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At2g02740.1/PDB

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&&&&&&&&&&&&&&&&&&&& 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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g02740-1l3aA.pir.txt

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

Assigned types to 268 residues in Sequence 2-02740, 0 remain unknown
Assigned types to 166 residues in Sequence 1l3aA, 102 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 At2g02740-1l3aA.pir.txt into sequence alignment.

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

>1L3A.pdb  Made from 5435 ATOM records in 1L3A.pdb
TPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAA
GVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRK
VLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVM
PYLLGWHTAVNSFKPETPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAF
KLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEF
FHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPV
TKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPEAELETPKVFVGYSIYKGK
AALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFS
LSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHF
FNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFK
PESGAELEWNLEHHHHHHTPKVFVGYSIYKGKAALTVEPRSPEFSPLDSG
AFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSC
EFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYI
PVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPEGAELE

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

Best alignment:
1L3A.pdb   327  NSFKPEAELETPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREG   376
                +S    AE+ +P+ +VG+SIYKGKAALT+EPR+PEF  L+SGAFKL++EG
2-02740     72  SSSSQNAEVSSPRFYVGHSIYKGKAALTIEPRAPEFVALESGAFKLTKEG   121

1L3A.pdb   377  MVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNK   426
                 ++LQFAPAAGVRQYDWSRKQVFSLSVTEIG+++SLG ++SCEFFHDP K
2-02740    122  FLLLQFAPAAGVRQYDWSRKQVFSLSVTEIGNLVSLGPRESCEFFHDPFK   171

1L3A.pdb   427  GR-SDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEF   475
                G+ SDEG+VRKVLKVEPLPDGSG FFNLSVQNKL+N+DE++YIP+TKAEF
2-02740    172  GKGSDEGKVRKVLKVEPLPDGSGRFFNLSVQNKLLNVDESVYIPITKAEF   221

1L3A.pdb   476  AVLVSAFNFVMPYLLGWHTAVNSFKPESGAEL   507
                AVL+SAFNFV+P+L+GW    NS KPE    L
2-02740    222  AVLISAFNFVLPHLIGWSAFANSIKPEDSNRL   253

