GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cadherin_pro - Cadherin prodomain like
Pfam: PF08758 (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: 90
Sequences: 5300
Seq/Len: 58.89
HH_delta: 0.099 (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
13_F26_G2.246195.182
49_R57_Y1.207692.786
39_V75_A1.175842.712
24_P55_S1.075542.481
30_F41_F1.013732.338
40_I78_S0.886192.044
42_E74_H0.863811.993
49_R59_K0.863671.992
27_K55_S0.853271.968
19_L58_A0.848251.957
58_A62_V0.83421.924
35_G38_R0.833041.922
34_T37_R0.830351.915
47_D60_R0.827231.908
42_E76_W0.79971.845
2_C33_C0.796461.837
8_Q11_Y0.779641.798
7_S29_N0.725821.674
17_S63_Q0.701491.618
50_V56_V0.69191.596
44_S74_H0.675641.559
38_R78_S0.671911.550
24_P57_Y0.634811.464
64_L67_E0.596531.376
24_P27_K0.5951.373
47_D69_R0.594521.371
48_F69_R0.584171.348
17_S64_L0.581741.342
19_L23_Q0.57881.335
17_S65_S0.540831.248
6_F75_A0.532721.229
28_V73_V0.529541.222
20_E23_Q0.517771.194
7_S31_E0.509441.175
50_V54_G0.502981.160
40_I52_E0.480761.109
51_L57_Y0.473791.093
5_G33_C0.456191.052
64_L69_R0.442511.021
30_F39_V0.441841.019
50_V73_V0.437591.009
11_Y26_G0.43721.009
35_G78_S0.417040.962
51_L55_S0.415140.958
4_P77_D0.407590.940
15_V25_L0.40520.935
63_Q66_S0.393770.908
4_P32_D0.39250.905
6_F11_Y0.387550.894
34_T38_R0.385510.889
30_F75_A0.375330.866
6_F30_F0.36390.839
58_A64_L0.359080.828
41_F54_G0.356470.822
43_S73_V0.354060.817
21_A61_P0.349470.806
5_G31_E0.342410.790
46_P59_K0.342060.789
28_V56_V0.324870.749
32_D77_D0.316240.730
43_S46_P0.315380.728
48_F71_F0.310190.716
18_N62_V0.303850.701
22_G57_Y0.30380.701
51_L54_G0.303010.699
17_S20_E0.296070.683
11_Y28_V0.281830.650
3_R81_Q0.280520.647
36_R81_Q0.278430.642
45_D70_S0.275590.636
23_Q58_A0.273110.630
7_S11_Y0.273010.630
2_C36_R0.266910.616
7_S10_K0.261710.604
37_R79_Q0.260540.601
47_D66_S0.258240.596
48_F62_V0.256320.591
37_R77_D0.253050.584
13_F56_V0.252010.581
25_L58_A0.251780.581
41_F75_A0.248920.574
72_T81_Q0.248910.574
21_A60_R0.248740.574
25_L56_V0.24820.573
62_V69_R0.248030.572
69_R72_T0.246980.570
25_L48_F0.245860.567
19_L24_P0.244020.563
21_A58_A0.243450.562
15_V19_L0.240780.555
43_S50_V0.239850.553
42_E52_E0.237710.548
14_E67_E0.236590.546
76_W80_T0.235630.544
3_R12_T0.235290.543
54_G73_V0.233650.539
7_S41_F0.232180.536
21_A59_K0.230.531
43_S76_W0.228730.528
29_N68_Q0.228510.527
2_C53_D0.227980.526
5_G29_N0.227610.525
2_C5_G0.226940.524
22_G49_R0.224810.519
10_K26_G0.223390.515
76_W79_Q0.22180.512
2_C37_R0.219080.505
18_N64_L0.216860.500
14_E27_K0.216120.499
33_C48_F0.214590.495
9_K53_D0.213140.492
8_Q29_N0.212070.489
21_A24_P0.211030.487
14_E68_Q0.208780.482
9_K61_P0.208160.480
49_R72_T0.208060.480
15_V23_Q0.207880.480
20_E38_R0.205880.475
23_Q33_C0.204890.473
32_D79_Q0.204640.472
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
1q55A0.977899.60.099
2ee0A0.988999.60.114
3ubhA199.60.142
2ystA199.60.146
3ubfA0.988999.50.161
4apxB199.50.173
2a4eA199.50.175
2qviA199.50.177
3ppeA199.50.179
2a62A199.50.18

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