At2g13810.1/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/At2g13810-1j32_A.pir.txt

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Assigned types to 456 residues in Sequence 2-13810, 8 remain unknown Assigned types to 378 residues in Sequence 1j32_A, 86 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 132 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 133 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 150 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 265 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 274 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 372 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 391 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 392 All residues are positively and negatively charged

Translated sequence file At2g13810-1j32_A.pir.txt into sequence alignment.

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>1J32.pdb Made from 5906 ATOM records in 1J32.pdb MKLAARVESVSPSMTLIIDAKAKAMKAEGIDVCSFSAGEPDFNTPKHIVE AAKAALEQGKTRYGPAAGEPRLREAIAQKLQRDNGLCYGADNILVTNGGK QSIFNLMLAMIEPGDEVIIPAPFWVSYPEMVKLAEGTPVILPTTVETQFK VSPEQIRQAITPKTKLLVFNTPSNPTGMVYTPDEVRAIAQVAVEAGLWVL SDEIYEKILYDDAQHLSIGAASPEAYERSVVCSGFAKTYAMTGWRVGFLA GPVPLVKAATKIQGHSTSNVCTFAQYGAIAAYENSQDCVQEMLAAFAERR RYMLDALNAMPGLECPKPDGAFYMFPSIAKTGRSSLDFCSELLDQHQVAT VPGAAFGADDCIRLSYATDLDTIKRGMERLEKFLHGILMKLAARVESVSP SMTLIIDAKAKAMKAEGIDVCSFSAGEPDFNTPKHIVEAAKAALEQGKTR YGPAAGEPRLREAIAQKLQRDNGLCYGADNILVTNGGKQSIFNLMLAMIE PGDEVIIPAPFWVSYPEMVKLAEGTPVILPTTVETQFKVSPEQIRQAITP KTKLLVFNTPSNPTGMVYTPDEVRAIAQVAVEAGLWVLSDEIYEKILYDD AQHLSIGAASPEAYERSVVCSGFAKTYAMTGWRVGFLAGPVPLVKAATKI QGHSTSNVCTFAQYGAIAAYENSQDCVQEMLAAFAERRRYMLDALNAMPG LECPKPDGAFYMFPSIAKTGRSSLDFCSELLDQHQVATVPGAAFGADDCI RLSYATDLDTIKRGMERLEKFLHGIL

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Best alignment: 1J32.pdb   58  QGKTRYGPAAGEPRLREAIAQKLQRDNGLCYGADNILVTNGGKQSIFNLM   107 +G  YG   G   LR+AIA+   RD  L   ++ + V++G +  I  L 2-13810    103  EGYRGYGLEQGNKTLRKAIAETFYRD--LHVKSNEVFVSDGAQSDISRLQ   150

1J32.pdb  108  LAMIEPGDEVIIPAPFWVSYPEMVKLAEGTPVILPTTVETQFKVSP   153 L ++    + +  P + +Y +   +   T      T + Q        P 2-13810    151  L-LLGSNVTIAVQDPTFPAYIDSSVIIGQTGHFHEKTKKYQNVVYMPCGP   199

1J32.pdb  153  ---EQIRQAITPKTKLLVFNTPSNPTGMVYTPDEVRAIAQVAVEAGLWVL   200 A+TP+T ++ F +P+NPTG V + ++  +   A   G  ++ 2-13810   200  NNSFFPDLAMTPRTDVIFFCSPNNPTGYVASRKQLHQLVDFAKTNGSIII   249

1J32.pdb  201  SDEIYEKILYDDAQHLSIGAASPEAYERSVVCSGFAKTYAMTGWRVGF--   248 D Y   + +D    SI    P A E ++  S F+K    TG R+G+ 2-13810   250  FDSAYAAFI-EDGSPRSI-YEIPGAREVAIEVSSFSKFAGFTGVRLGWSI   297

1J32.pdb  248  --LAGPVPLVKAATKIQGHSTSNVCTFAQYGAIAAYEN-SQDCVQE   291 +  P++    +I   S +     AQ G +A   +     ++ 2-13810   298  IPDELLYSNGFPIINDFHRIVTTSFNGASNIAQAGGLACLSSGGLKEIRS   347

1J32.pdb  292  MLAAFAERRRYMLDALNAMPGLECPKPDGAFYMFPSIAKTGRSSLDFCSE   341 +  + E R+ ++D L ++ GL+      A Y++  +   G  S D  +E 2-13810   348  VNNYYKENRKILMDTLVSL-GLKVYGGVNAPYLW--VHFKGSKSWDVFNE   394

