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At2g02540.1/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
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
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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/At2g02540-1wh5_A.pir.txt

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

Assigned types to 310 residues in Sequence 2-02540, 0 remain unknown
Assigned types to 78 residues in Sequence 1wh5_A, 232 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 At2g02540-1wh5_A.pir.txt into sequence alignment.

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

>1WH5.pdb  Made from 1242 ATOM records in 1WH5.pdb
GSSGSSGSSAEAGGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEV
IQRFCQETGVPRQVLKVWLHNNKHSGPSSG

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

Best alignment:
1WH5.pdb    13  GGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPR    62
                G   +KR RTKFT EQKE+M++ AER+GW+IQRQ++ V+Q+ CQE G+ R
2-02540    218  GHNQKKRFRTKFTQEQKEKMISFAERVGWKIQRQEESVVQQLCQEIGIRR   267

1WH5.pdb    63  QVLKVWLHNNKHS    75
                +VLKVW+HNNK +
2-02540    268  RVLKVWMHNNKQN   280

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

Highlighted IDENTICAL residue GLY   13  index1   13  path  218  %Seq 100.00
Highlighted IDENTICAL residue LYS   18  index1   18  path  223  %Seq 100.00
Highlighted IDENTICAL residue ARG   19  index1   19  path  224  %Seq 100.00
Highlighted IDENTICAL residue ARG   21  index1   21  path  226  %Seq 100.00
Highlighted IDENTICAL residue THR   22  index1   22  path  227  %Seq 100.00
Highlighted IDENTICAL residue LYS   23  index1   23  path  228  %Seq 100.00
Highlighted IDENTICAL residue PHE   24  index1   24  path  229  %Seq 100.00
Highlighted IDENTICAL residue THR   25  index1   25  path  230  %Seq 100.00
Highlighted IDENTICAL residue GLU   27  index1   27  path  232  %Seq 100.00
Highlighted IDENTICAL residue GLN   28  index1   28  path  233  %Seq 100.00
Highlighted IDENTICAL residue LYS   29  index1   29  path  234  %Seq 100.00
Highlighted IDENTICAL residue GLU   30  index1   30  path  235  %Seq 100.00
Highlighted IDENTICAL residue MET   32  index1   32  path  237  %Seq 100.00
Highlighted IDENTICAL residue ALA   36  index1   36  path  241  %Seq 100.00
Highlighted IDENTICAL residue GLU   37  index1   37  path  242  %Seq 100.00
Highlighted IDENTICAL residue ARG   38  index1   38  path  243  %Seq 100.00
Highlighted IDENTICAL residue GLY   40  index1   40  path  245  %Seq 100.00
Highlighted IDENTICAL residue TRP   41  index1   41  path  246  %Seq 100.00
Highlighted IDENTICAL residue ILE   43  index1   43  path  248  %Seq 100.00
Highlighted IDENTICAL residue GLN   44  index1   44  path  249  %Seq 100.00
Highlighted IDENTICAL residue ARG   45  index1   45  path  250  %Seq 100.00
Highlighted IDENTICAL residue GLN   46  index1   46  path  251  %Seq 100.00
Highlighted IDENTICAL residue VAL   50  index1   50  path  255  %Seq 100.00
Highlighted IDENTICAL residue GLN   52  index1   52  path  257  %Seq 100.00
Highlighted IDENTICAL residue CYS   55  index1   55  path  260  %Seq 100.00
Highlighted IDENTICAL residue GLN   56  index1   56  path  261  %Seq 100.00
Highlighted IDENTICAL residue GLU   57  index1   57  path  262  %Seq 100.00
Highlighted IDENTICAL residue GLY   59  index1   59  path  264  %Seq 100.00
Highlighted IDENTICAL residue ARG   62  index1   62  path  267  %Seq 100.00
Highlighted IDENTICAL residue VAL   64  index1   64  path  269  %Seq 100.00
Highlighted IDENTICAL residue LEU   65  index1   65  path  270  %Seq 100.00
Highlighted IDENTICAL residue LYS   66  index1   66  path  271  %Seq 100.00
Highlighted IDENTICAL residue VAL   67  index1   67  path  272  %Seq 100.00
Highlighted IDENTICAL residue TRP   68  index1   68  path  273  %Seq 100.00
Highlighted IDENTICAL residue HIS   70  index1   70  path  275  %Seq 100.00
Highlighted IDENTICAL residue ASN   71  index1   71  path  276  %Seq 100.00
Highlighted IDENTICAL residue ASN   72  index1   72  path  277  %Seq 100.00
Highlighted IDENTICAL residue LYS   73  index1   73  path  278  %Seq 100.00
Highlighted 38 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02540-1wh5_A.pir.txt.1WH5.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02540-1wh5_A.pir.txt PIR amino_acid 1WH5.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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