Pathway annotation using sequence alignment

Question

[sharmatina189059]

Dear all, I have 3652 bacterial protein sequences . I need to do pathway analysis. I have used BLASTKOALA, KASS, GeneSCF, DAVID and BioCyc for this purpose. But by using these tools only 50% genome is annotated in terms of getting pathway names or Ko numbers.

For remaining 50% genome annotation, I want to do sequence alignment of remaining protein sequences with the NR protein database of bacteria. Is it possible to do it with sequence alignment like this. and I am trying to download NR bacterial protein sequence database but it gives me a error. I am downloading it using ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/. Please tell me how can I download NR bacterial protein database and how can I assign pathways name to it?

Answer 1

[natasha.sernova]

To find bacterial genomes (there are much more now) see the post below:

where can I get environmental bacteria genome in fasta format (as many as possible)?

To look for KEGG-pathways see these recent papers:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210567/pdf/gkw1092.pdf

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5584762/

There are thousands of articles describing bacterial pathways, but often each one - some particular pathway only:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133246/pdf/fmicb-07-01945.pdf

To look for regulation in gram-positive bacteria, see Regprecise-site, for example:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840689/pdf/1471-2164-14-745.pdf

RegPrecise http://regprecise.lbl.gov