GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF938 - Protein of unknown function (DUF938)
Pfam: PF06080 (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: 204
Sequences: 17901
Seq/Len: 87.75
HH_delta: 0.151 (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
128_A185_L2.014993.603
131_L135_G1.691013.024
34_S54_P1.685343.014
53_Q103_F1.679163.003
30_L103_F1.477522.642
121_E182_A1.421592.542
126_G129_R1.36482.441
104_D132_K1.292622.311
40_A52_W1.251412.238
127_A137_L1.139252.037
59_D82_A1.099641.966
29_V105_A1.097611.963
59_D63_P1.064231.903
106_I131_L1.058141.892
33_A111_M1.05461.886
125_A183_H1.051691.881
106_I127_A0.966431.728
45_Q72_A0.936571.675
119_A122_G0.924731.654
121_E125_A0.92231.649
178_A182_A0.920371.646
58_D61_L0.912841.632
121_E183_H0.900211.610
121_E179_L0.900171.610
84_D87_A0.892441.596
53_Q81_L0.891811.595
40_A54_P0.888441.589
64_S67_A0.884071.581
23_P26_G0.882731.579
124_F180_A0.862761.543
63_P66_R0.862541.542
62_R66_R0.845731.512
29_V43_F0.836551.496
41_V45_Q0.83451.492
126_G130_L0.833921.491
177_E190_D0.827711.480
128_A183_H0.818951.464
62_R82_A0.814391.456
55_S83_L0.814171.456
100_P129_R0.805661.441
41_V68_W0.794691.421
177_E181_A0.791441.415
108_C111_M0.787491.408
172_D175_D0.785991.406
173_I177_E0.785441.405
178_A181_A0.768921.375
30_L106_I0.760091.359
56_D62_R0.754321.349
65_I80_P0.747831.337
113_H141_G0.740541.324
41_V69_I0.737331.319
42_Y45_Q0.732791.310
131_L137_L0.728781.303
26_G105_A0.72281.293
31_E34_S0.71561.280
67_A71_E0.714571.278
122_G125_A0.713921.277
110_N113_H0.71011.270
57_P84_D0.707691.266
32_I127_A0.704911.261
47_L50_L0.693071.239
66_R70_A0.688351.231
60_N63_P0.676661.210
108_C137_L0.674921.207
30_L55_S0.663121.186
105_A136_L0.652231.166
131_L185_L0.649661.162
62_R80_P0.649141.161
102_S132_K0.647511.158
125_A129_R0.636291.138
29_V107_F0.62761.122
124_F183_H0.622691.114
120_V179_L0.615381.100
39_H107_F0.614611.099
34_S65_I0.595151.064
54_P65_I0.593321.061
116_P119_A0.591251.057
173_I190_D0.586361.049
175_D178_A0.586071.048
110_N140_Y0.567971.016
83_L88_P0.567851.015
42_Y46_A0.567751.015
122_G126_G0.548560.981
56_D61_L0.546010.976
44_A52_W0.54060.967
31_E39_H0.531040.950
108_C127_A0.530890.949
51_T78_R0.522860.935
108_C123_L0.521590.933
67_A70_A0.520490.931
63_P67_A0.516930.924
32_I85_V0.516620.924
110_N114_I0.515310.921
106_I130_L0.510950.914
33_A108_C0.509860.912
34_S40_A0.506150.905
174_E178_A0.499820.894
115_S123_L0.498680.892
39_H43_F0.49690.889
68_W71_E0.489510.875
41_V44_A0.485980.869
175_D179_L0.485470.868
30_L130_L0.484930.867
64_S68_W0.483890.865
112_L124_F0.478730.856
177_E187_L0.478080.855
55_S81_L0.474130.848
40_A44_A0.473960.848
41_V72_A0.471210.843
129_R132_K0.467480.836
83_L87_A0.465720.833
106_I135_G0.459150.821
70_A75_P0.457080.817
39_H109_I0.450390.805
105_A138_F0.447250.800
34_S56_D0.44460.795
26_G104_D0.440870.788
