At2g05120.1/PDB

<pre_ &&&&&&&&&&&&&&&&&&&& 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 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 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 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 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/At2g05120-1xksA.pir.txt

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

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

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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

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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

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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.

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