FANDOM


&&&&&&&&&&&&&&&&&&&& 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
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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g04400-1pii_.pir.txt

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

Assigned types to 402 residues in Sequence 2-4400, 0 remain unknown
Assigned types to 259 residues in Sequence 1pii_, 143 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 At2g04400-1pii_.pir.txt into sequence alignment.

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

>1PII.pdb  Made from 3524 ATOM records in 1PII.pdb
MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQPSTRHFYDALQGARTAF
ILECKKASPSKGVIRDDFDPARIAAIYKHYASAISVLTDEKYFQGSFNFL
PIVSQIAPQPILCKDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLA
AVAHSLEMGVLTEVSNEEEQERAIALGAKVVGINNRDLRDLSIDLNRTRE
LAPKLGHNVTVISESGINTYAQVRELSHFANGFLIGSALMAHDDLHAAVR
RVLLGENKVCGLTRGQDAKAAYDAGAIYGGLIFVATSPRCVNVEQAQEVM
AAAPLQYVGVFRNHDIADVVDKAKVLSLAAVQLHGNEEQLYIDTLREALP
AHVAIWKALSVGETLPAREFQHVDKYVLDNGQGGSGQRFDWSLLNGQSLG
NVLLAGGLGADNCVEAAQTGCAGLDFNSAVESQPGIKDARLLASVFQTLR
AY

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

Best alignment:
1PII.pdb     2  QTVLAKIVADKAIWVEARKQQQPLASFQNEVQ--PSTRHFYDALQGA--R    47
                + +L +I   K + V   K+  PL   +  V+  P TR F  AL+ A  R
2-4400     127  RNILEEITWYKDVEVSRMKELNPLDVLKKAVEDAPPTRDFVGALRMAHKR   176

1PII.pdb    48  TAF---ILECKKASPSKGVIRDDFDPARIAAIY-KHYASAISVLTDEKYF    93
                T F   I E KKASPS+G+++++FDP  IA  Y K  A+ +SVLTD+KYF
2-4400     177  TGFPGLIAEVKKASPSRGILKENFDPVEIAQAYEKGGAACLSVLTDQKYF   226

1PII.pdb    94  QGSFNFLPIVSQIAPQ-PILCKDFIIDPYQIYLARYYQADACLLMLSVLD   142
                QG F  L  +     + P+LCK+F++DP+QIY AR   ADA LL+ +VL 
2-4400     227  QGGFENLEAIRSAGVKCPLLCKEFVVDPWQIYYARTKGADAVLLIAAVLA   276

1PII.pdb   143  DDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIAL-GAKVVGINNRDLRDL   191
                D +   L  +   L +  L EV +E E  R + + G ++VGINNR L   
2-4400     277  DLEITFLLKICKKLSLAALVEVHDEREMGRVLGIEGIELVGINNRSLETF   326

