An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations
Figure 4
A sequence similarity network shows how each Trx fold superfamily is distributed.
Sequence similarity network, containing 4,082 representative sequences that are a maximum of 40% identical and span the Trx fold class. Similarity is defined by pairwise BLAST alignments better than an E-value of 1×10−12; edges at this threshold represent alignments with a median 30% identity over 120 residues, while the rest of the edges represent better alignments. Each node is colored by a PFAM Thioredoxin-like Clan family if the sequence is a member. (Non-members are colored grey and labeled “No hit to Trx Clan.) These classes are discussed briefly in Table 1. Large nodes represent sequences that are associated with the 159 structures in Fig. 3. The sequences associated with the 15 representative structures in Fig. 3C are labeled using bold text and white arrows. The general locations of other sequences representing different superfamilies are noted using italicized text. Some edges representing similarity relationships from outside of the domain of interest are colored red, and are discussed in the text. Blue letters in parentheses correspond to the labels defining each group in Figures 5–7.