&&&&&&&&&&&&&&&&&&&& 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
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Got here 3
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Got here 3
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Got here 3
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Got here 3
Got here 4
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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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