Integrated proteogenomics database

Bacteria iconB. diazoefficiens 110spc4

Bradyrhizobium diazoefficiens 110spc4 (Genbank #CP032617) is a spontaneous spectinomycin resistant derivative of B. diazoefficiens USDA 110, which is widely used model organism to study rhizobial symbiosis [1,2,3].

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

Hierarchy Resource Link
1 NCBI RefSeq CP032617.1; from 24/04/2018
2 Prodigal [4] Ab initio gene predictions from Prodigal (v2.5)
3 in silico ORFs The in silico ORFs 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 > Prodigal > in silico. Files were parsed to extract the identifier, coordinates and sequences of bona fide protein-coding sequences (CDS) and pseudogene entries.

References

  1. Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T, Sasamoto S, Watanabe A, Idesawa K, Iriguchi M, Kawashima K, Kohara M, Matsumoto M, Shimpo S, Tsuruoka H, Wada T, Yamada M, Tabata S. 2002. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 9(6): 189-197.
  2. Pessi G, Ahrens CH, Rehrauer H, Lindemann A, Hauser F, Fischer HM, Hennecke H. 2007. Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules. Mol. Plant. Microbe. Interact. 20(11): 1353-63.
  3. Fernandez N, Cabrera JJ, Varadarajan AR, Lutz S, Ledermann R, Roschitzki B, Eberl L, Bedmar EJ, Fischer HM, Pessi G, Ahrens CH, Mesa S. 2019. An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens. Front. Microbiol. - Microbial Symbioses. (in press).
  4. 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.
  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
Version
Versions
1
Date
Calendar
13.02.2019

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TAR.GZ

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MD5
SHA1
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ZIP

Size
MD5
SHA1