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

Highlighted IDENTICAL residue ASN  249  index1  327  path   72  %Seq  50.00
Highlighted IDENTICAL residue SER  250  index1  328  path   73  %Seq  50.00
Highlighted IDENTICAL residue PHE  251  index1  329  path   74  %Seq  50.00
Highlighted IDENTICAL residue LYS  252  index1  330  path   75  %Seq  50.00
Highlighted IDENTICAL residue PRO  253  index1  331  path   76  %Seq  50.00
Highlighted IDENTICAL residue GLU  254  index1  332  path   77  %Seq  50.00
Highlighted IDENTICAL residue ALA  268  index1  333  path   78  %Seq  50.00
Highlighted IDENTICAL residue GLU  269  index1  334  path   79  %Seq  50.00
Highlighted IDENTICAL residue LEU  270  index1  335  path   80  %Seq  50.00
Highlighted IDENTICAL residue GLU  271  index1  336  path   81  %Seq  50.00
Highlighted IDENTICAL residue PRO   90  index1  338  path   83  %Seq 100.00
Highlighted IDENTICAL residue VAL   94  index1  342  path   87  %Seq 100.00
Highlighted IDENTICAL residue GLY   95  index1  343  path   88  %Seq 100.00
Highlighted IDENTICAL residue SER   97  index1  345  path   90  %Seq 100.00
Highlighted IDENTICAL residue ILE   98  index1  346  path   91  %Seq 100.00
Highlighted IDENTICAL residue TYR   99  index1  347  path   92  %Seq 100.00
Highlighted IDENTICAL residue LYS  100  index1  348  path   93  %Seq 100.00
Highlighted IDENTICAL residue GLY  101  index1  349  path   94  %Seq 100.00
Highlighted IDENTICAL residue LYS  102  index1  350  path   95  %Seq 100.00
Highlighted IDENTICAL residue ALA  103  index1  351  path   96  %Seq 100.00
Highlighted IDENTICAL residue ALA  104  index1  352  path   97  %Seq 100.00
Highlighted IDENTICAL residue LEU  105  index1  353  path   98  %Seq 100.00
Highlighted IDENTICAL residue THR  106  index1  354  path   99  %Seq 100.00
Highlighted IDENTICAL residue GLU  108  index1  356  path  101  %Seq 100.00
Highlighted IDENTICAL residue PRO  109  index1  357  path  102  %Seq 100.00
Highlighted IDENTICAL residue ARG  110  index1  358  path  103  %Seq 100.00
Highlighted IDENTICAL residue PRO  112  index1  360  path  105  %Seq 100.00
Highlighted IDENTICAL residue GLU  113  index1  361  path  106  %Seq 100.00
Highlighted IDENTICAL residue PHE  114  index1  362  path  107  %Seq 100.00
Highlighted IDENTICAL residue LEU  117  index1  365  path  110  %Seq 100.00
Highlighted IDENTICAL residue SER  119  index1  367  path  112  %Seq 100.00
Highlighted IDENTICAL residue GLY  120  index1  368  path  113  %Seq 100.00
Highlighted IDENTICAL residue ALA  121  index1  369  path  114  %Seq 100.00
Highlighted IDENTICAL residue PHE  122  index1  370  path  115  %Seq 100.00
Highlighted IDENTICAL residue LYS  123  index1  371  path  116  %Seq 100.00
Highlighted IDENTICAL residue LEU  124  index1  372  path  117  %Seq 100.00
Highlighted IDENTICAL residue GLU  127  index1  375  path  120  %Seq 100.00
Highlighted IDENTICAL residue GLY  128  index1  376  path  121  %Seq 100.00
Highlighted IDENTICAL residue LEU  132  index1  380  path  125  %Seq 100.00
Highlighted IDENTICAL residue GLN  133  index1  381  path  126  %Seq 100.00
Highlighted IDENTICAL residue PHE  134  index1  382  path  127  %Seq 100.00
Highlighted IDENTICAL residue ALA  135  index1  383  path  128  %Seq 100.00
Highlighted IDENTICAL residue PRO  136  index1  384  path  129  %Seq 100.00
Highlighted IDENTICAL residue ALA  137  index1  385  path  130  %Seq 100.00
Highlighted IDENTICAL residue ALA  138  index1  386  path  131  %Seq 100.00
Highlighted IDENTICAL residue GLY  139  index1  387  path  132  %Seq 100.00
Highlighted IDENTICAL residue VAL  140  index1  388  path  133  %Seq 100.00
Highlighted IDENTICAL residue ARG  141  index1  389  path  134  %Seq 100.00
