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Output format

Explanation box:

In this page, we will guide you through an example output, clarifying its meaning. For this example, we used the Purine nucleoside phosphorylase from Yersinia tuberculosis. This protein was submitted as a single protein in fasta, as shown in the "Instructions" page.
By hovering with the mouse cursor over each part of the output, you will be given an explanation. If you follow the links, you will have an example. Sometimes, in between the output, you will find explanation boxes (as this one). At the very end of this page you will find some more details of particular output files.
So, on top of the output page, you will find something like this:


Result for Q66EV7_DEOD_YERPS_Purine_nucleoside_phosphorylase_deoD_type

Results calculated from:
Row and Column Weighing of Mutual Information

Downloads:
Annotated tab Position listGFF report
Alignment report Neighbour-joining phylogenetic tree
GetStruct report PDB file 3D plot (png) PyMol script
Trees with leaf states (TAR archive)
All files (TAR archive)
Color mappings
Link to the corresponding PDB entry

Explanation box:

The color scheme used for highlighting the co-evolving residues ordered by score is as follows:

LetterDescriptionColorGraphics
C Conserved residue yellow .
1 co-evolving residue white/slate stick
2 co-evolving residue red stick
3 co-evolving residue cyan stick
4 co-evolving residue purple stick
5 co-evolving residue orange stick
6 co-evolving residue blue stick
7 co-evolving residue yellow stick
8 co-evolving residue brown stick
9 co-evolving residue black stick

If a group of residues (i.e., more than 2) are found to coevolve, all the residues in the group will be marked the same color.

Additional colors are available, and marked in the alignment as the letter [a-z], giving a total of 35 different colors (although many of them are similar).
The stick shape is maintained.The visualization of more than 9 interacting pairs or groups is therefore a little more attention-demanding.

A list with all the colors, and the associated symbols, can be found here.

Query : Q66EV7_DEOD_YERPS_Purine_nucleoside_phosphorylase_deoD_type___Y.1.1 (239 aa)
Hit   : 1PW7 (molecule: PURINE NUCLEOSIDE PHOSPHORYLASE;) (chain: c) (resolution: 2.00 ANGSTROMS.)
        Organism: ESCHERICHIA COLI, AND ESCHERICHIA

           C       8    a2 CCC C    C         8   C   6  C   6        C C  C   C 4CC 4  
      2 ATPHINAEMGDFADVVLMPGDPLRAKFIAETFLQDVREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYAKELITDF 81
        ||||||||||||||||||||||||||:||||||:|.||||||||||||||||||||||||||||||||||||.|||||||
      1 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDF 80
         BTTB   TTSS SEEEE S HHHHHHHHHHH EEEEEEE GGG  EEEEEETTEEEEEE   SSHHHHHHHHHHHHHHS
                                                                                        

            2 C C 1C                     3        3   8       5   5                   aC
     82 GVKKIIRVGSCGAVRTDVKLRDVVIGMGACTDSKVNRMRFKDHDYAAIADFEMTRNAVDAAKAKGVNVRVGNLFSADLFY 161
        ||||||||||||||   ||||||||||||||||||||:||||||:||||||:|.||||||||| |::.||||||||||||
     81 GVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFY 160
           EEEEEEEEEE STT  TT EEEEEEEEES SHHHHHTTTS    B  HHHHHHHHHHHHHTT   EEEEEEE S SS
                                                                                        

                           CC                    17             C   7  C    C       
    162 TPDPQMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTGEQTTAAERQTTFNDMIEIALESVLLGD 237
        :|| :||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||:||||||||||
    161 SPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGD 236
         S TTHHHHHHHTT  EEESSHHHHHHHHHHHT EEEEEEEEEEETTT  B  TTHHHHHHHHHHHHHHHHHHHHH
                                                                                    



Explanation box:

The above is an annotated alignment between the query sequence and the sequence of the protein whose sequence is graphically displayed.
The key to the annotation can be seen below:

                             N         A  A                                       <-- annotation 
    178 VAGVEYVDHWSYVDSIYETLGNATVNSYFPIDHTHTSPAGAEVVAEAFLKAVVCTGTSLKSVLTTTSFEGTCL <-- query sequence
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <-- match/mismatch
    161 VAGVEYVDHWSYVDSIYETLGNATVNSYFPIDHTHTSPAGAEVVAEAFLKAVVCTGTSLKSVLTTTSFEGTCL <-- hit (PDB) sequence
        HHT EEE HHHHHHHHHHHH HHHHHHT SSSSS   HHHHHHHHHHHHHHHHHHT GGGGGBS    SS    <-- DSSP secondary structure

The annotation codes used in InterMap3D correspond to the color codes explained before.

