Additional file 2: Figure S1.
Taxonomic classification of species for which a QSOX sequence was identified. The given classification is based on the NCBI taxonomy browser. Figure S2. QSOX orthologs, paralogs, and splice variants in various taxonomic classifications. To emphasize the hierarchy between orthologs and paralogs, Neighbor-joining (NJ) trees were constructed for QSOX sequences of Alveolata, Nematoda, Stramenopiles, Viridiplantae, Arthropoda, and Chordata. Figure S3. Consensus maximum likelihood tree of QSOX sequences, protists excluded. In an attempt to improve scores at the root of major branches, QSOX sequences of protists were removed from the dataset. Figure S4. Consensus maximum likelihood tree of the Trx domain of QSOX sequences. The Trx domains of QSOX sequences were retrieved using the pattern detailed in the methods section. Abbreviations correspond to species as listed in Figure S3. Figure S5. Consensus maximum likelihood tree of the Erv domain of QSOX sequences. The Erv domains of QSOX sequences were retrieved using the pattern detailed in the methods section. Abbreviations correspond to species as listed in Figure S3. Figure S6. Example of a neighbor-joining tree of the Trx domain/s of QSOX and PDI sequences. PDI sequences were retrieved from NCBI according to their annotation. Redox-active Trx domains were manually extracted from this set. Abbreviations for QSOX correspond to species as listed in Figure S3. Branches corresponding to Trx domains of QSOX sequences are indicated with a pale-blue background. Viridiplantae and Metazoa are indicated with a green and slate-blue background, respectively. Plant and animal parasites are indicated with green and orange asterisks, respectively. Figure S7. Identity of an amino-acid residue in the vicinity of the CXXC motif of QSOX and PDI Trx domains distinguishes the two families. Representative motif sequences of QSOX Trx1 domains are shown on the left, with the serine/threonine residue common in metazoan QSOXs highlighted in green, and the histidine characteristic of plant QSOXs highlighted in gray. For comparison, all CXXC motifs from H. sapiens and A. thaliana QSOXs are shown on the right to demonstrate the near universality of proline, highlighted in yellow, at this position in PDI enzymes in both plant and metazoan species. Only a few QSOXs contain a proline.
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Limor-Waisberg et al. BMC Evolutionary Biology 2013 13:70 doi:10.1186/1471-2148-13-70