At2g02480.1/PDB

&&&&&&&&&&&&&&&&&&&& 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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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g02480-1jr3_A.pir.txt
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Assigned types to 1218 residues in Sequence 2-02480, 4 remain unknown
Assigned types to 369 residues in Sequence 1jr3_A, 853 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 676 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 761 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 762 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 763 All residues are positively and negatively charged
Translated sequence file At2g02480-1jr3_A.pir.txt into sequence alignment.
======================================================
>1JR3.pdb Made from 13826 ATOM records in 1JR3.pdb
YQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKT
SIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVE
DTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKF
LLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRA
LQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDDQALSL
VEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAAL
GNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMT
LLRALAFHPRMPLPEPQVLARKWRPQTFADVVGQEHVLTALANGLSLGRI
HHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRF
VDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFN
ALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQL
EHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAV
SAMLGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLG
LLHRIAMVQLSPAALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRK
ELPYAPDRRMGVEMTLLRALAFHPRMPLPEPYQVLARKWRPQTFADVVGQ
EHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITAT
PCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFK
VYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCL
QFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLT
DQAIASGDGQVSTQAVSAMLGTLDDDQALSLVEAMVEANGERVMALINEA
AARGIEWEALLVEMLGLLHRIAMVQLSPAALGNDMAAIELRMRELARTIP
PTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRALAFHPRMPLPEPMIR
LYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTF
SIDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGL
LHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAA
RAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGKLTLPRVE
QAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEGSEPVILLRTLQRE
LLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQAVQ
LLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADMRWYPWLRPDFEKLV
ASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGC
QLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVT
DAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLA
PPPEQYAVTWLSREVTMSQDALLAALRLSAGSPGAALALFQGDNWQARET
LCQALAYSVPSGDWYSLLAALNHEQAPARLHWLATLLMDALKRHHGAAQV
TNVDVPGLVAELANHLSPSRLQAILGDVCHIREQLMSVTGINRELLITDL
LLRIEHYLQPGVVLPVPHL
======================================================
Best alignment:
1JR3.pdb 1 YQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKT 50
 YQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKT
1jr3_A 3 YQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKT 52
1JR3.pdb 51 SIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVE 100
 SIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVE
1jr3_A 53 SIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVE 102
1JR3.pdb 101 DTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKF 150
 DTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKF
1jr3_A 103 DTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKF 152
1JR3.pdb 151 LLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRA 200
 LLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRA
1jr3_A 153 LLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRA 202
1JR3.pdb 201 LQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDDQALSL 250
 LQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDDQALSL
1jr3_A 203 LQLLARAAEGSLRDALSLTDQAIASGXGQVSTQAVSAMLGTLDDDQALSL 252
