GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cadherin - Cadherin domain
Pfam: PF00028 (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: CL0159
Length: 93
Sequences: 6211
Seq/Len: 66.78
HH_delta: -0.014 (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
3_F16_G2.174034.556
61_R65_S1.377972.888
31_I73_A1.299322.723
36_L72_R1.153412.417
14_V52_E1.121322.350
20_A33_Y1.101252.308
45_S54_S1.067312.237
32_T76_S1.039412.178
34_S72_R0.962652.017
26_G29_S0.958692.009
55_L59_L0.945461.981
47_D50_T0.943441.977
17_Q52_E0.887691.860
72_R83_S0.854521.791
4_S91_N0.819231.717
2_S91_N0.812681.703
27_P30_Q0.797291.671
34_S74_T0.777411.629
9_A55_L0.765431.604
45_S56_K0.73921.549
43_L57_K0.714831.498
43_L67_Y0.69941.466
66_S89_T0.688121.442
70_T87_T0.677991.421
14_V54_S0.677011.419
9_A13_T0.669451.403
46_I53_I0.648641.359
74_T83_S0.62491.310
74_T81_P0.621141.302
68_Q89_T0.611351.281
64_Q67_Y0.610731.280
30_Q76_S0.60571.269
75_D78_G0.597671.252
7_E60_D0.597281.252
72_R85_T0.587011.230
68_Q87_T0.572161.199
30_Q49_N0.569811.194
18_V71_V0.567661.190
47_D54_S0.545191.143
14_V17_Q0.541761.135
7_E62_E0.541481.135
66_S91_N0.537581.127
53_I88_V0.526561.103
7_E61_R0.520691.091
69_L88_V0.517241.084
20_A24_D0.515691.081
10_P13_T0.51541.080
11_P57_K0.497721.043
47_D51_G0.493671.035
46_I71_V0.486961.020
20_A73_A0.486221.019
59_L92_V0.469860.985
2_S89_T0.448080.939
22_D75_D0.443570.930
78_G81_P0.439650.921
33_Y73_A0.432150.906
39_N42_G0.41790.876
46_I51_G0.406890.853
70_T85_T0.404620.848
20_A31_I0.397370.833
32_T48_P0.38870.815
44_F67_Y0.388190.814
33_Y51_G0.387940.813
44_F69_L0.384630.806
35_I46_I0.37590.788
71_V88_V0.373720.783
8_N58_P0.366940.769
27_P76_S0.362760.760
29_S75_D0.356180.746
11_P58_P0.356080.746
25_S29_S0.355210.744
31_I84_S0.350980.736
34_S48_P0.343740.720
35_I71_V0.337980.708
36_L39_N0.330630.693
18_V53_I0.330190.692
29_S76_S0.327720.687
47_D52_E0.325710.683
15_V55_L0.319640.670
42_G57_K0.31930.669
42_G56_K0.318940.668
32_T49_N0.317830.666
16_G88_V0.317290.665
5_V15_V0.316670.664
35_I38_G0.314350.659
41_D56_K0.299140.627
11_P14_V0.293950.616
37_G42_G0.292960.614
15_V44_F0.291990.612
38_G42_G0.289630.607
44_F90_I0.289250.606
24_D29_S0.285270.598
8_N61_R0.284920.597
70_T80_P0.284430.596
55_L92_V0.28420.596
12_G54_S0.280680.588
25_S28_N0.280620.588
38_G69_L0.280310.587
15_V18_V0.278610.584
3_F9_A0.277720.582
6_P14_V0.275260.577
39_N64_Q0.273450.573
8_N11_P0.271120.568
5_V92_V0.268990.564
76_S79_S0.268630.563
3_F88_V0.266260.558
18_V51_G0.262260.550
12_G45_S0.259910.545
71_V86_A0.258850.542
9_A14_V0.257880.540
58_P64_Q0.25740.539
5_V13_T0.253720.532
55_L58_P0.251240.527
75_D82_L0.251090.526
43_L63_T0.25080.526
44_F53_I0.250460.525
43_L56_K0.249830.524
38_G43_L0.248470.521
59_L67_Y0.245430.514
36_L70_T0.243910.511
13_T55_L0.24290.509
67_Y92_V0.24270.509
15_V53_I0.241940.507
22_D29_S0.240760.505
28_N76_S0.23820.499
41_D70_T0.236930.497
80_P83_S0.236030.495
27_P86_A0.234230.491
60_D63_T0.23320.489
26_G30_Q0.232120.486
25_S30_Q0.230820.484
51_G73_A0.228350.479
67_Y90_I0.2280.478
36_L85_T0.22570.473
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
2x2uA0.989299.6-0.014
2ystA0.989299.6-0.008
2ee0A0.967799.60.013
1q55A0.978599.50.027
3mvsA0.978599.50.032
3qrbA0.989299.50.033
1q55A0.989299.50.034
3q2wA0.978599.50.035
3q2vA0.978599.50.038
1zvnA0.967799.50.041

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