At2g01300.1/PDB

&&&&&&&&&&&&&&&&&&&& 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/

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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

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Assigned types to 156 residues in Sequence 2-01300, 7 remain unknown Assigned types to 106 residues in Sequence 1orjA, 57 remain unknown

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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

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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.

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

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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

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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

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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.

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