1JR3.pdb 251 VEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAAL 300
 VEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAAL
1jr3_A 253 VEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAAL 302
1JR3.pdb 301 GNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMT 350
 GNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMT
1jr3_A 303 GNDMAAIELRMXXXARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMT 352
1JR3.pdb 351 LLRALAFHPRMPLPEPQV 368
 LLRALAFHPRMPLPEP+V
1jr3_A 353 LLRALAFHPRMPLPEPEV 370
======================================================
Highlighted IDENTICAL residue LYS 9 index1 7 path 454 %Seq 100.00
Highlighted IDENTICAL residue ARG 11 index1 9 path 456 %Seq 100.00
Highlighted IDENTICAL residue PRO 12 index1 10 path 457 %Seq 100.00
Highlighted IDENTICAL residue PHE 15 index1 13 path 460 %Seq 100.00
Highlighted IDENTICAL residue GLY 20 index1 18 path 465 %Seq 100.00
Highlighted IDENTICAL residue GLN 21 index1 19 path 466 %Seq 100.00
Highlighted IDENTICAL residue VAL 24 index1 22 path 469 %Seq 100.00
Highlighted IDENTICAL residue LEU 28 index1 26 path 473 %Seq 100.00
Highlighted IDENTICAL residue ASN 30 index1 28 path 475 %Seq 100.00
Highlighted IDENTICAL residue ARG 36 index1 34 path 481 %Seq 100.00
Highlighted IDENTICAL residue ILE 37 index1 35 path 482 %Seq 100.00
Highlighted IDENTICAL residue TYR 41 index1 39 path 486 %Seq 100.00
Highlighted IDENTICAL residue LEU 42 index1 40 path 487 %Seq 100.00
Highlighted IDENTICAL residue PHE 43 index1 41 path 488 %Seq 100.00
Highlighted IDENTICAL residue GLY 45 index1 43 path 490 %Seq 100.00
Highlighted IDENTICAL residue ARG 47 index1 45 path 492 %Seq 100.00
Highlighted IDENTICAL residue GLY 48 index1 46 path 493 %Seq 100.00
Highlighted IDENTICAL residue GLY 50 index1 48 path 495 %Seq 100.00
Highlighted IDENTICAL residue LYS 51 index1 49 path 496 %Seq 100.00
Highlighted IDENTICAL residue THR 52 index1 50 path 497 %Seq 100.00
Highlighted IDENTICAL residue SER 53 index1 51 path 498 %Seq 100.00
Highlighted IDENTICAL residue ALA 55 index1 53 path 500 %Seq 100.00
Highlighted IDENTICAL residue ARG 56 index1 54 path 501 %Seq 100.00
Highlighted IDENTICAL residue LEU 62 index1 60 path 507 %Seq 100.00
Highlighted IDENTICAL residue ASN 63 index1 61 path 508 %Seq 100.00
Highlighted IDENTICAL residue CYS 64 index1 62 path 509 %Seq 100.00
Highlighted IDENTICAL residue PRO 72 index1 70 path 517 %Seq 100.00
Highlighted IDENTICAL residue CYS 73 index1 71 path 518 %Seq 100.00
Highlighted IDENTICAL residue GLY 74 index1 72 path 519 %Seq 100.00
Highlighted IDENTICAL residue CYS 76 index1 74 path 521 %Seq 100.00
Highlighted IDENTICAL residue CYS 79 index1 77 path 524 %Seq 100.00
Highlighted IDENTICAL residue GLY 85 index1 83 path 530 %Seq 100.00
Highlighted IDENTICAL residue ASP 89 index1 87 path 534 %Seq 100.00
Highlighted IDENTICAL residue GLU 92 index1 90 path 537 %Seq 100.00
Highlighted IDENTICAL residue ASP 94 index1 92 path 539 %Seq 100.00
Highlighted IDENTICAL residue ALA 96 index1 94 path 541 %Seq 100.00
Highlighted IDENTICAL residue ARG 105 index1 103 path 550 %Seq 100.00
Highlighted IDENTICAL residue LEU 107 index1 105 path 552 %Seq 100.00
Highlighted IDENTICAL residue LEU 108 index1 106 path 553 %Seq 100.00
Highlighted IDENTICAL residue ASN 110 index1 108 path 555 %Seq 100.00
Highlighted IDENTICAL residue LYS 121 index1 119 path 568 %Seq 100.00
Highlighted IDENTICAL residue VAL 122 index1 120 path 569 %Seq 100.00
Highlighted IDENTICAL residue ILE 125 index1 123 path 572 %Seq 100.00
Highlighted IDENTICAL residue ASP 126 index1 124 path 573 %Seq 100.00
Highlighted IDENTICAL residue GLU 127 index1 125 path 574 %Seq 100.00
Highlighted IDENTICAL residue HIS 129 index1 127 path 576 %Seq 100.00
Highlighted IDENTICAL residue LEU 131 index1 129 path 578 %Seq 100.00
Highlighted IDENTICAL residue LEU 140 index1 138 path 587 %Seq 100.00
Highlighted IDENTICAL residue LYS 141 index1 139 path 588 %Seq 100.00
Highlighted IDENTICAL residue LEU 143 index1 141 path 590 %Seq 100.00
