At2g02800.1/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 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 Got here 3 Got here 4 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/At2g02800-1b6cB.pir.txt

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Assigned types to 426 residues in Sequence 2-02800, 23 remain unknown Assigned types to 339 residues in Sequence 1b6cB, 110 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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Translated sequence file At2g02800-1b6cB.pir.txt into sequence alignment.

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>1B6C.pdb Made from 13732 ATOM records in 1B6C.pdb GVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFML GKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFD VELLKLETTLKDLIYDMTTSGSGSGLPLLVQRTIARTIVLQESIGKGRFG EVWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADN KDNGTWTQLWLVSDYHEHGSLFDYLNRYTVTVEGMIKLALSTASGLAHLH MEIVGTQGKPAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDI APNHRVGTKRYMAPEVLDDSINMKHFESFKRADIYAMGLVFWEIARRCSI GGIHEDYQLPYYDLVPSDPSVEEMRKVVCEQKLRPNIPNRWQSCEALRVM AKIMRECWYANGAARLTALRIKKTLSQLSQQEGGVQVETISPGDGRTFPK RGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMS VGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLETTLKDLIYDM TTSGSGSGLPLLVQRTIARTIVLQESIGKGRFGEVWRGKWRGEEVAVKIF SSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDYHE HGSLFDYLNRYTVTVEGMIKLALSTASGLAHLHMEIVGTQGKPAIAHRDL KSKNILVKKNGTCCIADLGLAVRHDSATDTIDIAPNHRVGTKRYMAPEVL DDSINMKHFESFKRADIYAMGLVFWEIARRCSIGGIHEDYQLPYYDLVPS DPSVEEMRKVVCEQKLRPNIPNRWQSCEALRVMAKIMRECWYANGAARLT ALRIKKTLSQLSQQEGGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGK KFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGA TGHPGIIPPHATLVFDVELLKLETTLKDLIYDMTTSGSGSGLPLLVQRTI ARTIVLQESIGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIYQT VMLRHENILGFIAADNKDNGTWTQLWLVSDYHEHGSLFDYLNRYTVTVEG MIKLALSTASGLAHLHMEIVGTQGKPAIAHRDLKSKNILVKKNGTCCIAD LGLAVRHDSATDTIDIAPNHRVGTKRYMAPEVLDDSINMKHFESFKRADI YAMGLVFWEIARRCSIGGIHEDYQLPYYDLVPSDPSVEEMRKVVCEQKLR PNIPNRWQSCEALRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQEGG VQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLG KQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDV ELLKLETTLKDLIYDMTTSGSGSGLPLLVQRTIARTIVLQESIGKGRFGE VWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNK DNGTWTQLWLVSDYHEHGSLFDYLNRYTVTVEGMIKLALSTASGLAHLHM EIVGTQGKPAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDIA PNHRVGTKRYMAPEVLDDSINMKHFESFKRADIYAMGLVFWEIARRCSIG GIHEDYQLPYYDLVPSDPSVEEMRKVVCEQKLRPNIPNRWQSCEALRVMA KIMRECWYANGAARLTALRIKKTLSQLSQQEG

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Best alignment: 1B6C.pdb  211  LVSDYHEHGSLFDYL---NRYTVTVEGMIKLALSTASGLAHLHMEIVGTQ   257 LV ++  GSL ++L       +T    +K+A+  A GL  LH       2-02800    164  LVYEFMPKGSLENHLFRRGAQPLTWAIRMKVAIGAAKGLTFLH--D   207

1B6C.pdb  258  GKPAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDIAPNHRVG   307 K + +RD K+ NIL+       ++D GLA +     D   ++    +G 2-02800   208  AKSQVIYRDFKAANILLDAEFNSKLSDFGLA-KAGPTGDKTHVS-TQVMG   255

1B6C.pdb  308  TKRYMAPE   315 T Y APE 2-02800   256  THGYAAPE   263

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Highlighted IDENTICAL residue LEU 278  index1  211  path  168  %Seq 100.00 Highlighted IDENTICAL residue VAL 279  index1  212  path  169  %Seq 100.00 Highlighted IDENTICAL residue GLY 286  index1  219  path  176  %Seq 100.00 Highlighted IDENTICAL residue SER 287  index1  220  path  177  %Seq 100.00 Highlighted IDENTICAL residue LEU 288  index1  221  path  178  %Seq 100.00 Highlighted IDENTICAL residue LEU 292  index1  225  path  182  %Seq 100.00 Highlighted IDENTICAL residue ASN 293  index1  226  path  186  %Seq  50.00 Highlighted IDENTICAL residue ARG 294  index1  227  path  187  %Seq  50.00 Highlighted IDENTICAL residue THR 298  index1  231  path  191  %Seq 100.00 Highlighted IDENTICAL residue LYS 304  index1  237  path  197  %Seq 100.00 Highlighted IDENTICAL residue ALA 306  index1  239  path  199  %Seq 100.00 Highlighted IDENTICAL residue ALA 310  index1  243  path  203  %Seq 100.00 Highlighted IDENTICAL residue GLY 312  index1  245  path  205  %Seq 100.00 Highlighted IDENTICAL residue LEU 313  index1  246  path  206  %Seq 100.00 Highlighted IDENTICAL residue LEU 316  index1  249  path  209  %Seq 100.00 Highlighted IDENTICAL residue HIS 317  index1  250  path  210  %Seq 100.00 Highlighted IDENTICAL residue LYS 326  index1  259  path  219  %Seq 100.00 Highlighted IDENTICAL residue ARG 332  index1  265  path  225  %Seq 100.00 Highlighted IDENTICAL residue ASP 333  index1  266  path  226  %Seq 100.00 Highlighted IDENTICAL residue LYS 335  index1  268  path  228  %Seq 100.00 Highlighted IDENTICAL residue ASN 338  index1  271  path  231  %Seq 100.00 Highlighted IDENTICAL residue ILE 339  index1  272  path  232  %Seq 100.00 Highlighted IDENTICAL residue LEU 340  index1  273  path  233  %Seq 100.00 Highlighted IDENTICAL residue ASP 351  index1  284  path  244  %Seq 100.00 Highlighted IDENTICAL residue GLY 353  index1  286  path  246  %Seq 100.00 Highlighted IDENTICAL residue LEU 354  index1  287  path  247  %Seq 100.00 Highlighted IDENTICAL residue ALA 355  index1  288  path  248  %Seq 100.00 Highlighted IDENTICAL residue GLY 374  index1  307  path  267  %Seq 100.00 Highlighted IDENTICAL residue THR 375  index1  308  path  268  %Seq 100.00 Highlighted IDENTICAL residue TYR 378  index1  311  path  271  %Seq 100.00 Highlighted IDENTICAL residue ALA 380  index1  313  path  273  %Seq 100.00 Highlighted IDENTICAL residue PRO 381  index1  314  path  274  %Seq 100.00 Highlighted IDENTICAL residue GLU 382  index1  315  path  275  %Seq 100.00 Highlighted 33 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02800-1b6cB.pir.txt.1B6C.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02800-1b6cB.pir.txt PIR amino_acid 1B6C.pdb A 100.0 BLOSUM62.dat

completed successfully.

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