The wording in the paper could perhaps be re-written, but this was the original
An objection might be raised that the psi-BLAST and SPARCLE results were artificially inflated by redundancies and spurious hits for NylB because of the search parameters we used. This objection would not be valid. First, these parameters were the defaults set by the NIH, and second, the point of the comparison was to show that even under relaxed and generous parameters, no remote potential homologs of PR.C could be detected
spurious hits are false positives. But the point was to give the most relaxed possible seach for PR.C and not NylB. And even then PR.C couldn’t register hits. NylB’s abundance and other nylonases was well demonstrated by the UniProt searches and didn’t require us to do a BLAST search at all. Establishing the homology of NylB to beta-lactamases was quite sufficient to establish the ubiquity of NylB and its homologs. The psi-BLAST was not done for the benefit of demonstraing NylB ubiquity, but rather PR.C’s abundance, and even under the most relaxed parameters, it didn’t return a single hit. Therefore it didn’t exist, and therefore the frame-shift hypothesis for NylB is wrong and should stop being cited.