GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HD_5 - HD domain
Pfam: PF13487 (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: 64
Sequences: 4656
Seq/Len: 72.75
HH_delta: 0.11 (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
38_Q58_P2.584983.636
8_R12_Q2.19853.093
19_A37_L1.730072.434
38_Q50_R1.61532.272
38_Q61_A1.576392.218
35_I60_G1.573072.213
37_L50_R1.520912.139
13_Q17_Y1.484142.088
43_W62_R1.466392.063
14_H40_H1.462742.058
10_I13_Q1.452182.043
22_L36_I1.345941.893
19_A33_A1.338081.882
42_R46_S1.258611.770
9_E12_Q1.17431.652
34_D38_Q1.041171.465
16_E20_E1.035061.456
13_Q16_E1.00831.418
35_I64_L1.00351.412
19_A23_S0.923451.299
8_R11_I0.904581.272
3_L11_I0.888941.250
17_Y20_E0.846141.190
18_G36_I0.835861.176
11_I48_Y0.826031.162
53_K56_E0.818141.151
14_H39_H0.77991.097
2_K8_R0.767731.080
34_D60_G0.765281.077
38_Q52_L0.74861.053
16_E50_R0.720061.013
41_E51_G0.702590.988
41_E47_G0.701550.987
20_E23_S0.696510.980
43_W54_G0.658440.926
23_S33_A0.630260.887
16_E37_L0.616390.867
54_G62_R0.601830.847
5_P9_E0.598430.842
19_A50_R0.594050.836
31_E60_G0.591770.832
41_E45_G0.591270.832
36_I64_L0.589430.829
28_L32_V0.586250.825
57_I61_A0.555290.781
59_L63_I0.543490.765
29_S32_V0.537880.757
41_E52_L0.529660.745
58_P61_A0.521470.734
43_W57_I0.520420.732
18_G39_H0.518670.730
4_T7_E0.513850.723
27_R32_V0.512140.720
14_H48_Y0.511250.719
9_E13_Q0.511140.719
6_E9_E0.508380.715
3_L7_E0.498170.701
52_L56_E0.486740.685
5_P8_R0.478420.673
34_D58_P0.47840.673
35_I61_A0.476210.670
15_P36_I0.475980.670
53_K57_I0.46870.659
22_L33_A0.457380.643
44_D47_G0.45130.635
31_E34_D0.447330.629
31_E36_I0.444370.625
43_W55_D0.415660.585
43_W58_P0.415140.584
32_V35_I0.413340.581
26_P29_S0.411580.579
32_V64_L0.406940.572
25_I31_E0.402140.566
1_G11_I0.398730.561
45_G49_P0.391570.551
12_Q48_Y0.389680.548
40_H48_Y0.385930.543
4_T8_R0.382260.538
15_P18_G0.377070.530
41_E49_P0.374190.526
19_A34_D0.372430.524
7_E10_I0.368490.518
43_W46_S0.358890.505
60_G64_L0.356210.501
28_L31_E0.354220.498
15_P19_A0.33780.475
22_L25_I0.336020.473
18_G37_L0.335080.471
46_S51_G0.329090.463
21_L25_I0.327930.461
18_G40_H0.324060.456
7_E11_I0.319990.450
3_L8_R0.319710.450
43_W61_A0.315370.444
2_K11_I0.314170.442
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
3tm8A0.968899.50.11
3hc1A0.859498.30.468
1vqrA0.859497.90.53
2ogiA0.828197.60.572
2o08A0.828197.50.577
3ccgA0.828197.50.579
3ljxA0.87596.90.629
3m1tA0.937596.70.639
3i7aA0.843896.20.659
3memA0.937595.90.668

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