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At2g14120.1/PDB

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&&&&&&&&&&&&&&&&&&&& 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
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Sequence 1
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Sequence 2
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g14120-1jwyB.pir.txt

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

Assigned types to 780 residues in Sequence 2-14120, 0 remain unknown
Assigned types to 315 residues in Sequence 1jwyB, 465 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 At2g14120-1jwyB.pir.txt into sequence alignment.

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

>1JWY.pdb  Made from 8297 ATOM records in 1JWY.pdb
DPIHDRTSDYHKYLKVKQFKLTVSDKRYIWYNPDPKERDSYECGEIVSET
SDSFTFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNL
RVRYNQDLIYTYSGLFLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIF
AISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQYLASVAGSGVLE
QQILQANPILEAFGNAKTTRNNNSSRFGKFIEIQFNSAGFISGASIQSYL
LEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAGPESFNYLNQSGC
VDIKGVSDSEEFKITRQAMDIVGFSQEEQMSIFKIIAGILHLGNIKFEKG
AGEGAVLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHLNVE
KSSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDISGFEIFK
VNSFEQLCINYTNEKLQQFFNHHMFKLEQEEYLKEKINWTFIDFGLDSQA
TIDLIDGRQPPGILALLDEQSVFPNATDNTLITKLHSHFSKKNAKYEEPR
FSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCFKDSSDNVVTKLF
NDPNIASRAKKGANFITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQ
LPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYADFVKRYYLLAPNV
PRDAEDSQKATDAVLKHLNIDPEQYRFGITKIFFRAGQLARIEEAREQRI
SEIDQLIPVINKLQDVFNTLGSDPLDLPQIVVVGSQSSGKSSVLENIVGR
DFLPRPLILQLTHLPIADDGSQTQEWGEFLHKPNDMFYDFSEIREEIIRD
TDISAQPINLKIYSPHVVNLTLVDLPGITDIEQQIRRMVMAYIKKQNAII
VAVTPANTDLANSDALQLAKEVDPEGKRTIGVITKLDLMDKGTDAMEVLT
GRVIPLTLGFIGVINRSQEDIIAKKSIRESLKSEILYFKNHPIYKSIANR
SGTAYLSKTLNKLLMFHIRDTLPDLKVKVSKMLSTRGLV

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

Best alignment:
1JWY.pdb   754  DQLIPVINKLQDVFNTLGS-DPLDLPQIVVVGSQSSGKSSVLENIVGRDF   802
                  +IP++NKLQD+F  LGS   + LPQ+ VVGSQSSGKSSVLE +VGRDF
2-14120     19  SSVIPIVNKLQDIFAQLGSQSTIALPQVAVVGSQSSGKSSVLEALVGRDF    68

1JWY.pdb   803  LP--------RPLILQLTHLPIADDGSQTQEWGEFL-HKPNDMFYDFSEI   843
                LP        RPL LQL     + DG   +EWGEFL H P    YDFSEI
2-14120     69  LPRGNDICTRRPLRLQLVQTKPSSDGGSDEEWGEFLHHDPVRRIYDFSEI   118

1JWY.pdb   844  REEIIRDTD-ISAQ-------PINLKIYSPHVVNLTLVDLPGIT------   879
                R EI  +T+ +S +       PI LKI+SP+V++++LVDLPGIT      
2-14120    119  RREIEAETNRVSGENKGVSDIPIGLKIFSPNVLDISLVDLPGITKVPVGD   168

1JWY.pdb   879  ---DIEQQIRRMVMAYIKKQNAIIVAVTPANTDLANSDALQLAKEVDPEG   926
                   DIE +IR M++ YIK+ + +I+AV+PANTDLANSDALQ+A   DP+G
2-14120    169  QPSDIEARIRTMILTYIKEPSCLILAVSPANTDLANSDALQIAGNADPDG   218

1JWY.pdb   927  KRTIGVITKLDLMDKGTDAMEVLTGRVIPLTLGFIGVINRSQEDIIAKKS   976
                 RTIGVITKLD+MD+GTDA   L G+ IPL LG++GV+NRSQEDI+  +S
2-14120    219  HRTIGVITKLDIMDRGTDARNHLLGKTIPLRLGYVGVVNRSQEDILMNRS   268

