E. coli BW25113

This is the parental strain (Genbank #CP009273) of the widely used Escherichia coli Keio gene knockout collection [1].

An iPtgxDB was created by hierarchically integrating protein coding sequences from the following annotation resources:

Hierarchy	Resource	Link
1	NCBI RefSeq	CP009273.1; from 30/10/2014
2	IMG [2]	Integrated Microbial Genomes (IMG) initiative of the Joint Genome Institute (JGI); Ga0058822, from 12/08/2014
3	Prodigal [3]	Ab initio gene predictions from Prodigal (v2.6)
4	ChemGenome [4]	Ab initio gene predictions from ChemGenome (v2.0, http://www.scfbio-iitd.res.in/chemgenome/chemgenomenew.jsp; with parameters: method, Swissprot space; length threshold, 70 nt; initiation codons, ATG, CTG, TTG, GTG)
5	in silico ORFs	The in silico ORF annotations were generated as described by Omasits and Varadarajan et al., 2017

Only ORFs above a selectable length threshold (here 18 aa) were considered. The iPtgxDB was created using the hierarchy RefSeq > JGI > Prodigal > ChemGenome > in silico. Files were parsed to extract the identifier, coordinates and sequences of bona fide protein-coding sequences (CDS) and pseudogene entries.

References

1. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K.A., Tomita, M., Wanner, B.L., and Mori, H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008.
2. Markowitz, V.M., Mavromatis, K., Ivanova, N.N., Chen, I.M., Chu, K., and Kyrpides, N.C. 2009. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25: 2271-2278.
3. Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
4. Singhal, P., Jayaram, B., Dixit, S.B., and Beveridge, D.L. 2008. Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations. Biophys J 94: 4173-4183.
5. Omasits, U., Varadarajan, A. R., Schmid, M., Goetze, S., Melidis, D., Bourqui, M., Nikolayeva, O., Quebatte, M., Patrignani, A., Dehio, C., Frey, J. E., Robinson, M. D., Wollscheid, B., and Ahrens., C. H. An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. bioRxiv, Cold Spring Harbor Labs Journals, 2017.