159_A163_S0.439240.785
112_L141_G0.439030.785
66_R69_I0.43740.782
31_E52_W0.437350.782
180_A187_L0.43680.781
44_A77_V0.434990.778
176_V180_A0.431660.772
31_E107_F0.431220.771
68_W72_A0.42960.768
179_L182_A0.428320.766
111_M115_S0.424750.760
187_L190_D0.423480.757
31_E37_G0.421470.754
128_A131_L0.417570.747
100_P126_G0.416520.745
136_L188_E0.41650.745
111_M114_I0.416150.744
174_E177_E0.414530.741
160_S163_S0.414390.741
29_V52_W0.414250.741
36_T64_S0.414240.741
108_C139_L0.411980.737
54_P80_P0.411650.736
155_A159_A0.410260.734
135_G185_L0.407180.728
60_N64_S0.405660.725
85_V111_M0.403810.722
34_S62_R0.40210.719
137_L185_L0.401740.718
61_L110_N0.40160.718
171_R175_D0.400850.717
110_N141_G0.400740.717
36_T68_W0.398890.713
179_L183_H0.397830.711
102_S130_L0.396720.709
112_L139_L0.389170.696
109_I140_Y0.388310.694
22_L105_A0.386770.692
43_F107_F0.384030.687
151_S154_N0.382480.684
36_T61_L0.380540.680
88_P126_G0.378650.677
120_V171_R0.378520.677
123_L127_A0.377020.674
80_P83_L0.376440.673
124_F128_A0.375520.672
22_L26_G0.373390.668
70_A73_G0.370410.662
125_A128_A0.36920.660
26_G50_L0.36770.658
113_H116_P0.36660.656
34_S80_P0.366390.655
69_I80_P0.366190.655
85_V88_P0.366050.655
155_A158_D0.361030.646
69_I74_L0.356390.637
125_A182_A0.3520.629
180_A183_H0.351720.629
124_F179_L0.35120.628
154_N158_D0.350170.626
156_A159_A0.347470.621
86_S119_A0.346950.620
69_I73_G0.342720.613
181_A187_L0.34260.613
113_H142_P0.342130.612
55_S88_P0.339820.608
86_S122_G0.336120.601
86_S115_S0.334390.598
22_L25_S0.33240.594
151_S155_A0.331430.593
36_T110_N0.331190.592
73_G76_N0.329460.589
158_D162_R0.328840.588
180_A185_L0.327590.586
157_F161_L0.326450.584
153_S156_A0.325970.583
62_R65_I0.324490.580
57_P62_R0.323890.579
40_A107_F0.321140.574
103_F130_L0.320010.572
150_T153_S0.318690.570
180_A188_E0.317940.569
111_M123_L0.316350.566
167_E171_R0.315720.565
177_E188_E0.314530.562
109_I138_F0.313630.561
110_N142_P0.313120.560
114_I141_G0.312480.559
112_L123_L0.310920.556
128_A184_G0.307230.549
168_W171_R0.307210.549
102_S129_R0.306780.549
44_A47_L0.305850.547
31_E40_A0.304990.545
181_A186_E0.30390.543
88_P130_L0.303270.542
185_L188_E0.302440.541
38_Q42_Y0.3010.538
41_V74_L0.300650.538
36_T39_H0.300590.538
162_R165_D0.299760.536
44_A74_L0.298580.534
152_E156_A0.296790.531
153_S159_A0.296470.530
154_N161_L0.296280.530
159_A162_R0.295110.528
57_P82_A0.294820.527
56_D80_P0.293730.525
100_P130_L0.293480.525
186_E189_E0.293310.525
152_E155_A0.291910.522
129_R133_P0.291610.521
87_A122_G0.290730.520
65_I68_W0.290330.519
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
4gekA0.946199.90.151
3mczA0.95199.90.201
2r3sA0.95199.90.206
3i53A0.916799.90.211
3gwzA0.931499.90.215
3dlcA0.946199.90.222
4a6dA0.936399.80.23
3dp7A0.95199.80.235
2ip2A0.926599.80.236
1x19A0.931499.80.24

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