GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Bin3 - Bicoid-interacting protein 3 (Bin3)
Pfam: PF06859 (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: 110
Sequences: 14955
Seq/Len: 135.95
HH_delta: 0.175 (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
31_Y85_F2.44883.361
34_L38_G1.9862.726
29_R32_S1.937882.660
30_I40_L1.912592.625
24_K80_E1.723662.366
3_D35_R1.658612.276
5_I30_I1.647442.261
29_R33_L1.584522.175
28_R81_P1.474982.024
75_E79_L1.467752.014
24_K81_P1.437471.973
7_C10_V1.404291.927
24_K77_Y1.403461.926
22_G25_R1.360811.868
5_I34_L1.339521.838
23_L77_Y1.207431.657
70_R73_Q1.168681.604
27_F78_L1.145391.572
34_L85_F1.139051.563
76_D80_E1.099171.509
24_K28_R1.056521.450
9_S15_H1.045891.435
34_L40_L1.034171.419
75_E90_E0.993981.364
4_V39_I0.974941.338
31_Y81_P0.972261.334
1_Q35_R0.938141.288
81_P84_G0.937361.286
17_N26_F0.892061.224
25_R29_R0.873411.199
25_R28_R0.847161.163
23_L69_L0.820241.126
9_S16_L0.796141.093
7_C30_I0.792181.087
76_D79_L0.789841.084
10_V17_N0.77561.064
26_F30_I0.773541.062
73_Q76_D0.764841.050
14_I17_N0.747091.025
28_R32_S0.743671.021
2_Y33_L0.73181.004
7_C26_F0.709860.974
10_V15_H0.707230.971
57_S61_R0.703820.966
39_I88_V0.702990.965
87_S90_E0.701210.962
1_Q33_L0.697950.958
7_C40_L0.69770.958
71_P92_G0.682110.936
42_L78_L0.680290.934
40_L85_F0.676860.929
5_I38_G0.669390.919
75_E87_S0.647770.889
5_I33_L0.646450.887
77_Y81_P0.643510.883
73_Q77_Y0.64190.881
77_Y80_E0.638270.876
71_P90_E0.634130.870
78_L81_P0.618450.849
28_R31_Y0.61190.840
14_I27_F0.607750.834
27_F81_P0.605180.831
4_V41_I0.599150.822
31_Y84_G0.592540.813
30_I34_L0.574180.788
71_P75_E0.566640.778
7_C42_L0.560930.770
69_L73_Q0.551190.756
8_L15_H0.548050.752
54_K58_E0.539340.740
15_H43_E0.535280.735
55_R59_E0.530830.729
8_L16_L0.522350.717
44_P48_K0.518430.712
15_H44_P0.517830.711
32_S36_P0.516550.709
52_K55_R0.513490.705
7_C17_N0.510190.700
50_Y53_A0.509670.700
27_F74_F0.508820.698
50_Y54_K0.508270.698
28_R80_E0.503420.691
2_Y5_I0.496940.682
86_S89_E0.496540.681
14_I26_F0.488660.671
32_S35_R0.486250.667
78_L87_S0.485690.667
69_L74_F0.482480.662
44_P47_W0.469920.645
79_L88_V0.466680.640
56_L59_E0.464530.638
27_F77_Y0.459220.630
10_V16_L0.456480.627
23_L26_F0.455940.626
55_R58_E0.452610.621
49_S52_K0.449630.617
10_V26_F0.440980.605
14_I42_L0.439810.604
15_H42_L0.437310.600
63_N66_S0.436530.599
72_D90_E0.435870.598
75_E88_V0.430080.590
27_F40_L0.429920.590
74_F78_L0.429730.590
52_K56_L0.428880.589
1_Q32_S0.425510.584
40_L78_L0.424330.582
55_R60_I0.423770.582
53_A58_E0.423710.582
9_S17_N0.422470.580
6_L9_S0.42170.579
79_L84_G0.416680.572
26_F40_L0.413460.567
6_L41_I0.407760.560
8_L41_I0.407710.560
43_E46_P0.407080.559
9_S66_S0.405760.557
80_E84_G0.397940.546
72_D75_E0.392450.539
72_D76_D0.389920.535
31_Y36_P0.38750.532
15_H65_K0.38480.528
47_W50_Y0.384680.528
79_L87_S0.384660.528
9_S43_E0.38270.525
35_R38_G0.38270.525
61_R64_Y0.381230.523
59_E62_E0.373770.513
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
3g07A0.981899.30.175
4e2xA0.881898.90.336
3ujcA0.945598.80.342
2o57A0.927398.80.35
2g72A0.998.80.357
3pfgA0.998.80.358
3l8dA0.927398.80.363
1y8cA0.954598.80.364
1nkvA0.927398.80.364
3dp7A0.998.80.364

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