GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
M20_dimer - Peptidase dimerisation domain
Pfam: PF07687 (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: 111
Sequences: 12524
Seq/Len: 112.83
HH_delta: 0.108 (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
12_T78_E2.372.852
12_T80_T2.301192.769
18_G26_G2.057932.477
13_I36_F1.919922.310
97_K101_E1.903992.291
10_R82_T1.899512.286
14_T78_E1.753742.110
10_R80_T1.738652.092
27_V32_A1.731252.083
33_A66_I1.646651.982
17_S77_D1.615211.944
101_E105_E1.605631.932
33_A79_A1.566691.885
33_A81_L1.553171.869
65_S82_T1.522881.833
98_A102_A1.515311.824
67_E80_T1.47171.771
34_A38_N1.434351.726
34_A37_L1.42571.716
35_R38_N1.378461.659
36_F104_V1.322131.591
31_E41_E1.316981.585
39_A103_A1.28361.545
99_E102_A1.27181.530
29_A79_A1.237381.489
16_K27_V1.233621.485
7_I93_L1.23231.483
95_E99_E1.198241.442
22_R25_K1.181681.422
92_D95_E1.17031.408
59_P96_I1.102081.326
13_I33_A1.079711.299
39_A106_K1.067931.285
9_F83_V1.042431.254
47_W99_E1.038031.249
30_I68_G1.017551.225
9_F97_K1.004071.208
95_E98_A0.971221.169
38_N42_E0.963151.159
39_A107_I0.944211.136
68_G79_A0.937761.128
13_I32_A0.924371.112
89_P92_D0.917951.105
10_R72_P0.907421.092
30_I66_I0.906751.091
39_A42_E0.902611.086
94_E98_A0.88531.065
98_A101_E0.875161.053
11_I81_L0.862841.038
72_P82_T0.85641.031
37_L81_L0.855051.029
103_A106_K0.848081.021
102_A106_K0.841511.013
8_W72_P0.828840.997
5_G87_Y0.823250.991
57_G89_P0.822820.990
71_A74_V0.813840.979
8_W84_D0.813790.979
87_Y93_L0.808550.973
30_I79_A0.798030.960
43_L99_E0.794480.956
63_I83_V0.788960.949
103_A107_I0.78680.947
66_I79_A0.777950.936
35_R39_A0.763170.918
14_T77_D0.761870.917
40_L100_I0.752030.905
7_I97_K0.749910.902
31_E34_A0.738650.889
85_I91_E0.735930.886
31_E37_L0.72740.875
90_G94_E0.722030.869
67_E70_T0.717660.864
28_N62_N0.690910.831
105_E108_A0.688140.828
11_I104_V0.680320.819
37_L63_I0.67570.813
102_A105_E0.671750.808
35_R42_E0.671380.808
13_I81_L0.63050.759
31_E42_E0.622680.749
33_A37_L0.615080.740
20_S62_N0.613120.738
32_A36_F0.607420.731
61_L85_I0.606410.730
99_E103_A0.605350.728
6_V84_D0.599380.721
35_R107_I0.596930.718
35_R41_E0.588530.708
11_I36_F0.586930.706
18_G23_P0.573710.690
94_E97_K0.571030.687
40_L61_L0.569040.685
32_A107_I0.567790.683
63_I81_L0.560730.675
93_L97_K0.560330.674
20_S60_T0.552580.665
4_R88_P0.550440.662
85_I96_I0.54970.662
47_W95_E0.545530.656
38_N41_E0.541560.652
65_S80_T0.540870.651
4_R60_T0.538230.648
13_I29_A0.526190.633
8_W82_T0.521850.628
32_A35_R0.521390.627
15_G29_A0.521260.627
62_N84_D0.513440.618
91_E95_E0.512460.617
104_V108_A0.501580.604
73_N86_R0.501540.604
87_Y92_D0.499770.601
98_A105_E0.494270.595
34_A66_I0.487810.587
67_E82_T0.484170.583
13_I108_A0.478690.576
87_Y96_I0.476310.573
7_I87_Y0.474890.571
20_S84_D0.470020.566
44_E47_W0.464950.560
36_F103_A0.46070.554
19_H86_R0.459660.553
13_I104_V0.459120.553
30_I37_L0.455960.549
11_I83_V0.448110.539
42_E45_F0.440620.530
6_V72_P0.44060.530
31_E35_R0.43990.529
29_A75_I0.438760.528
18_G75_I0.437660.527
20_S64_G0.43510.524
31_E38_N0.431040.519
44_E61_L0.431040.519
29_A76_P0.429670.517
59_P87_Y0.429060.516
91_E94_E0.425340.512
37_L83_V0.418930.504
37_L66_I0.41810.503
59_P85_I0.416180.501
31_E45_F0.414650.499
47_W102_A0.41420.498
28_N31_E0.411750.495
16_K25_K0.410370.494
34_A41_E0.409740.493
7_I90_G0.408620.492
19_H73_N0.406550.489
83_V100_I0.402540.484
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
3pfoA199.60.108
1ysjA0.95599.60.119
1xmbA0.936999.60.128
3tx8A0.97399.60.135
4ewtA0.95599.60.135
2f7vA0.99199.60.137
3ramA0.927999.60.142
3io1A0.927999.50.154
1vgyA0.96499.50.155
2rb7A0.909999.50.16

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