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At2g06555.1/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
Sequence 2
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/At2g06555-2haqt_C.pir.txt

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

Assigned types to 159 residues in Sequence 2-06555, 9 remain unknown
Assigned types to 125 residues in Sequence 2aqt_C, 43 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 52  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 53  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 54  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 55  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 56  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 100  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 101  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 136  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 137  All residues are positively and negatively charged

Translated sequence file At2g06555-2haqt_C.pir.txt into sequence alignment.

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

>2AQT.pdb  Made from 3456 ATOM records in 2AQT.pdb
ASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGLSEGLHGFHIH
ENPSCEPKEQEGQLTAGLGAGGHWDPKGAKQHGYPWQDDAHLGDLPALTV
LHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPAPLGGGGPRMA
CGVIKASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGLSEGLH
GFHIHENPSCEPKEQEGQLTAGLGAGGHWDPKGAKQHGYPWQDDAHLGDL
PALTVLHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPAPLGGG
GPRMACGVIKASIEVKVQQLDPVNGNKDVGTVTITESNYGLVFTPDLQGL
SEGLHGFHIHENPSCEPKEQEGQLTAGLGAGGHWDPKGAKQHGYPWQDDA
HLGDLPALTVLHDGTATNPVLAPRLKHLDDVRGHSIMIHTGGDNHSDHPA
PLGGGGPRMACGVIK

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

Best alignment:
2AQT.pdb   128  IHTGGDNHSDHPAPLGGGGPRMACGVIKASIEV   160
                +    + +SD        G    CGV+     V
2-06555    126  VFVSENEYSDFLLEASDVGKERRCGVLMLECRV   158

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

Highlighted IDENTICAL residue SER  167  index1  136  path  143  %Seq 100.00
Highlighted IDENTICAL residue ASP  168  index1  137  path  144  %Seq 100.00
Highlighted IDENTICAL residue GLY  177  index1  146  path  153  %Seq 100.00
Highlighted IDENTICAL residue CYS  182  index1  151  path  158  %Seq 100.00
Highlighted IDENTICAL residue GLY  183  index1  152  path  159  %Seq 100.00
Highlighted IDENTICAL residue VAL  184  index1  153  path  160  %Seq 100.00
Highlighted IDENTICAL residue LYS  186  index1  155  path  162  %Seq  50.00
Highlighted IDENTICAL residue ALA   32  index1  156  path  163  %Seq  50.00
Highlighted IDENTICAL residue SER   33  index1  157  path  164  %Seq  50.00
Highlighted IDENTICAL residue ILE   34  index1  158  path  165  %Seq  50.00
Highlighted IDENTICAL residue GLU   35  index1  159  path  166  %Seq  50.00
Highlighted IDENTICAL residue VAL   36  index1  160  path  167  %Seq  50.00
Highlighted 12 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g06555-2haqt_C.pir.txt.2AQT.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g06555-2haqt_C.pir.txt PIR amino_acid 2AQT.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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


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