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At2g01300.1/Structure

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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/At2g01300_1orjA.pir.txt

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

Assigned types to 156 residues in Sequence 2-01300, 7 remain unknown
Assigned types to 106 residues in Sequence 1orjA, 57 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 115  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 116  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 117  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 118  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 119  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 120  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 121  All residues are positively and negatively charged

Translated sequence file At2g01300_1orjA.pir.txt into sequence alignment.

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

>1ORJ.pdb  Made from 3847 ATOM records in 1ORJ.pdb
RNIAEAYFQNMVETATPLEQIILLYDKAIECLERAIEIYDQVNELEKRKE
FVENIDRVYDIISALKSFLDHEKGKEIAKNLDTIYTIILNTLVKVDKTKE
ELQKILEILKDLREAWEEVKKKVHHHPLEQIILLYDKAIECLERAIEIYD
QVNELEKRKEFVENIDRVYDIISALKSFLDHEKGKEIAKNLDTIYTIILN
TLVKVDKTKEELQKILEILKDLREAWEEVKKPLEQIILLYDKAIECLERA
IEIYDQVNELEKRKEFVENIDRVYDIISALKSFLDHEKGKEIAKNLDTIY
TIILNTLVKVDKTKEELQKILEILKDLREAWEEVKRNIAEAYFQNMVETA
TPLEQIILLYDKAIECLERAIEIYDQVNELEKRKEFVENIDRVYDIISAL
KSFLDHEKGKEIAKNLDTIYTIILNTLVKVDKTKEELQKILEILKDLREA
WEEVKKKVHH

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

Best alignment:
1ORJ.pdb   194  IYTIILNTLVKVDKTKEELQKILEILKDLREAWEEVKKPLEQIILLYDKA   243
                 + ++L+    + K K+   ++       ++ +    + +++ +++  K 
2-01300     17  FHPLVLSQRAIIPKKKKMTMRVSAAASSGKDHYYGGGRLVDENMIVLRKR    66

1ORJ.pdb   244  IECLERAIEIYDQVNE-LEKRKEFVENIDRVY-DIISALKSFL   284
                I  ++     Y+  +  ++  K F  + D V  D +  L+SFL
2-01300     67  IHEMKMVERNYEPPSHWMDWEKRFYNSYDSVICDSVGLLQSFL   109

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

Highlighted IDENTICAL residue ILE 2085  index1  194  path   17  %Seq  50.00
Highlighted IDENTICAL residue TYR 2086  index1  195  path   18  %Seq  50.00
Highlighted IDENTICAL residue THR 2087  index1  196  path   19  %Seq  50.00
Highlighted IDENTICAL residue ILE 2088  index1  197  path   20  %Seq  50.00
Highlighted IDENTICAL residue ILE 2089  index1  198  path   21  %Seq  50.00
Highlighted IDENTICAL residue LEU 2090  index1  199  path   22  %Seq  50.00
Highlighted IDENTICAL residue ASN 2091  index1  200  path   23  %Seq  50.00
Highlighted IDENTICAL residue THR 2092  index1  201  path   24  %Seq  50.00
Highlighted IDENTICAL residue LEU 2093  index1  202  path   25  %Seq  50.00
Highlighted IDENTICAL residue VAL 2094  index1  203  path   26  %Seq  50.00
Highlighted IDENTICAL residue LYS 2095  index1  204  path   27  %Seq  50.00
Highlighted IDENTICAL residue VAL 2096  index1  205  path   28  %Seq  50.00
Highlighted IDENTICAL residue ASP 2097  index1  206  path   29  %Seq  50.00
Highlighted IDENTICAL residue LYS 2098  index1  207  path   30  %Seq  50.00
Highlighted IDENTICAL residue THR 2099  index1  208  path   31  %Seq  50.00
Highlighted IDENTICAL residue LYS 2100  index1  209  path   32  %Seq  50.00
Highlighted IDENTICAL residue GLU 2101  index1  210  path   33  %Seq  50.00
Highlighted IDENTICAL residue GLU 2102  index1  211  path   34  %Seq  50.00
Highlighted IDENTICAL residue LEU 2103  index1  212  path   35  %Seq  50.00
Highlighted IDENTICAL residue GLN 2104  index1  213  path   36  %Seq  50.00
Highlighted IDENTICAL residue LYS 2105  index1  214  path   37  %Seq  50.00
Highlighted IDENTICAL residue ILE 2106  index1  215  path   38  %Seq  50.00
Highlighted IDENTICAL residue LEU 2107  index1  216  path   39  %Seq  50.00
Highlighted IDENTICAL residue GLU 2108  index1  217  path   40  %Seq  50.00
Highlighted IDENTICAL residue LEU 2110  index1  219  path   42  %Seq 100.00
Highlighted IDENTICAL residue LYS 3028  index1  242  path   65  %Seq 100.00
Highlighted IDENTICAL residue ILE 3030  index1  244  path   67  %Seq 100.00
Highlighted IDENTICAL residue TYR 3040  index1  254  path   77  %Seq 100.00
Highlighted IDENTICAL residue LYS 3050  index1  264  path   88  %Seq 100.00
Highlighted IDENTICAL residue PHE 3052  index1  266  path   90  %Seq 100.00
Highlighted IDENTICAL residue ASP 3057  index1  271  path   95  %Seq 100.00
Highlighted IDENTICAL residue VAL 3059  index1  273  path   97  %Seq  50.00
Highlighted IDENTICAL residue ASP 3061  index1  275  path  100  %Seq 100.00
Highlighted IDENTICAL residue LEU 3066  index1  280  path  105  %Seq 100.00
Highlighted IDENTICAL residue SER 3068  index1  282  path  107  %Seq 100.00
Highlighted IDENTICAL residue PHE 3069  index1  283  path  108  %Seq 100.00
Highlighted IDENTICAL residue LEU 3070  index1  284  path  109  %Seq 100.00
Highlighted 37 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01300_1orjA.pir.txt.1ORJ.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01300_1orjA.pir.txt PIR amino_acid 1ORJ.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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


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