GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Bromodomain - Bromodomain
Pfam: PF00439 (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. )
Length: 84
Sequences: 3232
Seq/Len: 38.48
HH_delta: -0.053 (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
28_D71_Y1.432783.272
38_D41_T1.400693.199
51_Y60_D1.359433.104
45_K50_K1.241592.835
23_P30_Y0.899572.054
73_P79_Y0.865951.978
9_M43_R0.827641.890
42_I61_V0.798461.823
9_M18_S0.797541.821
37_M64_I0.780561.783
58_E62_R0.766631.751
35_N63_L0.759891.735
69_R79_Y0.756281.727
5_L57_F0.738541.687
52_K56_E0.699791.598
76_S79_Y0.683621.561
45_K60_D0.667471.524
20_P38_D0.657881.502
22_D26_Y0.651621.488
22_D25_E0.648021.480
14_S18_S0.62441.426
35_N59_A0.615291.405
68_A72_N0.570951.304
19_K40_S0.570651.303
29_Y33_I0.564381.289
39_L64_I0.561051.281
16_P81_A0.550341.257
66_Q70_R0.535611.223
69_R82_A0.533851.219
73_P76_S0.532321.216
33_I70_R0.531471.214
8_L61_V0.517891.183
55_E59_A0.497011.135
42_I64_I0.473051.080
61_V65_F0.471371.076
37_M60_D0.469431.072
72_N78_I0.469351.072
29_Y71_Y0.451361.031
75_D80_K0.448421.024
53_S56_E0.447191.021
57_F61_V0.446271.019
77_P80_K0.439661.004
16_P78_I0.434780.993
68_A82_A0.424340.969
68_A79_Y0.423970.968
43_R47_E0.422640.965
20_P41_T0.406670.929
68_A78_I0.403880.922
37_M63_L0.391260.894
29_Y67_N0.379760.867
6_E43_R0.371140.848
13_I81_A0.370830.847
15_S19_K0.361530.826
63_L66_Q0.359860.822
21_V29_Y0.357160.816
45_K51_Y0.355660.812
44_K48_N0.353970.808
11_H15_S0.348390.796
26_Y72_N0.341610.780
77_P81_A0.33690.769
78_I82_A0.332330.759
26_Y71_Y0.325040.742
67_N72_N0.323240.738
74_P79_Y0.323230.738
79_Y82_A0.322880.737
11_H14_S0.319960.731
59_A62_R0.316090.722
59_A63_L0.31220.713
42_I45_K0.311640.712
37_M41_T0.310670.709
33_I36_P0.30740.702
40_S44_K0.302230.690
28_D31_E0.2980.681
40_S64_I0.297880.680
67_N71_Y0.296520.677
34_K70_R0.29530.674
69_R74_P0.290670.664
32_I70_R0.29040.663
42_I65_F0.289630.661
42_I46_L0.288640.659
23_P27_P0.287090.656
21_V72_N0.286540.654
5_L42_I0.285590.652
5_L46_L0.28440.649
65_F69_R0.281830.644
7_E10_K0.281520.643
54_I58_E0.280450.640
23_P26_Y0.275360.629
27_P71_Y0.274190.626
17_F72_N0.274050.626
23_P28_D0.273560.625
30_Y36_P0.26680.609
62_R66_Q0.265720.607
21_V26_Y0.262220.599
21_V71_Y0.261860.598
48_N52_K0.260570.595
7_E31_E0.254370.581
22_D27_P0.253380.579
7_E74_P0.251610.575
7_E11_H0.250770.573
19_K77_P0.247250.565
29_Y68_A0.245910.562
31_E34_K0.244450.558
33_I67_N0.243180.555
6_E10_K0.241580.552
22_D30_Y0.240820.550
6_E9_M0.238530.545
63_L67_N0.238440.545
26_Y30_Y0.238110.544
45_K56_E0.237620.543
73_P78_I0.237250.542
17_F29_Y0.236910.541
49_G52_K0.236670.540
28_D32_I0.236060.539
65_F81_A0.235730.538
17_F68_A0.235360.537
26_Y78_I0.234010.534
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
4ir5A199.8-0.053
1e6iA199.8-0.051
2i7kA199.8-0.05
2d9eA199.8-0.05
3g0lA199.8-0.047
3d7cA199.8-0.047
3fkmX199.8-0.041
3rcwA199.8-0.041
3uv5A199.8-0.038
3nxbA199.8-0.038

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