At2g14750.1/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 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/At2g14750-1i2d_A.pir.txt

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Assigned types to 276 residues in Sequence 2-14750, 20 remain unknown Assigned types to 271 residues in Sequence 1i2d_A, 25 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 11 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 12 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 13 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 14 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 15 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 16 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 17 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 18 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 19 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 20 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 73 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 74 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 75 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 76 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 77 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 78 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 79 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 80 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 152 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 219 All residues are positively and negatively charged

Translated sequence file At2g14750-1i2d_A.pir.txt into sequence alignment.

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>1I2D.pdb Made from 13407 ATOM records in 1I2D.pdb ANAPHGGVLKDLLARDAPRQAELAAEAESLPAVTLTERQLCDLELIMNGG FSPLEGFMNQADYDRVCEDNRLADGNVFSMPITLDASQEVIDEKKLQAGS RITLRDFRDDRNLAILTIDDIYRPDKTKEAKLVFGGDPEHPAIVYLNNTV KEFYIGGKIEAVNKLNHYDYVALRYTPAELRVHFDKLGWSRVVAFQTRNP MHRAHRELTVRAARSRQANVLIHPVVGLTKPGDIDHFTRVRAYQALLPRY PNGMAVLGLLGLAMRMGGPREAIWHAIIRKNHGATHFIVGRDHAGPGSNS KGEDFYGPYDAQHAVEKYKDELGIEVVEFQMVTYLPDTDEYRPVDQVPAG VKTLNISGTELRRRLRSGAHIPEWFSYPEVVKILRESNPPRATQGFTIFL TGYMNSGKDAIARALQVTLNQQGGRSVSLLLGDTVRHELSSELGFTREDR HTNIQRIAFVATELTRAGAAVIAAPIAPYEESRKFARDAVSQAGSFFLVH VATPLEHCEQSDKRGIYAAARRGEIKGFTGVDDPYETPEKADLVVDFSKQ SVRSIVHEIILVLESQGFLERQANAPHGGVLKDLLARDAPRQAELAAEAE SLPAVTLTERQLCDLELIMNGGFSPLEGFMNQADYDRVCEDNRLADGNVF SMPITLDASQEVIDEKKLQAGSRITLRDFRDDRNLAILTIDDIYRPDKTK EAKLVFGGDPEHPAIVYLNNTVKEFYIGGKIEAVNKLNHYDYVALRYTPA ELRVHFDKLGWSRVVAFQTRNPMHRAHRELTVRAARSRQANVLIHPVVGL TKPGDIDHFTRVRAYQALLPRYPNGMAVLGLLGLAMRMGGPREAIWHAII RKNHGATHFIVGRDHAGPGSNSKGEDFYGPYDAQHAVEKYKDELGIEVVE FQMVTYLPDTDEYRPVDQVPAGVKTLNISGTELRRRLRSGAHIPEWFSYP EVVKILRESNPPRATQGFTIFLTGYMNSGKDAIARALQVTLNQQGGRSVS LLLGDTVRHELSSELGFTREDRHTNIQRIAFVATELTRAGAAVIAAPIAP YEESRKFARDAVSQAGSFFLVHVATPLEHCEQSDKRGIYAAARRGEIKGF TGVDDPYETPEKADLVVDFSKQSVRSIVHEIILVLESQGFLERQANAPHG GVLKDLLARDAPRQAELAAEAESLPAVTLTERQLCDLELIMNGGFSPLEG FMNQADYDRVCEDNRLADGNVFSMPITLDASQEVIDEKKLQAGSRITLRD FRDDRNLAILTIDDIYRPDKTKEAKLVFGGDPEHPAIVYLNNTVKEFYIG GKIEAVNKLNHYDYVALRYTPAELRVHFDKLGWSRVVAFQTRNPMHRAHR ELTVRAARSRQANVLIHPVVGLTKPGDIDHFTRVRAYQALLPRYPNGMAV LGLLGLAMRMGGPREAIWHAIIRKNHGATHFIVGRDHAGPGSNSKGEDFY GPYDAQHAVEKYKDELGIEVVEFQMVTYLPDTDEYRPVDQVPAGVKTLNI SGTELRRRLRSGAHIPEWFSYPEVVKILRESNPPRATQGFTIFLTGYMNS GKDAIARALQVTLNQQGGRSVSLLLGDTVRHELSSELGFTREDRHTNIQR IAFVATELTRAGAAVIAAPIAPYEESRKFARDAVSQAGSFFLVHVATPLE HCEQSDKRGIYAAARRGEIKGFTGVDDPYETPEKADLVVDFSKQSVRSIV HEIILVLESQGFLERQ

