Integrated proteogenomics database

Bacteria iconB. diazoefficiens 110spc4_tryptic

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 [3] 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

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 C. H., Rehrauer H., Lindemann A., Hauser F., Fischer H. M., 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 J. J., Varadarajan A. R., Lutz S., Ledermann R., Roschitzki B., Eberl L., Bedmar E. J., Fischer H. M., Pessi G., Ahrens C. H., Mesa S. 2019. An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens. Front. Microbiol. 10:924.
  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
Versions

Version

1
Versions

Date

13.02.2019

Downloads icon Downloads

Compression icon

TAR.GZ

File icon

Size

16.4 MB
Data icon

MD5

638a792ad19b400c29dcbcec995a4cb1
Data icon

SHA1

29cb86d1b2170fc69641e06ef79cff9cefbc1209
Compression icon

ZIP

File icon

Size

16.8 MB
Data icon

MD5

47a5352ad0230e70583c0bd545c65b8f
Data icon

SHA1

f391fce7caa4d7ffb63809c4ea5ea2d587cc8434