At2g02740.1/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 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 Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g02740-1l3aA.pir.txt

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Assigned types to 268 residues in Sequence 2-02740, 0 remain unknown Assigned types to 166 residues in Sequence 1l3aA, 102 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 At2g02740-1l3aA.pir.txt into sequence alignment.

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>1L3A.pdb Made from 5435 ATOM records in 1L3A.pdb TPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAA GVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRK VLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVM PYLLGWHTAVNSFKPETPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAF KLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEF FHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPV TKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPEAELETPKVFVGYSIYKGK AALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFS LSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHF FNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFK PESGAELEWNLEHHHHHHTPKVFVGYSIYKGKAALTVEPRSPEFSPLDSG AFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSC EFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYI PVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPEGAELE

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Best alignment: 1L3A.pdb  327  NSFKPEAELETPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREG   376 +S   AE+ +P+ +VG+SIYKGKAALT+EPR+PEF  L+SGAFKL++EG 2-02740    72  SSSSQNAEVSSPRFYVGHSIYKGKAALTIEPRAPEFVALESGAFKLTKEG   121

1L3A.pdb  377  MVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNK   426 ++LQFAPAAGVRQYDWSRKQVFSLSVTEIG+++SLG ++SCEFFHDP K 2-02740   122  FLLLQFAPAAGVRQYDWSRKQVFSLSVTEIGNLVSLGPRESCEFFHDPFK   171

1L3A.pdb  427  GR-SDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEF   475 G+ SDEG+VRKVLKVEPLPDGSG FFNLSVQNKL+N+DE++YIP+TKAEF 2-02740   172  GKGSDEGKVRKVLKVEPLPDGSGRFFNLSVQNKLLNVDESVYIPITKAEF   221

1L3A.pdb  476  AVLVSAFNFVMPYLLGWHTAVNSFKPESGAEL   507 AVL+SAFNFV+P+L+GW   NS KPE    L 2-02740    222  AVLISAFNFVLPHLIGWSAFANSIKPEDSNRL   253

