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At2g13690.1/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

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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/At2g13690-1ejlI.pir.txt

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

Assigned types to 544 residues in Sequence 2-13690, 27 remain unknown
Assigned types to 361 residues in Sequence 1ejlI, 210 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

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

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 289  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 290  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 291  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 292  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 293  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 294  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 295  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 296  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 297  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 391  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 392  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 484  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 485  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 486  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 487  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 488  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 489  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 490  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 491  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 492  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 512  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 513  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 514  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 515  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 516  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 517  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 518  All residues are positively and negatively charged

Translated sequence file At2g13690-1ejlI.pir.txt into sequence alignment.

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

>1EJL.pdb  Made from 3368 ATOM records in 1EJL.pdb
PKKKRKVPKKKRKVGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSRE
KQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKA
VVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAID
PLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLV
RLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATEL
PIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATW
TMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSG
GTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGET
EKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYFS

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

Best alignment:
1EJL.pdb   148  AIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILP   197
                A+  +LA     +   L     + L W++++ C + NP   L ++ + L 
2-13690    284  AVSEILARFNSNETENLQDSLSKKLVWSITS-CSDVNPRNELKSLVKGLL   332

1EJL.pdb   198  TLVRLLHHNDPEV   210
                    +     PE+
2-13690    333  CKSSVYEKEQPEI   345

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

Highlighted IDENTICAL residue LEU  210  index1  153  path  298  %Seq 100.00
Highlighted IDENTICAL residue ALA  211  index1  154  path  299  %Seq 100.00
Highlighted IDENTICAL residue LEU  221  index1  164  path  309  %Seq 100.00
Highlighted IDENTICAL residue LEU  229  index1  172  path  317  %Seq 100.00
Highlighted IDENTICAL residue TRP  231  index1  174  path  319  %Seq 100.00
Highlighted IDENTICAL residue GLU  250  index1  193  path  337  %Seq 100.00
Highlighted IDENTICAL residue PRO  254  index1  197  path  341  %Seq 100.00
Highlighted 7 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13690-1ejlI.pir.txt.1EJL.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13690-1ejlI.pir.txt PIR amino_acid 1EJL.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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


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