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In conclusion, the isolate 9.1, tentatively identified as Pseudomonas deceptionensis based on gyrB alignment, appears to possess most of the major upper funneling pathways necessary for the conversion of lignin-related aromatic compounds.
A few cases of TvBspA proteins were inferred to possess distinctive domains identified by visual inspection of their alignments or through an InterProScan search.
Interestingly, it is the variable region of CBO0798 that is central to the CBO0798-CNT andgnmenthatnd that was predicted by 3D-PSSM to possess a jelly-roll fold similar to HCRn.
In fact, pairwise coarse alignment requires each couple of subsequent views in a dataset to possess a certain amount of overlap (from now on we address such requirement as the overlap constraint).
Alignments from two non-contiguous loci were required not to possess long similar sequences at the putative junction sites to discard false positive results from homologous, paralogous, or random spurious hits.
Clustal alignments of the Kir channel gene family revealed all members to possess a high degree of sequence similarity in core regions [ 9].
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