Integrated proteogenomics database

Bacteria iconS. meliloti 2011_Lys-C_custom

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

A small custom iPtgxDB was created by hierarchically integrating protein coding sequences from three annotation resources (1-3) and two 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)
5 276 RiboSeq predictions The RiboSeq candidates were selected as described by Hadjeras et al., 2022 [4]

Only ORFs above a selectable length threshold (here 18 aa) were considered. The iPtgxDB was created using the hierarchy RefSeq > Genbank > Genoscope > Prodigal > RiboSeq. 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. Hadjeras, L., Heiniger, B., Maaß, S., Scheuer, R., Gelhausen, R., Azarderakhsh, S., Barth-Weber, S., Backofen, R., Becher, D., Ahrens, C.H., Sharma, C.M., Evguenieva-Hackenberg, E. 2022. Small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti. bioRxiv 2022.11.12.516264
  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.
iPtgxDB Release Info
Versions

Version

1
Versions

Date

02.02.2022

Downloads icon Downloads

Compression icon

TAR.GZ

File icon

Size

1.8 MB
Data icon

MD5

48b34aa7026e8aa2592b6f8e9f965346
Data icon

SHA1

2f14c0bbcb0551047cadd0a6cf7c22002f7b9225
Compression icon

ZIP

File icon

Size

1.9 MB
Data icon

MD5

4603aec2e1621e0d4e651569f4abd14f
Data icon

SHA1

22544409b1460551958d8eaa6174b970cc5e906a