Words similar to psi-blast

Example sentences for: psi-blast

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To determine the entire extant of the N1pC/P60 family we initiated PSI-BLAST [ 28] searches of the non-redundant database (expect (E)-value for inclusion in threshold = 0.01, iterated to convergence) with a number of starting points, such as the catalytic domains of B. subtilis LytF (C1wE) and LytE (C1wF), L. monocytogenes P60 and P45 and E. coli N1pC.
As a step beyond PSI-BLAST or PFAM profiles, we have used 123D+ [ 17 18 ] , which not only performs target-template profile-profile alignment, but also uses secondary structure and contact capacity potential information for protein fold recognition.
For example, A. thaliana has at least three superfamily members in the PSI-BLAST output, including carbamoyl phosphate synthetase, 3-methylcrotonyl-CoA carboxylase, and acetyl CoA carboxylase.
Using PSI-BLAST [ 27 ] with different inteins as seeds, divergent inteins with less than ten percent sequence identity as compared to the query sequence are recovered (data not shown); however, using this approach we did not discover any additional intein or homing endonuclease encoding genes in T. acidophilum.
A multiple alignment of the N-terminal-most domain of the SGCs and its bacterial homologs was prepared using the T_coffee program and adjusted manually based on the PSI-BLAST HSPs (Fig.