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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g01480_1llzA.pir.txt

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

Assigned types to 567 residues in Sequence 2-01480, 21 remain unknown
Assigned types to 446 residues in Sequence 1llzA, 142 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 At2g01480_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   109  EVPVNSDVLGIQAKNNQPHIEQILVTCPEGCAGDELDRRLYIARSIIGKK   158
                EVPVNSDVLGIQAKNNQPHIEQILVTCPEGCAGDELDRRLYIARSIIGKK
1llzA        1  EVPVNSDVLGIQAKNNQPHIEQILVTCPEGCAGDELDRRLYIARSIIGKK    50

1LLZ.pdb   159  LAEDFYVCSFSCRTIVYKGMVRSIILGEFYLDLKNPGYTSNFAVYHRRFS   208
                LAEDFYVCSFSCRTIVYKGMVRSIILGEFYLDLKNPGYTSNFAVYHRRFS
1llzA       51  LAEDFYVCSFSCRTIVYKGMVRSIILGEFYLDLKNPGYTSNFAVYHRRFS   100

1LLZ.pdb   209  TNTMPKWPLAQPMRLLGHNGEINTLLGNINWMAAREKELEVSGWTKAELE   258
                TNTMPKWPLAQPMRLLGHNGEINTLLGNINWMAAREKELEVSGWTKAELE
1llzA      101  TNTMPKWPLAQPMRLLGHNGEINTLLGNINWMAAREKELEVSGWTKAELE   150

1LLZ.pdb   259  ALTPIVNQANSDSYNLDSALELLVRTGRSPLEAAMILVPEAYKNQPALKD   308
                ALTPIVNQANSDSYNLDSALELLVRTGRSPLEAAMILVPEAYKNQPALKD
1llzA      151  ALTPIVNQANSDSYNLDSALELLVRTGRSPLEAAMILVPEAYKNQPALKD   200

1LLZ.pdb   309  YPEISDFHDYYSGLQEPWDGPALLVFSDGKIVGAGLDRNGLRPARYCITK   358
                YPEISDFHDYYSGLQEPWDGPALLVFSDGKIVGAGLDRNGLRPARYCITK
1llzA      201  YPEISDFHDYYSGLQEPWDGPALLVFSDGKIVGAGLDRNGLRPARYCITK   250

1LLZ.pdb   359  DDYIVLGSEAGVVDLPEVDIVEKGRLAPGQMIAVDLAEQKILKNYQIKQQ   408
                DDYIVLGSEAGVVDLPEVDIVEKGRLAPGQMIAVDLAEQKILKNYQIKQQ
1llzA      251  DDYIVLGSEAGVVDLPEVDIVEKGRLAPGQMIAVDLAEQKILKNYQIKQQ   300

1LLZ.pdb   409  AAQKYPYGEWIKI----------------QDAQTVLQQQAAFGYTAEDVE   442
                AAQKYPYGEWIKI                 DAQTVLQQQAAFGYTAEDVE
1llzA      301  AAQKYPYGEWIKIQRQTVASDSFAEKTLFNDAQTVLQQQAAFGYTAEDVE   350

1LLZ.pdb   443  MVVVPMASQGKEPTFCMGDDTPLAVLSHKPRLLYDYFKQRFAQVTNPPID   492
                MVVVPMASQGKEPTFCMGDDTPLAVLSHKPRLLYDYFKQRFAQVTNPPID
1llzA      351  MVVVPMASQGKEPTFCMGDDTPLAVLSHKPRLLYDYFKQRFAQVTNPPID   400

1LLZ.pdb   493  PLRENLVMSLAMFLGKRGNLLEPKAE-----KLRSPLVNEVELQAI   533
                PLRENLVMSLAMFLGKRGNLLEPKAE     KLRSPLVNEVELQAI
1llzA      401  PLRENLVMSLAMFLGKRGNLLEPKAESARTIKLRSPLVNEVELQAI   446

