FANDOM


&&&&&&&&&&&&&&&&&&&& 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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g04360-1oe9A.pir.txt

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

Assigned types to 320 residues in Sequence 2-4360, 34 remain unknown
Assigned types to 245 residues in Sequence 1oe9A, 109 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 At2g04360-1oe9A.pir.txt into sequence alignment.

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

>1OE9.pdb  Made from 6925 ATOM records in 1OE9.pdb
ELYTKYARVWIPDPEEVWKSAELLKDYKPGDKVLQLRLDLEYCLKELPPL
RNPDILVGENDLTALSYLHEPAVLHNLKVRFIDSKLIYTYCGIVLVAINP
YEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVS
GESGAGKTVSAKYAMRYFATVSNVEEKVLASNPIMESIGNAKTTRNDNSS
RFGKYIEIGFDKRYRIIGANMRTYLLEKSRVVFQAEEERNYHIFYQLCAS
AALPEFKTLRLGNANYFHYTKQGGSPVIDGIDDAKEMVNTRQACTLLGIS
DSYQMGIFRILAGILHLGNVEFASRDSDSCAIPPKHDPLTIFCDLMGVDY
EEMAHWLCHRKLATYIKPISKLHAINARDALAKHIYANLFNWIVDHVNKA
LHSTVKQHSFIGVLDIYGFETFEINSFEQFCINYANEKLQQQFNMHVFKL
EQEEYMKEQIPDFYDNQPCINLIEAKMGVLDLLDEECKMPKGSDDTWAQK
LYNTHLNKCALFEKPRLSNKAFIIKHFADKVEYQCEGFLEKNKDTVYEEQ
IKVLKSSKKFKLLPELFHKKTVGHQFRNSLHLLMETLNATTPHYVRCIKP
NDFKFPFTFDEKRAVQQLRACGVLETIRISAAGFPSRWTYQEFFSRYRVL
MKQKDVLSDRKQTCKNVLEKLILDKDKYQFGKTKIFFRAGQVAYLEKIRA
DKLRAACIRIQKTIRGWLMRKKYMRMRRGDAFNKDQLEEFKEAFELFDRV
GDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDELKSRRVDFETFLP
MLQAVAKYEDYLEGFRVFDGNGKVMGAELRHVLTTLGEKMTEEEVETVLA
GHEDSNGCINYEAFLKHILS

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

Best alignment:
1OE9.pdb    90  YCGIVLVAINPYEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMA   139
                YCGIVLVAINPYEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMA
1oe9A        1  YCGIVLVAINPYEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMA    50

1OE9.pdb   140  RDERNQSIIVSGESGAGKTVSAKYAMRYFATV------SNVEEKVLASNP   183
                RDERNQSIIVSGESGAGKTVSAKYAMRYFATV      +NVEEKVLASNP
1oe9A       51  RDERNQSIIVSGESGAGKTVSAKYAMRYFATVSGSASEANVEEKVLASNP   100

1OE9.pdb   184  IMESIGNAKTTRNDNSSRFGKYIEIGFDKRYRIIGANMRTYLLEKSRVVF   233
                IMESIGNAKTTRNDNSSRFGKYIEIGFDKRYRIIGANMRTYLLEKSRVVF
1oe9A      101  IMESIGNAKTTRNDNSSRFGKYIEIGFDKRYRIIGANMRTYLLEKSRVVF   150

1OE9.pdb   234  QAEEERNYHIFYQLCASAALPEFKTLRLGNANYFHYTKQGGSPVIDGIDD   283
                QAEEERNYHIFYQLCASAALPEFKTLRLGNANYFHYTKQGGSPVIDGIDD
1oe9A      151  QAEEERNYHIFYQLCASAALPEFKTLRLGNANYFHYTKQGGSPVIDGIDD   200

1OE9.pdb   284  AKEMVNTRQACTLLGISDSYQMGIFRILAGILHLGNVEFASRDSD   328
                AKEMVNTRQACTLLGISDSYQMGIFRILAGILHLGNVEFASRDSD
1oe9A      201  AKEMVNTRQACTLLGISDSYQMGIFRILAGILHLGNVEFASRDSD   245

