GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PDZ_1 - PDZ-like domain
Pfam: PF12812 (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: CL0466
Length: 78
Sequences: 5065
Seq/Len: 64.94
HH_delta: 0.22 (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
63_P67_D1.267752.648
58_N75_I1.247462.606
15_F65_L1.041162.175
17_D65_L1.006072.101
14_V36_A1.005342.100
60_K71_V0.919671.921
19_S22_Q0.917811.917
57_V75_I0.903141.886
32_G35_V0.897061.874
56_S59_G0.852061.780
56_S61_P0.84461.764
15_F68_F0.835191.744
39_G44_F0.804521.680
10_V42_L0.787761.645
64_D67_D0.778321.626
49_S52_F0.761471.591
57_V68_F0.726481.517
40_G44_F0.675841.412
69_I73_K0.651211.360
66_D69_I0.644691.347
42_L46_G0.631551.319
16_H35_V0.628111.312
20_Y23_A0.626281.308
65_L69_I0.607991.270
32_G37_V0.55611.162
34_Y37_V0.549411.148
37_V41_S0.542031.132
14_V38_S0.523441.093
66_D73_K0.522981.092
37_V50_K0.522161.091
67_D70_K0.507221.059
48_I52_F0.498651.042
72_V75_I0.485971.015
17_D64_D0.482751.008
16_H22_Q0.478270.999
20_Y24_R0.472630.987
10_V15_F0.468510.979
67_D71_V0.451720.944
44_F49_S0.448030.936
37_V43_A0.440970.921
15_F32_G0.439780.919
34_Y48_I0.430260.899
65_L68_F0.430180.899
69_I72_V0.428740.896
70_K73_K0.423730.885
17_D32_G0.416920.871
70_K74_K0.415330.868
22_Q33_V0.406320.849
71_V74_K0.400850.837
54_I62_T0.400380.836
43_A47_G0.398840.833
18_L23_A0.395050.825
31_G53_I0.383260.801
57_V72_V0.37790.789
16_H33_V0.374970.783
10_V38_S0.369110.771
32_G62_T0.365790.764
57_V62_T0.361630.755
38_S41_S0.356240.744
71_V75_I0.347930.727
38_S44_F0.346030.723
19_S26_Y0.345830.722
60_K74_K0.337780.706
18_L22_Q0.328390.686
62_T67_D0.324440.678
42_L52_F0.323840.676
66_D70_K0.316840.662
48_I54_I0.315440.659
18_L53_I0.313820.655
33_V51_G0.313680.655
19_S23_A0.312480.653
28_I53_I0.312230.652
13_A42_L0.30440.636
52_F55_T0.304170.635
54_I68_F0.300540.628
43_A48_I0.298910.624
58_N71_V0.297050.620
35_V50_K0.296420.619
57_V71_V0.296350.619
22_Q26_Y0.294440.615
60_K67_D0.290890.608
33_V36_A0.285940.597
32_G68_F0.281280.588
20_Y26_Y0.280360.586
52_F59_G0.280220.585
39_G49_S0.280.585
13_A48_I0.279770.584
43_A52_F0.278880.583
42_L45_A0.275990.576
62_T71_V0.275920.576
21_Q25_Q0.274260.573
37_V44_F0.271930.568
41_S47_G0.270190.564
36_A39_G0.26910.562
14_V50_K0.267220.558
10_V69_I0.262220.548
10_V14_V0.25870.540
68_F73_K0.248460.519
62_T68_F0.247150.516
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
3stjA199.20.22
3pv2A199.20.226
4a8cA199.10.255
1ky9A199.10.257
1te0A199.10.259
2l97A0.9872990.292
4ic6A0.9744990.296
2pzdA0.9487990.301
1lcyA1990.301
2p3wA0.948798.90.319

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