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At2g10070.2/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
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/At2g10070-2-1wmrA.pir.txt

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

Assigned types to 208 residues in Sequence 2-10070-208, 11 remain unknown
Assigned types to 78 residues in Sequence 1wmrA, 141 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 At2g10070-2-1wmrA.pir.txt into sequence alignment.

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

>1WMR.pdb  Made from 8484 ATOM records in 1WMR.pdb
REFMAVTANNSQLLTWWHNTGEINTQTPVADGNVRQSGLYSVKVQTTPAS
SSLYYDSFVYLAIPGNGMSDQLQYTQGYNQTQAWTSFLYSHDATVKISRN
GSSANSNVVIRPTSLNFPVRYDNQSVYITVPYSPTGYRFSVEFDDDLISL
APSGARQPENALLIFASPFENSSTKPQPGSPNSIAPAPGRVLGLNTTSAS
TVVFNPGVYYFTGHDHMVLSSSVTWVYFAPGAYVKGAVEFLSTASEVKAS
GHGVLSGEQYVWYADPDEGYQKASGANNNGLRMWRGTLGNSSQTFVLNGV
TVSAPPFNSMDWSGNSLDLITCRVDDYKQVGAFYGQTDGLEMYPGTILQD
VFYHTDDDGLKMYYSNVTARNIVMWKESVAPVVEFGWTPRNTENVLFDNV
DVIHQAYANAGNNPGIFGAVNNYLYAPDGLSSNHSTGNSNMTVRNITWSN
FRAEGSSSALFRINPIQNLDNISIKNVSIESFEPLSINTTESWMPVWYDL
NNGKQITVTDFSIEGFTVGNTTITASNAASVGRIDGVDPAYAGSVHYIDR
EFMAVTANNSQLLTWWHNTGEINTQTPVADGNVRQSGLYSVKVQTTPASS
SLYYDSFVYLAIPGNGMSDQLQYTQGYNQTQAWTSFLYSHDATVKISRNG
SSANSNVVIRPTSLNFPVRYDNQSVYITVPYSPTGYRFSVEFDDDLISLA
PSGARQPENALLIFASPFENSSTKPQPGSPNSIAPAPGRVLGLNTTSAST
VVFNPGVYYFTGHDHMVLSSSVTWVYFAPGAYVKGAVEFLSTASEVKASG
HGVLSGEQYVWYADPDEGYQKASGANNNGLRMWRGTLGNSSQTFVLNGVT
VSAPPFNSMDWSGNSLDLITCRVDDYKQVGAFYGQTDGLEMYPGTILQDV
FYHTDDDGLKMYYSNVTARNIVMWKESVAPVVEFGWTPRNTENVLFDNVD
VIHQAYANAGNNPGIFGAVNNYLYAPDGLSSNHSTGNSNMTVRNITWSNF
RAEGSSSALFRINPIQNLDNISIKNVSIESFEPLSINTTESWMPVWYDLN
NGKQITVTDFSIEGFTVGNTTITASNAASVGRIDGVDPAYAGSVHYID

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

Best alignment:
1WMR.pdb       17  WHNTGEINTQTPVADGNVRQSGLYSVKVQTTPASSSLYYDSFVYLAIPGN    66
                   + N+       P+    V+         Q  P+SS L      Y +  GN
2-10070-208    54  FQNSSNREVPVPLLSEEVQNEASNRPIPQQDPSSSPLQNSHASYPSSQGN   103

1WMR.pdb       67  GMSD    70
                      +
2-10070-208   104  NFHE   107

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

Highlighted IDENTICAL residue TRP   32  index1   17  path   65  %Seq 100.00
Highlighted IDENTICAL residue ASN   34  index1   19  path   67  %Seq 100.00
Highlighted IDENTICAL residue THR   35  index1   20  path   68  %Seq 100.00
Highlighted IDENTICAL residue GLY   36  index1   21  path   69  %Seq 100.00
Highlighted IDENTICAL residue GLN   41  index1   26  path   74  %Seq 100.00
Highlighted IDENTICAL residue ASP   46  index1   31  path   79  %Seq 100.00
Highlighted IDENTICAL residue SER   52  index1   37  path   85  %Seq  50.00
Highlighted IDENTICAL residue GLY   53  index1   38  path   86  %Seq  50.00
Highlighted IDENTICAL residue LEU   54  index1   39  path   87  %Seq  50.00
Highlighted IDENTICAL residue TYR   55  index1   40  path   88  %Seq  50.00
Highlighted IDENTICAL residue SER   56  index1   41  path   89  %Seq  50.00
Highlighted IDENTICAL residue VAL   57  index1   42  path   90  %Seq  50.00
Highlighted IDENTICAL residue LYS   58  index1   43  path   91  %Seq  50.00
Highlighted IDENTICAL residue VAL   59  index1   44  path   92  %Seq  50.00
Highlighted IDENTICAL residue GLN   60  index1   45  path   93  %Seq  50.00
Highlighted IDENTICAL residue THR   61  index1   46  path   94  %Seq  50.00
Highlighted IDENTICAL residue THR   62  index1   47  path   95  %Seq  50.00
Highlighted IDENTICAL residue PRO   63  index1   48  path   96  %Seq  50.00
Highlighted IDENTICAL residue ALA   64  index1   49  path   97  %Seq  50.00
Highlighted IDENTICAL residue SER   65  index1   50  path   98  %Seq  50.00
Highlighted IDENTICAL residue SER   66  index1   51  path   99  %Seq  50.00
Highlighted IDENTICAL residue SER   67  index1   52  path  100  %Seq  50.00
Highlighted IDENTICAL residue LEU   68  index1   53  path  101  %Seq  50.00
Highlighted IDENTICAL residue TYR   69  index1   54  path  102  %Seq  50.00
Highlighted IDENTICAL residue TYR   70  index1   55  path  103  %Seq  50.00
Highlighted IDENTICAL residue ASP   71  index1   56  path  104  %Seq  50.00
Highlighted IDENTICAL residue SER   72  index1   57  path  105  %Seq  50.00
Highlighted IDENTICAL residue PHE   73  index1   58  path  106  %Seq  50.00
Highlighted IDENTICAL residue VAL   74  index1   59  path  107  %Seq  50.00
Highlighted IDENTICAL residue TYR   75  index1   60  path  108  %Seq  50.00
Highlighted IDENTICAL residue LEU   76  index1   61  path  109  %Seq  50.00
Highlighted IDENTICAL residue ALA   77  index1   62  path  110  %Seq  50.00
Highlighted IDENTICAL residue ILE   78  index1   63  path  111  %Seq  50.00
Highlighted IDENTICAL residue PRO   79  index1   64  path  112  %Seq  50.00
Highlighted IDENTICAL residue GLY   80  index1   65  path  113  %Seq  50.00
Highlighted IDENTICAL residue ASN   81  index1   66  path  114  %Seq  50.00
Highlighted IDENTICAL residue GLY   82  index1   67  path  115  %Seq  50.00
Highlighted IDENTICAL residue MET   83  index1   68  path  116  %Seq  50.00
Highlighted IDENTICAL residue SER   84  index1   69  path  117  %Seq  50.00
Highlighted IDENTICAL residue ASP   85  index1   70  path  118  %Seq  50.00
Highlighted 40 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g10070-2-1wmrA.pir.txt.1WMR.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g10070-2-1wmrA.pir.txt PIR amino_acid 1WMR.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

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