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 Got here 4 Got here 3 Got here 4 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  DCILDDKLQSLLHSALNQTLEHRKGKKTPATHSTSHSTTWVEYS   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

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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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