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Highlighted IDENTICAL residue ASN 249  index1  327  path   72  %Seq  50.00 Highlighted IDENTICAL residue SER 250  index1  328  path   73  %Seq  50.00 Highlighted IDENTICAL residue PHE 251  index1  329  path   74  %Seq  50.00 Highlighted IDENTICAL residue LYS 252  index1  330  path   75  %Seq  50.00 Highlighted IDENTICAL residue PRO 253  index1  331  path   76  %Seq  50.00 Highlighted IDENTICAL residue GLU 254  index1  332  path   77  %Seq  50.00 Highlighted IDENTICAL residue ALA 268  index1  333  path   78  %Seq  50.00 Highlighted IDENTICAL residue GLU 269  index1  334  path   79  %Seq  50.00 Highlighted IDENTICAL residue LEU 270  index1  335  path   80  %Seq  50.00 Highlighted IDENTICAL residue GLU 271  index1  336  path   81  %Seq  50.00 Highlighted IDENTICAL residue PRO  90  index1  338  path   83  %Seq 100.00 Highlighted IDENTICAL residue VAL  94  index1  342  path   87  %Seq 100.00 Highlighted IDENTICAL residue GLY  95  index1  343  path   88  %Seq 100.00 Highlighted IDENTICAL residue SER  97  index1  345  path   90  %Seq 100.00 Highlighted IDENTICAL residue ILE  98  index1  346  path   91  %Seq 100.00 Highlighted IDENTICAL residue TYR  99  index1  347  path   92  %Seq 100.00 Highlighted IDENTICAL residue LYS 100  index1  348  path   93  %Seq 100.00 Highlighted IDENTICAL residue GLY 101  index1  349  path   94  %Seq 100.00 Highlighted IDENTICAL residue LYS 102  index1  350  path   95  %Seq 100.00 Highlighted IDENTICAL residue ALA 103  index1  351  path   96  %Seq 100.00 Highlighted IDENTICAL residue ALA 104  index1  352  path   97  %Seq 100.00 Highlighted IDENTICAL residue LEU 105  index1  353  path   98  %Seq 100.00 Highlighted IDENTICAL residue THR 106  index1  354  path   99  %Seq 100.00 Highlighted IDENTICAL residue GLU 108  index1  356  path  101  %Seq 100.00 Highlighted IDENTICAL residue PRO 109  index1  357  path  102  %Seq 100.00 Highlighted IDENTICAL residue ARG 110  index1  358  path  103  %Seq 100.00 Highlighted IDENTICAL residue PRO 112  index1  360  path  105  %Seq 100.00 Highlighted IDENTICAL residue GLU 113  index1  361  path  106  %Seq 100.00 Highlighted IDENTICAL residue PHE 114  index1  362  path  107  %Seq 100.00 Highlighted IDENTICAL residue LEU 117  index1  365  path  110  %Seq 100.00 Highlighted IDENTICAL residue SER 119  index1  367  path  112  %Seq 100.00 Highlighted IDENTICAL residue GLY 120  index1  368  path  113  %Seq 100.00 Highlighted IDENTICAL residue ALA 121  index1  369  path  114  %Seq 100.00 Highlighted IDENTICAL residue PHE 122  index1  370  path  115  %Seq 100.00 Highlighted IDENTICAL residue LYS 123  index1  371  path  116  %Seq 100.00 Highlighted IDENTICAL residue LEU 124  index1  372  path  117  %Seq 100.00 Highlighted IDENTICAL residue GLU 127  index1  375  path  120  %Seq 100.00 Highlighted IDENTICAL residue GLY 128  index1  376  path  121  %Seq 100.00 Highlighted IDENTICAL residue LEU 132  index1  380  path  125  %Seq 100.00 Highlighted IDENTICAL residue GLN 133  index1  381  path  126  %Seq 100.00 Highlighted IDENTICAL residue PHE 134  index1  382  path  127  %Seq 100.00 Highlighted IDENTICAL residue ALA 135  index1  383  path  128  %Seq 100.00 Highlighted IDENTICAL residue PRO 136  index1  384  path  129  %Seq 100.00 Highlighted IDENTICAL residue ALA 137  index1  385  path  130  %Seq 100.00 Highlighted IDENTICAL residue ALA 138  index1  386  path  131  %Seq 100.00 Highlighted IDENTICAL residue GLY 139  index1  387  path  132  %Seq 100.00 Highlighted IDENTICAL residue VAL 140  index1  388  path  133  %Seq 100.00 Highlighted IDENTICAL residue ARG 141  index1  389  path  134  %Seq 100.00 Highlighted