1JWY.pdb   977  IRESLKSEILYFKNHPIYKSIANRSGTAYLSKTLNKLLMFHIRDTLPDLK  1026
                I+++L +E  +F++ P+Y  + +R G   L+K LN++L+ HI+  LP LK
2-14120    269  IKDALVAEEKFFRSRPVYSGLTDRLGVPQLAKKLNQVLVQHIKALLPSLK   318

1JWY.pdb  1027  VKVSKML  1033
                 +++  L
2-14120    319  SRINNAL   325

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

Highlighted IDENTICAL residue ILE    5  index1  757  path   22  %Seq 100.00
Highlighted IDENTICAL residue PRO    6  index1  758  path   23  %Seq 100.00
Highlighted IDENTICAL residue ASN    9  index1  761  path   26  %Seq 100.00
Highlighted IDENTICAL residue LYS   10  index1  762  path   27  %Seq 100.00
Highlighted IDENTICAL residue LEU   11  index1  763  path   28  %Seq 100.00
Highlighted IDENTICAL residue GLN   12  index1  764  path   29  %Seq 100.00
Highlighted IDENTICAL residue ASP   13  index1  765  path   30  %Seq 100.00
Highlighted IDENTICAL residue PHE   15  index1  767  path   32  %Seq 100.00
Highlighted IDENTICAL residue LEU   18  index1  770  path   35  %Seq 100.00
Highlighted IDENTICAL residue GLY   19  index1  771  path   36  %Seq 100.00
Highlighted IDENTICAL residue SER   20  index1  772  path   37  %Seq  50.00
Highlighted IDENTICAL residue LEU   25  index1  777  path   43  %Seq 100.00
Highlighted IDENTICAL residue PRO   26  index1  778  path   44  %Seq 100.00
Highlighted IDENTICAL residue GLN   27  index1  779  path   45  %Seq 100.00
Highlighted IDENTICAL residue VAL   30  index1  782  path   48  %Seq 100.00
Highlighted IDENTICAL residue VAL   31  index1  783  path   49  %Seq 100.00
Highlighted IDENTICAL residue GLY   32  index1  784  path   50  %Seq 100.00
Highlighted IDENTICAL residue SER   33  index1  785  path   51  %Seq 100.00
Highlighted IDENTICAL residue GLN   34  index1  786  path   52  %Seq 100.00
Highlighted IDENTICAL residue SER   35  index1  787  path   53  %Seq 100.00
Highlighted IDENTICAL residue SER   36  index1  788  path   54  %Seq 100.00
Highlighted IDENTICAL residue GLY   37  index1  789  path   55  %Seq 100.00
Highlighted IDENTICAL residue LYS   38  index1  790  path   56  %Seq 100.00
Highlighted IDENTICAL residue SER   39  index1  791  path   57  %Seq 100.00
Highlighted IDENTICAL residue SER   40  index1  792  path   58  %Seq 100.00
Highlighted IDENTICAL residue VAL   41  index1  793  path   59  %Seq 100.00
Highlighted IDENTICAL residue LEU   42  index1  794  path   60  %Seq 100.00
Highlighted IDENTICAL residue GLU   43  index1  795  path   61  %Seq 100.00
Highlighted IDENTICAL residue VAL   46  index1  798  path   64  %Seq 100.00
Highlighted IDENTICAL residue GLY   47  index1  799  path   65  %Seq 100.00
Highlighted IDENTICAL residue ARG   48  index1  800  path   66  %Seq 100.00
Highlighted IDENTICAL residue ASP   49  index1  801  path   67  %Seq 100.00
Highlighted IDENTICAL residue PHE   50  index1  802  path   68  %Seq 100.00
Highlighted IDENTICAL residue LEU   51  index1  803  path   69  %Seq 100.00
Highlighted IDENTICAL residue PRO   52  index1  804  path   70  %Seq 100.00
Highlighted IDENTICAL residue ARG   61  index1  805  path   79  %Seq 100.00
Highlighted IDENTICAL residue PRO   62  index1  806  path   80  %Seq 100.00
Highlighted IDENTICAL residue LEU   63  index1  807  path   81  %Seq 100.00