1PII.pdb   192  SIDLNRTREL   201
                 +D++ T++L
2-4400     327  EVDISNTKKL   336

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

Highlighted IDENTICAL residue LEU    5  index1    5  path  130  %Seq 100.00
Highlighted IDENTICAL residue ILE    8  index1    8  path  133  %Seq 100.00
Highlighted IDENTICAL residue LYS   12  index1   12  path  137  %Seq 100.00
Highlighted IDENTICAL residue VAL   16  index1   16  path  141  %Seq 100.00
Highlighted IDENTICAL residue LYS   20  index1   20  path  145  %Seq 100.00
Highlighted IDENTICAL residue PRO   24  index1   24  path  149  %Seq 100.00
Highlighted IDENTICAL residue LEU   25  index1   25  path  150  %Seq 100.00
Highlighted IDENTICAL residue VAL   32  index1   32  path  157  %Seq 100.00
Highlighted IDENTICAL residue GLN   33  index1   33  path  158  %Seq  50.00
Highlighted IDENTICAL residue PRO   34  index1   34  path  161  %Seq 100.00
Highlighted IDENTICAL residue THR   36  index1   36  path  163  %Seq 100.00
Highlighted IDENTICAL residue ARG   37  index1   37  path  164  %Seq 100.00
Highlighted IDENTICAL residue PHE   39  index1   39  path  166  %Seq 100.00
Highlighted IDENTICAL residue ALA   42  index1   42  path  169  %Seq 100.00
Highlighted IDENTICAL residue LEU   43  index1   43  path  170  %Seq 100.00
Highlighted IDENTICAL residue ALA   46  index1   46  path  173  %Seq  50.00
Highlighted IDENTICAL residue ARG   47  index1   47  path  176  %Seq  50.00
Highlighted IDENTICAL residue THR   48  index1   48  path  177  %Seq  50.00
Highlighted IDENTICAL residue ILE   51  index1   51  path  183  %Seq 100.00
Highlighted IDENTICAL residue GLU   53  index1   53  path  185  %Seq 100.00
Highlighted IDENTICAL residue LYS   55  index1   55  path  187  %Seq 100.00
Highlighted IDENTICAL residue LYS   56  index1   56  path  188  %Seq 100.00
Highlighted IDENTICAL residue ALA   57  index1   57  path  189  %Seq 100.00
Highlighted IDENTICAL residue SER   58  index1   58  path  190  %Seq 100.00
Highlighted IDENTICAL residue PRO   59  index1   59  path  191  %Seq 100.00
Highlighted IDENTICAL residue SER   60  index1   60  path  192  %Seq 100.00
Highlighted IDENTICAL residue GLY   62  index1   62  path  194  %Seq 100.00
Highlighted IDENTICAL residue PHE   68  index1   68  path  200  %Seq 100.00
Highlighted IDENTICAL residue ASP   69  index1   69  path  201  %Seq 100.00
Highlighted IDENTICAL residue PRO   70  index1   70  path  202  %Seq 100.00
Highlighted IDENTICAL residue ILE   73  index1   73  path  205  %Seq 100.00
Highlighted IDENTICAL residue ALA   74  index1   74  path  206  %Seq 100.00
Highlighted IDENTICAL residue TYR   77  index1   77  path  209  %Seq 100.00
Highlighted IDENTICAL residue LYS   78  index1   78  path  211  %Seq  50.00
Highlighted IDENTICAL residue ALA   81  index1   81  path  214  %Seq 100.00
Highlighted IDENTICAL residue SER   85  index1   85  path  218  %Seq 100.00
Highlighted IDENTICAL residue VAL   86  index1   86  path  219  %Seq 100.00
Highlighted IDENTICAL residue LEU   87  index1   87  path  220  %Seq 100.00
Highlighted IDENTICAL residue THR   88  index1   88  path  221  %Seq 100.00
Highlighted IDENTICAL residue ASP   89  index1   89  path  222  %Seq 100.00
Highlighted IDENTICAL residue LYS   91  index1   91  path  224  %Seq 100.00
Highlighted IDENTICAL residue TYR   92  index1   92  path  225  %Seq 100.00
Highlighted IDENTICAL residue PHE   93  index1   93  path  226  %Seq 100.00
Highlighted IDENTICAL residue GLN   94  index1   94  path  227  %Seq 100.00
Highlighted IDENTICAL residue GLY   95  index1   95  path  228  %Seq 100.00
Highlighted IDENTICAL residue PHE   97  index1   97  path  230  %Seq 100.00
Highlighted IDENTICAL residue LEU  100  index1  100  path  233  %Seq 100.00
Highlighted IDENTICAL residue ALA  107  index1  107  path  240  %Seq  50.00
Highlighted IDENTICAL residue PRO  110  index1  110  path  244  %Seq 100.00
Highlighted IDENTICAL residue LEU  112  index1  112  path  246  %Seq 100.00
Highlighted IDENTICAL residue CYS  113  index1  113  path  247  %Seq 100.00
Highlighted IDENTICAL residue LYS  114  index1  114  path  248  %Seq 100.00
Highlighted IDENTICAL residue PHE  116  index1  116  path  250  %Seq 100.00
Highlighted IDENTICAL residue ASP  119  index1  119  path  253  %Seq 100.00
Highlighted IDENTICAL residue PRO  120  index1  120  path  254  %Seq 100.00
Highlighted IDENTICAL residue GLN  122  index1  122  path  256  %Seq 100.00
Highlighted IDENTICAL residue ILE  123  index1  123  path  257  %Seq 100.00
Highlighted IDENTICAL residue TYR  124  index1  124  path  258  %Seq 100.00
Highlighted IDENTICAL residue ALA  126  index1  126  path  260  %Seq 100.00
Highlighted IDENTICAL residue ARG  127  index1  127  path  261  %Seq 100.00
Highlighted IDENTICAL residue ALA  131  index1  131  path  265  %Seq 100.00
Highlighted IDENTICAL residue ASP  132  index1  132  path  266  %Seq 100.00
Highlighted IDENTICAL residue ALA  133  index1  133  path  267  %Seq 100.00
Highlighted IDENTICAL residue LEU  135  index1  135  path  269  %Seq 100.00
Highlighted IDENTICAL residue LEU  136  index1  136  path  270  %Seq 100.00
Highlighted IDENTICAL residue VAL  140  index1  140  path  274  %Seq 100.00
Highlighted IDENTICAL residue LEU  141  index1  141  path  275  %Seq 100.00
Highlighted IDENTICAL residue ASP  143  index1  143  path  277  %Seq 100.00
Highlighted IDENTICAL residue LEU  149  index1  149  path  283  %Seq 100.00
Highlighted IDENTICAL residue LEU  156  index1  156  path  290  %Seq 100.00
Highlighted IDENTICAL residue LEU  161  index1  161  path  295  %Seq 100.00
Highlighted IDENTICAL residue GLU  163  index1  163  path  297  %Seq 100.00
Highlighted IDENTICAL residue VAL  164  index1  164  path  298  %Seq 100.00
Highlighted IDENTICAL residue GLU  167  index1  167  path  301  %Seq 100.00
Highlighted IDENTICAL residue GLU  169  index1  169  path  303  %Seq 100.00
Highlighted IDENTICAL residue ARG  172  index1  172  path  306  %Seq 100.00
Highlighted IDENTICAL residue GLY  177  index1  177  path  312  %Seq 100.00
Highlighted IDENTICAL residue VAL  181  index1  181  path  316  %Seq 100.00
Highlighted IDENTICAL residue GLY  182  index1  182  path  317  %Seq 100.00
Highlighted IDENTICAL residue ILE  183  index1  183  path  318  %Seq 100.00
Highlighted IDENTICAL residue ASN  184  index1  184  path  319  %Seq 100.00
Highlighted IDENTICAL residue ASN  185  index1  185  path  320  %Seq 100.00
Highlighted IDENTICAL residue ARG  186  index1  186  path  321  %Seq 100.00
Highlighted IDENTICAL residue LEU  188  index1  188  path  323  %Seq 100.00
Highlighted IDENTICAL residue ASP  194  index1  194  path  329  %Seq 100.00
Highlighted IDENTICAL residue THR  198  index1  198  path  333  %Seq 100.00
Highlighted IDENTICAL residue LEU  201  index1  201  path  336  %Seq 100.00
Highlighted 87 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g04400-1pii_.pir.txt.1PII.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g04400-1pii_.pir.txt PIR amino_acid 1PII.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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