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At2g09865.1/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
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Sequence 2
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g09865-1jas_A.pir.txt

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

Assigned types to 339 residues in Sequence 2-09865, 17 remain unknown
Assigned types to 108 residues in Sequence 1jas_A, 248 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 261  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 262  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 263  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 264  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 265  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 266  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 281  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 282  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 283  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 297  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 310  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 311  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 312  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 313  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 314  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 315  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 316  All residues are positively and negatively charged

Translated sequence file At2g09865-1jas_A.pir.txt into sequence alignment.

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

>1JAS.pdb  Made from 2391 ATOM records in 1JAS.pdb
MSTPARRRLMRDFKRLQEDPPVGVSGAPSENNIMQWNAVIFGPEGTPFED
GTFKLVIEFSEEYPNKPPTVRFLSKMFHPNVYADGSICLDILQNRWSPTY
DVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSWN
DS

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

Best alignment:
1JAS.pdb   133  NKREYEKRVSAIV   145
                 KR+  KRV +++
2-09865    192  RKRKKSKRVGSLL   204

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

Highlighted IDENTICAL residue ASN  133  index1  133  path  192  %Seq  50.00
Highlighted IDENTICAL residue LYS  134  index1  134  path  193  %Seq  50.00
Highlighted IDENTICAL residue ARG  135  index1  135  path  194  %Seq  50.00
Highlighted IDENTICAL residue GLU  136  index1  136  path  195  %Seq  50.00
Highlighted IDENTICAL residue TYR  137  index1  137  path  196  %Seq  50.00
Highlighted IDENTICAL residue GLU  138  index1  138  path  197  %Seq  50.00
Highlighted IDENTICAL residue LYS  139  index1  139  path  198  %Seq  50.00
Highlighted IDENTICAL residue ARG  140  index1  140  path  199  %Seq  50.00
Highlighted IDENTICAL residue VAL  141  index1  141  path  200  %Seq  50.00
Highlighted IDENTICAL residue SER  142  index1  142  path  201  %Seq  50.00
Highlighted IDENTICAL residue ALA  143  index1  143  path  202  %Seq  50.00
Highlighted IDENTICAL residue ILE  144  index1  144  path  203  %Seq  50.00
Highlighted IDENTICAL residue VAL  145  index1  145  path  204  %Seq  50.00
Highlighted 13 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g09865-1jas_A.pir.txt.1JAS.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g09865-1jas_A.pir.txt PIR amino_acid 1JAS.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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