B. 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.