GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cadherin-like - Cadherin-like beta sandwich domain
Pfam: PF12733 (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: 88
Sequences: 434
Seq/Len: 4.93
HH_delta: 0.716 (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
58_L63_N0.303562.491
72_A77_T0.289272.374
19_T86_T0.244762.008
38_A70_V0.234221.922
22_N60_E0.228621.876
58_L87_R0.207541.703
14_T79_K0.188271.545
20_V24_V0.185811.525
7_P13_T0.183741.508
38_A72_A0.180691.483
64_T84_T0.179851.476
27_V85_V0.178431.464
33_P40_V0.178051.461
68_I75_G0.174211.429
21_P24_V0.165881.361
37_G73_E0.165841.361
69_T80_T0.160691.319
17_T84_T0.160651.318
18_V86_T0.154221.265
20_V87_R0.1541.264
26_S55_T0.147421.210
71_T75_G0.143241.175
31_A40_V0.14321.175
66_I85_V0.138591.137
25_D86_T0.138251.134
35_D42_V0.137531.129
41_T69_T0.135061.108
7_P27_V0.134251.102
20_V63_N0.132851.090
54_A70_V0.132061.084
67_T85_V0.131451.079
32_T39_T0.130311.069
7_P16_Y0.128751.056
17_T86_T0.128451.054
28_T53_S0.125461.029
62_E85_V0.124051.018
33_P53_S0.122631.006
29_V66_I0.120360.988
17_T78_T0.120350.988
60_E63_N0.120090.985
25_D57_P0.119270.979
34_E37_G0.118380.971
62_E84_T0.117020.960
40_V87_R0.115920.951
36_S42_V0.115710.949
27_V57_P0.114510.940
82_T86_T0.113310.930
25_D41_T0.113120.928
13_T26_S0.112040.919
27_V34_E0.111090.912
18_V29_V0.110710.908
29_V68_I0.110120.904
17_T59_N0.109990.903
44_G75_G0.109940.902
9_F79_K0.109150.896
29_V83_I0.107530.882
58_L85_V0.106890.877
13_T32_T0.106090.871
35_D79_K0.105530.866
53_S56_I0.105390.865
56_I66_I0.105070.862
63_N87_R0.105040.862
62_E74_D0.104580.858
15_E76_T0.104290.856
8_A33_P0.103860.852
42_V54_A0.103840.852
24_V58_L0.103650.851
11_P18_V0.103520.849
10_S40_V0.102330.840
23_D44_G0.101810.835
27_V83_I0.101570.833
36_S73_E0.101530.833
43_N64_T0.100630.826
10_S55_T0.100510.825
28_T74_D0.100360.824
15_E82_T0.10.821
20_V85_V0.099990.820
61_G87_R0.09870.810
20_V66_I0.098370.807
39_T69_T0.098270.806
31_A60_E0.09820.806
34_E74_D0.097070.797
21_P37_G0.09610.789
43_N56_I0.095420.783
21_P66_I0.095090.780
62_E80_T0.094750.777
44_G58_L0.094450.775
45_V59_N0.094290.774
36_S64_T0.093290.766
29_V82_T0.093130.764
21_P87_R0.092150.756
55_T79_K0.09180.753
25_D48_N0.091410.750
36_S54_A0.090940.746
58_L66_I0.090890.746
57_P83_I0.090630.744
43_N72_A0.089710.736
30_T42_V0.089680.736
59_N63_N0.089650.736
24_V54_A0.089280.733
24_V87_R0.088810.729
11_P83_I0.088450.726
29_V85_V0.087710.720
72_A76_T0.08760.719
19_T63_N0.087560.718
20_V57_P0.087310.716
8_A14_T0.086780.712
20_V41_T0.086760.712
25_D54_A0.086740.712
34_E71_T0.085480.701
37_G75_G0.085250.700
59_N73_E0.085060.698
18_V35_D0.084710.695
17_T22_N0.084510.693
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
4hetA0.965995.90.716
3hbzA0.863677.30.808
3s30A0.863672.20.815
4ftdA0.87567.10.821
3owrA0.863656.30.832
1tg7A0.988646.30.842
1qhoA0.943227.30.859
4kmqA0.977323.30.863
2w47A0.977320.20.867
3bgaA0.988618.80.869
If you are interested in a protein containing this domain,
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