GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
KH_2 - KH domain
Pfam: PF07650 (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: CL0007
Length: 78
Sequences: 3423
Seq/Len: 43.88
HH_delta: 0.115 (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
51_R70_V0.780712.413
46_N49_K0.737642.280
9_E53_E0.714392.208
52_E56_K0.712742.203
41_G44_G0.676152.090
49_K53_E0.62271.924
5_F35_Q0.616671.906
36_P40_I0.523361.617
18_I64_K0.512911.585
25_D69_N0.480551.485
33_A37_G0.4761.471
7_F11_K0.456231.410
10_I26_Q0.453911.403
5_F54_L0.415511.284
10_I39_V0.410231.268
1_E4_Y0.40311.246
51_R55_R0.402821.245
1_E57_E0.392221.212
40_I44_G0.39221.212
11_K27_I0.385441.191
4_Y8_K0.3791.171
29_I74_K0.371351.148
30_V69_N0.368471.139
49_K52_E0.36181.118
35_Q38_I0.353421.092
58_L66_V0.349091.079
19_E32_K0.345161.067
45_S49_K0.342821.059
52_E55_R0.339181.048
71_V74_K0.338851.047
42_K45_S0.33591.038
33_A73_V0.335221.036
16_S33_A0.333121.030
31_I35_Q0.332161.027
35_Q77_W0.331981.026
19_E69_N0.331321.024
53_E56_K0.328571.015
40_I47_I0.321740.994
53_E57_E0.319520.987
19_E25_D0.315580.975
48_K51_R0.314790.973
25_D67_F0.307320.950
47_I71_V0.306460.947
37_G42_K0.303930.939
37_G40_I0.302440.935
58_L65_K0.30020.928
9_E29_I0.299950.927
3_R20_I0.297670.920
27_I71_V0.295250.912
58_L64_K0.290580.898
17_D32_K0.28960.895
26_Q68_L0.284850.880
4_Y12_K0.283590.876
48_K55_R0.282970.875
28_I67_F0.2810.868
2_I46_N0.278890.862
9_E50_I0.275120.850
33_A36_P0.274030.847
6_L50_I0.273180.844
33_A39_V0.268710.830
10_I48_K0.266950.825
38_I42_K0.265380.820
5_F31_I0.262270.811
32_K71_V0.26050.805
4_Y7_F0.260360.805
25_D75_K0.25890.800
11_K18_I0.258620.799
5_F9_E0.258380.799
12_K75_K0.25770.796
8_K20_I0.257010.794
15_I64_K0.254170.786
37_G44_G0.253240.783
6_L10_I0.252230.780
8_K11_K0.250890.775
11_K14_G0.250680.775
50_I55_R0.24970.772
2_I6_L0.248510.768
27_I64_K0.247780.766
2_I5_F0.247260.764
42_K46_N0.245550.759
31_I37_G0.244560.756
10_I29_I0.242420.749
54_L57_E0.240640.744
39_V47_I0.240370.743
2_I29_I0.237140.733
55_R67_F0.23460.725
6_L18_I0.2340.723
43_K46_N0.226270.699
54_L68_L0.223490.691
29_I72_K0.222560.688
12_K25_D0.221990.686
19_E46_N0.221260.684
55_R65_K0.219730.679
9_E33_A0.217450.672
26_Q32_K0.216150.668
12_K58_L0.215550.666
26_Q67_F0.214320.662
40_I51_R0.212920.658
20_I36_P0.211240.653
14_G17_D0.210390.650
37_G70_V0.209050.646
9_E46_N0.206910.639
1_E55_R0.206320.638
17_D65_K0.205630.636
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
1wh9A0.987299.30.115
3iz6B0.987299.30.134
3u5cD0.987299.20.139
3j3aD0.987299.20.141
2zkqc0.987299.20.145
2xzmC0.987299.20.159
3zeyX0.987299.20.159
3j20C0.961599.20.165
3i1mC0.948799.20.173
3r8nC0.948799.20.175

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