Results

[summary] [cytoscape] [jmol] [files] [input]

Summary

17 groups of coevolution were detected with a total of 50 amino acids involved.
See the full text output as well as HTML tables of pairs and groups of coevolving amino acids.

Cytoscape

This Cytoscape plugin is interactive. Please allow to load, which might take a few moments.
Larger nodes correspond to greater numbers of connected (coevolving) sites  [tip]. Cytoscape Web example
The xgmml file listed below can be used with the stand-alone Cytoscape application.

Jmol

For interactive viewing you can use the following Jmol plugin:


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Listing of groups with residues covered by 3-D structure (click on headers to sort):

o Group [?] Mean distance [?] Sites [?] 3-D sites [?] Residue indices [?] Residues [?]
138.17339911, 172, 254, 305, 306, 362, 369, 379, 483D, E, V, I, G, R, V, I, E
240.38299811, 254, 305, 306, 362, 369, 379, 483, 530D, V, I, G, R, V, I, E, A
332.56144348, 100, 133, 530T, I, A, A
446.558133100, 133, 239I, A, A
533.440977101, 145, 171, 219, 441, 466, 491T, A, K, F, K, A, M
636.353944126, 212, 344, 354A, A, G, E
725.19454145, 441, 466, 491, 536A, K, A, M, G
837.44132172, 471, 529E, G, A
934.406844179, 217, 458, 487D, S, C, N
1026.959165188, 212, 251, 344, 354, 536D, A, A, G, E, G
1137.786265188, 251, 344, 354, 456, 536D, A, G, E, L, G
1237.714244213, 236, 298, 484V, V, G, E
1339.00733251, 366, 420A, Q, I
1448.9133307, 462, 481M, P, A
1564.954532338, 430, 534E, R, A
1616.58543340, 346, 362, 527A, V, R, N
1720.388232456, 471, 529L, G, A

Files

Listing of files generated (hover with mouse over file name for description):

Input

The following input was submitted:
Analysis type:intra-protein
Input file 1:name: groel.aln
sequences: 12 (DNA)
alignment length: 1695
protein lengths: 547 - 553 aa
Reference sequence:E.coli
Structure file:PDB: 2EU1 (local copy)
chain A: atoms 1 - 3855, residues 2 - 525, 523 matches
WARNING: 1 mismatch between reference and PDB sequence (alignment)
tree file:
tree file 2:
bootstrap value:0.8
gap threshold:0.8
alpha threshold:0.01
number of simulated alignments:100
inter-protein analysis:off
await convergence:off
time correction:off

Generated on Fri Jun 13 19:37:21 2014 (Eire), overall processing time: 15 seconds.

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