GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1776 - Fungal family of unknown function (DUF1776)
Pfam: PF08643 (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: CL0063
Length: 299
Sequences: 5948
Seq/Len: 19.89
HH_delta: 0.259 (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
118_A122_N1.485624.085
128_P175_L1.08562.985
61_D64_S1.058082.910
152_F179_F1.03022.833
173_S177_S0.927522.551
125_L174_A0.910372.503
124_R171_V0.883262.429
16_L201_L0.879262.418
23_D262_N0.841332.314
27_R269_Y0.789972.172
179_F193_V0.760752.092
18_R22_L0.750812.065
121_L125_L0.742532.042
23_D27_R0.730392.008
38_A42_K0.720881.982
154_P176_S0.69851.921
73_A138_L0.695591.913
23_D265_F0.687491.891
5_V30_I0.672531.849
121_L126_L0.651581.792
122_N126_L0.651531.792
13_H35_V0.649851.787
37_S40_D0.644831.773
33_V52_I0.625631.720
149_I194_T0.620721.707
6_V24_L0.620021.705
30_I53_R0.609891.677
19_S258_R0.609251.675
70_S74_S0.604611.663
8_I21_A0.60341.659
22_L47_E0.596981.642
117_W167_P0.595591.638
42_K45_E0.587761.616
114_P133_Q0.579641.594
34_T57_L0.578711.591
18_R43_Y0.574711.580
32_Y72_F0.5731.576
62_P130_L0.568821.564
20_L264_V0.566361.557
23_D26_R0.563561.550
69_L135_L0.559421.538
125_L129_I0.548961.510
132_I178_F0.546871.504
71_R74_S0.54661.503
109_I166_S0.542781.493
38_A56_W0.5361.474
66_H134_G0.531511.462
6_V29_F0.523011.438
179_F195_Q0.522311.436
168_E172_S0.522021.435
136_L186_L0.521641.434
62_P66_H0.519381.428
110_E140_R0.519241.428
97_I268_L0.516721.421
113_S116_S0.513771.413
71_R75_L0.511911.408
66_H70_S0.51061.404
53_R75_L0.510421.404
109_I178_F0.507341.395
57_L68_S0.507211.395
24_L265_F0.504011.386
148_K151_L0.493621.357
19_S23_D0.492311.354
19_S261_H0.489811.347
67_A71_R0.489431.346
121_L170_I0.489161.345
29_F269_Y0.48251.327
118_A126_L0.480321.321
18_R44_V0.47081.295
30_I51_D0.468911.289
99_I153_N0.467631.286
186_L191_I0.464111.276
13_H36_S0.463361.274
121_L171_V0.46271.272
19_S22_L0.462431.272
22_L26_R0.457571.258
280_G283_S0.457411.258
274_G277_V0.452681.245
129_I178_F0.451281.241
267_A277_V0.450591.239
176_S197_K0.448111.232
24_L29_F0.442321.216
32_Y76_L0.4421.215
114_P130_L0.43831.205
121_L174_A0.435771.198
192_D273_K0.434071.194
158_S176_S0.43361.192
98_F101_S0.43141.186
158_S173_S0.429151.180
45_E54_P0.427251.175
14_D204_G0.425811.171
100_P179_F0.425221.169
138_L145_Q0.423821.165
265_F269_Y0.42381.165
266_D270_G0.421431.159
64_S67_A0.417151.147
256_S259_E0.406611.118
57_L64_S0.403381.109
35_V41_E0.401131.103
118_A130_L0.400091.100
25_E52_I0.395721.088
24_L268_L0.394941.086
7_V93_L0.392571.080
42_K46_S0.391961.078
55_L68_S0.390751.075
257_L261_H0.390181.073
62_P114_P0.388911.069
32_Y53_R0.386751.064
100_P152_F0.386321.062
149_I192_D0.385341.060
59_D128_P0.377861.039
157_S169_S0.376211.035
110_E136_L0.37451.030
129_I174_A0.374391.030
98_F131_T0.374381.030
154_P195_Q0.373011.026
21_A33_V0.372651.025
151_L179_F0.370791.020
108_P111_T0.370441.019
128_P132_I0.369341.016
100_P132_I0.363741.000
161_N180_T0.362910.998
166_S181_S0.362820.998
27_R265_F0.355660.978
60_S123_T0.355410.977
176_S276_V0.354180.974
32_Y55_L0.353540.972
53_R76_L0.353470.972
99_I102_L0.352880.970
63_S66_H0.352110.968
202_D256_S0.351930.968
67_A70_S0.350490.964
120_E171_V0.348350.958
7_V34_T0.347640.956
173_S176_S0.345790.951
116_S119_D0.34540.950
135_L139_L0.340880.937
125_L170_I0.340160.935
105_P116_S0.340060.935
159_S197_K0.339840.935
166_S185_E0.337420.928
59_D131_T0.334580.920
8_I24_L0.334470.920
115_S119_D0.3330.916
60_S119_D0.332180.913
41_E54_P0.330450.909
132_I182_L0.329920.907
18_R47_E0.329760.907
34_T65_I0.329730.907
20_L261_H0.329610.906
148_K153_N0.327820.901
180_T275_S0.323950.891
63_S67_A0.322690.887
20_L24_L0.322380.887
196_I264_V0.32050.881
93_L135_L0.317230.872
104_Y120_E0.316530.870
39_E42_K0.315780.868
161_N173_S0.315710.868
159_S278_Y0.312490.859
151_L268_L0.310740.854
115_S118_A0.308230.848
263_A279_V0.304290.837
139_L148_K0.303710.835
161_N177_S0.303560.835
5_V32_Y0.303350.834
