Figure 3. A structure-based similarity network describes a map of the Trx fold class.

A Structure similarity network, containing 159 structures that are a maximum of 60% identical (by sequence) that span the Trx fold class. Similarity is defined by FAST scores better than a score of 4.5; edges at this threshold represent alignments with a median of 2.75 Å RMSD across 72 aligned positions, while the rest of the edges represent better alignments. As given in the key, each node is colored by a PFAM Thioredoxin-like Clan family if the chain sequence is a member. (Non-members are colored grey and labeled “No hit to Trx Clan.) These classes are discussed briefly in Table 1. Nodes with thick white borders and bold labels denote chains present in the hierarchical clustering tree in D. Labels like “1ON4_A” denote PDB ID 1ON4, chain A. Some additional proteins that may be of interest are labeled with plain face text and labels. B Structure similarity network containing the same structures as in A, shown at the more stringent threshold of 7.5. Edges at this threshold correspond to alignments with a median of 2.45 Å RMSD across 89 aligned positions. Nodes are colored as in A. C Structure similarity network containing the 105 structures from the large connected cluster in B, displayed at a FAST score cutoff of 12.0; edges at this threshold represent alignments with a median of 2.21 Å RMSD across 102 aligned positions. Nodes are colored as in A. D Complete linkage hierarchical clustering tree based on pairwise FAST scores for 15 representative structures singled out in the networks in A–C, with PDB IDs in bold, and associated SwissProt sequence IDs in plain text. Note: this is a static figure generated from interactive protein similarity networks that can be downloaded and viewed from http://babbittlab.compbio.ucsf.edu/resources/TrxFold/.