At2g02590.1/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
Got here 4
Got here 3
Got here 4
Got here 3
Sequence 2
Got here 3
Got here 4
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g02590-1fx8A.pir.txt
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Assigned types to 324 residues in Sequence 2-02590, 24 remain unknown
Assigned types to 184 residues in Sequence 1fx8A, 164 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 230 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 231 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 232 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 233 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 234 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 235 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 286 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 287 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 288 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 289 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 290 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 291 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 292 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 293 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 294 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 295 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 322 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 323 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 324 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 325 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 326 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 327 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 328 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 329 All residues are positively and negatively charged
Translated sequence file At2g02590-1fx8A.pir.txt into sequence alignment.
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>1FX8.pdb Made from 1895 ATOM records in 1FX8.pdb
TLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIWGLGVAMA
IYLTAGVSGAHLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVY
GLYYNLFFDFEQTHHIVRGSVESVDLAGTFSTYPNPHINFVQAFAVEMVI
TAILMGLILALTDDGNGVPRGPLAPLLIGLLIAVIGASMGPLTGFAMNPA
RDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIVGAIVGAFAYRKLI
GRHL
======================================================
Best alignment:
1FX8.pdb 34 FGQWEISVIWGLGVAMAIYLTAGVSGAHLNPAVTIALWLFACFDKRKVIP 83
 FG + +V++ L I L + + + L F+ +P
2-02590 143 FGWPDEAVVFALATLPVIELRGAIPVGYWMQLKPVVLTSFSVLGNMVPVP 192
1FX8.pdb 84 FIV 86
 FIV
2-02590 193 FIV 195
======================================================
Highlighted IDENTICAL residue PHE 39 index1 34 path 143 %Seq 100.00
Highlighted IDENTICAL residue GLY 40 index1 35 path 144 %Seq 100.00
Highlighted IDENTICAL residue VAL 46 index1 41 path 150 %Seq 100.00
Highlighted IDENTICAL residue LEU 50 index1 45 path 154 %Seq 100.00
Highlighted IDENTICAL residue ILE 56 index1 51 path 160 %Seq 100.00
Highlighted IDENTICAL residue LEU 58 index1 53 path 162 %Seq 100.00
Highlighted IDENTICAL residue LEU 67 index1 62 path 171 %Seq 50.00
Highlighted IDENTICAL residue ASN 68 index1 63 path 172 %Seq 50.00
Highlighted IDENTICAL residue PRO 69 index1 64 path 173 %Seq 50.00
Highlighted IDENTICAL residue ALA 70 index1 65 path 174 %Seq 100.00
Highlighted IDENTICAL residue THR 72 index1 67 path 176 %Seq 100.00
Highlighted IDENTICAL residue ALA 74 index1 69 path 178 %Seq 100.00
Highlighted IDENTICAL residue LYS 85 index1 80 path 189 %Seq 50.00
Highlighted 13 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02590-1fx8A.pir.txt.1FX8.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02590-1fx8A.pir.txt PIR amino_acid 1FX8.pdb A 100.0 BLOSUM62.dat 
completed successfully.
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