GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CUB - CUB domain
Pfam: PF00431 (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. )
Clan: CL0164
Length: 110
Sequences: 3774
Seq/Len: 34.31
HH_delta: -0.111 (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
54_C76_C1.647434.767
45_S104_R0.930842.693
86_S91_L0.83692.421
26_D94_R0.826032.390
62_Y92_F0.753222.179
48_L76_C0.747142.162
49_E56_Q0.704162.037
60_E74_R0.695052.011
44_L107_K0.68811.991
5_L29_W0.682271.974
58_Y96_H0.673041.947
26_D96_H0.624631.807
60_E94_R0.62431.806
44_L109_T0.624161.806
43_F46_F0.606881.756
60_E71_L0.606761.756
23_S102_S0.601691.741
29_W106_F0.599381.734
12_I108_A0.598131.731
21_Y95_F0.595351.723
47_D103_S0.593761.718
63_D87_S0.573891.660
28_T92_F0.55361.602
32_T90_S0.550051.591
42_T83_S0.530661.535
13_S107_K0.526481.523
41_L61_V0.51651.494
14_S17_Y0.500871.449
49_E98_D0.500731.449
14_S18_P0.492561.425
59_L93_I0.472391.367
22_P25_S0.463741.342
91_L108_A0.453031.311
30_T92_F0.446331.291
11_I107_K0.440581.275
41_L91_L0.439861.273
62_Y71_L0.426931.235
34_P37_H0.423691.226
33_A39_I0.420611.217
5_L110_Y0.417111.207
17_Y45_S0.408991.183
33_A37_H0.399191.155
58_Y74_R0.39411.140
40_R83_S0.390021.128
40_R85_I0.384161.111
21_Y24_N0.38181.105
21_Y57_D0.379091.097
42_T109_T0.377481.092
28_T94_R0.363921.053
47_D104_R0.357991.036
43_F59_L0.34981.012
33_A89_N0.341320.988
20_N102_S0.333960.966
56_Q98_D0.332710.963
95_F105_G0.331490.959
48_L95_F0.327870.949
31_I39_I0.32690.946
57_D98_D0.325330.941
43_F108_A0.324990.940
62_Y94_R0.318620.922
15_P18_P0.31450.910
5_L31_I0.31210.903
21_Y97_S0.311470.901
61_V84_I0.310520.898
32_T89_N0.30410.880
63_D72_L0.302540.875
72_L84_I0.299940.868
16_N22_P0.29740.860
46_F75_F0.295490.855
97_S105_G0.295030.854
57_D105_G0.293650.850
12_I93_I0.293480.849
46_F59_L0.290610.841
10_G110_Y0.290260.840
45_S107_K0.289410.837
54_C58_Y0.289290.837
62_Y72_L0.282710.818
98_D105_G0.280140.811
21_Y49_E0.279920.810
43_F61_V0.277290.802
25_S97_S0.275510.797
65_N90_S0.26960.780
63_D86_S0.266070.770
47_D78_S0.261230.756
14_S22_P0.260490.754
30_T90_S0.256330.742
48_L58_Y0.253830.734
49_E57_D0.251150.727
29_W93_I0.250150.724
27_C31_I0.245890.711
5_L10_G0.245740.711
58_Y76_C0.245350.710
38_R85_I0.244270.707
93_I108_A0.244070.706
33_A36_G0.243370.704
64_G70_P0.239830.694
98_D101_N0.236860.685
66_D92_F0.234010.677
48_L77_G0.233790.676
49_E101_N0.232460.673
38_R89_N0.23120.669
14_S21_Y0.230580.667
67_E92_F0.229990.665
48_L54_C0.22870.662
75_F84_I0.226820.656
56_Q100_S0.226380.655
72_L87_S0.222090.643
61_V93_I0.220980.639
57_D97_S0.218410.632
49_E103_S0.218030.631
86_S89_N0.217820.630
46_F77_G0.217580.630
7_N110_Y0.213170.617
41_L108_A0.211670.612
43_F81_P0.210560.609
70_P92_F0.207030.599
10_G31_I0.203870.590
39_I86_S0.202740.587
8_N37_H0.201760.584
55_C99_S0.201620.583
6_T11_I0.198180.573
18_P21_Y0.196320.568
46_F106_F0.194720.563
95_F106_F0.194620.563
38_R87_S0.194260.562
66_D70_P0.190540.551
23_S97_S0.187790.543
43_F83_S0.186390.539
16_N25_S0.185590.537
23_S100_S0.182650.528
65_N70_P0.182170.527
67_E70_P0.181550.525
20_N103_S0.181520.525
62_Y66_D0.181480.525
14_S29_W0.180980.524
33_A86_S0.17960.520
5_L8_N0.179450.519
20_N47_D0.1790.518
63_D71_L0.178580.517
13_S35_P0.176590.511
37_H90_S0.176480.511
43_F48_L0.172410.499
57_D95_F0.172140.498
14_S59_L0.170580.494
5_L12_I0.170170.492
11_I44_L0.167690.485
59_L105_G0.167460.485
99_S103_S0.167230.484
19_S22_P0.166070.480
49_E97_S0.164930.477
59_L108_A0.164910.477
10_G33_A0.16370.474
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
2qqmA199.8-0.111
2qqoA199.8-0.101
2wnoA199.8-0.1
4gz9A199.8-0.099
3kq4B0.981899.8-0.084
3kq4B199.8-0.081
4gz9A0.990999.8-0.081
2qqkA199.8-0.066
2qqkA0.990999.7-0.049
1nt0A0.963699.7-0.032

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