The Redox System in C. elegans, a Phylogenetic Approach

Figure 5

Maximum likelihood majority-rule bootstrap consensus tree of thioredoxin (TRX) and nucleoredoxin (NXN) proteins. A blast (blastp) search of known Homo sapiens (H.s), Saccharomyces cerevisiae (S.c), and Drosophila melanogaster (D.m) proteins was undertaken to identify all the homologs within these three species. The proteins from these species were then blasted against Caenorhabditis elegans (C.e) to identify homologues in the Genbank database. Identified sequences with significant expected value (≤~1E − 10) were used to generate a multiple sequence alignment (MSA) via ClustalW 2.1. The MSAs were then trimmed and used to produce a maximum likelihood majority-rule bootstrap consensus tree inferred from 1000 replicates via Mega 5.10. Proteins with sequences greater that ~350aa that were more closely related to other families discussed in this paper, such as GRX or PDI, were removed from this analysis. Some proteins fit equally well with TRX and TRX-related families, for example, DPY11 can be found in both the TRX and protein disulfide isomerase (PDI) trees.