Highlighted IDENTICAL residue GLN  142  index1  390  path  135  %Seq 100.00
Highlighted IDENTICAL residue TYR  143  index1  391  path  136  %Seq 100.00
Highlighted IDENTICAL residue ASP  144  index1  392  path  137  %Seq 100.00
Highlighted IDENTICAL residue TRP  145  index1  393  path  138  %Seq 100.00
Highlighted IDENTICAL residue SER  146  index1  394  path  139  %Seq 100.00
Highlighted IDENTICAL residue ARG  147  index1  395  path  140  %Seq 100.00
Highlighted IDENTICAL residue LYS  148  index1  396  path  141  %Seq 100.00
Highlighted IDENTICAL residue GLN  149  index1  397  path  142  %Seq 100.00
Highlighted IDENTICAL residue VAL  150  index1  398  path  143  %Seq 100.00
Highlighted IDENTICAL residue PHE  151  index1  399  path  144  %Seq 100.00
Highlighted IDENTICAL residue SER  152  index1  400  path  145  %Seq 100.00
Highlighted IDENTICAL residue LEU  153  index1  401  path  146  %Seq 100.00
Highlighted IDENTICAL residue SER  154  index1  402  path  147  %Seq 100.00
Highlighted IDENTICAL residue VAL  155  index1  403  path  148  %Seq 100.00
Highlighted IDENTICAL residue THR  156  index1  404  path  149  %Seq 100.00
Highlighted IDENTICAL residue GLU  157  index1  405  path  150  %Seq 100.00
Highlighted IDENTICAL residue ILE  158  index1  406  path  151  %Seq 100.00
Highlighted IDENTICAL residue GLY  159  index1  407  path  152  %Seq 100.00
Highlighted IDENTICAL residue SER  163  index1  411  path  156  %Seq 100.00
Highlighted IDENTICAL residue LEU  164  index1  412  path  157  %Seq 100.00
Highlighted IDENTICAL residue GLY  165  index1  413  path  158  %Seq 100.00
Highlighted IDENTICAL residue SER  169  index1  417  path  162  %Seq 100.00
Highlighted IDENTICAL residue CYS  170  index1  418  path  163  %Seq 100.00
Highlighted IDENTICAL residue GLU  171  index1  419  path  164  %Seq 100.00
Highlighted IDENTICAL residue PHE  172  index1  420  path  165  %Seq 100.00
Highlighted IDENTICAL residue PHE  173  index1  421  path  166  %Seq 100.00
Highlighted IDENTICAL residue HIS  174  index1  422  path  167  %Seq 100.00
Highlighted IDENTICAL residue ASP  175  index1  423  path  168  %Seq 100.00
Highlighted IDENTICAL residue PRO  176  index1  424  path  169  %Seq 100.00
Highlighted IDENTICAL residue LYS  178  index1  426  path  171  %Seq 100.00
Highlighted IDENTICAL residue GLY  179  index1  427  path  172  %Seq 100.00
Highlighted IDENTICAL residue SER  181  index1  429  path  175  %Seq 100.00
Highlighted IDENTICAL residue ASP  182  index1  430  path  176  %Seq 100.00
Highlighted IDENTICAL residue GLU  183  index1  431  path  177  %Seq 100.00
Highlighted IDENTICAL residue GLY  184  index1  432  path  178  %Seq 100.00
Highlighted IDENTICAL residue VAL  186  index1  434  path  180  %Seq 100.00
Highlighted IDENTICAL residue ARG  187  index1  435  path  181  %Seq 100.00
Highlighted IDENTICAL residue LYS  188  index1  436  path  182  %Seq 100.00
Highlighted IDENTICAL residue VAL  189  index1  437  path  183  %Seq 100.00
Highlighted IDENTICAL residue LEU  190  index1  438  path  184  %Seq 100.00
Highlighted IDENTICAL residue LYS  191  index1  439  path  185  %Seq 100.00
Highlighted IDENTICAL residue VAL  192  index1  440  path  186  %Seq 100.00
Highlighted IDENTICAL residue GLU  193  index1  441  path  187  %Seq 100.00
Highlighted IDENTICAL residue PRO  194  index1  442  path  188  %Seq 100.00
Highlighted IDENTICAL residue LEU  195  index1  443  path  189  %Seq 100.00
Highlighted IDENTICAL residue PRO  196  index1  444  path  190  %Seq 100.00
Highlighted IDENTICAL residue ASP  197  index1  445  path  191  %Seq 100.00
Highlighted IDENTICAL residue GLY  198  index1  446  path  192  %Seq 100.00
Highlighted IDENTICAL residue SER  199  index1  447  path  193  %Seq 100.00
