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
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Sequence 2
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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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