Highlighted IDENTICAL residue LEU   65  index1  809  path   83  %Seq 100.00
Highlighted IDENTICAL residue GLN   66  index1  810  path   84  %Seq 100.00
Highlighted IDENTICAL residue LEU   67  index1  811  path   85  %Seq 100.00
Highlighted IDENTICAL residue ASP   75  index1  819  path   93  %Seq 100.00
Highlighted IDENTICAL residue GLY   76  index1  820  path   94  %Seq 100.00
Highlighted IDENTICAL residue GLU   81  index1  825  path   99  %Seq 100.00
Highlighted IDENTICAL residue TRP   82  index1  826  path  100  %Seq 100.00
Highlighted IDENTICAL residue GLY   83  index1  827  path  101  %Seq 100.00
Highlighted IDENTICAL residue GLU   84  index1  828  path  102  %Seq 100.00
Highlighted IDENTICAL residue PHE   85  index1  829  path  103  %Seq 100.00
Highlighted IDENTICAL residue LEU   86  index1  830  path  104  %Seq 100.00
Highlighted IDENTICAL residue HIS   87  index1  831  path  106  %Seq  50.00
Highlighted IDENTICAL residue PRO   89  index1  833  path  108  %Seq 100.00
Highlighted IDENTICAL residue TYR   94  index1  838  path  113  %Seq 100.00
Highlighted IDENTICAL residue ASP   95  index1  839  path  114  %Seq 100.00
Highlighted IDENTICAL residue PHE   96  index1  840  path  115  %Seq 100.00
Highlighted IDENTICAL residue SER   97  index1  841  path  116  %Seq 100.00
Highlighted IDENTICAL residue GLU   98  index1  842  path  117  %Seq 100.00
Highlighted IDENTICAL residue ILE   99  index1  843  path  118  %Seq 100.00
Highlighted IDENTICAL residue ARG  100  index1  844  path  119  %Seq 100.00
Highlighted IDENTICAL residue GLU  102  index1  846  path  121  %Seq 100.00
Highlighted IDENTICAL residue ILE  103  index1  847  path  122  %Seq 100.00
Highlighted IDENTICAL residue THR  107  index1  851  path  126  %Seq 100.00
Highlighted IDENTICAL residue ALA  119  index1  855  path  131  %Seq 100.00
Highlighted IDENTICAL residue PRO  121  index1  857  path  140  %Seq 100.00
Highlighted IDENTICAL residue ILE  122  index1  858  path  141  %Seq 100.00
Highlighted IDENTICAL residue LEU  124  index1  860  path  143  %Seq 100.00
Highlighted IDENTICAL residue LYS  125  index1  861  path  144  %Seq 100.00
Highlighted IDENTICAL residue ILE  126  index1  862  path  145  %Seq 100.00
Highlighted IDENTICAL residue SER  128  index1  864  path  147  %Seq 100.00
Highlighted IDENTICAL residue PRO  129  index1  865  path  148  %Seq 100.00
Highlighted IDENTICAL residue VAL  131  index1  867  path  150  %Seq 100.00
Highlighted IDENTICAL residue LEU  136  index1  872  path  155  %Seq 100.00
Highlighted IDENTICAL residue VAL  137  index1  873  path  156  %Seq 100.00
Highlighted IDENTICAL residue ASP  138  index1  874  path  157  %Seq 100.00
Highlighted IDENTICAL residue LEU  139  index1  875  path  158  %Seq 100.00
Highlighted IDENTICAL residue PRO  140  index1  876  path  159  %Seq 100.00
Highlighted IDENTICAL residue GLY  141  index1  877  path  160  %Seq 100.00
Highlighted IDENTICAL residue ILE  142  index1  878  path  161  %Seq 100.00
Highlighted IDENTICAL residue THR  152  index1  879  path  162  %Seq 100.00
Highlighted IDENTICAL residue ASP  153  index1  880  path  172  %Seq 100.00
Highlighted IDENTICAL residue ILE  154  index1  881  path  173  %Seq 100.00
