GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4174 - Domain of unknown function (DUF4174)
Pfam: PF13778 (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: CL0172
Length: 118
Sequences: 22518
Seq/Len: 190.83
HH_delta: 0.142 (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
10_N87_K2.527073.227
38_G105_F2.259852.886
105_F109_D2.015012.573
86_G90_G1.997522.551
93_L107_T1.864562.381
9_K45_V1.855732.370
86_G92_K1.815892.319
36_R40_D1.542981.970
20_A57_P1.518551.939
35_N38_G1.488241.900
12_L45_V1.45051.852
42_R109_D1.433461.830
91_V94_R1.4061.795
22_D25_Y1.39871.786
85_I91_V1.384331.768
68_A72_R1.336271.706
17_A48_V1.318791.684
34_N101_P1.258231.607
4_D7_R1.206341.540
81_T94_R1.136211.451
15_V82_V1.109241.416
95_W107_T1.100331.405
51_G70_R1.074391.372
33_Q37_C1.052431.344
7_R12_L1.039181.327
28_Q82_V0.992111.267
30_E34_N0.991611.266
83_V91_V0.988171.262
100_D103_E0.976531.247
48_V59_K0.968271.236
101_P105_F0.963421.230
102_E106_D0.944411.206
12_L47_I0.942571.204
6_F12_L0.935411.194
13_L84_L0.919351.174
31_E101_P0.893251.141
30_E33_Q0.890111.137
17_A29_L0.87831.121
103_E106_D0.876691.119
64_E67_Q0.875861.118
31_E34_N0.87581.118
75_I81_T0.852681.089
106_D109_D0.831191.061
39_L105_F0.830561.061
69_L73_L0.826221.055
29_L48_V0.823091.051
17_A20_A0.820341.047
15_V29_L0.808981.033
39_L109_D0.805481.029
13_L82_V0.80451.027
10_N45_V0.800771.022
16_F73_L0.796921.018
40_D43_D0.790941.010
14_V85_I0.781650.998
68_A71_K0.779160.995
10_N92_K0.778520.994
40_D45_V0.773260.987
19_S22_D0.771550.985
54_A58_G0.766620.979
37_C40_D0.75840.968
7_R10_N0.757810.968
51_G67_Q0.750220.958
12_L89_G0.748080.955
31_E35_N0.741990.947
6_F47_I0.738780.943
16_F49_I0.73570.939
83_V94_R0.732880.936
59_K62_S0.721770.922
33_Q36_R0.714890.913
15_V28_Q0.708480.905
81_T96_P0.699440.893
15_V24_R0.698170.891
13_L32_L0.688110.879
35_N102_E0.684020.873
67_Q71_K0.682290.871
20_A50_T0.67910.867
48_V61_L0.669940.855
17_A50_T0.665410.850
27_Q98_P0.663110.847
50_T53_G0.655060.836
35_N39_L0.643720.822
36_R46_V0.63820.815
7_R89_G0.634660.810
29_L33_Q0.633750.809
103_E107_T0.621520.794
33_Q59_K0.616420.787
10_N84_L0.612930.783
32_L46_V0.604340.772
38_G41_E0.60320.770
38_G42_R0.599180.765
34_N37_C0.598890.765
27_Q30_E0.595070.760
19_S79_G0.591870.756
12_L85_I0.590810.754
71_K74_R0.583380.745
44_I108_I0.58260.744
35_N101_P0.581710.743
15_V32_L0.577650.738
45_V60_P0.576730.736
73_L85_I0.56990.728
19_S52_D0.567390.724
22_D80_F0.562520.718
6_F45_V0.560740.716
102_E105_F0.560420.716
51_G79_G0.556870.711
24_R27_Q0.553070.706
27_Q31_E0.546550.698
16_F75_I0.545950.697
8_W89_G0.538450.688
49_I62_S0.538290.687
49_I69_L0.536990.686
38_G109_D0.534790.683
84_L107_T0.533810.682
85_I89_G0.531350.678
43_D87_K0.526970.673
25_Y28_Q0.521010.665
39_L42_R0.519910.664
60_P63_P0.519230.663
13_L44_I0.518730.662
82_V104_L0.518690.662
16_F83_V0.518210.662
69_L72_R0.518070.662
95_W99_I0.517970.661
64_E68_A0.513230.655
15_V48_V0.512760.655
38_G101_P0.512120.654
10_N44_I0.508860.650
24_R98_P0.508350.649
44_I84_L0.504140.644
10_N86_G0.500710.639
37_C41_E0.488870.624
34_N38_G0.488670.624
20_A23_P0.486480.621
31_E102_E0.483850.618
65_D68_A0.48230.616
14_V49_I0.477450.610
39_L44_I0.472640.604
23_P26_Q0.47130.602
8_W86_G0.471270.602
55_R58_G0.470440.601
13_L46_V0.467690.597
70_R75_I0.467020.596
54_A63_P0.462990.591
35_N105_F0.459270.586
26_Q29_L0.457590.584
99_I107_T0.455860.582
84_L95_W0.454980.581
36_R45_V0.451660.577
23_P27_Q0.448360.573
84_L104_L0.447710.572
66_I71_K0.447590.572
28_Q32_L0.447530.571
21_D56_S0.443520.566
99_I103_E0.442710.565
54_A57_P0.440020.562
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
2hyxA0.974699.60.142
2h30A0.974699.60.158
1zofA0.983199.60.159
1zyeA0.983199.60.159
2i81A0.983199.60.161
1we0A0.983199.60.163
3eytA0.974699.60.166
2bmxA0.966199.60.167
3lorA0.974699.60.167
2f9sA0.974699.60.168

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