S. meliloti 2011_Lys-C

Sinorhizobium meliloti strain 2011 (Genbank #NC_020528 is the reference strain [1] which includes two plasmids #NC_020527 and #NC_020560.

An iPtgxDB was created by hierarchically integrating protein coding sequences from three annotation resources (1-3) and three predictions:

Hierarchy	Resource	Link
1	NCBI RefSeq	GCF_000346065.1_ASM34606v1; from 19/05/2017
2	NCBI Genbank	GCA_000346065.1_ASM34606v1; from 31/01/2014
3	Genoscope [2]	v2.7.3, accessed 14/11/2018
4	Prodigal [3]	Ab initio gene predictions from Prodigal (v2.6)
5	ChemGenome [4]	Ab initio gene predictions from ChemGenome (v2.0; with parameters method: Swissprot, length threshold: 70 nt, initiation codons: ATG, CTG, TTG, GTG)
6	in silico ORFs	The in silico ORF annotations were generated as described by Omasits and Varadarajan et al., 2017 [5]

Only ORFs above a selectable length threshold (here 18 aa) were considered. The iPtgxDB was created using the hierarchy RefSeq > Genbank > Genoscope > Prodigal > ChemGenome > in silico. Files were parsed to extract the identifier, coordinates and sequences of bona fide protein-coding sequences (CDS) and pseudogene entries. For extensions or reductions to already annotated CDSs, sequences were only included up to the first LysC cleavage site, allowing to identify such proteins using the proteomics data obtained by using this protease. For more detail on how we generate iPtgxDBs and how the identifiers can be interpreted, please see reference [5].

References

1. Sallet, E., Roux, B., Sauviac, L., Jardinaud, M. F., Carrere, S., Faraut, T., de Carvalho-Niebel, F., Gouzy, J., Gamas, P., Capela, D., Bruand, C. and Schiex, T. 2013. Next-generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011. DNA Res 20(4): 339-354.
2. Vallenet, D., Belda, E., Calteau, A., Cruveiller, S., Engelen, S., Lajus, A., Le Fevre, F., Longin, C., Mornico, D., Roche, D. et al. 2013. MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res 41: D636-647.
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. 2017. An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. Genome Research. 27: 2083-2095.