36_S58_D0.303130.834
183_R275_S0.30240.832
7_V68_S0.300890.827
139_L145_Q0.300530.826
64_S68_S0.299810.824
62_P133_Q0.299150.823
72_F77_S0.297180.817
69_L134_G0.297040.817
15_P203_I0.296740.816
194_T277_V0.296570.816
43_Y46_S0.294840.811
55_L71_R0.293240.806
155_S168_E0.292530.804
130_L134_G0.291430.801
258_R262_N0.290740.800
93_L139_L0.290190.798
196_I267_A0.290010.797
180_T276_V0.289180.795
7_V72_F0.287950.792
69_L98_F0.287760.791
145_Q148_K0.285780.786
182_L193_V0.28520.784
23_D261_H0.285150.784
65_I130_L0.28490.783
176_S195_Q0.28390.781
132_I150_I0.283630.780
56_W64_S0.281740.775
23_D258_R0.280970.773
261_H265_F0.280120.770
104_Y123_T0.279540.769
65_I131_T0.278170.765
123_T127_T0.276850.761
4_E94_K0.276840.761
34_T55_L0.276560.761
6_V97_I0.276050.759
169_S173_S0.276020.759
112_I167_P0.275810.758
33_V54_P0.275140.757
135_L138_L0.274530.755
169_S181_S0.27350.752
33_V41_E0.273490.752
129_I167_P0.273480.752
59_D102_L0.272370.749
65_I134_G0.271550.747
98_F139_L0.269280.740
148_K152_F0.268670.739
43_Y47_E0.268530.738
100_P103_S0.266880.734
153_N264_V0.266840.734
147_S151_L0.265570.730
72_F76_L0.263410.724
104_Y205_N0.26310.723
16_L20_L0.263040.723
4_E147_S0.262910.723
25_E48_D0.26210.721
201_L255_S0.261570.719
155_S172_S0.25910.712
153_N196_I0.258330.710
260_L264_V0.258120.710
94_K145_Q0.257430.708
35_V56_W0.256980.707
73_A76_L0.256470.705
140_R189_H0.256250.705
8_I20_L0.255220.702
154_P197_K0.254610.700
99_I103_S0.253490.697
259_E263_A0.248780.684
128_P131_T0.247060.679
16_L153_N0.246610.678
45_E52_I0.246250.677
62_P118_A0.245870.676
6_V99_I0.244870.673
22_L48_D0.244030.671
57_L65_I0.243860.671
35_V54_P0.243720.670
195_Q276_V0.243660.670
136_L140_R0.242820.668
22_L25_E0.240520.661
40_D43_Y0.23940.658
141_S145_Q0.239390.658
98_F102_L0.239020.657
200_N206_F0.238170.655
59_D127_T0.23790.654
25_E31_V0.236370.650
186_L193_V0.235310.647
34_T64_S0.233540.642
133_Q136_L0.232640.640
29_F265_F0.232440.639
180_T183_R0.232310.639
161_N181_S0.231230.636
98_F150_I0.231070.635
29_F94_K0.229590.631
134_G137_P0.229120.630
21_A31_V0.229010.630
124_R172_S0.228370.628
9_A168_E0.227170.625
31_V52_I0.22650.623
55_L75_L0.226130.622
138_L141_S0.225640.620
230_R234_G0.22560.620
133_Q178_F0.225560.620
14_D18_R0.225160.619
126_L130_L0.225150.619
114_P118_A0.224880.618
168_E171_V0.224040.616
24_L31_V0.224020.616
8_I99_I0.222850.613
173_S180_T0.222840.613
8_I31_V0.222680.612
112_I117_W0.22230.611
109_I133_Q0.221790.610
40_D204_G0.221640.609
197_K276_V0.219930.605
119_D122_N0.219870.605
183_R187_R0.218480.601
73_A77_S0.217810.599
199_G280_G0.217490.598
139_L191_I0.217310.598
104_Y119_D0.216540.595
30_I50_P0.216040.594
7_V131_T0.215650.593
165_H184_R0.215560.593
20_L99_I0.215260.592
149_I153_N0.213580.587
281_R284_R0.213110.586
198_L260_L0.213020.586
33_V48_D0.211770.582
174_A177_S0.211670.582
275_S278_Y0.21060.579
155_S198_L0.21020.578
113_S133_Q0.209540.576
201_L260_L0.209010.575
149_I268_L0.208870.574
147_S190_N0.208840.574
130_L133_Q0.208320.573
186_L189_H0.205230.564
65_I127_T0.204860.563
20_L265_F0.20460.563
25_E51_D0.204530.562
109_I129_I0.204390.562
161_N169_S0.203990.561
154_P175_L0.203970.561
117_W129_I0.203960.561
140_R191_I0.20380.560
169_S177_S0.203630.560
44_V48_D0.203610.560
278_Y283_S0.203240.559
72_F75_L0.202720.557
7_V135_L0.202460.557
124_R168_E0.202360.556
162_P165_H0.201510.554
14_D37_S0.200010.550
137_P140_R0.20.550
5_V94_K0.199980.550
157_S165_H0.199880.550
9_A172_S0.199770.549
203_I257_L0.199690.549
126_L174_A0.199580.549
6_V268_L0.199480.549
194_T267_A0.199090.547
29_F97_I0.19890.547
60_S122_N0.198850.547
200_N282_G0.198430.546
184_R187_R0.198290.545
46_S50_P0.197850.544
273_K277_V0.197520.543
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
4fgsA0.81271000.259
4ag3A0.7961000.267
4g81D0.80941000.269
4iuyA0.80941000.275
4gkbA0.83281000.292
4iqgC0.79931000.299
3gedA0.80941000.303
4h15A0.82271000.305
4hp8A0.7861000.307
3u49A0.84281000.31

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