At2g13690.1/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
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Sequence 1
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Sequence 2
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g13690-1ejlI.pir.txt
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Assigned types to 544 residues in Sequence 2-13690, 27 remain unknown
Assigned types to 361 residues in Sequence 1ejlI, 210 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 289 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 290 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 291 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 292 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 293 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 294 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 295 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 296 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 391 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 392 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 484 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 485 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 486 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 487 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 488 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 489 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 490 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 491 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 492 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 512 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 513 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 514 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 515 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 516 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 517 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 518 All residues are positively and negatively charged
Translated sequence file At2g13690-1ejlI.pir.txt into sequence alignment.
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>1EJL.pdb Made from 3368 ATOM records in 1EJL.pdb
PKKKRKVPKKKRKVGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSRE
KQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKA
VVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAID
PLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLV
RLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATEL
PIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATW
TMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSG
GTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGET
EKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYFS
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Best alignment:
1EJL.pdb 148 AIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILP 197
 A+ +LA + L + L W++++ C + NP L ++ + L 
2-13690 284 AVSEILARFNSNETENLQDSLSKKLVWSITS-CSDVNPRNELKSLVKGLL 332
1EJL.pdb 198 TLVRLLHHNDPEV 210
 + PE+
2-13690 333 CKSSVYEKEQPEI 345
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Highlighted IDENTICAL residue LEU 210 index1 153 path 298 %Seq 100.00
Highlighted IDENTICAL residue ALA 211 index1 154 path 299 %Seq 100.00
Highlighted IDENTICAL residue LEU 221 index1 164 path 309 %Seq 100.00
Highlighted IDENTICAL residue LEU 229 index1 172 path 317 %Seq 100.00
Highlighted IDENTICAL residue TRP 231 index1 174 path 319 %Seq 100.00
Highlighted IDENTICAL residue GLU 250 index1 193 path 337 %Seq 100.00
Highlighted IDENTICAL residue PRO 254 index1 197 path 341 %Seq 100.00
Highlighted 7 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13690-1ejlI.pir.txt.1EJL.pdb.conservation.pml
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The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13690-1ejlI.pir.txt PIR amino_acid 1EJL.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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