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At2g02800.1/PDB

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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
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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

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

Assigned types to 426 residues in Sequence 2-02800, 23 remain unknown
Assigned types to 339 residues in Sequence 1b6cB, 110 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

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

Translated sequence file At2g02800-1b6cB.pir.txt into sequence alignment.

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

>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

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

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

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

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

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

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.

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

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