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

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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g02410-1llzA.pir.txt

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

Assigned types to 308 residues in Sequence 2-02410, 42 remain unknown
Assigned types to 275 residues in Sequence 1llzA, 75 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 At2g02410-1llzA.pir.txt into sequence alignment.

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

>1LLZ.pdb  Made from 11311 ATOM records in 1LLZ.pdb
CGVGFIANLRGKPDHTLVEQALKALGCMEHRGGCSADNDSGDGAGVMTAI
PRELLAQWFNTRNLPMPDGDRLGVGMVFLPQEPSAREVARAYVEEVVRLE
KLTVLGWREVPVNSDVLGIQAKNNQPHIEQILVTCPEGCAGDELDRRLYI
ARSIIGKKLAEDFYVCSFSCRTIVYKGMVRSIILGEFYLDLKNPGYTSNF
AVYHRRFSTNTMPKWPLAQPMRLLGHNGEINTLLGNINWMAAREKELEVS
GWTKAELEALTPIVNQANSDSYNLDSALELLVRTGRSPLEAAMILVPEAY
KNQPALKDYPEISDFHDYYSGLQEPWDGPALLVFSDGKIVGAGLDRNGLR
PARYCITKDDYIVLGSEAGVVDLPEVDIVEKGRLAPGQMIAVDLAEQKIL
KNYQIKQQAAQKYPYGEWIKIQDAQTVLQQQAAFGYTAEDVEMVVVPMAS
QGKEPTFCMGDDTPLAVLSHKPRLLYDYFKQRFAQVTNPPIDPLRENLVM
SLAMFLGKRGNLLEPKAEKLRSPLVNEVELQAIKTGQLQVAEVSTLYDLD
GVNSLEDALTNLVKTAIATVQAGAEILVLTDRPNGAILTENQSFIPPLLA
VGAVHHHLIRAGLRLKASLIVDTAQCWSTHHFACLVGYGASAICPYLALE
SVRQWWLDEKTQKLMENGRLDRIDLPTALKNYRQSVEAGLFKILSKMGIS
LLASYHGAQIFEAIGLGAELVEYAFAGTTSRVGGLTIADVAGEVMVFHGM
AFPEMAKKLENFGFVNYRPGGEYHMNSPEMSKSLHKAVAAYYDHYELYRQ
YLKDRPVTALRDLLDFNADQPAISLEEVESVESIVKRFCTGGMSLGALSR
EAHETLAIAMNRLGAKSNSGEGGEDVVRYLTLDDVDSEGNSPTLPHLHGL
QNGDTANSAIKQIASGRFGVTPEYLMSGKQLEIKMAQGAKPGEGGQLPGK
KVSEYIAMLRRSKPGVTLISPPPHHDIYSIEDLAQLIYDLHQINPEAQVS
VKLVAEIGIGTIAAGVAKANADIIQISGHDGGTGASPLSSIKHAGSPWEL
GVTEVHRVLMENQLRDRVLLRADGGLKTGWDVVMAALMGAEEYGFGSIAM
IAEGCIMARVCHTNNCPVGVATQQERLRQRFKGVPGQVVNFFYFIAEEVR
SLLAHLGYRSLDDIIGRTDLLKVRSDVQLSKTQNLTLDCLLNLPDTKQNR
QWLNHEPVHSNGPVLDDDILADPDIQEAINHQTTATKTYRLVNTDRTVGT
RLSGAIAKKYGNNGFEGNITLNFQGAAGQSFGAFNLDGMTLHLQGEANDY
VGKGMNGGEIVIVPHPQASFAPEDNVIIGNTCLYGATGGNLYANGRAGER
FAVRNSVGKAVIEGAGDHCCEYMTGGVIVVLGPVGRNVGAGMTGGLAYFL
DEVGDLPEKINPEIITLQRITASKGEEQLKSLITAHVEHTGSPKGKAILA
NWSDYLGKFWQAVPPSEKDSPEANN

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

Best alignment:
1LLZ.pdb   697  MGISLLASYHGAQIFEAIGLGAELVEYAFAGTTSRVGGLTIAD   739
                +  S++       +F+A+  G    +  FAG      G T AD
2-02410    168  VSFSMVKEVKVVVVFDALMSGLPTHKEDFAGVDVIFSGETCAD   210

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

Highlighted IDENTICAL residue ILE  720  index1  699  path  202  %Seq  50.00
Highlighted IDENTICAL residue SER  721  index1  700  path  203  %Seq  50.00
Highlighted IDENTICAL residue GLY  728  index1  707  path  210  %Seq 100.00
Highlighted IDENTICAL residue GLU  733  index1  712  path  215  %Seq 100.00
Highlighted IDENTICAL residue ALA  739  index1  718  path  221  %Seq  50.00
Highlighted IDENTICAL residue GLU  740  index1  719  path  222  %Seq  50.00
Highlighted IDENTICAL residue LEU  741  index1  720  path  223  %Seq  50.00
Highlighted IDENTICAL residue VAL  742  index1  721  path  224  %Seq  50.00
Highlighted IDENTICAL residue GLU  743  index1  722  path  225  %Seq  50.00
Highlighted IDENTICAL residue TYR  744  index1  723  path  226  %Seq  50.00
Highlighted IDENTICAL residue ALA  745  index1  724  path  227  %Seq  50.00
Highlighted IDENTICAL residue THR  749  index1  728  path  231  %Seq 100.00
Highlighted 12 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02410-1llzA.pir.txt.1LLZ.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02410-1llzA.pir.txt PIR amino_acid 1LLZ.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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