Hello everyone! Welcome to the list! I have a question regrding a psi-blast result using scop sunid 81250 against SPTremble ac Q8WTS6 (using a quite NR SPTremble as the search space). I get only a single HSP, but two itterations, and the exact same HSP has a better E-Value in the second itteration. Is this a bug or is there some reason why the scoring system can vary in this way? I am using the latest version of psiblast ca one month ago. The important bits of the results are... <Iteration_iter-num>1</Iteration_iter-num> <Hit_num>1</Hit_num> <Hsp_evalue>2.73238e-112</Hsp_evalue> <Hsp_num>1</Hsp_num> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>173</Hsp_query-to> <Hsp_hit-from>194</Hsp_hit-from> <Hsp_hit-to>366</Hsp_hit-to> <Hsp_identity>173</Hsp_identity> <Hsp_positive>173</Hsp_positive> <Hsp_gaps>0</Hsp_gaps> <Hsp_align-len>173</Hsp_align-len> <Iteration_iter-num>2</Iteration_iter-num> <Hit_num>1</Hit_num> <Hsp> <Hsp_num>1</Hsp_num> <Hsp_evalue>2.41558e-119</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>173</Hsp_query-to> <Hsp_hit-from>194</Hsp_hit-from> <Hsp_hit-to>366</Hsp_hit-to> <Hsp_identity>173</Hsp_identity> <Hsp_positive>173</Hsp_positive> <Hsp_gaps>0</Hsp_gaps> <Hsp_align-len>173</Hsp_align-len> Cheers, Dan.