GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cupin_7 - ChrR Cupin-like domain
Pfam: PF12973 (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: CL0029
Length: 91
Sequences: 6922
Seq/Len: 76.07
HH_delta: 0.135 (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
54_E63_G1.658333.469
56_S61_R1.625863.401
54_E61_R1.452613.039
56_S79_R1.420242.971
63_G66_D1.30182.723
52_E64_A1.090472.281
32_E83_G1.087872.276
36_S79_R0.9932.077
11_S30_R0.872961.826
42_H76_H0.868271.816
48_I68_L0.831831.740
11_S32_E0.825961.728
57_D68_L0.790721.654
49_L67_W0.779911.632
30_R83_G0.771641.614
47_E67_W0.771491.614
36_S77_T0.689021.441
55_L62_Y0.684221.431
26_V47_E0.664171.389
12_V27_S0.636421.331
33_P82_E0.612391.281
41_R75_S0.605351.266
31_L35_A0.598481.252
40_H76_H0.592821.240
13_K30_R0.573411.200
13_K28_L0.556671.165
42_H46_E0.55421.159
52_E82_E0.55071.152
9_G32_E0.537181.124
28_L51_L0.535721.121
54_E82_E0.520131.088
39_R75_S0.500281.047
56_S81_D0.500261.047
50_V55_L0.498691.043
80_S83_G0.472070.988
39_R77_T0.455910.954
34_G81_D0.447060.935
46_E76_H0.44540.932
62_Y68_L0.441370.923
45_G69_R0.436740.914
52_E83_G0.431510.903
10_V31_L0.418250.875
33_P83_G0.416890.872
54_E81_D0.414180.866
55_L61_R0.413340.865
48_I70_L0.411970.862
45_G71_P0.401380.840
16_H67_W0.397410.831
55_L78_P0.393690.824
24_E45_G0.383240.802
26_V69_R0.382620.800
16_H26_V0.379740.794
58_G77_T0.377070.789
62_Y66_D0.376020.787
28_L52_E0.367570.769
43_P73_G0.36430.762
46_E78_P0.364030.762
57_D62_Y0.362410.758
16_H27_S0.351180.735
41_R73_G0.350980.734
47_E69_R0.347830.728
46_E70_L0.344360.720
17_R25_R0.336250.703
57_D70_L0.336140.703
70_L76_H0.335210.701
38_P77_T0.333960.699
33_P80_S0.333890.698
11_S14_P0.330650.692
14_P27_S0.329840.690
28_L49_L0.322140.674
26_V29_L0.31970.669
50_V62_Y0.318550.666
14_P18_D0.317810.665
12_V29_L0.315880.661
38_P42_H0.315470.660
27_S46_E0.314090.657
48_I57_D0.312540.654
47_E68_L0.310090.649
50_V53_G0.30840.645
25_R28_L0.305590.639
58_G74_S0.304770.638
15_L49_L0.303240.634
19_E22_T0.302450.633
24_E69_R0.301520.631
26_V67_W0.299150.626
70_L74_S0.29710.622
16_H69_R0.296450.620
10_V32_E0.292750.612
32_E35_A0.286330.599
18_D25_R0.285520.597
75_S79_R0.28470.596
48_I55_L0.282880.592
9_G14_P0.282320.591
45_G72_P0.281720.589
29_L46_E0.281140.588
56_S59_D0.277180.580
15_L51_L0.276930.579
26_V49_L0.275330.576
10_V37_L0.274860.575
37_L77_T0.274030.573
15_L28_L0.27140.568
61_R81_D0.270010.565
19_E69_R0.269520.564
14_P25_R0.26290.550
10_V29_L0.258320.540
48_I78_P0.252980.529
12_V44_G0.252550.528
19_E23_G0.24490.512
57_D77_T0.241890.506
55_L66_D0.239780.502
14_P62_Y0.237890.498
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
3o14A199.40.135
2q1zB0.95699.20.198
3cjxA0.98999.20.233
3ebrA0.98999.10.237
3o14A0.95699.10.243
2o1qA0.98999.10.25
4e2qA0.98999.10.265
3balA0.989990.287
3i7dA0.989990.291
2bnmA0.989990.298

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