Glyceraldehyde3PhosphateDehydrogenase

blastpgp -I T -m 4 -e 1E-40 -b 3000 -v 3000 -j 10 -d /data/nr -i 1GAD.faa -o 1GAD_BL.out 1GAD_BL.out
- note used an E value cutoff of 1E-40 to ensure convergence
structure based alignment file for guiding clustalw GAP_struct.aln
sequences aligned and processed as for ChorismateSynthase
alignment statistics: 1GAD_BL_90_trim_alistat.txt
phylogeny determined for the alignment
- get_web_tx.pl 1GAD_BL_90_trim.mfa > 1GAD_90_phylogeny.txt
MI, Z score, distances, and linkages determined
- peerZ_3.pl -i 1GD1.MI.txt > 1GD1_P0.txt
- structure_assign.pl -i 1GD1_P0.txt -j 1GD1.pdb -m O -k "P Q R" > 1GD1_P0_dist.txt
- linkage.pl 1GD1_P0_dist.txt > 1GD1_P0_dist_link.txt
graph.pl -i 1GD1_P0_dist.txt > 1GD1.dot