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

Highlighted IDENTICAL residue PRO  111  index1  111  path   17  %Seq 100.00
Highlighted IDENTICAL residue SER  114  index1  114  path   20  %Seq 100.00
Highlighted IDENTICAL residue ARG  146  index1  146  path   52  %Seq 100.00
Highlighted IDENTICAL residue ILE  150  index1  150  path   56  %Seq 100.00
Highlighted IDENTICAL residue SER  153  index1  153  path   59  %Seq 100.00
Highlighted IDENTICAL residue GLU  161  index1  161  path   70  %Seq  50.00
Highlighted IDENTICAL residue ASP  162  index1  162  path   71  %Seq  50.00
Highlighted IDENTICAL residue PHE  163  index1  163  path   72  %Seq 100.00
Highlighted IDENTICAL residue TYR  175  index1  175  path   84  %Seq 100.00
Highlighted IDENTICAL residue GLY  177  index1  177  path   86  %Seq 100.00
Highlighted IDENTICAL residue VAL  179  index1  179  path   88  %Seq 100.00
Highlighted IDENTICAL residue TYR  196  index1  196  path  106  %Seq 100.00
Highlighted IDENTICAL residue SER  198  index1  198  path  108  %Seq 100.00
Highlighted IDENTICAL residue ARG  206  index1  206  path  116  %Seq 100.00
Highlighted IDENTICAL residue TRP  215  index1  215  path  142  %Seq 100.00
Highlighted IDENTICAL residue LEU  217  index1  217  path  158  %Seq  50.00
Highlighted IDENTICAL residue ALA  218  index1  218  path  159  %Seq  50.00
Highlighted IDENTICAL residue GLN  219  index1  219  path  160  %Seq  50.00
Highlighted IDENTICAL residue ASN  227  index1  227  path  168  %Seq 100.00
Highlighted IDENTICAL residue GLY  228  index1  228  path  169  %Seq 100.00
Highlighted IDENTICAL residue ASN  231  index1  231  path  172  %Seq 100.00
Highlighted IDENTICAL residue ILE  237  index1  237  path  178  %Seq 100.00
Highlighted IDENTICAL residue ALA  242  index1  242  path  183  %Seq 100.00
Highlighted IDENTICAL residue LEU  247  index1  247  path  188  %Seq 100.00
Highlighted IDENTICAL residue ASP  270  index1  270  path  211  %Seq 100.00
Highlighted IDENTICAL residue TYR  272  index1  272  path  213  %Seq 100.00
Highlighted IDENTICAL residue LEU  281  index1  281  path  222  %Seq 100.00
Highlighted IDENTICAL residue VAL  282  index1  282  path  223  %Seq  50.00
Highlighted IDENTICAL residue ARG  283  index1  283  path  224  %Seq  50.00
Highlighted IDENTICAL residue THR  284  index1  284  path  225  %Seq  50.00
Highlighted IDENTICAL residue GLY  285  index1  285  path  226  %Seq  50.00
Highlighted IDENTICAL residue PRO  310  index1  310  path  261  %Seq 100.00
Highlighted IDENTICAL residue LEU  322  index1  322  path  273  %Seq 100.00
Highlighted IDENTICAL residue GLU  324  index1  324  path  275  %Seq 100.00
Highlighted IDENTICAL residue ASP  327  index1  327  path  278  %Seq  50.00
Highlighted IDENTICAL residue GLY  328  index1  328  path  279  %Seq  50.00
Highlighted IDENTICAL residue PRO  329  index1  329  path  280  %Seq  50.00
Highlighted IDENTICAL residue ALA  330  index1  330  path  281  %Seq  50.00
Highlighted IDENTICAL residue SER  335  index1  335  path  286  %Seq 100.00
Highlighted IDENTICAL residue ARG  353  index1  353  path  304  %Seq 100.00
Highlighted IDENTICAL residue THR  357  index1  357  path  309  %Seq  50.00
Highlighted IDENTICAL residue LYS  358  index1  358  path  310  %Seq  50.00
Highlighted IDENTICAL residue ASP  359  index1  359  path  311  %Seq  50.00
Highlighted IDENTICAL residue ASP  360  index1  360  path  312  %Seq  50.00
Highlighted IDENTICAL residue TYR  361  index1  361  path  313  %Seq 100.00
Highlighted IDENTICAL residue LEU  364  index1  364  path  316  %Seq 100.00
Highlighted IDENTICAL residue LEU  373  index1  373  path  325  %Seq 100.00
Highlighted IDENTICAL residue GLU  375  index1  375  path  327  %Seq 100.00
Highlighted IDENTICAL residue GLU  380  index1  380  path  335  %Seq 100.00
Highlighted IDENTICAL residue VAL  392  index1  392  path  347  %Seq 100.00
Highlighted IDENTICAL residue LEU  394  index1  394  path  349  %Seq 100.00
Highlighted IDENTICAL residue GLU  396  index1  396  path  352  %Seq 100.00
Highlighted IDENTICAL residue ASN  402  index1  402  path  367  %Seq 100.00
Highlighted IDENTICAL residue ALA  410  index1  410  path  375  %Seq 100.00
Highlighted IDENTICAL residue TYR  413  index1  413  path  378  %Seq  50.00
Highlighted IDENTICAL residue PRO  414  index1  414  path  379  %Seq  50.00
Highlighted IDENTICAL residue TRP  418  index1  418  path  383  %Seq 100.00
Highlighted IDENTICAL residue ILE  419  index1  419  path  384  %Seq  50.00
Highlighted IDENTICAL residue LYS  420  index1  420  path  385  %Seq 100.00
Highlighted IDENTICAL residue GLN  422  index1  422  path  403  %Seq 100.00
Highlighted IDENTICAL residue VAL  443  index1  427  path  413  %Seq 100.00
Highlighted IDENTICAL residue GLY  451  index1  435  path  421  %Seq 100.00
Highlighted IDENTICAL residue TYR  452  index1  436  path  436  %Seq 100.00
Highlighted IDENTICAL residue ALA  454  index1  438  path  438  %Seq 100.00
Highlighted IDENTICAL residue MET  464  index1  448  path  448  %Seq 100.00
Highlighted IDENTICAL residue LYS  469  index1  453  path  455  %Seq 100.00
Highlighted IDENTICAL residue GLU  470  index1  454  path  456  %Seq 100.00
Highlighted IDENTICAL residue PRO  480  index1  464  path  466  %Seq 100.00
Highlighted IDENTICAL residue SER  485  index1  469  path  471  %Seq 100.00
Highlighted IDENTICAL residue PRO  488  index1  472  path  474  %Seq  50.00
Highlighted IDENTICAL residue ASP  493  index1  477  path  479  %Seq 100.00
Highlighted IDENTICAL residue TYR  494  index1  478  path  480  %Seq 100.00
Highlighted IDENTICAL residue VAL  502  index1  486  path  488  %Seq 100.00
Highlighted IDENTICAL residue MET  516  index1  500  path  502  %Seq 100.00
Highlighted IDENTICAL residue PRO  544  index1  523  path  530  %Seq 100.00
Highlighted 75 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01480_1llzA.pir.txt.1LLZ.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01480_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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