How should I proceed to calculate the percentage of conserved proteins (POCP)?

There could be several reasons why some bacteria do not give any results when using BLASTP to search for homologous proteins:

Lack of sequence information: It is possible that the genome of the bacteria you are searching for does not have any protein-coding sequences that match the query sequence used in the BLASTP search. This could be due to a number of factors, such as incomplete genome sequencing or differences in gene content between different bacterial species.

Low sequence identity: Even if there are homologous proteins in the genome, the level of sequence identity between the query sequence and the bacterial protein may be too low for BLASTP to detect a significant match. In such cases, it may be necessary to adjust the BLASTP parameters or use a different search algorithm that is more sensitive to low sequence identity.

Errors in the input data: It is possible that errors were introduced during the download or preparation of the protein sequences, which could result in incomplete or incorrect data that may not match the query sequence.

Technical issues: Finally, technical issues such as network connectivity, server downtime, or other factors could prevent the BLASTP search from completing successfully.

To further investigate why some bacteria did not give any results, you may need to carefully examine your data, adjust your BLASTP parameters, and try different search algorithms. Additionally, you can consult the BLASTP documentation or seek help from bioinformatics experts.

Hadj Ahmed Belaouni

For some annotators, the syntax/methodology might be different, thus, downloading annotated genomes from NCBI can lead to incompatibility between annotation outputs. It would be wise to have the .fna* files, and try to re-annotate them all using the same annotator, this could fix your issue.

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