnline database [27] for E.coli K12 orphans identified in this study.
A search within the MicrobesOnline database demonstrates the presence of EBPs in 1435 bacterial species [ 10].
Annotations of TF protein domains were collected from the MicrobesOnline database [ 39].
255 complete genomes of bacteria analyzed in this study (Additional file 1) were downloaded from the MicrobesOnline database [ 43].
For each taxonomic collection including manually curated regulons in the selected subset of genomes, we selected an expanded set of genomes from the same taxonomic lineage that are available in the MicrobesOnline database [ 39].