IDENTICAL residue GLN 142  index1  390  path  135  %Seq 100.00 Highlighted IDENTICAL residue TYR 143  index1  391  path  136  %Seq 100.00 Highlighted IDENTICAL residue ASP 144  index1  392  path  137  %Seq 100.00 Highlighted IDENTICAL residue TRP 145  index1  393  path  138  %Seq 100.00 Highlighted IDENTICAL residue SER 146  index1  394  path  139  %Seq 100.00 Highlighted IDENTICAL residue ARG 147  index1  395  path  140  %Seq 100.00 Highlighted IDENTICAL residue LYS 148  index1  396  path  141  %Seq 100.00 Highlighted IDENTICAL residue GLN 149  index1  397  path  142  %Seq 100.00 Highlighted IDENTICAL residue VAL 150  index1  398  path  143  %Seq 100.00 Highlighted IDENTICAL residue PHE 151  index1  399  path  144  %Seq 100.00 Highlighted IDENTICAL residue SER 152  index1  400  path  145  %Seq 100.00 Highlighted IDENTICAL residue LEU 153  index1  401  path  146  %Seq 100.00 Highlighted IDENTICAL residue SER 154  index1  402  path  147  %Seq 100.00 Highlighted IDENTICAL residue VAL 155  index1  403  path  148  %Seq 100.00 Highlighted IDENTICAL residue THR 156  index1  404  path  149  %Seq 100.00 Highlighted IDENTICAL residue GLU 157  index1  405  path  150  %Seq 100.00 Highlighted IDENTICAL residue ILE 158  index1  406  path  151  %Seq 100.00 Highlighted IDENTICAL residue GLY 159  index1  407  path  152  %Seq 100.00 Highlighted IDENTICAL residue SER 163  index1  411  path  156  %Seq 100.00 Highlighted IDENTICAL residue LEU 164  index1  412  path  157  %Seq 100.00 Highlighted IDENTICAL residue GLY 165  index1  413  path  158  %Seq 100.00 Highlighted IDENTICAL residue SER 169  index1  417  path  162  %Seq 100.00 Highlighted IDENTICAL residue CYS 170  index1  418  path  163  %Seq 100.00 Highlighted IDENTICAL residue GLU 171  index1  419  path  164  %Seq 100.00 Highlighted IDENTICAL residue PHE 172  index1  420  path  165  %Seq 100.00 Highlighted IDENTICAL residue PHE 173  index1  421  path  166  %Seq 100.00 Highlighted IDENTICAL residue HIS 174  index1  422  path  167  %Seq 100.00 Highlighted IDENTICAL residue ASP 175  index1  423  path  168  %Seq 100.00 Highlighted IDENTICAL residue PRO 176  index1  424  path  169  %Seq 100.00 Highlighted IDENTICAL residue LYS 178  index1  426  path  171  %Seq 100.00 Highlighted IDENTICAL residue GLY 179  index1  427  path  172  %Seq 100.00 Highlighted IDENTICAL residue SER 181  index1  429  path  175  %Seq 100.00 Highlighted IDENTICAL residue ASP 182  index1  430  path  176  %Seq 100.00 Highlighted IDENTICAL residue GLU 183  index1  431  path  177  %Seq 100.00 Highlighted IDENTICAL residue GLY 184  index1  432  path  178  %Seq 100.00 Highlighted IDENTICAL residue VAL 186  index1  434  path  180  %Seq 100.00 Highlighted IDENTICAL residue ARG 187  index1  435  path  181  %Seq 100.00 Highlighted IDENTICAL residue LYS 188  index1  436  path  182  %Seq 100.00 Highlighted IDENTICAL residue VAL 189  index1  437  path  183  %Seq 100.00 Highlighted IDENTICAL residue LEU 190  index1  438  path  184  %Seq 100.00 Highlighted IDENTICAL residue LYS 191  index1  439  path  185  %Seq 100.00 Highlighted IDENTICAL residue VAL 192  index1  440  path  186  %Seq 100.00 Highlighted IDENTICAL residue GLU 193  index1  441  path  187  %Seq 100.00 Highlighted IDENTICAL residue PRO 194  index1  442  path  188  %Seq 100.00 Highlighted IDENTICAL residue LEU 195  index1  443  path  189  %Seq 100.00 Highlighted IDENTICAL residue PRO 196  index1  444  path  190  %Seq 100.00 Highlighted IDENTICAL residue ASP 197  index1  445  path  191  %Seq 100.00 Highlighted IDENTICAL residue GLY 198  index1  446  path  192  %Seq 100.00 Highlighted IDENTICAL residue SER 199  index1  447  path  193  %Seq 100.00 