GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
La - La domain
Pfam: PF05383 (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. )
Length: 61
Sequences: 670
Seq/Len: 10.98
HH_delta: -0.041 (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
47_T50_D0.496492.269
8_Y40_F0.415171.898
14_L24_M0.405761.855
23_Q26_S0.395081.806
20_L32_V0.356591.630
2_K6_E0.340861.558
20_L40_F0.324651.484
9_F16_R0.298561.365
2_K60_D0.29481.347
13_N17_D0.279941.280
52_E56_D0.277181.267
34_I55_V0.275441.259
41_N44_K0.273891.252
50_D53_L0.273531.250
5_V30_G0.268991.230
18_K22_S0.255781.169
9_F40_F0.255651.169
15_P18_K0.254411.163
6_E61_S0.251071.148
23_Q36_T0.243381.112
17_D40_F0.2411.102
38_L51_I0.239911.097
8_Y17_D0.237731.087
21_R25_D0.237521.086
5_V37_I0.237321.085
4_Q7_F0.236021.079
3_K49_T0.234451.072
4_Q8_Y0.232881.064
2_K57_A0.228761.046
19_F36_T0.226391.035
56_D59_R0.223121.020
13_N40_F0.222351.016
4_Q13_N0.220951.010
39_S44_K0.220141.006
4_Q40_F0.218420.998
1_I43_M0.216180.988
35_S51_I0.21520.984
9_F37_I0.212270.970
5_V26_S0.210310.961
7_F12_E0.209810.959
57_A61_S0.209580.958
30_G42_R0.200490.916
38_L54_I0.198790.909
51_I54_I0.198290.906
2_K31_W0.198190.906
26_S55_V0.19530.893
41_N45_A0.19490.891
24_M32_V0.19240.879
55_V59_R0.191770.877
33_P36_T0.189440.866
11_D58_L0.18830.861
37_I43_M0.188230.860
19_F42_R0.187930.859
13_N19_F0.186840.854
10_S37_I0.185660.849
12_E24_M0.185630.848
52_E58_L0.183360.838
8_Y13_N0.183060.837
47_T54_I0.181640.830
2_K59_R0.18140.829
26_S56_D0.180320.824
11_D42_R0.180120.823
31_W46_L0.179270.819
26_S29_D0.17870.817
10_S31_W0.177790.813
45_A55_V0.175210.801
9_F59_R0.173810.794
12_E34_I0.172840.790
18_K21_R0.168170.769
35_S58_L0.167470.765
21_R41_N0.166480.761
5_V58_L0.165790.758
7_F40_F0.165040.754
19_F23_Q0.16270.744
33_P54_I0.162450.743
1_I46_L0.161770.739
36_T39_S0.159960.731
33_P51_I0.159330.728
10_S22_S0.158150.723
35_S49_T0.157120.718
32_V51_I0.156750.716
26_S41_N0.156540.716
32_V41_N0.156460.715
18_K60_D0.154280.705
45_A51_I0.154140.705
56_D60_D0.152410.697
29_D53_L0.151290.692
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
1s29A0.983699.8-0.041
2cqkA0.950899.8-0.012
2vooA0.967299.80.06
1wfxA0.868960.90.835
3htxA145.20.849
1c07A0.868935.70.857
4gd5A0.426235.50.858
3qr0A0.934423.10.87
3ohmB0.8852210.871
2lvvA0.983616.90.877

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