Integrated proteogenomics database

Bacteria iconB. longum NCC2705_tryptic

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].

A tryptic iPtgxDB of Bifidobacterium longum (NCC 2705) was created by hierarchically integrating protein coding sequences from the following annotation resources:

Hierarchy Resource Link
1 NCBI RefSeq NC_004307.2 / NC_004943.1; from 06-APR-2020
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

12.08.2020

Downloads icon Downloads

Compression icon

TAR.GZ

File icon

Size

4.1 MB
Data icon

MD5

0b3e97af7d47e3ab3a8572f012fa4b7d
Data icon

SHA1

3a7325b1055d6f2b686ba5c31b03b4101a50581b
Compression icon

ZIP

File icon

Size

4.2 MB
Data icon

MD5

1cb2d0530d88ba213d7d7b21e3e34b18
Data icon

SHA1

aaf803f2ed5626dd97069f56af0ce79fdd82c43d