At2g09865.1/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
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Sequence 1
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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/At2g09865-1jas_A.pir.txt
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Assigned types to 339 residues in Sequence 2-09865, 17 remain unknown
Assigned types to 108 residues in Sequence 1jas_A, 248 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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Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 261 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 262 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 263 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 264 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 265 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 266 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 281 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 282 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 283 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 297 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 310 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 311 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 312 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 313 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 314 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 315 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 316 All residues are positively and negatively charged
Translated sequence file At2g09865-1jas_A.pir.txt into sequence alignment.
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>1JAS.pdb Made from 2391 ATOM records in 1JAS.pdb
MSTPARRRLMRDFKRLQEDPPVGVSGAPSENNIMQWNAVIFGPEGTPFED
GTFKLVIEFSEEYPNKPPTVRFLSKMFHPNVYADGSICLDILQNRWSPTY
DVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSWN
DS
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Best alignment:
1JAS.pdb 133 NKREYEKRVSAIV 145
 KR+ KRV +++
2-09865 192 RKRKKSKRVGSLL 204
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Highlighted IDENTICAL residue ASN 133 index1 133 path 192 %Seq 50.00
Highlighted IDENTICAL residue LYS 134 index1 134 path 193 %Seq 50.00
Highlighted IDENTICAL residue ARG 135 index1 135 path 194 %Seq 50.00
Highlighted IDENTICAL residue GLU 136 index1 136 path 195 %Seq 50.00
Highlighted IDENTICAL residue TYR 137 index1 137 path 196 %Seq 50.00
Highlighted IDENTICAL residue GLU 138 index1 138 path 197 %Seq 50.00
Highlighted IDENTICAL residue LYS 139 index1 139 path 198 %Seq 50.00
Highlighted IDENTICAL residue ARG 140 index1 140 path 199 %Seq 50.00
Highlighted IDENTICAL residue VAL 141 index1 141 path 200 %Seq 50.00
Highlighted IDENTICAL residue SER 142 index1 142 path 201 %Seq 50.00
Highlighted IDENTICAL residue ALA 143 index1 143 path 202 %Seq 50.00
Highlighted IDENTICAL residue ILE 144 index1 144 path 203 %Seq 50.00
Highlighted IDENTICAL residue VAL 145 index1 145 path 204 %Seq 50.00
Highlighted 13 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g09865-1jas_A.pir.txt.1JAS.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g09865-1jas_A.pir.txt PIR amino_acid 1JAS.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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