FANDOM


&&&&&&&&&&&&&&&&&&&& 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

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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/At2g05120-1xksA.pir.txt

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

Assigned types to 1234 residues in Sequence 2-05120, 28 remain unknown
Assigned types to 412 residues in Sequence 1xksA, 850 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 At2g05120-1xksA.pir.txt into sequence alignment.

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

>1XKS.pdb  Made from 2845 ATOM records in 1XKS.pdb
ESVNYDVKTFGSSLPVKVMEALTLAEVDDQLTINIDEGGWACLVCKEKLI
IWKIALSPITKLSVCKELQLPPSDFHWSADLVALSYSSTQAVAVMVATRE
GSIRYWPSLAGEDTYTEAFVDKTYSFLTAVQGGSFILSSSGSQLIRLIPE
SSGKIHQHILPQGQGMSDLTLSSVLWDRERSSFYSLTSSNISKWELDDSS
EKHAYSWDINRALKENITDAIWGSESNYEAIKEGVNIRYLDLKQNCDGLV
ILAAAWHSADNPCLIYYSLITIEDNGCQMSDAVTVEVTQYNPPFQSEDLI
LCQLTVPNFSNQTAYLYNESAVYVCSTGTGKFSLPQEKIVFNAQGDSVLG
AGACGGVPIIFSRNSGLVSITSRE

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

Best alignment:
1XKS.pdb   132  GGSFILSSSGSQLIRLIPESSGKIHQHILPQGQG-MSDLTLSSVLWDRER   180
                G + ILS  G+  +     SS ++++  LP   G + D ++ S   + E 
2-05120    447  GSAIILSGDGTATVCYCHGSSTRLYKFDLPYDAGKVLDASVLSSTDEHEY   496

1XKS.pdb   181  SSFYSLT   187
                 ++  LT
2-05120    497  GAWTVLT   503

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

Highlighted IDENTICAL residue LEU  222  index1  137  path  476  %Seq 100.00
Highlighted IDENTICAL residue ILE  230  index1  145  path  484  %Seq 100.00
Highlighted IDENTICAL residue ARG  231  index1  146  path  485  %Seq 100.00
Highlighted IDENTICAL residue HIS  243  index1  158  path  501  %Seq 100.00
Highlighted IDENTICAL residue GLY  248  index1  163  path  506  %Seq 100.00
Highlighted IDENTICAL residue GLN  249  index1  164  path  507  %Seq  50.00
Highlighted IDENTICAL residue GLY  250  index1  165  path  508  %Seq  50.00
Highlighted IDENTICAL residue MET  251  index1  166  path  510  %Seq 100.00
Highlighted IDENTICAL residue SER  270  index1  167  path  511  %Seq 100.00
Highlighted IDENTICAL residue LEU  272  index1  169  path  513  %Seq 100.00
Highlighted IDENTICAL residue SER  275  index1  172  path  516  %Seq  50.00
Highlighted IDENTICAL residue SER  276  index1  173  path  517  %Seq  50.00
Highlighted IDENTICAL residue VAL  277  index1  174  path  518  %Seq  50.00
Highlighted IDENTICAL residue LEU  278  index1  175  path  519  %Seq  50.00
Highlighted IDENTICAL residue TRP  279  index1  176  path  520  %Seq  50.00
Highlighted IDENTICAL residue ASP  280  index1  177  path  521  %Seq  50.00
Highlighted IDENTICAL residue ARG  281  index1  178  path  522  %Seq  50.00
Highlighted IDENTICAL residue SER  284  index1  181  path  525  %Seq 100.00
Highlighted 18 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g05120-1xksA.pir.txt.1XKS.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g05120-1xksA.pir.txt PIR amino_acid 1XKS.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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