Highlighted IDENTICAL residue GLY  200  index1  448  path  194  %Seq 100.00
Highlighted IDENTICAL residue PHE  202  index1  450  path  196  %Seq 100.00
Highlighted IDENTICAL residue PHE  203  index1  451  path  197  %Seq 100.00
Highlighted IDENTICAL residue ASN  204  index1  452  path  198  %Seq 100.00
Highlighted IDENTICAL residue LEU  205  index1  453  path  199  %Seq 100.00
Highlighted IDENTICAL residue SER  206  index1  454  path  200  %Seq 100.00
Highlighted IDENTICAL residue VAL  207  index1  455  path  201  %Seq 100.00
Highlighted IDENTICAL residue GLN  208  index1  456  path  202  %Seq 100.00
Highlighted IDENTICAL residue ASN  209  index1  457  path  203  %Seq 100.00
Highlighted IDENTICAL residue LYS  210  index1  458  path  204  %Seq 100.00
Highlighted IDENTICAL residue LEU  211  index1  459  path  205  %Seq 100.00
Highlighted IDENTICAL residue ASN  213  index1  461  path  207  %Seq 100.00
Highlighted IDENTICAL residue ASP  215  index1  463  path  209  %Seq 100.00
Highlighted IDENTICAL residue GLU  216  index1  464  path  210  %Seq 100.00
Highlighted IDENTICAL residue TYR  219  index1  467  path  213  %Seq 100.00
Highlighted IDENTICAL residue ILE  220  index1  468  path  214  %Seq 100.00
Highlighted IDENTICAL residue PRO  221  index1  469  path  215  %Seq 100.00
Highlighted IDENTICAL residue THR  223  index1  471  path  217  %Seq 100.00
Highlighted IDENTICAL residue LYS  224  index1  472  path  218  %Seq 100.00
Highlighted IDENTICAL residue ALA  225  index1  473  path  219  %Seq 100.00
Highlighted IDENTICAL residue GLU  226  index1  474  path  220  %Seq 100.00
Highlighted IDENTICAL residue PHE  227  index1  475  path  221  %Seq 100.00
Highlighted IDENTICAL residue ALA  228  index1  476  path  222  %Seq 100.00
Highlighted IDENTICAL residue VAL  229  index1  477  path  223  %Seq 100.00
Highlighted IDENTICAL residue LEU  230  index1  478  path  224  %Seq 100.00
Highlighted IDENTICAL residue SER  232  index1  480  path  226  %Seq 100.00
Highlighted IDENTICAL residue ALA  233  index1  481  path  227  %Seq 100.00
Highlighted IDENTICAL residue PHE  234  index1  482  path  228  %Seq 100.00
Highlighted IDENTICAL residue ASN  235  index1  483  path  229  %Seq 100.00
Highlighted IDENTICAL residue PHE  236  index1  484  path  230  %Seq 100.00
Highlighted IDENTICAL residue VAL  237  index1  485  path  231  %Seq 100.00
Highlighted IDENTICAL residue PRO  239  index1  487  path  233  %Seq 100.00
Highlighted IDENTICAL residue LEU  241  index1  489  path  235  %Seq 100.00
Highlighted IDENTICAL residue GLY  243  index1  491  path  237  %Seq 100.00
Highlighted IDENTICAL residue TRP  244  index1  492  path  238  %Seq 100.00
Highlighted IDENTICAL residue ASN  249  index1  497  path  243  %Seq 100.00
Highlighted IDENTICAL residue SER  250  index1  498  path  244  %Seq 100.00
Highlighted IDENTICAL residue LYS  252  index1  500  path  246  %Seq 100.00
Highlighted IDENTICAL residue PRO  253  index1  501  path  247  %Seq 100.00
Highlighted IDENTICAL residue GLU  254  index1  502  path  248  %Seq 100.00
Highlighted IDENTICAL residue SER  266  index1  503  path  249  %Seq  50.00
Highlighted IDENTICAL residue GLY  267  index1  504  path  250  %Seq  50.00
Highlighted IDENTICAL residue ALA  268  index1  505  path  251  %Seq  50.00
Highlighted IDENTICAL residue GLU  269  index1  506  path  252  %Seq  50.00
Highlighted IDENTICAL residue LEU  270  index1  507  path  253  %Seq  50.00
Highlighted 142 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02740-1l3aA.pir.txt.1L3A.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02740-1l3aA.pir.txt PIR amino_acid 1L3A.pdb A 100.0 BLOSUM62.dat 

completed successfully.

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

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