GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Mad3_BUB1_I - Mad3BUB1 homology region 1
Pfam: PF08311 (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: 126
Sequences: 29179
Seq/Len: 231.58
HH_delta: -0.032 (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
114_N117_K3.616652.614
41_K44_G3.576362.585
102_Y121_I3.498962.529
25_W48_L3.281932.372
29_I49_L3.25632.354
105_W121_I2.992352.163
87_K105_W2.940922.126
28_Y48_L2.922812.113
9_E28_Y2.784572.013
106_A122_Y2.746361.985
72_W85_I2.740981.981
32_I44_G2.627651.899
75_Y85_I2.513061.816
8_F27_R2.493171.802
109_L121_I2.398271.734
109_L117_K2.333081.686
46_L50_E2.255861.631
86_F104_E2.18681.581
50_E75_Y2.149521.554
32_I48_L2.071851.498
83_R87_K2.040281.475
5_R9_E2.028821.466
76_A86_F1.95021.410
83_R109_L1.923471.390
5_R35_N1.911381.382
21_P24_P1.902391.375
83_R112_R1.899841.373
89_L101_F1.814821.312
98_L101_F1.763771.275
90_Y102_Y1.717621.242
119_D123_Q1.711691.237
109_L114_N1.70641.233
105_W109_L1.680391.215
5_R32_I1.680311.215
11_Q24_P1.674161.210
75_Y79_S1.603821.159
83_R105_W1.586851.147
56_F59_D1.581111.143
25_W51_R1.572571.137
102_Y124_L1.566471.132
12_I25_W1.558011.126
83_R108_F1.551481.121
28_Y32_I1.532921.108
22_L56_F1.514181.094
49_L74_K1.502391.086
88_F91_S1.49321.079
51_R54_R1.485171.074
79_S85_I1.480251.070
35_N41_K1.47931.069
32_I41_K1.474721.066
12_I24_P1.462741.057
51_R55_K1.462091.057
22_L52_C1.411451.020
59_D71_I1.403281.014
110_E122_Y1.38391.000
25_W52_C1.370490.991
103_E107_E1.368440.989
15_Y21_P1.367330.988
10_E14_S1.364440.986
11_Q14_S1.340.969
52_C71_I1.338330.967
26_L30_K1.333760.964
90_Y101_F1.312960.949
102_Y125_G1.306720.945
117_K120_E1.302530.941
5_R31_W1.298360.938
44_G47_E1.27220.920
10_E13_R1.271050.919
108_F112_R1.25480.907
46_L78_L1.250010.904
107_E110_E1.244080.899
15_Y20_D1.185860.857
53_I72_W1.185670.857
73_I104_E1.184010.856
53_I71_I1.181750.854
31_W35_N1.17310.848
30_K34_E1.170040.846
46_L75_Y1.133630.819
104_E107_E1.13310.819
106_A118_A1.1240.812
5_R28_Y1.122160.811
107_E111_K1.119590.809
46_L79_S1.117860.808
42_Q78_L1.105410.799
80_S111_K1.102330.797
72_W88_F1.088440.787
77_D104_E1.087830.786
77_D80_S1.08760.786
25_W55_K1.086190.785
73_I101_F1.085630.785
110_E115_F1.07850.780
74_K77_D1.078440.780
99_A125_G1.068740.773
81_D84_E1.065850.770
30_K33_E1.057340.764
73_I77_D1.031260.745
85_I88_F1.029570.744
7_E11_Q1.024090.740
7_E10_E1.021710.739
4_Q31_W1.019770.737
3_Q7_E1.006840.728
9_E48_L1.003170.725
6_Q10_E1.000940.723
72_W89_L0.995710.720
106_A125_G0.992120.717
29_I52_C0.99180.717
26_L74_K0.989740.715
29_I45_L0.984580.712
27_R30_K0.978950.708
26_L59_D0.973140.703
115_F119_D0.970960.702
30_K74_K0.962140.695
33_E45_L0.961620.695
33_E78_L0.959810.694
5_R41_K0.955190.690
48_L51_R0.948680.686
3_Q6_Q0.947980.685
80_S104_E0.941260.680
22_L59_D0.938250.678
76_A79_S0.934550.676
82_P108_F0.92320.667
83_R114_N0.913590.660
121_I124_L0.900520.651
109_L112_R0.898390.649
8_F31_W0.891630.644
59_D70_K0.877980.635
87_K121_I0.876920.634
33_E42_Q0.876050.633
90_Y105_W0.869870.629
47_E51_R0.868570.628
84_E88_F0.865740.626
42_Q46_L0.862970.624
50_E85_I0.851850.616
87_K109_L0.846610.612
86_F108_F0.846260.612
9_E44_G0.838530.606
94_I98_L0.8380.606
80_S108_F0.827360.598
4_Q11_Q0.825710.597
33_E74_K0.821690.594
107_E122_Y0.819010.592
33_E49_L0.817640.591
81_D85_I0.815170.589
52_C55_K0.813350.588
45_L49_L0.809710.585
110_E118_A0.805710.582
4_Q8_F0.801860.580
103_E125_G0.784570.567
82_P86_F0.781290.565
16_E20_D0.779390.563
30_K49_L0.769310.556
95_G98_L0.763110.552
120_E124_L0.760870.550
20_D55_K0.758810.548
26_L71_I0.757180.547
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
4gywA0.857199.4-0.032
4gywA0.857199.20.03
2h6fA0.857199.20.062
2pziA0.849299.20.068
3gyzA0.857199.10.076
2pl2A0.857199.10.099
2h6fA0.8571990.123
2vsyA0.8571990.124
4abnA0.8968990.125
2pziA0.8492990.134

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