GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HD - HD domain
Pfam: PF01966 (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: CL0237
Length: 122
Sequences: 11896
Seq/Len: 97.51
HH_delta: 0.13 (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
13_E29_R2.094762.946
64_A86_R2.002152.816
87_Y107_S1.636462.302
53_R57_Y1.611652.267
7_R120_D1.611432.267
67_L85_I1.590222.237
68_K82_A1.5882.234
64_A82_A1.520152.138
17_D25_R1.483012.086
13_E25_R1.359631.912
27_L80_I1.344981.892
16_A25_R1.328571.869
16_A28_L1.29811.826
31_A84_A1.284611.807
12_A32_A1.2211.717
8_V32_A1.214951.709
9_A29_R1.202171.691
64_A68_K1.168321.643
87_Y110_A1.129081.588
83_N87_Y1.109331.560
41_P62_I1.077911.516
62_I65_E1.057961.488
55_K58_R1.042461.466
84_A109_E1.039261.462
12_A112_I0.982481.382
15_L116_A0.96531.358
59_H88_H0.961121.352
54_G57_Y0.948391.334
58_R62_I0.923081.298
4_H35_H0.901421.268
24_D109_E0.892311.255
38_G63_G0.888631.250
9_A32_A0.873511.229
13_E17_D0.870741.225
43_P55_K0.843041.186
12_A113_V0.83791.179
12_A28_L0.802631.129
58_R61_E0.802461.129
41_P66_I0.797291.121
28_L109_E0.791731.114
91_P114_K0.785261.105
5_S9_A0.779451.096
3_E7_R0.768351.081
15_L112_I0.761751.071
10_E29_R0.755671.063
61_E65_E0.749341.054
14_R18_R0.738661.039
61_E86_R0.735741.035
108_L111_R0.734611.033
84_A113_V0.731141.028
63_G85_I0.726631.022
92_W111_R0.720251.013
36_D117_D0.683560.961
8_V116_A0.675710.950
4_H36_D0.67480.949
65_E68_K0.665910.937
53_R56_F0.663820.934
11_L116_A0.659250.927
4_H117_D0.654270.920
9_A33_L0.6510.916
28_L32_A0.648130.912
60_E64_A0.63980.900
9_A13_E0.617830.869
11_L120_D0.612930.862
32_A113_V0.612270.861
83_N109_E0.609820.858
84_A110_A0.606250.853
82_A86_R0.603680.849
114_K118_R0.590590.831
107_S110_A0.587540.826
25_R29_R0.586940.826
36_D88_H0.57760.812
36_D59_H0.574030.807
5_S32_A0.568940.800
37_I63_G0.564370.794
70_F73_E0.554630.780
90_G93_N0.554220.780
31_A113_V0.546510.769
12_A16_A0.541360.761
90_G114_K0.534090.751
80_I83_N0.534040.751
24_D108_L0.532510.749
28_L113_V0.53230.749
24_D80_I0.528140.743
7_R10_E0.52760.742
106_I110_A0.525780.740
6_L33_L0.524740.738
67_L82_A0.523160.736
88_H117_D0.516920.727
38_G66_I0.514110.723
71_L74_L0.50920.716
59_H89_H0.508770.716
111_R114_K0.496050.698
16_A32_A0.495070.696
34_L67_L0.495020.696
59_H63_G0.493230.694
27_L30_I0.488340.687
83_N107_S0.487690.686
24_D27_L0.486810.685
41_P44_D0.481490.677
91_P118_R0.477490.672
3_E6_L0.474840.668
108_L112_I0.470850.662
5_S33_L0.468620.659
10_E14_R0.460730.648
14_R17_D0.460180.647
42_T62_I0.45540.641
2_F5_S0.453620.638
11_L14_R0.448330.631
30_I81_I0.448230.630
27_L81_I0.444970.626
26_E30_I0.44420.625
7_R11_L0.442530.622
11_L119_L0.441940.622
6_L10_E0.440530.620
12_A116_A0.439430.618
2_F6_L0.438170.616
59_H117_D0.434950.612
8_V33_L0.432260.608
15_L115_L0.430950.606
27_L74_L0.428880.603
56_F118_R0.426850.600
15_L19_L0.424590.597
16_A20_G0.424140.597
29_R33_L0.422160.594
19_L115_L0.421020.592
80_I109_E0.415160.584
37_I66_I0.414490.583
36_D89_H0.413660.582
26_E29_R0.410990.578
31_A109_E0.410540.577
23_E108_L0.406340.572
31_A34_L0.403560.568
66_I69_E0.401330.564
15_L18_R0.400270.563
82_A85_I0.393570.554
67_L71_L0.39140.551
16_A112_I0.391270.550
74_L80_I0.387650.545
65_E69_E0.385030.542
27_L31_A0.38440.541
10_E13_E0.379440.534
111_R115_L0.376470.530
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
3tm8A0.950899.50.13
3hc1A0.885299.20.252
2ogiA0.860799.20.283
3ccgA0.860799.20.283
2o08A0.852599.10.288
2pq7A0.827999.10.302
3djbA0.811599.10.308
3dtoA0.811599.10.309
3gw7A0.836199.10.316
3memA0.885299.10.316

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