Highlighted IDENTICAL residue GLY 200  index1  448  path  194  %Seq 100.00 Highlighted IDENTICAL residue PHE 202  index1  450  path  196  %Seq 100.00 Highlighted IDENTICAL residue PHE 203  index1  451  path  197  %Seq 100.00 Highlighted IDENTICAL residue ASN 204  index1  452  path  198  %Seq 100.00 Highlighted IDENTICAL residue LEU 205  index1  453  path  199  %Seq 100.00 Highlighted IDENTICAL residue SER 206  index1  454  path  200  %Seq 100.00 Highlighted IDENTICAL residue VAL 207  index1  455  path  201  %Seq 100.00 Highlighted IDENTICAL residue GLN 208  index1  456  path  202  %Seq 100.00 Highlighted IDENTICAL residue ASN 209  index1  457  path  203  %Seq 100.00 Highlighted IDENTICAL residue LYS 210  index1  458  path  204  %Seq 100.00 Highlighted IDENTICAL residue LEU 211  index1  459  path  205  %Seq 100.00 Highlighted IDENTICAL residue ASN 213  index1  461  path  207  %Seq 100.00 Highlighted IDENTICAL residue ASP 215  index1  463  path  209  %Seq 100.00 Highlighted IDENTICAL residue GLU 216  index1  464  path  210  %Seq 100.00 Highlighted IDENTICAL residue TYR 219  index1  467  path  213  %Seq 100.00 Highlighted IDENTICAL residue ILE 220  index1  468  path  214  %Seq 100.00 Highlighted IDENTICAL residue PRO 221  index1  469  path  215  %Seq 100.00 Highlighted IDENTICAL residue THR 223  index1  471  path  217  %Seq 100.00 Highlighted IDENTICAL residue LYS 224  index1  472  path  218  %Seq 100.00 Highlighted IDENTICAL residue ALA 225  index1  473  path  219  %Seq 100.00 Highlighted IDENTICAL residue GLU 226  index1  474  path  220  %Seq 100.00 Highlighted IDENTICAL residue PHE 227  index1  475  path  221  %Seq 100.00 Highlighted IDENTICAL residue ALA 228  index1  476  path  222  %Seq 100.00 Highlighted IDENTICAL residue VAL 229  index1  477  path  223  %Seq 100.00 Highlighted IDENTICAL residue LEU 230  index1  478  path  224  %Seq 100.00 Highlighted IDENTICAL residue SER 232  index1  480  path  226  %Seq 100.00 Highlighted IDENTICAL residue ALA 233  index1  481  path  227  %Seq 100.00 Highlighted IDENTICAL residue PHE 234  index1  482  path  228  %Seq 100.00 Highlighted IDENTICAL residue ASN 235  index1  483  path  229  %Seq 100.00 Highlighted IDENTICAL residue PHE 236  index1  484  path  230  %Seq 100.00 Highlighted IDENTICAL residue VAL 237  index1  485  path  231  %Seq 100.00 Highlighted IDENTICAL residue PRO 239  index1  487  path  233  %Seq 100.00 Highlighted IDENTICAL residue LEU 241  index1  489  path  235  %Seq 100.00 Highlighted IDENTICAL residue GLY 243  index1  491  path  237  %Seq 100.00 Highlighted IDENTICAL residue TRP 244  index1  492  path  238  %Seq 100.00 Highlighted IDENTICAL residue ASN 249  index1  497  path  243  %Seq 100.00 Highlighted IDENTICAL residue SER 250  index1  498  path  244  %Seq 100.00 Highlighted IDENTICAL residue LYS 252  index1  500  path  246  %Seq 100.00 Highlighted IDENTICAL residue PRO 253  index1  501  path  247  %Seq 100.00 Highlighted IDENTICAL residue GLU 254  index1  502  path  248  %Seq 100.00 Highlighted IDENTICAL residue SER 266  index1  503  path  249  %Seq  50.00 Highlighted IDENTICAL residue GLY 267  index1  504  path  250  %Seq  50.00 Highlighted IDENTICAL residue ALA 268  index1  505  path  251  %Seq  50.00 Highlighted IDENTICAL residue GLU 269  index1  506  path  252  %Seq  50.00 Highlighted IDENTICAL residue LEU 270  index1  507  path  253  %Seq  50.00 Highlighted 142 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02740-1l3aA.pir.txt.1L3A.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02740-1l3aA.pir.txt PIR amino_acid 1L3A.pdb A 100.0 BLOSUM62.dat

completed successfully.

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