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/

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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 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 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/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

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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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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.

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>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

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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

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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

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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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