Protein structure modeling, phylogenetic analysis, and sequence comparison.

LX Linan Xie
DX Dongliang Xiao
XW Xiaojing Wang
CW Chen Wang
JB Jing Bai
QY Qun Yue
HY Haitao Yue
YL Ye Li
IM István Molnár
YX Yuquan Xu
LZ Liwen Zhang
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The FgSULT1 homology protein structure model was built with I-TASSER (62), and the resulting model was optimized using Discovery Studio v2.7 as described in reference 36. Protein structures were compared using the Dali server (63), cavity volumes were measured using the GHECOM 1.0 server (54), and sequence alignments were performed with MUSCLE v3.6 (64). Phylogenetic relationships were reconstructed using the maximum likelihood and the neighbor joining methods in MEGA v5.2 (65). Statistical support was generated by bootstrap analysis with 1,000 pseudoreplicates. SULTs with confirmed functions were obtained from the UniProtKB database (Table S6 in reference 36).

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