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Best alignment: 1I2D.pdb  394  QGFTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLLGDTVRHELSSEL   443 +G I++TG   SGK  +A AL   L Q+ G+   +L GD VRH L+ +L 2-14750   100  KGCVIWVTGLSGSGKSTLACALNQMLYQK-GKLCYILDGDNVRHGLNRDL   148

1I2D.pdb  444  GFTREDRHTNIQRIAFVATELTRAGAAVIAAPIAPYEESRKFARDAVSQA   493 F EDR  NI+R+  VA     AG   IA+ I+PY   R   R  + + 2-14750   149  SFKAEDRAENIRRVGEVAKLFADAGIICIASLISPYRTDRDACRSLLPE-   197

1I2D.pdb  494  GSFFLVHVATPLEHCEQSDKRGIYAAARRGEIKGFTGVDDPYETPEKADL   543 G F V +  PL  CE  D +G+Y  AR G+IKGFTG+DDPYE P   ++ 2-14750   198  GDFVEVFMDVPLSVCEARDPKGLYKLARAGKIKGFTGIDDPYEPPLNCEI   247

1I2D.pdb  544  VVD-FSKQSVRSIVHEIILVLESQGFLE   570 +     S   +  +++  L+++G+L+ 2-14750   248  SLGREGGTSPIEMAEKVVGYLDNKGYLQ   275