1J32.pdb  342  LLDQHQVATVPGAAF--GADDCIRLSYATDLDTIKRGMERLEKFLH   385 +L+  + TVPG+ F  G ++ +R+S     D I    +RL+ F + 2-13810   395  ILENTHIITVPGSGFGPGGEEYLRISGFGRRDHIVEASKRLQNFFN   440

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Highlighted IDENTICAL residue GLY  59  index1   59  path  104  %Seq 100.00 Highlighted IDENTICAL residue TYR  63  index1   63  path  108  %Seq 100.00 Highlighted IDENTICAL residue GLY  64  index1   64  path  109  %Seq 100.00 Highlighted IDENTICAL residue GLY  68  index1   68  path  113  %Seq 100.00 Highlighted IDENTICAL residue LEU  72  index1   72  path  117  %Seq 100.00 Highlighted IDENTICAL residue ARG  73  index1   73  path  118  %Seq 100.00 Highlighted IDENTICAL residue ALA  75  index1   75  path  120  %Seq 100.00 Highlighted IDENTICAL residue ILE  76  index1   76  path  121  %Seq 100.00 Highlighted IDENTICAL residue ALA  77  index1   77  path  122  %Seq 100.00 Highlighted IDENTICAL residue ARG  82  index1   82  path  127  %Seq 100.00 Highlighted IDENTICAL residue ASP  83  index1   83  path  128  %Seq 100.00 Highlighted IDENTICAL residue VAL  95  index1   95  path  140  %Seq 100.00 Highlighted IDENTICAL residue GLY  98  index1   98  path  143  %Seq 100.00 Highlighted IDENTICAL residue ILE 103  index1  103  path  148  %Seq 100.00 Highlighted IDENTICAL residue PRO 122  index1  122  path  167  %Seq 100.00 Highlighted IDENTICAL residue TYR 127  index1  127  path  172  %Seq 100.00 Highlighted IDENTICAL residue THR 137  index1  137  path  182  %Seq 100.00 Highlighted IDENTICAL residue THR 144  index1  144  path  189  %Seq 100.00 Highlighted IDENTICAL residue GLN 148  index1  148  path  193  %Seq 100.00 Highlighted IDENTICAL residue VAL 151  index1  151  path  200  %Seq  50.00 Highlighted IDENTICAL residue SER 152  index1  152  path  201  %Seq  50.00 Highlighted IDENTICAL residue PRO 153  index1  153  path  202  %Seq  50.00 Highlighted IDENTICAL residue GLU 154  index1  154  path  206  %Seq  50.00 Highlighted IDENTICAL residue ALA 159  index1  159  path  211  %Seq 100.00 Highlighted IDENTICAL residue THR 161  index1  161  path  213  %Seq 100.00 Highlighted IDENTICAL residue PRO 162  index1  162  path  214  %Seq 100.00 Highlighted IDENTICAL residue THR 164  index1  164  path  216  %Seq 100.00 Highlighted IDENTICAL residue PHE 169  index1  169  path  221  %Seq 100.00 Highlighted IDENTICAL residue PRO 172  index1  172  path  224  %Seq 100.00 Highlighted IDENTICAL residue ASN 174  index1  174  path  226  %Seq 100.00 Highlighted IDENTICAL residue PRO 175  index1  175  path  227  %Seq 100.00 Highlighted IDENTICAL residue THR 176  index1  176  path  228  %Seq 100.00 Highlighted IDENTICAL residue GLY 177  index1  177  path  229  %Seq 100.00 Highlighted IDENTICAL residue VAL 179  index1  179  path  231  %Seq 100.00 Highlighted IDENTICAL residue ALA 192  index1  192  path  244  %Seq 100.00 Highlighted IDENTICAL residue GLY 196  index1  196  path  248  %Seq 100.00 Highlighted IDENTICAL residue ASP 202  index1  202  path  254  %Seq 100.00 Highlighted IDENTICAL residue TYR 205  index1  205  path  257  %Seq 100.00 Highlighted IDENTICAL residue ASP 212  index1  212  path  263  %Seq 100.00 Highlighted IDENTICAL residue SER 217  index1  217  path  269  %Seq 100.00 Highlighted IDENTICAL residue ILE 218  index1  218  path  270  %Seq 100.00 Highlighted IDENTICAL residue PRO 223  index1  223  path  275  %Seq 100.00 Highlighted IDENTICAL residue ALA 225  index1  225  path  277  %Seq 100.00 Highlighted IDENTICAL residue GLU 227  index1  227  path  279  %Seq 100.00 Highlighted IDENTICAL residue SER 233  index1  233  path  285  %Seq 100.00 Highlighted IDENTICAL residue PHE 235  index1  235  path  287  %Seq 