The DSSP code for secondary structure:

    * H = alpha helix
    * B = residue in isolated beta-bridge
    * E = extended strand, participates in beta ladder
    * G = 3-helix (3/10 helix)
    * I = 5 helix (pi helix)
    * T = hydrogen bonded turn
    * S = bend 
Predicted co-evolving residues:
Position 1 Position 2 PredictionScoreDistance
92203co-evolution 4.38 4.983 Å Co-evolving pair mapped on treePair frequencies
1986co-evolution 3.70 7.332 Å Co-evolving pair mapped on treePair frequencies
115124co-evolution 3.63 10.501 Å Co-evolving pair mapped on treePair frequencies
7579co-evolution 3.58 6.196 Å Co-evolving pair mapped on treePair frequencies
136140co-evolution 3.52 6.212 Å Co-evolving pair mapped on treePair frequencies
4855co-evolution 3.43 18.880 Å Co-evolving pair mapped on treePair frequencies
204222co-evolution 3.41 9.505 Å Co-evolving pair mapped on treePair frequencies
1340co-evolution 3.37 7.644 Å Co-evolving pair mapped on treePair frequencies
13128co-evolution 3.34 25.554 Å Co-evolving pair mapped on treePair frequencies
18160co-evolution 3.34 22.860 Å Co-evolving pair mapped on treePair frequencies
55conserved.
2121conserved.
2222conserved.
2323conserved.
2525conserved.
3030conserved.
4444conserved.
5151conserved.
6464conserved.
6666conserved.
6969conserved.
7373conserved.
7676conserved.
7777conserved.
8888conserved.
9090conserved.
9393conserved.
161161conserved.
181181conserved.
182182conserved.
218218conserved.
225225conserved.
230230conserved.

Explanation box:

How to interpret the results in the ranked list of coevolving pairs:

After the alignment comes the list with the results. This list shows the pairs predicted to be coevolving, ordered by the strenght of our belief in their coevolution. That is, by the score (not a significance measure). The score changes with the method used.

Meaning of the scores by method:

RCW MI: The score is the Mutual Information between the residues in position 1 and 2 divided by their background Mutual Information to all other sites.

MI / Entropy: The score is the Mutual Information between the residues in position 1 and 2 divided by the entropy of positions 1 and 2.

Dependency: The score is the entropy-weighed dependency ratio. Basically, is the Mutual Information between the residues in position 1 and 2 divided by their background Mutual Information and then by a factor dependent on the entropy of positions 1 and 2.

Intersection of different methods: In case of intersection, the score is the average rank of the positions in the results list of different methods. If a pair, for instance, was the top hit according to RCW MI, and the 2nd hit on the other method used in the intersection (for instance, Dependency), then its score will be 1.5.

The generated phylogenetic trees:

The trees are generated from the full alignment. When the link (with a depiction of a phylogenetic tree, in pink) is clicked, the software ATV (Zmasek et al., 2001) will be executed in a new window, and the tree file is loaded.
For each sequence depicted on the tree, the amino-acids present on the positions predicted as co-evolving will be shown as node labels. This feature can be turned on or off in the ATV applet.

Tips for better visualization of the phylogenetic trees:

Unchecking the "show taxonomy" box will remove the pair residues names.
Checking the "show seq names" box will display the sequence names.
Unchecking the "color species" box will remove coloring for the labels.
If the tree contains many leaves, it is convenient to "Zoom it on Y" for a better visualization.

Frequencies of occuring pairs:

Clicking on the right-most link (with a depiction of a spreasheet) will open a page showing the frequencies at which each aminoacid pairs occur (for the pair predicted to be co-evolving).




Explanation box:

Explanation of the GetStruct report

The output from GetStruct is in COL (column) format, a modified protein version of the column format described here. The output is mostly self-explanatory. The κ, t and τ parameters are defined in D.M. Soumpasis and M.C. Strahm (2000) J Biomol Struct Dyn. 17(6):965-79.
The DSSP code for secondary structure:

    * H = alpha helix
    * B = residue in isolated beta-bridge
    * E = extended strand, participates in beta ladder
    * G = 3-helix (3/10 helix)
    * I = 5 helix (pi helix)
    * T = hydrogen bonded turn
    * S = bend 

