At2g05620.1/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
Sequence 2
Got here 3
Got here 4
Got here 3
Got here 4
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g05620-1h2vC.pir.txt
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Assigned types to 133 residues in Sequence 2-05620, 0 remain unknown
Assigned types to 71 residues in Sequence 1h2vC, 62 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 At2g05620-1h2vC.pir.txt into sequence alignment.
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>1H2V.pdb Made from 6667 ATOM records in 1H2V.pdb
DHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARL
LPEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLV
RFLSDLVNCHVIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLP
WVGKELYEKKDAEMDRIFANTESYLKRRQKTHVPMLQVWTADKPHPQEEY
LDCLWAQIQKLKKDRWQERHILRPYLAFDSILCEALQHNLPPFTPPPHTE
DSVYPMPRVIFRMFDYTDDPEGPVMPGSHSVERFVIEENLHCIIKSHWKE
RKTCAAQLVSYPGKNKIPLNYHIVEVIFAELFQLPAPPHIDVMYTTLLIE
LCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHHLSNFQFRW
SWEDWSDCLSQDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCP
SNPTCIYKYGDESSNSLPGHSVALCLAVAFKSKATNDEIFSILKDVPNFN
PLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVLRVM
FEVWRNHPQMIAVLVDKMIRTQIVDCAAVANWIFSSELSRDFTRLFVWEI
LHSTIRKMNKHVLKIQKELEEAKIERLQEKVESAQSEQKNLFLVIFQRFI
MILTEHLVRCETDGTSVLTPWYKNCIERLQQIFLQHHQIIQQYMVTLENL
LFTAELDPHILAVFQQFCALQAEKLLKKSCTLYVGNLSFYTTEEQIYELF
SKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI
IRTDWDAGFKEGRQY
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Best alignment:
1H2V.pdb 498 NFNPLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVL 547
 +FNPLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVL
1h2vC 4 SFNPLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVL 53
1H2V.pdb 548 RVMFEVWRNHPQMIAVLV 565
 RVMFEVWRNHPQMIAVLV
1h2vC 54 RVMFEVWRNHPQMIAVLV 71
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Highlighted IDENTICAL residue LEU 542 index1 502 path 69 %Seq 100.00
Highlighted IDENTICAL residue VAL 548 index1 508 path 75 %Seq 100.00
Highlighted IDENTICAL residue THR 550 index1 510 path 77 %Seq 100.00
Highlighted IDENTICAL residue LYS 557 index1 517 path 84 %Seq 100.00
Highlighted IDENTICAL residue PHE 559 index1 519 path 86 %Seq 100.00
Highlighted IDENTICAL residue ALA 565 index1 525 path 93 %Seq 100.00
Highlighted IDENTICAL residue ALA 567 index1 527 path 95 %Seq 100.00
Highlighted IDENTICAL residue VAL 572 index1 532 path 100 %Seq 100.00
Highlighted IDENTICAL residue SER 579 index1 539 path 107 %Seq 100.00
Highlighted IDENTICAL residue LEU 604 index1 564 path 132 %Seq 100.00
Highlighted 10 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g05620-1h2vC.pir.txt.1H2V.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g05620-1h2vC.pir.txt PIR amino_acid 1H2V.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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