Integrated proteogenomics database

Bacteria iconB. henselae CHDE101_tryptic

Bartonella henselae strain ATCC49882 variant-1 (CHDE101; Genbank #CP020742) is a laboratory variant of B. henselae strain Houston-1. It encodes for a frame-shifted BadA, which is not expressed on the surface of the bacteria (Lu et al., 2013).

An iPtgxDB was created for this lab strain by hierarchically integrating protein coding sequences from the ab initio gene prediction software Prodigal (Hyatt et al. 2010) (v2.6) and in silico ORFs on top.

Hierarchy Resource Link
1 Prodigal [2] Ab initio gene predictions from Prodigal (v2.6)
2 in silico ORFs The in silico ORF 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 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. Lu, Y.Y., Franz, B., Truttmann, M.C., Riess, T., Gay-Fraret, J., Faustmann, M., Kempf, V.A., and Dehio, C. 2013. Bartonella henselae trimeric autotransporter adhesin BadA expression interferes with effector translocation by the VirB/D4 type IV secretion system. Cell Microbiol 15: 759-778.
  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. 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

10.11.2016

Downloads icon Downloads

Compression icon

TAR.GZ

File icon

Size

2.9 MB
Data icon

MD5

2f3512304a98b8603a93cef0d147fdc1
Data icon

SHA1

e6c40ced583222dc817b22f5fd42ddd20157cc56
Compression icon

ZIP

File icon

Size

3.0 MB
Data icon

MD5

5b6f2431019087d58b3df14a42151609
Data icon

SHA1

26786fca84a97fd37b94d4d24664d1ee9c0ed2a8