Fandom

Proteins Wiki

At2g02480.1/PDB

< At2g02480.1

47,922pages on
this wiki
Add New Page
Talk0 Share
&&&&&&&&&&&&&&&&&&&& 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
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

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

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.

@@@@@@@@@@@@@@@@@@@@ END  /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@

Ad blocker interference detected!


Wikia is a free-to-use site that makes money from advertising. We have a modified experience for viewers using ad blockers

Wikia is not accessible if you’ve made further modifications. Remove the custom ad blocker rule(s) and the page will load as expected.