Highlighted IDENTICAL residue GLU  155  index1  882  path  174  %Seq 100.00
Highlighted IDENTICAL residue ILE  158  index1  885  path  177  %Seq 100.00
Highlighted IDENTICAL residue ARG  159  index1  886  path  178  %Seq 100.00
Highlighted IDENTICAL residue MET  161  index1  888  path  180  %Seq 100.00
Highlighted IDENTICAL residue TYR  165  index1  892  path  184  %Seq 100.00
Highlighted IDENTICAL residue ILE  166  index1  893  path  185  %Seq 100.00
Highlighted IDENTICAL residue LYS  167  index1  894  path  186  %Seq 100.00
Highlighted IDENTICAL residue ILE  173  index1  900  path  192  %Seq 100.00
Highlighted IDENTICAL residue ALA  175  index1  902  path  194  %Seq 100.00
Highlighted IDENTICAL residue VAL  176  index1  903  path  195  %Seq 100.00
Highlighted IDENTICAL residue PRO  178  index1  905  path  197  %Seq 100.00
Highlighted IDENTICAL residue ALA  179  index1  906  path  198  %Seq 100.00
Highlighted IDENTICAL residue ASN  180  index1  907  path  199  %Seq 100.00
Highlighted IDENTICAL residue THR  181  index1  908  path  200  %Seq 100.00
Highlighted IDENTICAL residue ASP  182  index1  909  path  201  %Seq 100.00
Highlighted IDENTICAL residue LEU  183  index1  910  path  202  %Seq 100.00
Highlighted IDENTICAL residue ALA  184  index1  911  path  203  %Seq 100.00
Highlighted IDENTICAL residue ASN  185  index1  912  path  204  %Seq 100.00
Highlighted IDENTICAL residue SER  186  index1  913  path  205  %Seq 100.00
Highlighted IDENTICAL residue ASP  187  index1  914  path  206  %Seq 100.00
Highlighted IDENTICAL residue ALA  188  index1  915  path  207  %Seq 100.00
Highlighted IDENTICAL residue LEU  189  index1  916  path  208  %Seq 100.00
Highlighted IDENTICAL residue GLN  190  index1  917  path  209  %Seq 100.00
Highlighted IDENTICAL residue ALA  192  index1  919  path  211  %Seq 100.00
Highlighted IDENTICAL residue ASP  196  index1  923  path  215  %Seq 100.00
Highlighted IDENTICAL residue PRO  197  index1  924  path  216  %Seq 100.00
Highlighted IDENTICAL residue GLY  199  index1  926  path  218  %Seq 100.00
Highlighted IDENTICAL residue ARG  201  index1  928  path  220  %Seq 100.00
Highlighted IDENTICAL residue THR  202  index1  929  path  221  %Seq 100.00
Highlighted IDENTICAL residue ILE  203  index1  930  path  222  %Seq 100.00
Highlighted IDENTICAL residue GLY  204  index1  931  path  223  %Seq 100.00
Highlighted IDENTICAL residue VAL  205  index1  932  path  224  %Seq 100.00
Highlighted IDENTICAL residue ILE  206  index1  933  path  225  %Seq 100.00
Highlighted IDENTICAL residue THR  207  index1  934  path  226  %Seq 100.00
Highlighted IDENTICAL residue LYS  208  index1  935  path  227  %Seq 100.00
Highlighted IDENTICAL residue LEU  209  index1  936  path  228  %Seq 100.00
Highlighted IDENTICAL residue ASP  210  index1  937  path  229  %Seq 100.00
Highlighted IDENTICAL residue MET  212  index1  939  path  231  %Seq 100.00
Highlighted IDENTICAL residue ASP  213  index1  940  path  232  %Seq 100.00
Highlighted IDENTICAL residue GLY  215  index1  942  path  234  %Seq 100.00
Highlighted IDENTICAL residue THR  216  index1  943  path  235  %Seq 100.00
Highlighted IDENTICAL residue ASP  217  index1  944  path  236  %Seq 100.00
