I have been given the task of protein sequence PSI BLASTing a histidine kinase in Vibrio Cholerae. I have to do two rounds of PSI BLAST and observe the top three hits in each. I noticed that these hits all start with "Vibrio Cholerae Histidine kinase" but after that they have different accession numbers e.g. EEO20674.1 vs WP_001121906. Also between the 1st and 2nd round of iterations the only hit that has remained is that with the accession number EEO20674.1(moving from 2nd to 1st best hit between the rounds). Does this mean that EEO20674.1 is likely to be the best distant related homologue for comparison or is the BLAST just reproducing redundant sequences (note the Identity rates is 100% for one of the top 3 in first round and 99% for the other 2 and 99% for all three in the 2nd round) between the hits?
Is this "task" a homework question? Are you starting this search with a known "histidine kinase" from V. cholerae?
If the identities between the sequence and your query is close to 100% (over the entire length?) do you think that can represent a "distant" homolog?
Yes, and yes the sequence is known. As the Identity is usually 99% over the entire sequence, it is my understanding that they are distant homologs as that's what I thought PSI was for... also while the query is a "sensor histidine kinase", some of the hits returned are "signal transduction his kinases".
Yes, and yes the sequence is known. As the Identity is usually 99% over the entire sequence, it is my understanding that they are distant homologs as that's what I thought PSI was for... also while the query is a "sensor histidine kinase", some of the hits returned are "signal transduction his kinases".
Check this tutorial on PSI-blast: http://www.ncbi.nlm.nih.gov/books/NBK2590/
Though PSI-blast can be used to find distant homologs you are not going to see them in iteration 1 since that performs a plain blastp search. I don't know what is expected in the deliverable from this assignment but just two rounds of blasting may not be enough to find true distant homologs.
NCBI has since released DELTA-blast which provides results as good as (or better) than PSI-BLAST.