GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3856 - Domain of Unknown Function (DUF3856)
Pfam: PF12968 (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: CL0020
Length: 144
Sequences: 33699
Seq/Len: 234.02
HH_delta: -0.079 (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
24_A27_E3.559872.949
70_R73_E3.48792.889
115_R118_E3.418392.831
58_H77_S3.347272.773
62_S78_A3.333052.761
10_Y31_S2.976392.465
107_A123_F2.82192.337
106_R122_E2.744132.273
14_S32_C2.739182.269
61_L77_S2.608712.161
65_L73_E2.459432.037
33_R61_L2.425372.009
110_L122_E2.402791.990
65_L77_S2.40151.989
13_L31_S2.193941.817
75_L79_D2.155661.786
17_E27_E2.138661.771
110_L118_E2.131941.766
120_L124_R2.020071.673
32_C60_G1.928621.597
17_E31_S1.829071.515
29_A33_R1.815111.503
58_H80_R1.783781.478
110_L115_R1.768461.465
16_A20_L1.684921.396
65_L70_R1.63451.354
29_A68_L1.586321.314
10_Y34_K1.549141.283
106_R110_L1.542461.278
29_A65_L1.541571.277
104_F108_V1.467391.215
109_A113_L1.424451.180
61_L65_L1.35781.125
118_E121_K1.349681.118
125_M129_M1.343891.113
11_M15_D1.339481.110
39_S42_I1.332651.104
26_E68_L1.327331.099
122_E125_M1.312511.087
64_A68_L1.29591.073
66_A71_Y1.289971.068
13_L17_E1.280871.061
73_E76_Q1.251171.036
107_A126_A1.251111.036
55_A81_A1.250141.036
29_A64_A1.247081.033
125_M128_E1.245221.031
20_L24_A1.243731.030
111_E123_F1.23431.022
80_R84_Y1.219241.010
85_F88_R1.207281.000
80_R83_R1.189790.986
79_D95_E1.180450.978
17_E24_A1.177350.975
79_D106_R1.175950.974
29_A61_L1.163940.964
34_K37_E1.153330.955
27_E31_S1.150780.953
63_G66_A1.13970.944
36_M58_H1.139220.944
108_V111_E1.133430.939
15_D19_Q1.126130.933
34_K38_V1.113830.923
35_A57_C1.102610.913
27_E30_A1.100830.912
111_E116_K1.080590.895
66_A78_A1.080260.895
59_A63_G1.06940.886
105_S108_V1.048720.869
15_D18_R1.048070.868
11_M60_G1.046690.867
124_R128_E1.042030.863
15_D60_G1.039760.861
63_G67_G1.026810.851
95_E99_W1.02410.848
93_Q97_K1.004710.832
77_S80_R1.004150.832
111_E119_A0.999420.828
10_Y35_A0.997570.826
25_Y64_A0.992410.822
118_E122_E0.964160.799
73_E77_S0.958660.794
17_E20_L0.955270.791
76_Q80_R0.953090.789
36_M57_C0.947070.784
66_A74_C0.946320.784
33_R37_E0.937280.776
58_H84_Y0.93560.775
62_S81_A0.927210.768
33_R77_S0.926130.767
31_S34_K0.925250.766
55_A85_F0.919920.762
12_A15_D0.917540.760
78_A105_S0.90970.754
35_A38_V0.898440.744
104_F126_A0.896090.742
16_A19_Q0.893680.740
107_A119_A0.893310.740
108_V112_G0.887890.735
30_A34_K0.88170.730
58_H81_A0.878820.728
116_K120_L0.875980.726
110_L113_L0.866810.718
82_L92_H0.866390.718
108_V123_F0.864670.716
96_G99_W0.863850.716
62_S74_C0.859940.712
126_A129_M0.854450.708
25_Y68_L0.845570.700
121_K125_M0.843940.699
32_C64_A0.831010.688
28_A32_C0.829420.687
25_Y67_G0.827790.686
76_Q79_D0.819690.679
122_E126_A0.818680.678
30_A33_R0.818330.678
63_G78_A0.817920.677
18_R67_G0.81680.677
13_L16_A0.816540.676
29_A70_R0.814170.674
60_G63_G0.813440.674
74_C78_A0.811480.672
78_A94_D0.805930.668
72_D76_Q0.804290.666
15_D32_C0.800660.663
14_S18_R0.799630.662
92_H95_E0.798610.661
39_S57_C0.791420.656
26_E72_D0.785330.650
75_L113_L0.781940.648
18_R60_G0.781360.647
18_R64_A0.778850.645
18_R32_C0.777970.644
71_Y75_L0.767310.636
97_K105_S0.766440.635
121_K124_R0.765110.634
14_S17_E0.764060.633
124_R127_G0.763460.632
26_E29_A0.763050.632
99_W122_E0.758080.628
59_A81_A0.752720.623
18_R25_Y0.747620.619
92_H96_G0.740840.614
81_A84_Y0.740140.613
63_G105_S0.731490.606
26_E30_A0.730770.605
79_D82_L0.730050.605
8_M12_A0.728450.603
33_R36_M0.725740.601
75_L110_L0.722760.599
93_Q96_G0.715110.592
25_Y29_A0.714880.592
119_A123_F0.712960.591
65_L68_L0.712160.590
72_D117_E0.711190.589
117_E121_K0.705880.585
72_D113_L0.70540.584
14_S35_A0.69580.576
28_A64_A0.69170.573
39_S43_P0.677130.561
86_N95_E0.674820.559
79_D83_R0.674730.559
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
4gywA0.826499.5-0.079
4gywA0.826499.4-0.044
4i2zA0.861199.4-0.037
4gcnA0.868199.4-0.021
2hr2A0.937599.4-0.02
3gyzA0.826499.40.001
4ga2A0.826499.30.016
1kt0A0.909799.30.046
2h6fA0.826499.30.051
1p5qA0.909799.30.057

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