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At2g04039.1/PDB

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&&&&&&&&&&&&&&&&&&&& 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/

======================================================

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
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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

======================================================

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

======================================================

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

======================================================

Translated sequence file At2g04039-1-2bkv_A.pir.txt into sequence alignment.

======================================================

>2BKV.pdb  Made from 3889 ATOM records in 2BKV.pdb
MKVMECQTYEELSQIAARITADTIKEKPDAVLGLATGGTPEGTYRQLIRL
HQTENLSFQNITTVNLDEYAGLSSDDPNSYHFYMNDRFFQHIDSKPSRHF
IPNGNADDLEAECRRYEQLVDSLGDTDIQLLGIGRNGHIGFNEPGTSFKS
RTHVVTLNEQTRQANARYFPSIDSVPKKALTMGIQTILSSKRILLLISGK
SKAEAVRKLLEGNISEDFPASALHLHSDVTVLIDREAASLRMKVMECQTY
EELSQIAARITADTIKEKPDAVLGLATGGTPEGTYRQLIRLHQTENLSFQ
NITTVNLDEYAGLSSDDPNSYHFYMNDRFFQHIDSKPSRHFIPNGNADDL
EAECRRYEQLVDSLGDTDIQLLGIGRNGHIGFNEPGTSFKSRTHVVTLNE
QTRQANARYFPSIDSVPKKALTMGIQTILSSKRILLLISGKSKAEAVRKL
LEGNISEDFPASALHLHSDVTVLIDREAASLRP

======================================================

Best alignment:
2BKV.pdb    174  SVPKKALTMGIQTILSSKRI--LLLISGKSKAEAVRKLLE   211
                  VP   +++   T+ SS  +  L L SG  K   +R  L+
2-04039-1    10  GVPSSRISITTPTLSSSSLLPPLTLQSGTRKDNLLRCALQ    49

======================================================

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.

@@@@@@@@@@@@@@@@@@@@ END  /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@

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