GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF218 - DUF218 domain
Pfam: PF02698 (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: 155
Sequences: 2522
Seq/Len: 16.27
HH_delta: 0.204 (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
86_A117_F0.89663.244
33_Y72_R0.827742.994
43_F63_L0.741052.681
5_I38_A0.713452.581
7_V29_A0.682582.469
28_E31_R0.677472.451
2_A102_I0.599252.168
60_R70_E0.585032.116
76_E85_N0.578572.093
79_S85_N0.564222.041
64_I70_E0.557792.018
5_I104_V0.553992.004
27_D62_Y0.534971.935
54_S57_E0.504881.826
43_F73_I0.496961.798
76_E79_S0.492831.783
80_T84_E0.479111.733
60_R64_I0.473221.712
30_A34_K0.457721.656
83_Y87_R0.440241.593
30_A63_L0.438981.588
53_R61_D0.438551.587
33_Y69_P0.438381.586
114_R118_R0.432411.564
69_P72_R0.419521.518
42_L89_S0.41891.515
105_T110_M0.416741.508
90_K94_K0.415141.502
3_D100_S0.41141.488
40_R74_I0.409171.480
6_V101_I0.396661.435
40_R72_R0.39371.424
6_V89_S0.390621.413
60_R75_L0.390271.412
30_A66_L0.387471.402
81_N84_E0.379251.372
41_I63_L0.378051.368
8_L113_A0.376861.363
23_R27_D0.375451.358
93_L101_I0.370251.339
85_N89_S0.367551.330
84_E88_F0.360471.304
86_A120_V0.359431.300
76_E88_F0.35651.290
18_L26_L0.353771.280
82_T109_H0.343691.243
26_L59_M0.342671.240
85_N88_F0.340421.232
31_R35_A0.337471.221
110_M126_F0.334391.210
103_L117_F0.327751.186
107_P111_R0.321711.164
7_V43_F0.319251.155
27_D66_L0.315251.140
26_L43_F0.314081.136
57_E77_P0.313091.133
5_I32_L0.311.121
105_T109_H0.308671.117
78_K88_F0.307781.113
29_A41_I0.306141.108
44_S89_S0.304651.102
110_M128_P0.293531.062
4_A42_L0.292141.057
8_L109_H0.285761.034
25_R105_T0.284241.028
57_E61_D0.283011.024
115_M119_K0.282221.021
87_R91_R0.278941.009
33_Y36_G0.278441.007
36_G39_P0.278191.006
4_A101_I0.276831.001
114_R126_F0.273930.991
32_L104_V0.272530.986
22_S59_M0.266040.962
30_A62_Y0.264320.956
30_A68_V0.263870.955
68_V73_I0.262210.949
28_E127_I0.26190.947
49_H52_G0.260250.941
26_L62_Y0.260220.941
55_E85_N0.249550.903
33_Y68_V0.24950.903
79_S84_E0.247380.895
37_Y102_I0.247070.894
6_V86_A0.24610.890
4_A98_W0.243360.880
5_I39_P0.242850.879
105_T113_A0.240440.870
45_G85_N0.238730.864
63_L67_G0.238730.864
8_L103_L0.238440.863
12_L18_L0.237650.860
83_Y120_V0.237610.860
62_Y66_L0.237270.858
26_L63_L0.237150.858
118_R123_D0.237150.858
44_S79_S0.236140.854
54_S77_P0.232040.839
44_S59_M0.231490.837
93_L98_W0.229250.829
79_S88_F0.224160.811
68_V72_R0.223240.808
48_G80_T0.222170.804
2_A125_V0.220050.796
46_G79_S0.220.796
128_P131_P0.217280.786
27_D30_A0.212520.769
3_D99_Q0.211110.764
101_I122_P0.210020.760
38_A104_V0.209760.759
44_S76_E0.208890.756
43_F59_M0.206270.746
60_R73_I0.20580.745
33_Y41_I0.20450.740
91_R94_K0.204370.739
114_R124_A0.203980.738
44_S85_N0.20370.737
24_E133_T0.201970.731
33_Y37_Y0.201560.729
9_G55_E0.201220.728
114_R128_P0.199990.723
42_L93_L0.199110.720
5_I41_I0.198750.719
22_S62_Y0.196320.710
82_T85_N0.196190.710
29_A63_L0.196010.709
25_R106_S0.195830.708
116_I120_V0.195530.707
13_D16_G0.192290.696
43_F79_S0.191780.694
56_A75_L0.190950.691
57_E75_L0.190440.689
64_I73_I0.189350.685
56_A76_E0.187610.679
124_A128_P0.187150.677
55_E59_M0.187140.677
84_E116_I0.185860.672
38_A72_R0.185430.671
8_L25_R0.185110.670
8_L82_T0.184970.669
61_D64_I0.184020.666
8_L105_T0.183380.663
55_E76_E0.183250.663
24_E27_D0.183110.662
56_A77_P0.182210.659
57_E95_E0.181990.658
13_D17_Q0.181860.658
88_F91_R0.181130.655
21_E106_S0.18110.655
3_D98_W0.17790.644
32_L102_I0.177260.641
108_Y132_P0.175870.636
18_L22_S0.175140.634
83_Y116_I0.174160.630
24_E130_P0.174030.630
25_R109_H0.173770.629
47_Y77_P0.173590.628
74_I92_L0.170260.616
11_A22_S0.170050.615
24_E106_S0.169140.612
46_G56_A0.168840.611
46_G85_N0.168670.610
107_P131_P0.16640.602
79_S89_S0.16610.601
47_Y54_S0.165380.598
28_E129_A0.165270.598
31_R34_K0.165210.598
8_L81_N0.164910.597
53_R58_A0.164520.595
45_G76_E0.164250.594
7_V25_R0.163230.591
22_S26_L0.162890.589
25_R104_V0.162880.589
128_P132_P0.162640.588
50_G58_A0.161960.586
64_I67_G0.161890.586
121_G124_A0.161860.586
27_D136_S0.161460.584
45_G79_S0.161120.583
76_E89_S0.160860.582
81_N115_M0.160650.581
11_A19_S0.160220.580
8_L112_R0.160010.579
7_V26_L0.159890.578
90_K122_P0.158120.572
109_H112_R0.15810.572
18_L23_R0.158060.572
17_Q20_P0.157370.569
41_I68_V0.157280.569
103_L126_F0.157050.568
5_I37_Y0.156690.567
131_P134_P0.156260.565
18_L58_A0.155990.564
86_A89_S0.155830.564
103_L113_A0.155230.562
9_G46_G0.154960.561
110_M114_R0.154710.560
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
3ca8A0.92261000.204
2hqsH0.683987.20.885
2aizP0.632384.90.888
3qi7A0.9742810.893
3dbiA176.40.897
3gv0A0.993574.20.899
2kgwA0.6387740.899
3ff1A0.8903730.9
4eh1A0.477472.90.9
3g85A0.993572.70.9

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