Integrated proteogenomics database

Bacteria iconB. thetaiotaomicron DSM2079_Asp-N

The extended simplified human intestinal microbiota (SIHUMIx) consists of eight bacterial members (Anaerostipes caccae (DSMZ 14662); Bacteroides thetaiotaomicron (DSMZ 2079); Bifidobacterium longum (NCC 2705); Blautia producta (DSMZ 2950); Clostridium butyricum (DSMZ 10702); Clostridium ramosum (DSMZ 1402); Escherichia coli K-12 (MG1655); Lactobacillus plantarum (DSMZ 20174)) of the human intestine and thus represents a model community to analyze such microbial interactions [1].

An Asp-N iPtgxDB of Bacteroides thetaiotaomicron (DSM 2079) was created by hierarchically integrating protein coding sequences from the following annotation resources:

Hierarchy Resource Link
1 NCBI RefSeq CP040529.1 / CP040530.1 from 20-MAY-2019 (NCBI Prokaryotic Genome Annotation Pipeline (PGAP v.4.7)
2 Prodigal [2] ab initio gene predictions from Prodigal (v2.6)
3 ChemGenome [3] ab initio gene predictions from ChemGenome (v2.0, http://www.scfbio-iitd.res.in/chemgenome/chemgenomenew.jsp; with parameters: method, Swissprot space; length threshold, 70 nt; initiation codons, ATG, CTG, TTG, GTG)
4 in silico ORFs in silico ORF annotations were generated as described by Omasits and Varadarajan et al., 2017 (v2.0, Only ORFs above a selectable length threshold (here 18 aa) were considered.)

The iPtgxDB was created using the hierarchy RefSeq > Prodigal > ChemGenome > in silico. Files were parsed to extract the identifier, coordinates and sequences of bona fide protein-coding sequences (CDS) and pseudogene entries.

References

  1. Becker, N., Kunath, J., Loh, G. & Blaut, M. Human intestinal microbiota: Characterization of a simplified and stable gnotobiotic rat model. Gut Microbes 2, 25-33, doi:10.4161/gmic.2.1.14651 (2011).
  2. 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.
  3. 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.
  4. 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. An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. bioRxiv, Cold Spring Harbor Labs Journals, 2017.
iPtgxDB Release Info
Versions

Version

1
Versions

Date

10.08.2020

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Compression icon

TAR.GZ

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Size

9.5 MB
Data icon

MD5

5a6953e89e1bdcbf7275d4e9c5130be5
Data icon

SHA1

8905ac40871bf75b33244df1bbfd92241d6cec4c
Compression icon

ZIP

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Size

9.7 MB
Data icon

MD5

ba51ab204ace78e30a8233a79947ea08
Data icon

SHA1

57a78ae54578a86012dbf41ac6afb9ca2e57159e