At2g09900.1/PDB

&&&&&&&&&&&&&&&&&&&& BEGIN /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues &&&&&&&&&&&&&&&&&&&&
Successfully read 2 file paths from WYRM_file_paths.txt
generic_input /usr/local/www/html/proteins/workspace/
generic_output /usr/local/www/html/proteins/htdocs/results/
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Sequence file type = 3
Sequence type = 3
Got here 1
Got here 2
Got here 3
Sequence 1
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Sequence 2
Got here 3
Got here 4
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g09900-1q4kB.pir.txt
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Assigned types to 175 residues in Sequence 2-09900, 5 remain unknown
Assigned types to 48 residues in Sequence 1q4kB, 132 remain unknown
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Successfully read 576 entries for residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat
Read the residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat
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Translated sequence file At2g09900-1q4kB.pir.txt into sequence alignment.
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>1Q4K.pdb Made from 5483 ATOM records in 1Q4K.pdb
DCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDK
YGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPN
SLMKKITLLKYFRNYMSEHLLKAGANITPREGDELARLPYLRTWFRTRSA
IILHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEY
GCCKELASRLRYARTMVDKLLSSRCHLSDMLQQLHSVNASKPSERGLVRQ
EEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYND
GDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANI
TPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLM
AAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSCHLS
DMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGY
QLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKK
ITLLKYFRNYMSEHLLKAGDELARLPYLRTWFRTRSAIILHLSNGSVQIN
FFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYA
RTMVDKLLSSMQSPLMQSPLMQSPL
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Best alignment:
1Q4K.pdb 1 DCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYS 48
 DC L D LQ L + L ++ + PA + WV+YS
2-09900 120 DCILDDKLQSL----LHSALNQTLEHRKGKKTPATHSTSHSTTWVEYS 163
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Highlighted IDENTICAL residue ASP 371 index1 1 path 120 %Seq 100.00
Highlighted IDENTICAL residue CYS 372 index1 2 path 121 %Seq 100.00
Highlighted IDENTICAL residue LEU 374 index1 4 path 123 %Seq 100.00
Highlighted IDENTICAL residue ASP 376 index1 6 path 125 %Seq 100.00
Highlighted IDENTICAL residue LEU 378 index1 8 path 127 %Seq 100.00
Highlighted IDENTICAL residue GLN 379 index1 9 path 128 %Seq 100.00
Highlighted IDENTICAL residue LEU 381 index1 11 path 130 %Seq 100.00
Highlighted IDENTICAL residue ALA 386 index1 16 path 131 %Seq 50.00
Highlighted IDENTICAL residue SER 387 index1 17 path 132 %Seq 100.00
Highlighted IDENTICAL residue LYS 388 index1 18 path 133 %Seq 100.00
Highlighted IDENTICAL residue LEU 394 index1 24 path 144 %Seq 100.00
Highlighted IDENTICAL residue PRO 403 index1 33 path 153 %Seq 100.00
Highlighted IDENTICAL residue ALA 404 index1 34 path 154 %Seq 100.00
Highlighted IDENTICAL residue TRP 414 index1 44 path 164 %Seq 100.00
Highlighted IDENTICAL residue VAL 415 index1 45 path 165 %Seq 100.00
Highlighted IDENTICAL residue TYR 417 index1 47 path 167 %Seq 100.00
Highlighted IDENTICAL residue SER 418 index1 48 path 168 %Seq 100.00
Highlighted 17 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g09900-1q4kB.pir.txt.1Q4K.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g09900-1q4kB.pir.txt PIR amino_acid 1Q4K.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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