GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Oligomerisation - Oligomerisation domain
Pfam: PF02410 (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: 100
Sequences: 1724
Seq/Len: 17.24
HH_delta: -0.028 (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
95_D98_S0.869673.166
9_L46_I0.79352.889
9_L14_A0.771422.808
14_A35_A0.69672.536
53_A57_E0.688832.508
37_G43_V0.587612.139
54_L78_Y0.497511.811
17_I35_A0.494351.800
35_A85_I0.4721.718
22_V29_A0.459611.673
72_D87_T0.454691.655
38_R42_H0.438061.595
62_P78_Y0.41951.527
49_E53_A0.417651.520
4_E58_Y0.413281.505
72_D90_A0.397891.448
2_L6_V0.397571.447
47_A74_V0.395441.440
9_L35_A0.392221.428
75_L82_V0.392211.428
16_D36_T0.38311.395
47_A85_I0.381071.387
2_L33_I0.379061.380
4_E8_A0.374521.363
10_E17_I0.373671.360
6_V10_E0.365231.330
51_E65_I0.364631.327
54_L60_E0.364611.327
9_L50_V0.364221.326
66_E75_L0.363241.322
5_I78_Y0.344721.255
51_E76_V0.34451.254
87_T90_A0.344351.254
65_I76_V0.342211.246
34_I96_L0.33781.230
14_A46_I0.32741.192
48_D68_L0.32541.185
22_V26_S0.320791.168
43_V85_I0.319351.163
5_I33_I0.317541.156
63_L79_G0.314251.144
3_E6_V0.307191.118
36_T88_P0.2991.088
37_G46_I0.298561.087
8_A49_E0.297571.083
46_I85_I0.296791.080
6_V17_I0.293021.067
32_F82_V0.288571.051
92_E95_D0.283291.031
6_V19_V0.282861.030
49_E52_K0.278211.013
29_A82_V0.27561.003
19_V33_I0.273680.996
3_E7_E0.272430.992
50_V83_V0.269910.983
43_V71_S0.268860.979
19_V31_Y0.268850.979
8_A50_V0.267890.975
15_E38_R0.267050.972
30_D66_E0.265550.967
43_V87_T0.265470.966
68_L74_V0.265320.966
33_I81_I0.263840.960
5_I81_I0.262560.956
42_H45_A0.260540.948
52_K57_E0.259730.946
44_R71_S0.255270.929
68_L71_S0.253010.921
42_H46_I0.2530.921
41_R44_R0.248920.906
71_S74_V0.247090.900
15_E36_T0.245190.893
37_G74_V0.244360.890
36_T43_V0.239370.871
39_S42_H0.238580.869
51_E78_Y0.237140.863
8_A53_A0.237050.863
9_L33_I0.230340.839
35_A46_I0.229580.836
6_V9_L0.229520.836
88_P92_E0.227270.827
75_L93_Y0.221970.808
21_D24_E0.221580.807
17_I33_I0.220690.803
37_G88_P0.220470.803
43_V74_V0.219290.798
32_F84_H0.219080.798
2_L19_V0.211380.770
41_R66_E0.209680.763
12_K49_E0.204780.745
25_K29_A0.202760.738
7_E11_D0.200310.729
40_E87_T0.198980.724
30_D80_D0.19670.716
23_R31_Y0.196510.715
28_W82_V0.196390.715
70_E85_I0.19570.712
52_K92_E0.195220.711
86_F94_Y0.1950.710
39_S81_I0.193490.704
22_V27_S0.193480.704
5_I54_L0.193260.704
33_I83_V0.192390.700
12_K40_E0.191940.699
56_K61_R0.189940.691
12_K86_F0.188170.685
44_R68_L0.18810.685
36_T41_R0.183880.669
77_D80_D0.183330.667
45_A94_Y0.182980.666
20_L34_I0.182470.664
54_L81_I0.180720.658
38_R87_T0.179290.653
4_E54_L0.177650.647
8_A12_K0.177570.646
97_E100_W0.177130.645
51_E68_L0.17670.643
48_D56_K0.176480.642
38_R88_P0.175840.640
86_F97_E0.173460.631
12_K42_H0.172890.629
38_R99_L0.172680.629
62_P65_I0.172230.627
20_L25_K0.171210.623
22_V90_A0.170120.619
34_I97_E0.170020.619
7_E69_D0.168990.615
72_D89_E0.168480.613
39_S100_W0.166510.606
64_R82_V0.165770.603
15_E88_P0.165560.603
5_I8_A0.164660.599
20_L32_F0.164560.599
58_Y61_R0.164470.599
30_D75_L0.163830.596
28_W54_L0.163750.596
7_E10_E0.163280.594
77_D93_Y0.163090.594
5_I83_V0.162860.593
38_R41_R0.162150.590
40_E72_D0.16170.589
3_E10_E0.159330.580
48_D52_K0.159210.580
36_T87_T0.158050.575
4_E7_E0.1570.572
28_W83_V0.156840.571
30_D77_D0.156740.571
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
2o5aA0.99100-0.028
2id1A0.99100-0.028
3upsA0.99100-0.027
2qipA0.8238.60.906
3f41A0.9537.70.907
3subA0.57230.916
2iu4A0.8620.80.918
3pg5A0.9520.20.918
3mf7A0.7419.50.919
3ct4A0.8418.40.919

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