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?