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Highlighted IDENTICAL residue GLY 396  index1  395  path  119  %Seq 100.00 Highlighted IDENTICAL residue ILE 399  index1  398  path  122  %Seq 100.00 Highlighted IDENTICAL residue THR 402  index1  401  path  125  %Seq 100.00 Highlighted IDENTICAL residue GLY 403  index1  402  path  126  %Seq 100.00 Highlighted IDENTICAL residue SER 407  index1  406  path  130  %Seq 100.00 Highlighted IDENTICAL residue GLY 408  index1  407  path  131  %Seq 100.00 Highlighted IDENTICAL residue LYS 409  index1  408  path  132  %Seq 100.00 Highlighted IDENTICAL residue ALA 413  index1  412  path  136  %Seq 100.00 Highlighted IDENTICAL residue ALA 415  index1  414  path  138  %Seq 100.00 Highlighted IDENTICAL residue LEU 416  index1  415  path  139  %Seq 100.00 Highlighted IDENTICAL residue LEU 420  index1  419  path  143  %Seq 100.00 Highlighted IDENTICAL residue GLN 422  index1  421  path  145  %Seq 100.00 Highlighted IDENTICAL residue GLY 425  index1  424  path  147  %Seq 100.00 Highlighted IDENTICAL residue LEU 431  index1  430  path  154  %Seq 100.00 Highlighted IDENTICAL residue GLY 433  index1  432  path  156  %Seq 100.00 Highlighted IDENTICAL residue ASP 434  index1  433  path  157  %Seq 100.00 Highlighted IDENTICAL residue VAL 436  index1  435  path  159  %Seq 100.00 Highlighted IDENTICAL residue ARG 437  index1  436  path  160  %Seq 100.00 Highlighted IDENTICAL residue HIS 438  index1  437  path  161  %Seq 100.00 Highlighted IDENTICAL residue LEU 440  index1  439  path  163  %Seq 100.00 Highlighted IDENTICAL residue LEU 444  index1  443  path  167  %Seq 100.00 Highlighted IDENTICAL residue PHE 446  index1  445  path  169  %Seq 100.00 Highlighted IDENTICAL residue GLU 449  index1  448  path  172  %Seq 100.00 Highlighted IDENTICAL residue ASP 450  index1  449  path  173  %Seq 100.00 Highlighted IDENTICAL residue ARG 451  index1  450  path  174  %Seq 100.00 Highlighted IDENTICAL residue ASN 454  index1  453  path  177  %Seq 100.00 Highlighted IDENTICAL residue ILE 455  index1  454  path  178  %Seq 100.00 Highlighted IDENTICAL residue ARG 457  index1  456  path  180  %Seq 100.00 Highlighted IDENTICAL residue VAL 461  index1  460  path  184  %Seq 100.00 Highlighted IDENTICAL residue ALA 462  index1  461  path  185  %Seq 100.00 Highlighted IDENTICAL residue ALA 468  index1  467  path  191  %Seq 100.00 Highlighted IDENTICAL residue GLY 469  index1  468  path  192  %Seq 100.00 Highlighted IDENTICAL residue ILE 473  index1  472  path  196  %Seq 100.00 Highlighted IDENTICAL residue ALA 474  index1  473  path  197  %Seq 100.00 Highlighted IDENTICAL residue ILE 477  index1  476  path  200  %Seq 100.00 Highlighted IDENTICAL residue PRO 479  index1  478  path  202  %Seq 100.00 Highlighted IDENTICAL residue TYR 480  index1  479  path  203  %Seq 100.00 Highlighted IDENTICAL residue ARG 484  index1  483  path  207  %Seq 100.00 Highlighted IDENTICAL residue ARG 488  index1  487  path  211  %Seq 100.00 Highlighted IDENTICAL residue PHE 497  index1  496  path  220  %Seq 100.00 Highlighted IDENTICAL residue VAL 500  index1  499  path  223  %Seq 100.00 Highlighted IDENTICAL residue PRO 505  index1  504  path  228  %Seq 100.00 Highlighted IDENTICAL residue LEU 506  index1  505  path  229  %Seq 100.00 Highlighted IDENTICAL residue CYS 509  index1  508  path  232  %Seq 100.00 Highlighted IDENTICAL residue GLU 510  index1  509  path  233  %Seq 100.00 Highlighted IDENTICAL residue ASP 513  index1  512  path  236  %Seq 100.00 Highlighted IDENTICAL residue GLY 516  index1  515  path  239  %Seq 100.00 Highlighted IDENTICAL residue TYR 518  index1  517  path  241  %Seq 100.00 Highlighted IDENTICAL residue ALA 521  index1  520  path  244  %Seq 100.00 Highlighted IDENTICAL residue ARG 522  index1  521  path  245  %Seq 100.00 Highlighted IDENTICAL residue GLY 524  index1  523  path  247  %Seq 100.00 Highlighted IDENTICAL residue ILE 526  index1  525  path  249  %Seq 100.00 Highlighted IDENTICAL residue LYS 527  index1  526  path  250  %Seq 100.00 Highlighted IDENTICAL residue GLY 528  index1  527  path  251  %Seq 100.00 Highlighted IDENTICAL residue PHE 529  index1  528  path  252  %Seq 100.00 Highlighted IDENTICAL residue THR 530  index1  529  path  253  %Seq 100.00 Highlighted IDENTICAL residue GLY 531  index1  530  path  254  %Seq 100.00 Highlighted IDENTICAL residue ASP 533  index1  532  path  256  %Seq 100.00 Highlighted IDENTICAL residue ASP 534  index1  533  path  257  %Seq 100.00 Highlighted IDENTICAL residue PRO 535  index1  534  path  258  %Seq 100.00 Highlighted IDENTICAL residue TYR 536  index1  535  path  259  %Seq 100.00 Highlighted IDENTICAL residue GLU 537  index1  536  path  260  %Seq 100.00 Highlighted IDENTICAL residue PRO 539  index1  538  path  262  %Seq 100.00 Highlighted IDENTICAL residue SER 549  index1  548  path  273  %Seq  50.00 Highlighted IDENTICAL residue SER 552  index1  551  path  276  %Seq 100.00 Highlighted IDENTICAL residue LEU 564  index1  563  path  288  %Seq 100.00 Highlighted IDENTICAL residue GLY 568  index1  567  path  292  %Seq 100.00 Highlighted IDENTICAL residue LEU 570  index1  569  path  294  %Seq 100.00 Highlighted 68 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g14750-1i2d_A.pir.txt.1I2D.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g14750-1i2d_A.pir.txt PIR amino_acid 1I2D.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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