Highlighted IDENTICAL residue ALA  218  index1  945  path  237  %Seq 100.00
Highlighted IDENTICAL residue LEU  222  index1  949  path  241  %Seq 100.00
Highlighted IDENTICAL residue GLY  224  index1  951  path  243  %Seq 100.00
Highlighted IDENTICAL residue ILE  227  index1  954  path  246  %Seq 100.00
Highlighted IDENTICAL residue PRO  228  index1  955  path  247  %Seq 100.00
Highlighted IDENTICAL residue LEU  229  index1  956  path  248  %Seq 100.00
Highlighted IDENTICAL residue LEU  231  index1  958  path  250  %Seq 100.00
Highlighted IDENTICAL residue GLY  232  index1  959  path  251  %Seq 100.00
Highlighted IDENTICAL residue GLY  235  index1  962  path  254  %Seq 100.00
Highlighted IDENTICAL residue VAL  236  index1  963  path  255  %Seq 100.00
Highlighted IDENTICAL residue ASN  238  index1  965  path  257  %Seq 100.00
Highlighted IDENTICAL residue ARG  239  index1  966  path  258  %Seq 100.00
Highlighted IDENTICAL residue SER  240  index1  967  path  259  %Seq 100.00
Highlighted IDENTICAL residue GLN  241  index1  968  path  260  %Seq 100.00
Highlighted IDENTICAL residue GLU  242  index1  969  path  261  %Seq 100.00
Highlighted IDENTICAL residue ASP  243  index1  970  path  262  %Seq 100.00
Highlighted IDENTICAL residue ILE  244  index1  971  path  263  %Seq 100.00
Highlighted IDENTICAL residue SER  249  index1  976  path  268  %Seq 100.00
Highlighted IDENTICAL residue ILE  250  index1  977  path  269  %Seq 100.00
Highlighted IDENTICAL residue LEU  254  index1  981  path  273  %Seq 100.00
Highlighted IDENTICAL residue GLU  257  index1  984  path  276  %Seq 100.00
Highlighted IDENTICAL residue PHE  261  index1  988  path  280  %Seq 100.00
Highlighted IDENTICAL residue PRO  265  index1  992  path  284  %Seq 100.00
Highlighted IDENTICAL residue TYR  267  index1  994  path  286  %Seq 100.00
Highlighted IDENTICAL residue ARG  273  index1 1000  path  292  %Seq 100.00
Highlighted IDENTICAL residue GLY  275  index1 1002  path  294  %Seq 100.00
Highlighted IDENTICAL residue LEU  279  index1 1006  path  298  %Seq 100.00
Highlighted IDENTICAL residue LYS  281  index1 1008  path  300  %Seq 100.00
Highlighted IDENTICAL residue LEU  283  index1 1010  path  302  %Seq 100.00
Highlighted IDENTICAL residue ASN  284  index1 1011  path  303  %Seq 100.00
Highlighted IDENTICAL residue LEU  287  index1 1014  path  306  %Seq 100.00
Highlighted IDENTICAL residue HIS  290  index1 1017  path  309  %Seq 100.00
Highlighted IDENTICAL residue ILE  291  index1 1018  path  310  %Seq 100.00
Highlighted IDENTICAL residue LEU  295  index1 1022  path  314  %Seq 100.00
Highlighted IDENTICAL residue PRO  296  index1 1023  path  315  %Seq 100.00
Highlighted IDENTICAL residue LEU  298  index1 1025  path  317  %Seq 100.00
Highlighted IDENTICAL residue LYS  299  index1 1026  path  318  %Seq 100.00
Highlighted IDENTICAL residue LEU  306  index1 1033  path  325  %Seq 100.00
Highlighted 160 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g14120-1jwyB.pir.txt.1JWY.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g14120-1jwyB.pir.txt PIR amino_acid 1JWY.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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


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