Highlighted IDENTICAL residue GLU 144 index1 142 path 591 %Seq 100.00
Highlighted IDENTICAL residue PRO 146 index1 144 path 593 %Seq 100.00
Highlighted IDENTICAL residue VAL 150 index1 148 path 597 %Seq 100.00
Highlighted IDENTICAL residue PHE 152 index1 150 path 599 %Seq 100.00
Highlighted IDENTICAL residue THR 156 index1 154 path 603 %Seq 100.00
Highlighted IDENTICAL residue THR 157 index1 155 path 604 %Seq 100.00
Highlighted IDENTICAL residue ASP 158 index1 156 path 605 %Seq 100.00
Highlighted IDENTICAL residue PRO 163 index1 161 path 610 %Seq 100.00
Highlighted IDENTICAL residue THR 165 index1 163 path 612 %Seq 100.00
Highlighted IDENTICAL residue ILE 166 index1 164 path 613 %Seq 100.00
Highlighted IDENTICAL residue SER 168 index1 166 path 615 %Seq 100.00
Highlighted IDENTICAL residue ARG 169 index1 167 path 616 %Seq 100.00
Highlighted IDENTICAL residue CYS 170 index1 168 path 617 %Seq 100.00
Highlighted IDENTICAL residue PHE 173 index1 171 path 620 %Seq 100.00
Highlighted IDENTICAL residue LEU 178 index1 176 path 625 %Seq 100.00
Highlighted IDENTICAL residue ILE 183 index1 181 path 630 %Seq 100.00
Highlighted IDENTICAL residue LEU 187 index1 185 path 634 %Seq 100.00
Highlighted IDENTICAL residue ILE 190 index1 188 path 637 %Seq 100.00
Highlighted IDENTICAL residue GLU 194 index1 192 path 641 %Seq 100.00
Highlighted IDENTICAL residue ALA 202 index1 200 path 649 %Seq 100.00
Highlighted IDENTICAL residue LEU 203 index1 201 path 650 %Seq 100.00
Highlighted IDENTICAL residue LEU 205 index1 203 path 652 %Seq 100.00
Highlighted IDENTICAL residue ALA 207 index1 205 path 654 %Seq 100.00
Highlighted IDENTICAL residue ALA 210 index1 208 path 657 %Seq 100.00
Highlighted IDENTICAL residue GLY 212 index1 210 path 659 %Seq 100.00
Highlighted IDENTICAL residue SER 213 index1 211 path 660 %Seq 100.00
Highlighted IDENTICAL residue LEU 214 index1 212 path 661 %Seq 100.00
Highlighted IDENTICAL residue ARG 215 index1 213 path 662 %Seq 100.00
Highlighted IDENTICAL residue ASP 216 index1 214 path 663 %Seq 100.00
Highlighted IDENTICAL residue ALA 217 index1 215 path 664 %Seq 100.00
Highlighted IDENTICAL residue GLN 223 index1 221 path 670 %Seq 100.00
Highlighted IDENTICAL residue GLY 228 index1 226 path 675 %Seq 100.00
Highlighted IDENTICAL residue THR 234 index1 232 path 681 %Seq 100.00
Highlighted IDENTICAL residue VAL 237 index1 235 path 684 %Seq 100.00
Highlighted IDENTICAL residue GLY 242 index1 240 path 689 %Seq 100.00
Highlighted IDENTICAL residue ASP 246 index1 244 path 693 %Seq 100.00
Highlighted IDENTICAL residue LEU 250 index1 248 path 697 %Seq 100.00
Highlighted IDENTICAL residue LEU 252 index1 250 path 699 %Seq 100.00
Highlighted IDENTICAL residue GLU 254 index1 252 path 701 %Seq 100.00
Highlighted IDENTICAL residue GLU 270 index1 268 path 717 %Seq 100.00
Highlighted IDENTICAL residue GLY 275 index1 273 path 722 %Seq 100.00
Highlighted IDENTICAL residue LEU 281 index1 279 path 728 %Seq 100.00
Highlighted IDENTICAL residue LEU 288 index1 286 path 735 %Seq 100.00
Highlighted IDENTICAL residue ILE 292 index1 290 path 739 %Seq 100.00
Highlighted IDENTICAL residue ALA 307 index1 305 path 754 %Seq 100.00
Highlighted IDENTICAL residue ARG 312 index1 310 path 759 %Seq 100.00
Highlighted IDENTICAL residue LEU 332 index1 330 path 779 %Seq 100.00
Highlighted IDENTICAL residue LYS 337 index1 335 path 784 %Seq 100.00
Highlighted IDENTICAL residue LEU 339 index1 337 path 786 %Seq 100.00
Highlighted IDENTICAL residue ASP 344 index1 342 path 791 %Seq 100.00
Highlighted IDENTICAL residue ARG 345 index1 343 path 792 %Seq 100.00
Highlighted IDENTICAL residue THR 352 index1 350 path 799 %Seq 100.00
Highlighted IDENTICAL residue LEU 353 index1 351 path 800 %Seq 100.00
Highlighted IDENTICAL residue LEU 354 index1 352 path 801 %Seq 100.00
Highlighted 104 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02480-1jr3_A.pir.txt.1JR3.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02480-1jr3_A.pir.txt PIR amino_acid 1JR3.pdb A 100.0 BLOSUM62.dat 
completed successfully.
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