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Displaying 3D alignements

In order to visualize results with the Jmol applet, you must have Java enabled in your browser
In order to visualize results in Rasmol, you need Rasmol installed on your machine and you have to configure your browser.How to configure your browser to use Rasmol scripts encoded in the YAKUSA result page
You can also save rasmol script on your computer wich contains also CA coordinates ( right click on rasmol icon and save target, default name: getRasmol.pl) and open it with your own rasmol (run rasmol from terminal with "rasmol -script [downloaded file]").
In Jmol popup window or in Rasmol query structure is colored in red, database structure is colored in blue, and SHSPs are colored in various bright colors
Other explanations of our result page:

1e9x_A: rank 7: score : 255.54 zscore: 16.17 (PDBsum/RCSB)

1e9x_A: PDB code (with chain) of the database structure found
rank: rank of 1e9x_A protein for this scan of the database
score: ranking score, based upon MTD, computed for "spatially compatible" SHSPsor for all SHSPs found (input option)
zscore: the Z-score of the ranking score (the Z-score is computed in the usual manner over all scores of protein structures in the scanned database). Usually, one can see a fall in this Z-score between significant structural matches and random ones. At a first glance, matches giving Z-score above 6 or 7 are likely to be significant matches.
PDBsum/RCSB: link to PDBSum or Protein Databank at RCSB

1E9X: 1E9X Cytochrome P450 51-Like Rv0764C (see equivalent proteins in our database)

This line is a description of the biological fonction of 1E9X

Length: 449 residues, 247/449 residus aligned ( 55.0%)

Length: length of the database structure found.
100: aligned residue number
55.0%: aligned residue percentage (55.0 = 247/449*100)

SHSPs: 9 SHSPs found

Id      pos_query  chain     pos_bank  chain   score  shift  length    RMSD     MTD_proba  RGBcolor 
[  1]   24  -   61  (A)    25  -   62  (A)     666     -1      38     1.5  1.649179E-46  #FFAAAA 
[  2]   95  -  126  (A)    93  -  124  (A)     623      2      32     2.8  7.913895E-29  #B4B4F5 
[  3]  139  -  158  (A)   134  -  153  (A)     365      5      20     0.7  8.730852E-22  #EABFBF 
[  4]  232  -  241  (A)   224  -  233  (A)     222      8      10     0.7  1.580246E-11  #C9C9E0 
[  5]  249  -  300  (A)   241  -  292  (A)    1183      8      52     3.0  1.015930E-42  #D5D4D4 
[  6]  311  -  342  (A)   304  -  335  (A)     616      7      32     1.2  2.823627E-38  #DFDFCA 
[  7]  345  -  367  (A)   337  -  359  (A)     429      8      23     1.2  5.585958E-31  #C0E9E9 
[  8]  371  -  379  (A)   362  -  370  (A)     220      9       9     0.2  4.118291E-14  #F4F4B5 
[  9]  396  -  426  (A)   390  -  420  (A)     637      6      31     1.0  3.797677E-38  #AAFFFF

Id: SHSP id
pos-query: first and last residue pdb number of SHSP in the query structure
chain: chain in the query structure (main chain if blank)
pos-bank: first and last residue pdb number of SHSP in the database structure
chain: chain in the database structure (main chain if blank)
score: score computed for SHSP, based on α angle differences
shift: SHSP shift between database and query, i.e. [database structure residue index] minus [query structure residue index]
lenght: SHSP length
RMSD: SHSP RMS, i.e. RMS between database and query fragment of SHSP
MTD_proba: SHSP probability (MTD based)
RGBColor: SHSP color (for use in jmol)

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Group of SHSPs spatially compatible: 1  2  3  5  6  7  8  9 (score   255.54, 52.78% residues aligned)

This line is the group of "spatially compatible" SHSPs, which is found by computing crossed RMS. The score is the overall score of compatible SHSPs, i.e. the sum of logarithm of the compatible SHSP MTD probabilities

SHSPs amino acid sequences
SHSP 1

The color of this line is the one used for this SHPS (in query and database structures) in jmol and rasmol.

Outside SHSP residues which are in light colors, residues in query structure are colored in red in jmol and rasmol, and residues in database structure are colored in blue.

query KPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEA |: : :: || |:: |: |: || . database DPIGLMQRVRDECGDVGTFQLAGKQVVLLSGSHANEFF

Alignment of the sequences of query and database fragments of one SHSP:

vertical lines ('|') group identical residues (.i.e. whose score >= 4 in BLOSUM62),

Semicolons (':') group residues with BLOSUM62 score >= 2,

Points ('.') group residues with BLOSUM62 score >= 1

Last modified: Tue Dec 7 18:41:39 CET 2004

Displaying 3D alignements

In order to visualize results with the Jmol applet, you must have Java enabled in your browser

In order to visualize results in Rasmol, you need Rasmol installed on your machine and you have to configure your browser.How to configure your browser to use Rasmol scripts encoded in the YAKUSA result page

You can also save rasmol script on your computer wich contains also CA coordinates ( right click on rasmol icon and save target, default name: getRasmol.pl) and open it with your own rasmol (run rasmol from terminal with "rasmol -script [downloaded file]").

In Jmol popup window or in Rasmol query structure is colored in red, database structure is colored in blue, and SHSPs are colored in various bright colors

Other explanations of our result page: