Fandom

Proteins Wiki

At2g13810.1/PDB

< At2g13810.1

47,922pages on
this wiki
Add New Page
Talk0 Share
&&&&&&&&&&&&&&&&&&&& 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
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

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

Assigned types to 456 residues in Sequence 2-13810, 8 remain unknown
Assigned types to 378 residues in Sequence 1j32_A, 86 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

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

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.

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

>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

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

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  LAMIEPGDEVIIPAPFWVSYPEMVKLAEGTPVILPTTVETQ----FKVSP   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

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

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

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

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.

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


Ad blocker interference detected!


Wikia is a free-to-use site that makes money from advertising. We have a modified experience for viewers using ad blockers

Wikia is not accessible if you’ve made further modifications. Remove the custom ad blocker rule(s) and the page will load as expected.