GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Vir_act_alpha_C - Virulence activator alpha C-term
Pfam: PF10400 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Length: 90
Sequences: 1163
Seq/Len: 12.92
HH_delta: 0.215 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
30_R80_E0.82653.592
73_Q77_E0.569892.477
34_E80_E0.559512.432
14_G22_A0.508542.210
41_E69_I0.492062.139
33_H72_E0.484252.105
23_I83_I0.478282.079
63_L82_A0.442421.923
8_L67_Y0.437691.902
70_R77_E0.437151.900
37_L73_Q0.435551.893
41_E73_Q0.428261.861
27_E83_I0.425091.848
30_R76_I0.422141.835
37_L69_I0.416811.812
66_E81_E0.408591.776
23_I27_E0.378231.644
30_R79_C0.358061.556
29_R75_E0.345351.501
30_R34_E0.34131.484
70_R74_A0.334111.452
38_A41_E0.304761.325
18_D21_E0.289551.259
31_E35_E0.283691.233
59_F85_E0.274661.194
30_R83_I0.271241.179
7_F29_R0.27081.177
14_G60_Y0.267941.165
34_E76_I0.263131.144
42_E45_Q0.260391.132
24_E27_E0.255571.111
70_R81_E0.247591.076
20_E24_E0.231591.007
8_L64_T0.230391.001
19_P23_I0.225590.981
71_Y75_E0.225180.979
41_E44_E0.222650.968
29_R33_H0.220250.957
40_Y68_G0.215410.936
17_L22_A0.213670.929
36_R39_E0.213560.928
34_E38_A0.213080.926
80_E84_E0.208520.906
76_I80_E0.208270.905
31_E34_E0.204670.890
28_E32_Q0.203790.886
33_H75_E0.202470.880
40_Y65_L0.197390.858
32_Q35_E0.195530.850
62_Y79_C0.19440.845
11_L63_L0.190290.827
8_L68_G0.190130.826
38_A42_E0.189040.822
63_L67_Y0.185820.808
72_E75_E0.181250.788
70_R73_Q0.18050.785
23_I86_L0.180220.783
63_L66_E0.178970.778
29_R32_Q0.178540.776
66_E85_E0.175130.761
29_R79_C0.174060.757
5_D16_H0.173340.753
12_F64_T0.17210.748
33_H79_C0.170280.740
21_E24_E0.168770.734
10_K58_A0.16790.730
6_E63_L0.166860.725
37_L76_I0.166550.724
61_W64_T0.166230.723
17_L21_E0.161980.704
32_Q36_R0.161580.702
19_P85_E0.160820.699
40_Y72_E0.15960.694
67_Y71_Y0.156250.679
26_L79_C0.156220.679
24_E31_E0.1540.669
10_K68_G0.153690.668
4_R10_K0.15170.659
9_L68_G0.150990.656
59_F63_L0.149980.652
27_E31_E0.149440.650
65_L68_G0.149220.649
26_L83_I0.149090.648
68_G71_Y0.14880.647
41_E45_Q0.147130.640
65_L69_I0.146910.639
7_F14_G0.146630.637
27_E35_E0.146620.637
10_K22_A0.14620.635
15_G60_Y0.145390.632
42_E80_E0.144020.626
12_F68_G0.142550.620
5_D78_W0.141940.617
9_L29_R0.141670.616
24_E84_E0.141530.615
5_D67_Y0.141470.615
33_H36_R0.140090.609
13_F16_H0.140020.609
64_T68_G0.139730.607
10_K18_D0.13970.607
28_E31_E0.139320.606
44_E69_I0.139260.605
67_Y75_E0.1390.604
33_H67_Y0.138240.601
46_E62_Y0.137680.598
76_I83_I0.137650.598
41_E66_E0.137390.597
10_K29_R0.137380.597
44_E66_E0.137250.597
56_P60_Y0.137210.596
68_G72_E0.136060.591
60_Y63_L0.135490.589
25_L47_I0.134550.585
76_I79_C0.134280.584
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
3l9fA0.998.90.215
1yg2A198.80.237
2rkhA0.877898.40.34
2p4wA0.966749.60.775
2kq9A0.8778200.815
2z90A0.877819.10.817
2fjcA0.877811.20.834
4eveA0.866710.60.835
2clbA0.922210.50.836
2c2jA0.922210.50.836

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