GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cadherin_2 - Cadherin-like
Pfam: PF08266 (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: 84
Sequences: 2670
Seq/Len: 31.79
HH_delta: 0.107 (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
5_Y18_G1.617775.849
64_R68_C0.770752.787
50_N53_T0.613522.218
16_V55_D0.569272.058
11_M15_T0.553512.001
58_V62_I0.550271.990
49_V56_L0.541971.960
19_N55_D0.533541.929
48_R57_F0.531111.920
5_Y23_D0.417321.509
36_F49_V0.410081.483
58_V64_R0.393581.423
17_I47_F0.383551.387
30_S33_S0.375961.359
16_V57_F0.367231.328
46_Y60_E0.366481.325
3_I7_V0.362681.311
48_R59_S0.362171.310
25_G31_L0.338571.224
13_P59_S0.334781.210
11_M58_V0.328171.187
27_D32_S0.297331.075
3_I18_G0.295231.067
19_N68_C0.290071.049
8_P11_M0.278311.006
35_N51_E0.278141.006
10_E62_I0.271940.983
26_L31_L0.265560.960
9_E63_D0.265230.959
44_S66_E0.262840.950
50_N54_G0.256720.928
22_K53_T0.255380.923
44_S69_G0.251510.909
25_G36_F0.25150.909
15_T36_F0.250170.905
10_E61_R0.248650.899
39_V66_E0.246240.890
50_N57_F0.244330.883
25_G34_R0.24340.880
21_A25_G0.242940.878
45_Q60_E0.241280.872
3_I21_A0.240470.869
38_I42_G0.240210.869
12_P22_K0.232160.839
31_L36_F0.231930.839
51_E57_F0.224430.811
27_D52_K0.221330.800
38_I56_L0.219540.794
33_S52_K0.218960.792
24_L64_R0.218280.789
33_S36_F0.217480.786
17_I58_V0.217420.786
45_Q50_N0.217030.785
38_I41_E0.215840.780
16_V19_N0.211310.764
9_E65_E0.210.759
26_L34_R0.2090.756
25_G32_S0.207850.752
20_I55_D0.205320.742
10_E65_E0.204650.740
14_G48_R0.203850.737
47_F50_N0.202590.733
36_F43_N0.201960.730
53_T57_F0.201860.730
7_V14_G0.201010.727
30_S60_E0.200780.726
12_P15_T0.198390.717
46_Y59_S0.19830.717
13_P60_E0.197380.714
21_A54_G0.196310.710
22_K55_D0.194730.704
44_S59_S0.194280.702
44_S60_E0.194140.702
63_D66_E0.188060.680
10_E64_R0.186370.674
27_D31_L0.184410.667
37_R51_E0.182310.659
15_T47_F0.181450.656
26_L32_S0.179680.650
42_G49_V0.179560.649
5_Y8_P0.178920.647
41_E46_Y0.178240.644
12_P61_R0.178150.644
25_G38_I0.176880.640
56_L61_R0.176550.638
14_G57_F0.176070.637
62_I67_L0.175240.634
52_K59_S0.173990.629
3_I8_P0.173820.628
46_Y67_L0.172670.624
46_Y66_E0.171510.620
24_L68_C0.170930.618
66_E69_G0.169680.614
35_N52_K0.169190.612
40_S67_L0.168970.611
9_E17_I0.168360.609
13_P16_V0.168130.608
11_M16_V0.166650.603
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
1wuzA199.60.107
1wyjA199.50.136
2x2uA0.964399.30.244
2ee0A0.976299.30.247
2x2uA0.988199.30.253
2ystA0.976299.30.253
2yqgA0.976299.20.265
1q55A199.20.267
3q2wA199.20.275
1l3wA199.20.285

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