GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4480 - Domain of unknown function (DUF4480)
Pfam: PF13715 (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: CL0287
Length: 88
Sequences: 12639
Seq/Len: 143.62
HH_delta: -0.018 (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
4_G37_F2.868773.221
32_D36_R2.752163.090
5_K36_R2.515172.824
23_K49_K2.500352.808
50_I74_I2.306622.590
49_K59_T2.184692.453
23_K59_T2.130862.393
47_T59_T2.066012.320
56_E79_K1.864642.094
56_E77_E1.804452.026
7_V75_Y1.797252.018
49_K57_T1.775671.994
7_V73_N1.655851.859
23_K47_T1.613331.812
37_F73_N1.505331.690
21_Y49_K1.375381.544
12_G75_Y1.353471.520
1_T38_S1.326391.489
15_L18_A1.323041.486
3_S38_S1.322721.485
18_A50_I1.311481.473
47_T61_T1.275841.433
1_T40_K1.252631.407
18_A52_Y1.249251.403
22_L27_K1.249071.403
5_K73_N1.21451.364
16_P33_E1.2011.349
58_K77_E1.170911.315
9_S78_P1.112131.249
15_L52_Y1.090551.225
19_T28_G1.063611.194
29_T39_I1.052491.182
22_L41_L1.044431.173
3_S36_R1.024691.151
10_D78_P1.022151.148
51_S57_T1.018811.144
44_G64_V0.999521.122
9_S77_E0.994921.117
37_F50_I0.970571.090
45_D61_T0.964781.083
58_K74_I0.960811.079
22_L39_I0.94971.066
3_S71_N0.944711.061
22_L45_D0.943521.059
18_A31_T0.913411.026
7_V12_G0.911711.024
13_E16_P0.862820.969
19_T51_S0.851480.956
9_S75_Y0.819290.920
60_I74_I0.814550.915
65_N70_T0.802950.902
55_Y78_P0.795790.894
42_P45_D0.754330.847
45_D63_S0.743680.835
21_Y51_S0.740620.832
21_Y28_G0.740580.832
2_I72_L0.727690.817
41_L44_G0.727550.817
5_K14_P0.708840.796
17_G30_V0.708570.796
13_E33_E0.702270.789
10_D13_E0.690660.776
79_K82_Q0.689290.774
32_D35_G0.686510.771
62_I72_L0.68390.768
82_Q85_E0.678860.762
6_V31_T0.673690.756
16_P30_V0.671910.754
60_I64_V0.669190.751
64_V70_T0.654980.735
84_D87_V0.649330.729
37_F72_L0.639520.718
60_I72_L0.639330.718
19_T30_V0.636060.714
83_L86_V0.634540.712
55_Y76_L0.632660.710
6_V18_A0.629720.707
36_R71_N0.586670.659
41_L45_D0.575280.646
31_T35_G0.563620.633
17_G52_Y0.558320.627
15_L76_L0.557240.626
15_L55_Y0.556990.625
28_G53_I0.540160.607
81_N85_E0.537350.603
37_F71_N0.535330.601
22_L42_P0.532750.598
61_T64_V0.530520.596
4_G20_V0.525960.591
27_K42_P0.525380.590
8_D15_L0.511260.574
52_Y55_Y0.50660.569
56_E81_N0.506050.568
16_P52_Y0.495460.556
17_G33_E0.492380.553
20_V31_T0.491680.552
6_V50_I0.466720.524
27_K41_L0.464220.521
2_I62_I0.454060.510
60_I65_N0.446430.501
81_N88_V0.44480.499
4_G29_T0.444150.499
2_I48_L0.443030.497
50_I58_K0.438040.492
83_L88_V0.436670.490
53_I83_L0.434750.488
17_G28_G0.432990.486
43_E64_V0.429140.482
45_D64_V0.427350.480
22_L25_T0.42590.478
58_K76_L0.423420.475
21_Y26_K0.422080.474
8_D12_G0.420470.472
62_I65_N0.417280.469
8_D55_Y0.416290.467
19_T53_I0.414230.465
24_N47_T0.400630.450
79_K83_L0.393460.442
44_G63_S0.392280.440
20_V29_T0.386430.434
63_S71_N0.385940.433
20_V37_F0.371720.417
25_T45_D0.370930.416
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
3mn8A0.988698.9-0.018
2nsmA0.977398.8-0.008
1uwyA0.988698.8-0.008
1h8lA0.897798.50.101
1nkgA0.909194.80.525
3kcpA0.943290.50.588
2xsuA0.988690.40.589
3e8vA0.840984.30.627
2boyA0.943282.30.636
3g3lA0.931876.30.655

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