>CDK2_HUMAN.1.1 (298 aa), hit 1 alignment 1
# Hit sequence name .............. 2EXM.A
# Hit sequence comment ........... TRANSFERASE                            
# Hit sequence length ............ 298
# Hit entry resolution ........... 1.80
# Alignment length ............... 298
# Alignment interval in query .... 1-298
# Alignment interval in hit ...... 1-298
# BLAST score .................... 605
# BLAST exp value ................ e-173
# BLAST ident regime ............. 298/298=100%
# 
# Column  1 ...................... Q#,    query residue #
# Column  2 ...................... QA,    query annotation
# Column  3 ...................... Q,     query residue
# Column  4 ...................... I,     identity
# Column  5 ...................... H,     hit residue
# Column  6 ...................... S,     secondary structure
# Column  7 ...................... ACC,   solvent accessibility
# Column  8 ...................... H#,    hit residue #
# Column  9 ...................... H#C,   hit residue # native
# Column 10 ...................... X,     atomic coordinate x
# Column 11 ...................... Y,     atomic coordinate y
# Column 12 ...................... Z,     atomic coordinate z
# Column 13 ...................... K,     KAPPA
# Column 14 ...................... t,     t
# Column 15 ...................... T,     TAV
# Column 16 ...................... Phi,   torsion angle
# Column 17 ...................... Psi,   torsion angle
# Column 18 ...................... Bfact, B factor
# Column 19 ...................... Occ,   occupancy
# 
# /CDK2_HUMAN/1/1/100/1.80/e-173/298/298/1/298/48/2EXM.A/
# 
# Q#  A  Q I H  S    ACC    H#   H#C     X        Y       Z          K       t       T      Phi       Psi       Bfact  Occ
# ------------------------------------------------------------------------------------------------------------------------
   1  .  M = M  .     27     1     1   103.736  111.276   93.725  (undef) (undef) (undef)    (undef)  170.1962  69.35 1.00
   2  .  E = E  .    126     2     2   105.169  114.841   93.811  (undef)    0.24    0.47  -104.6923  -11.6199  58.56 1.00
   3  .  N = N  S     77     3     3   108.467  114.674   91.927     0.38    0.21    0.38   -92.2273    4.6679  47.15 1.00
   4  .  F = F  E     12     4     4   106.535  113.718   88.835     0.21    0.51   -0.38  -131.5151  149.8276  42.90 1.00
   5  .  Q = Q  E     95     5     5   103.834  115.410   86.809     0.30    0.41   -0.44  -112.7757  112.2643  49.77 1.00
   6  .  K = K  E     77     6     6   101.359  112.839   85.567     0.30    0.82    0.01   -62.4825  143.0278  42.78 1.00
   7  .  V = V  E     61     7     7   100.654  113.362   81.907     0.35    0.32   -0.10  -124.5373   -1.7162  46.03 1.00
   8  .  E = E  E    120     8     8    98.229  110.463   81.416     0.14    0.10   -0.39   174.0266  168.2736  45.87 1.00
   9  .  K = K  E    103     9     9    96.743  107.183   82.619     0.31    0.80   -0.15  -113.2600  108.3539  43.82 1.00
  10  .  I = I  E     74    10    10    98.271  104.443   80.470     0.38    0.04   -0.40   -73.5653  -17.6334  42.89 1.00
  11  C  G = G  E     26    11    11    95.773  102.022   81.929     0.16    0.16   -0.32   146.5818 -167.5758  41.43 1.00
  12  C  E = E  E     72    12    12    95.074   99.768   84.855     0.27    0.86   -0.13  -125.7959  106.4560  48.42 1.00
  13  C  G = G  .     26    13    13    97.405   96.860   85.441     0.20    0.06   -0.43   -83.2946 -164.8109  42.19 1.00
  14  4  T = T  S     16    14    14    97.420   93.848   87.749     0.37    0.48    0.30   -67.4280  -35.3884  45.14 1.00
  15  4  Y = Y  S     22    15    15    98.811   95.909   90.640     0.32    0.20   -0.31  -102.6491  -14.5752  38.77 1.00
  (...)
  295  .  H = H  .     88   295   295   104.767   99.631   61.462     0.31    0.59    0.35  -101.6250   89.4394  62.12 1.00
  296  .  L = L  .     23   296   296   103.557  102.037   64.123     0.19    0.94   -0.16  -137.2310  135.2956  60.00 1.00
  297  .  R = R  .    246   297   297   101.894  105.419   64.247     0.29 (undef) (undef)  -117.0606  111.2114  66.66 1.00
  298  .  L = L  .    150   298   298   101.772  106.937   67.724  (undef) (undef) (undef)   -86.8988   (undef)  56.47 1.00
//

How to use the compressed archive containing all files "All files (TAR archive)"

Use a decompression program to recover all the files included in the .tgz compressed archive. In Windows, suitable programs are PowerArchiver 6.1, 7-zip (freeware), WinRar or Winzip. In some of these, you might have to decompress the archive two times in a row. In Macintosh, suitable programs are BOMArchiveHelper or Stuffit expander. In Unix, use gunzip.
This will extract all the output files contained in the archive to a folder. Sometimes - depending on your machine configurations - a simple double-click on the file will cause the appropriate program to decompress the archive and create the folder.
If you have Pymol installed, the PyMol script (".pml" file) can be opened in PyMol by double-clicking on it. This will load the PDB structure and color it. The structure can then be rotated to a better angle, and a new ray-trace image created by clicking on the "ray" button (a warning, ray-tracing may take a long time and it might seem your computer has frozen).




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