100.00 Highlighted IDENTICAL residue LYS 237  index1  237  path  289  %Seq 100.00 Highlighted IDENTICAL residue THR 242  index1  242  path  294  %Seq 100.00 Highlighted IDENTICAL residue GLY 243  index1  243  path  295  %Seq 100.00 Highlighted IDENTICAL residue ARG 245  index1  245  path  297  %Seq 100.00 Highlighted IDENTICAL residue GLY 247  index1  247  path  299  %Seq 100.00 Highlighted IDENTICAL residue LEU 249  index1  249  path  309  %Seq  50.00 Highlighted IDENTICAL residue ALA 250  index1  250  path  310  %Seq  50.00 Highlighted IDENTICAL residue GLY 251  index1  251  path  311  %Seq  50.00 Highlighted IDENTICAL residue PRO 252  index1  252  path  312  %Seq  50.00 Highlighted IDENTICAL residue VAL 253  index1  253  path  313  %Seq  50.00 Highlighted IDENTICAL residue PRO 254  index1  254  path  314  %Seq  50.00 Highlighted IDENTICAL residue LEU 255  index1  255  path  315  %Seq  50.00 Highlighted IDENTICAL residue ILE 262  index1  262  path  322  %Seq 100.00 Highlighted IDENTICAL residue SER 266  index1  266  path  326  %Seq 100.00 Highlighted IDENTICAL residue ALA 274  index1  274  path  334  %Seq 100.00 Highlighted IDENTICAL residue GLN 275  index1  275  path  335  %Seq 100.00 Highlighted IDENTICAL residue GLY 277  index1  277  path  337  %Seq 100.00 Highlighted IDENTICAL residue ALA 280  index1  280  path  340  %Seq 100.00 Highlighted IDENTICAL residue ASN 284  index1  284  path  344  %Seq  50.00 Highlighted IDENTICAL residue GLU 298  index1  298  path  359  %Seq 100.00 Highlighted IDENTICAL residue ARG 300  index1  300  path  361  %Seq 100.00 Highlighted IDENTICAL residue ASP 305  index1  305  path  366  %Seq 100.00 Highlighted IDENTICAL residue LEU 307  index1  307  path  368  %Seq 100.00 Highlighted IDENTICAL residue GLY 312  index1  312  path  373  %Seq 100.00 Highlighted IDENTICAL residue LEU 313  index1  313  path  374  %Seq 100.00 Highlighted IDENTICAL residue ALA 321  index1  321  path  382  %Seq 100.00 Highlighted IDENTICAL residue TYR 323  index1  323  path  384  %Seq 100.00 Highlighted IDENTICAL residue GLY 332  index1  332  path  393  %Seq 100.00 Highlighted IDENTICAL residue SER 335  index1  335  path  396  %Seq 100.00 Highlighted IDENTICAL residue ASP 337  index1  337  path  398  %Seq 100.00 Highlighted IDENTICAL residue GLU 341  index1  341  path  402  %Seq 100.00 Highlighted IDENTICAL residue LEU 343  index1  343  path  404  %Seq 100.00 Highlighted IDENTICAL residue THR 350  index1  350  path  411  %Seq 100.00 Highlighted IDENTICAL residue VAL 351  index1  351  path  412  %Seq 100.00 Highlighted IDENTICAL residue PRO 352  index1  352  path  413  %Seq 100.00 Highlighted IDENTICAL residue GLY 353  index1  353  path  414  %Seq 100.00 Highlighted IDENTICAL residue PHE 356  index1  356  path  417  %Seq 100.00 Highlighted IDENTICAL residue GLY 357  index1  357  path  420  %Seq  50.00 Highlighted IDENTICAL residue ARG 363  index1  363  path  426  %Seq 100.00 Highlighted IDENTICAL residue SER 365  index1  365  path  428  %Seq 100.00 Highlighted IDENTICAL residue ASP 371  index1  371  path  434  %Seq 100.00 Highlighted IDENTICAL residue ILE 373  index1  373  path  436  %Seq 100.00 Highlighted IDENTICAL residue ARG 379  index1  379  path  442  %Seq 100.00 Highlighted IDENTICAL residue LEU 380  index1  380  path  443  %Seq 100.00 Highlighted IDENTICAL residue PHE 383  index1  383  path  446  %Seq 100.00 Highlighted 91 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13810-1j32_A.pir.txt.1J32.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13810-1j32_A.pir.txt PIR amino_acid 1J32.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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