At2g04039.1/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
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Got here 3
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Sequence 2
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g04039-1-2bkv_A.pir.txt
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Assigned types to 199 residues in Sequence 2-04039-1, 0 remain unknown
Assigned types to 68 residues in Sequence 2bkv_A, 131 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 At2g04039-1-2bkv_A.pir.txt into sequence alignment.
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>2BKV.pdb Made from 3889 ATOM records in 2BKV.pdb
MKVMECQTYEELSQIAARITADTIKEKPDAVLGLATGGTPEGTYRQLIRL
HQTENLSFQNITTVNLDEYAGLSSDDPNSYHFYMNDRFFQHIDSKPSRHF
IPNGNADDLEAECRRYEQLVDSLGDTDIQLLGIGRNGHIGFNEPGTSFKS
RTHVVTLNEQTRQANARYFPSIDSVPKKALTMGIQTILSSKRILLLISGK
SKAEAVRKLLEGNISEDFPASALHLHSDVTVLIDREAASLRMKVMECQTY
EELSQIAARITADTIKEKPDAVLGLATGGTPEGTYRQLIRLHQTENLSFQ
NITTVNLDEYAGLSSDDPNSYHFYMNDRFFQHIDSKPSRHFIPNGNADDL
EAECRRYEQLVDSLGDTDIQLLGIGRNGHIGFNEPGTSFKSRTHVVTLNE
QTRQANARYFPSIDSVPKKALTMGIQTILSSKRILLLISGKSKAEAVRKL
LEGNISEDFPASALHLHSDVTVLIDREAASLRP
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Best alignment:
2BKV.pdb 174 SVPKKALTMGIQTILSSKRI--LLLISGKSKAEAVRKLLE 211
 VP +++ T+ SS + L L SG K +R L+
2-04039-1 10 GVPSSRISITTPTLSSSSLLPPLTLQSGTRKDNLLRCALQ 49
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Highlighted IDENTICAL residue SER 174 index1 174 path 10 %Seq 50.00
Highlighted IDENTICAL residue VAL 175 index1 175 path 11 %Seq 100.00
Highlighted IDENTICAL residue PRO 176 index1 176 path 12 %Seq 100.00
Highlighted IDENTICAL residue THR 186 index1 186 path 22 %Seq 100.00
Highlighted IDENTICAL residue SER 189 index1 189 path 25 %Seq 100.00
Highlighted IDENTICAL residue SER 190 index1 190 path 26 %Seq 100.00
Highlighted IDENTICAL residue LEU 194 index1 194 path 32 %Seq 100.00
Highlighted IDENTICAL residue LEU 196 index1 196 path 34 %Seq 100.00
Highlighted IDENTICAL residue SER 198 index1 198 path 36 %Seq 100.00
Highlighted IDENTICAL residue GLY 199 index1 199 path 37 %Seq 100.00
Highlighted IDENTICAL residue LYS 202 index1 202 path 40 %Seq 100.00
Highlighted IDENTICAL residue ARG 207 index1 207 path 45 %Seq 100.00
Highlighted IDENTICAL residue LEU 210 index1 210 path 48 %Seq 100.00
Highlighted 13 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g04039-1-2bkv_A.pir.txt.2BKV.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g04039-1-2bkv_A.pir.txt PIR amino_acid 2BKV.pdb A 100.0 BLOSUM62.dat 
completed successfully.
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