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At2g10836.1/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
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Sequence 1
Got here 3
Got here 4
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Got here 4
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Got here 4
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Got here 4
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Sequence 2
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g10836-1fgu_A.pir.txt

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

Assigned types to 282 residues in Sequence 2-10836, 37 remain unknown
Assigned types to 213 residues in Sequence 1fgu_A, 106 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 64  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 65  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 66  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 67  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 68  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 69  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 70  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 71  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 72  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 73  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 74  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 75  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 76  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 77  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 156  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 157  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 158  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 159  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 160  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 161  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 162  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 163  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 164  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 165  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 166  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 167  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 168  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 169  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 170  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 171  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 172  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 173  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 174  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 175  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 176  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 177  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 178  All residues are positively and negatively charged

Translated sequence file At2g10836-1fgu_A.pir.txt into sequence alignment.

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

>1FGU.pdb  Made from 3793 ATOM records in 1FGU.pdb
MSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDES
GEIRATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTF
NNETSVMPCEDDHHLPTVQFDFTGIDDLENKSKDSLVDIIGICKSYEDAT
KITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADKFDGSRQPVLAIKG
ARVSDFGGRSLSVLSSSTIIANPDIPEAYKLRGWFDAEGQALDGVSMSKV
VPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESGEIR
ATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNET
SVMPCVQFDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVA
KRNIYLMDTSGKVVTATLWGEDADKFDGSRQPVLAIKGARVSDFGGRSLS
VLSSSTIIANPDIPEAYKLRGWFDAEGQALDGVS

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

Best alignment:
1FGU.pdb     2  SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESG    51
                SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESG
1fgu_A       1  SKVVPIASLTPYQSKWTICARVXXXXXXXXXXXXXXEGKLFSLELVDESG    50

1FGU.pdb    52  EIRATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFN   101
                EIRATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFN
1fgu_A      51  EIRATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFN   100

1FGU.pdb   102  NETSVMPCEDDHHLPTVQFDFTGIDDLENKSKDSLVDIIGICKSYEDATK   151
                NETSVMPCEDDHHLPTVQFDFTGIDDLENKSKDSLVDIIGICKSYEDATK
1fgu_A     101  NETSVMPCEDXXXXXXXXXXXXXXXXXXXXXXXSLVDIIGICKSYEDATK   150

1FGU.pdb   152  ITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADKFDGSRQPVLAIKGA   201
                ITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADKFDGSRQPVLAIKGA
1fgu_A     151  ITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADKFDGSRQPVLAIKGA   200

1FGU.pdb   202  RVSDFGGRSLSVLSSSTIIANPDIPEAYKLRGWFDAEGQALDGVSMS   248
                RVSDFGGRSLSVLSSSTIIANPDIPEAYKLRGWFDAEGQALDGVS+S
1fgu_A     201  RVSDFGGRSLSVLSSSTIIANPDIPEAYKLRGWFDAEGQALDGVSIS   247

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

Highlighted IDENTICAL residue ILE  187  index1    7  path   47  %Seq 100.00
Highlighted IDENTICAL residue LEU  190  index1   10  path   50  %Seq 100.00
Highlighted IDENTICAL residue SER  195  index1   15  path   55  %Seq 100.00
Highlighted IDENTICAL residue GLU  225  index1   45  path   85  %Seq 100.00
Highlighted IDENTICAL residue VAL  227  index1   47  path   87  %Seq 100.00
Highlighted IDENTICAL residue GLY  231  index1   51  path   91  %Seq 100.00
Highlighted IDENTICAL residue ILE  233  index1   53  path   94  %Seq 100.00
Highlighted IDENTICAL residue ALA  235  index1   55  path   96  %Seq 100.00
Highlighted IDENTICAL residue LEU  262  index1   82  path  124  %Seq 100.00
Highlighted IDENTICAL residue ASN  274  index1   94  path  138  %Seq 100.00
Highlighted IDENTICAL residue PHE  280  index1  100  path  144  %Seq 100.00
Highlighted IDENTICAL residue THR  284  index1  104  path  148  %Seq 100.00
Highlighted IDENTICAL residue PRO  288  index1  108  path  152  %Seq 100.00
Highlighted IDENTICAL residue GLY  321  index1  141  path  185  %Seq 100.00
Highlighted IDENTICAL residue GLU  327  index1  147  path  191  %Seq 100.00
Highlighted IDENTICAL residue THR  330  index1  150  path  194  %Seq 100.00
Highlighted IDENTICAL residue VAL  334  index1  154  path  202  %Seq 100.00
Highlighted IDENTICAL residue ASN  337  index1  157  path  205  %Seq 100.00
Highlighted IDENTICAL residue THR  351  index1  171  path  219  %Seq 100.00
Highlighted IDENTICAL residue GLY  353  index1  173  path  221  %Seq 100.00
Highlighted IDENTICAL residue LYS  354  index1  174  path  222  %Seq 100.00
Highlighted IDENTICAL residue GLY  362  index1  182  path  230  %Seq 100.00
Highlighted IDENTICAL residue PHE  368  index1  188  path  236  %Seq 100.00
Highlighted IDENTICAL residue VAL  383  index1  203  path  267  %Seq 100.00
Highlighted IDENTICAL residue ASP  385  index1  205  path  269  %Seq 100.00
Highlighted IDENTICAL residue GLY  388  index1  208  path  272  %Seq 100.00
Highlighted IDENTICAL residue ARG  389  index1  209  path  273  %Seq 100.00
Highlighted IDENTICAL residue SER  392  index1  212  path  278  %Seq 100.00
Highlighted IDENTICAL residue SER  397  index1  217  path  283  %Seq 100.00
Highlighted IDENTICAL residue ILE  399  index1  219  path  285  %Seq 100.00
Highlighted IDENTICAL residue ASN  402  index1  222  path  288  %Seq 100.00
Highlighted IDENTICAL residue PRO  406  index1  226  path  292  %Seq 100.00
Highlighted IDENTICAL residue GLU  407  index1  227  path  293  %Seq 100.00
Highlighted IDENTICAL residue ARG  412  index1  232  path  298  %Seq 100.00
Highlighted IDENTICAL residue PHE  415  index1  235  path  303  %Seq 100.00
Highlighted IDENTICAL residue GLN  420  index1  240  path  308  %Seq 100.00
Highlighted 36 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g10836-1fgu_A.pir.txt.1FGU.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g10836-1fgu_A.pir.txt PIR amino_acid 1FGU.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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