# *Clostridium ramosum* DSM1402

| iPtgxDB Release     ||
| ------: | :--------: |
| Version | 1          |
| Date    | 10.08.2020 |

## Downloaded from
[/database/annotations/c-ramosum-dsm1402-2](/database/annotations/c-ramosum-dsm1402-2)

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 Clostridium ramosum (DSM 1402) was created by hierarchically integrating protein coding sequences from the following annotation resources:

| Hierarchy | Resource | Link |
| :---: | :--- | :--- |
| 1 | NCBI RefSeq | CP036346.1 from 22-FEB-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.
