Predicting bacteria pathway based on whole genome sequence

Question

[21afiq]

Hi, I already obtain a whole genome sequence of my bacteria (already done the annotation and assembly). Is there any way for me to know what type of pathway that presence in my bacteria based on my whole genome sequence? I am new in bioinformatic field. Thanks

Answer 1

[natasha.sernova]

What do you know about your bacterium?

As far as I have understood, its genome was assembled. What do you know in termes of annotation?

Do you have predicted protein sequences? How did you predict them?

To learn the phylum I would suggest to run blastp with some of them.

Its site is

www.ncbi.nlm.nih.gov - NCBI, from there go to BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi).

There are many sites for determining pathways. KEGG (http://www.genome.jp/kegg/),

REACTOME (http://www.reactome.org/),

BioCyc via Pathway Tools software (https://metacyc.org), etc

Answer 2

[dago]

The easiest way is to blast the protiens against db as KEGG. YOu can use web tools like BlastKOALA. In the results then you can navigate amongst the different pathways identified. Of course this will require some manual curation to be sure that eventually missing enzyme are coded in the genome. Another option is to use pathway tools, but you need a license for that.