GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-C2H2_2 - C2H2 type zinc-finger (2 copies)
Pfam: PF12756 (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: CL0361
Length: 100
Sequences: 11482
Seq/Len: 114.82
HH_delta: 0.159 (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
82_S85_S2.001793.332
54_P70_M1.558632.594
52_R59_T1.55632.590
3_L19_M1.457152.425
29_D42_Y1.265732.107
4_F19_M1.239212.062
52_R57_N1.197741.993
11_S14_D1.148721.912
35_D38_R1.085271.806
5_C18_H1.066551.775
53_C56_C1.062011.767
63_R67_Q1.05151.750
81_E86_W1.050941.749
3_L54_P0.999161.663
62_S65_A0.990431.648
55_Y70_M0.974761.622
12_V16_L0.951681.584
36_P40_L0.924921.539
38_R41_N0.902591.502
2_C5_C0.873091.453
65_A68_E0.850451.415
54_P83_E0.836031.391
2_C18_H0.835031.390
17_Q68_E0.824981.373
3_L83_E0.816981.360
39_L43_L0.816891.360
56_C69_H0.781991.301
40_L67_Q0.764861.273
66_L70_M0.759351.264
42_Y46_K0.757341.260
39_L42_Y0.749681.248
80_S85_S0.747461.244
14_D17_Q0.74661.243
16_L40_L0.724521.206
50_S59_T0.719471.197
52_R81_E0.716461.192
53_C69_H0.707151.177
16_L67_Q0.67691.127
55_Y84_E0.669611.114
67_Q70_M0.665861.108
15_L19_M0.653581.088
29_D33_L0.634761.056
24_G27_I0.599410.998
32_Y59_T0.595810.992
30_Q33_L0.587220.977
11_S62_S0.584390.973
8_S59_T0.581850.968
10_S14_D0.581110.967
18_H22_K0.577290.961
23_H28_P0.563850.938
4_F55_Y0.561410.934
15_L18_H0.551210.917
12_V36_P0.550640.916
34_V38_R0.541990.902
40_L43_L0.538290.896
51_F63_R0.53090.884
61_R65_A0.529220.881
12_V63_R0.526180.876
74_H77_K0.516480.860
18_H23_H0.516110.859
8_S32_Y0.507140.844
13_D17_Q0.506350.843
36_P63_R0.495670.825
16_L19_M0.494660.823
41_N44_R0.494030.822
19_M70_M0.493650.822
19_M43_L0.486560.810
64_E68_E0.468610.780
83_E86_W0.467170.778
76_K79_N0.463480.771
42_Y47_V0.461620.768
17_Q41_N0.45790.762
37_N64_E0.457280.761
9_F15_L0.448490.746
11_S35_D0.445390.741
29_D35_D0.441890.735
67_Q71_R0.440950.734
43_L70_M0.428570.713
5_C8_S0.427230.711
2_C9_F0.424160.706
41_N68_E0.417990.696
20_K23_H0.416860.694
62_S68_E0.41130.685
34_V61_R0.408660.680
4_F84_E0.404270.673
25_F28_P0.401910.669
17_Q20_K0.397680.662
64_E67_Q0.395410.658
17_Q37_N0.394320.656
45_K61_R0.393930.656
44_R47_V0.392790.654
38_R65_A0.391850.652
37_N41_N0.390470.650
44_R50_S0.390270.650
8_S11_S0.388780.647
71_R74_H0.384240.639
9_F18_H0.384030.639
10_S34_V0.383510.638
63_R66_L0.381850.636
24_G28_P0.377510.628
7_E58_K0.372690.620
51_F66_L0.370380.616
24_G34_V0.370180.616
74_H79_N0.369880.616
68_E71_R0.366180.609
14_D65_A0.365630.609
41_N62_S0.363640.605
43_L49_E0.363370.605
10_S61_R0.363340.605
23_H26_D0.363340.605
50_S61_R0.359880.599
6_D30_Q0.359620.599
35_D62_S0.359210.598
44_R48_K0.356330.593
66_L69_H0.355630.592
16_L20_K0.353120.588
84_E87_E0.347740.579
13_D64_E0.345890.576
13_D16_L0.344660.574
41_N64_E0.344450.573
82_S86_W0.339380.565
60_F69_H0.339060.564
5_C15_L0.331830.552
6_D57_N0.331160.551
55_Y74_H0.329490.548
43_L47_V0.328020.546
4_F8_S0.327620.545
23_H27_I0.322380.537
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
3zmsC0.9999.50.159
3zmsC199.40.205
2i13A0.9999.30.211
2i13A0.9999.30.231
2lt7A199.30.233
2dlqA0.9999.30.244
2jp9A0.9999.20.259
1tf6A0.9999.20.263
2rpcA0.9999.20.27
2gliA0.9999.20.283

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