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

Highlighted IDENTICAL residue GLY  104  index1   92  path    3  %Seq 100.00
Highlighted IDENTICAL residue LEU  116  index1  104  path   15  %Seq 100.00
Highlighted IDENTICAL residue PRO  117  index1  105  path   16  %Seq 100.00
Highlighted IDENTICAL residue ILE  118  index1  106  path   29  %Seq  50.00
Highlighted IDENTICAL residue TYR  119  index1  107  path   30  %Seq  50.00
Highlighted IDENTICAL residue GLN  130  index1  118  path   41  %Seq 100.00
Highlighted IDENTICAL residue PRO  137  index1  125  path   48  %Seq 100.00
Highlighted IDENTICAL residue HIS  138  index1  126  path   49  %Seq 100.00
Highlighted IDENTICAL residue ALA  141  index1  129  path   52  %Seq 100.00
Highlighted IDENTICAL residue ALA  146  index1  134  path   57  %Seq  50.00
Highlighted IDENTICAL residue TYR  147  index1  135  path   58  %Seq  50.00
Highlighted IDENTICAL residue LYS  148  index1  136  path   59  %Seq  50.00
Highlighted IDENTICAL residue GLN  149  index1  137  path   60  %Seq  50.00
Highlighted IDENTICAL residue MET  150  index1  138  path   61  %Seq  50.00
Highlighted IDENTICAL residue ALA  151  index1  139  path   62  %Seq  50.00
Highlighted IDENTICAL residue SER  165  index1  153  path   76  %Seq 100.00
Highlighted IDENTICAL residue LYS  174  index1  162  path   85  %Seq 100.00
Highlighted IDENTICAL residue PHE  180  index1  168  path   91  %Seq  50.00
Highlighted IDENTICAL residue ALA  181  index1  169  path   92  %Seq  50.00
Highlighted IDENTICAL residue THR  182  index1  170  path   93  %Seq  50.00
Highlighted IDENTICAL residue VAL  183  index1  171  path   94  %Seq  50.00
Highlighted IDENTICAL residue LEU  197  index1  179  path  108  %Seq 100.00
Highlighted IDENTICAL residue ALA  209  index1  191  path  120  %Seq 100.00
Highlighted IDENTICAL residue THR  211  index1  193  path  122  %Seq  50.00
Highlighted IDENTICAL residue THR  212  index1  194  path  123  %Seq  50.00
Highlighted IDENTICAL residue ARG  213  index1  195  path  124  %Seq  50.00
Highlighted IDENTICAL residue GLY  236  index1  218  path  155  %Seq 100.00
Highlighted IDENTICAL residue LEU  243  index1  225  path  162  %Seq 100.00
Highlighted IDENTICAL residue PHE  262  index1  244  path  184  %Seq 100.00
Highlighted IDENTICAL residue LEU  265  index1  247  path  187  %Seq 100.00
Highlighted IDENTICAL residue LEU  279  index1  261  path  202  %Seq 100.00
Highlighted IDENTICAL residue ASN  281  index1  263  path  204  %Seq 100.00
Highlighted IDENTICAL residue PHE  285  index1  267  path  208  %Seq  50.00
Highlighted IDENTICAL residue HIS  286  index1  268  path  209  %Seq  50.00
Highlighted IDENTICAL residue TYR  287  index1  269  path  210  %Seq  50.00
Highlighted IDENTICAL residue THR  288  index1  270  path  211  %Seq  50.00
Highlighted IDENTICAL residue LYS  289  index1  271  path  212  %Seq  50.00
Highlighted IDENTICAL residue GLN  290  index1  272  path  213  %Seq  50.00
Highlighted IDENTICAL residue GLY  291  index1  273  path  214  %Seq  50.00
Highlighted IDENTICAL residue GLY  292  index1  274  path  215  %Seq  50.00
Highlighted IDENTICAL residue SER  293  index1  275  path  216  %Seq  50.00
Highlighted IDENTICAL residue PRO  294  index1  276  path  217  %Seq  50.00
Highlighted IDENTICAL residue VAL  295  index1  277  path  218  %Seq  50.00
Highlighted IDENTICAL residue ILE  296  index1  278  path  219  %Seq  50.00
Highlighted IDENTICAL residue THR  313  index1  295  path  236  %Seq  50.00
Highlighted IDENTICAL residue LEU  314  index1  296  path  237  %Seq  50.00
Highlighted IDENTICAL residue LEU  315  index1  297  path  238  %Seq  50.00
Highlighted IDENTICAL residue GLY  316  index1  298  path  239  %Seq  50.00
Highlighted IDENTICAL residue ILE  317  index1  299  path  240  %Seq  50.00
Highlighted IDENTICAL residue SER  318  index1  300  path  241  %Seq  50.00
Highlighted IDENTICAL residue ASP  319  index1  301  path  242  %Seq  50.00
Highlighted IDENTICAL residue LEU  329  index1  311  path  252  %Seq 100.00
Highlighted IDENTICAL residue LEU  333  index1  315  path  256  %Seq 100.00
Highlighted IDENTICAL residue ASP  346  index1  328  path  269  %Seq 100.00
Highlighted 54 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g04360-1oe9A.pir.txt.1OE9.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g04360-1oe9A.pir.txt PIR amino_acid 1OE9.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.