At2g01580.1/Structure

&&&&&&&&&&&&&&&&&&&& 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 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

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Assigned types to 567 residues in Sequence 2-01480, 21 remain unknown Assigned types to 446 residues in Sequence 1llzA, 142 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 At2g01480_1llzA.pir.txt into sequence alignment.

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>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

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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  AAQKYPYGEWIKIQDAQTVLQQQAAFGYTAEDVE   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

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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

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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.

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