GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
WHG - WHG domain
Pfam: PF13305 (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: 81
Sequences: 3104
Seq/Len: 38.32
HH_delta: 0.386 (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
9_R13_E0.761682.658
8_I76_F0.735942.568
11_A73_A0.640252.234
7_Y70_H0.545161.903
11_A18_F0.528991.846
67_A71_G0.486831.699
45_E49_A0.486041.696
14_H17_L0.440121.536
18_F70_H0.438481.530
64_A68_A0.432111.508
18_F66_W0.427531.492
38_E42_E0.427061.490
2_A6_A0.425141.484
48_I58_A0.417891.458
47_L51_G0.415831.451
8_I73_A0.415311.449
66_W75_L0.39981.395
6_A9_R0.394591.377
70_H75_L0.393731.374
46_A49_A0.392531.370
10_F14_H0.389761.360
66_W70_H0.379461.324
19_R77_L0.376431.314
37_F40_L0.359771.256
46_A50_E0.343481.199
42_E46_A0.340881.190
42_E45_E0.339081.183
4_G69_V0.3351.169
7_Y66_W0.332661.161
22_F70_H0.32581.137
30_D36_A0.31741.108
8_I12_R0.312811.092
3_M43_L0.312341.090
47_L53_L0.311491.087
5_R9_R0.303661.060
20_L23_M0.3021.054
7_Y73_A0.300781.050
41_V62_A0.299791.046
71_G75_L0.292491.021
43_L47_L0.289891.012
45_E58_A0.289221.009
58_A62_A0.289181.009
67_A75_L0.286821.001
29_E33_F0.281440.982
23_M27_I0.279590.976
12_R76_F0.278060.970
24_S54_S0.269170.939
15_P19_R0.267430.933
22_F66_W0.263880.921
10_F17_L0.263520.920
55_P59_R0.261720.913
2_A5_R0.255750.893
39_L46_A0.253190.884
18_F73_A0.252560.881
38_E59_R0.251210.877
43_L53_L0.250230.873
16_E20_L0.247890.865
31_P35_E0.246740.861
63_L72_L0.245010.855
41_V45_E0.242550.846
45_E48_I0.2390.834
64_A72_L0.234680.819
17_L21_M0.23450.818
59_R63_L0.232290.811
55_P58_A0.231630.808
67_A70_H0.230490.804
47_L52_N0.227320.793
41_V59_R0.227230.793
27_I30_D0.226150.789
67_A77_L0.225150.786
63_L66_W0.224240.783
43_L46_A0.224080.782
16_E19_R0.223860.781
16_E23_M0.221780.774
4_G65_L0.219970.768
73_A77_L0.21710.758
54_S57_D0.216820.757
40_L44_I0.215670.753
11_A75_L0.213970.747
40_L43_L0.210630.735
21_M71_G0.209780.732
23_M26_I0.209560.731
44_I58_A0.209220.730
32_E35_E0.208240.727
70_H74_S0.204670.714
51_G54_S0.204310.713
17_L68_A0.203550.710
11_A66_W0.203540.710
58_A68_A0.203230.709
23_M77_L0.202070.705
69_V76_F0.201350.703
44_I53_L0.200920.701
48_I61_I0.200290.699
37_F41_V0.199750.697
58_A61_I0.19870.693
63_L74_S0.198470.693
45_E51_G0.196370.685
47_L54_S0.194390.678
31_P34_Q0.192290.671
44_I48_I0.191790.669
3_M77_L0.191040.667
49_A52_N0.190840.666
39_L42_E0.189330.661
46_A52_N0.188580.658
4_G12_R0.186910.652
17_L74_S0.186740.652
39_L47_L0.185960.649
26_I32_E0.182810.638
5_R50_E0.181330.633
30_D33_F0.180790.631
69_V73_A0.180650.630
67_A72_L0.180380.630
5_R20_L0.179660.627
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
3cjdA0.975397.40.386
2oi8A1970.44
3aqtA0.987796.90.447
3on2A196.80.452
3he0A196.70.458
1zk8A0.938396.70.461
2genA196.70.465
2iu5A196.50.477
3colA196.40.481
3qkxA196.40.485

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