GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DrsE - DsrEDsrF-like family
Pfam: PF02635 (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: CL0394
Length: 122
Sequences: 2138
Seq/Len: 17.52
HH_delta: 0.153 (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
41_F49_A0.526462.592
91_D94_E0.470212.315
82_E86_K0.469822.313
77_K102_V0.442242.177
17_A48_L0.440992.171
7_V20_A0.437882.156
44_D88_R0.430332.119
4_F116_G0.415352.045
82_E103_P0.406762.003
38_V77_K0.397061.955
38_V112_L0.39561.948
70_L76_V0.372451.834
46_V80_V0.3711.827
3_V27_A0.356691.756
41_F45_G0.348731.717
105_G108_E0.343061.689
62_P65_E0.322211.586
49_A80_V0.32041.577
40_F109_L0.317431.563
36_D77_K0.302131.487
85_L103_P0.300841.481
64_Q68_K0.298761.471
108_E112_L0.297511.465
46_V84_C0.29381.446
108_E111_E0.289541.426
28_A76_V0.287391.415
4_F40_F0.287081.413
46_V85_L0.282211.389
21_L67_L0.265081.305
71_K78_I0.260521.283
26_A29_A0.253691.249
111_E115_E0.246291.213
25_N73_A0.241541.189
42_H45_G0.234751.156
38_V79_Y0.23381.151
102_V108_E0.228571.125
85_L101_V0.228381.124
47_K88_R0.227771.121
38_V116_G0.226281.114
20_A23_L0.220381.085
61_P65_E0.220361.085
109_L113_Q0.218691.077
5_F24_A0.214951.058
79_Y108_E0.214591.057
83_T106_M0.21151.041
23_L26_A0.205361.011
68_K72_E0.204141.005
18_K22_R0.203911.004
86_K91_D0.203281.001
90_L96_L0.197060.970
71_K100_G0.196680.968
81_C106_M0.196620.968
8_T16_R0.195690.963
91_D95_D0.195130.961
109_L118_A0.194590.958
39_V78_I0.194190.956
41_F78_I0.192790.949
38_V115_E0.19050.938
83_T104_S0.188960.930
113_Q119_V0.188840.930
67_L78_I0.188460.928
45_G84_C0.187930.925
45_G48_L0.187930.925
81_C105_G0.187320.922
79_Y112_L0.178520.879
68_K100_G0.178110.877
79_Y104_S0.177910.876
69_E72_E0.176840.871
113_Q118_A0.1760.867
68_K71_K0.174610.860
7_V39_V0.174470.859
40_F81_C0.173870.856
69_E74_G0.172090.847
8_T110_A0.17190.846
83_T105_G0.169980.837
45_G107_D0.169730.836
15_E19_I0.169170.833
111_E114_A0.168460.829
25_N70_L0.166690.821
19_I22_R0.164860.812
20_A39_V0.164030.808
103_P109_L0.163790.806
28_A36_D0.162280.799
20_A24_A0.161480.795
61_P66_L0.160880.792
85_L91_D0.160740.791
96_L99_V0.160660.791
17_A45_G0.160320.789
65_E69_E0.159820.787
42_H106_M0.158580.781
68_K91_D0.158570.781
28_A31_G0.157110.774
21_L41_F0.156890.772
25_N29_A0.156060.768
15_E45_G0.155610.766
22_R25_N0.155240.764
50_L90_L0.153290.755
31_G37_V0.152650.752
71_K101_V0.151630.747
17_A21_L0.151550.746
37_V70_L0.150320.740
35_H114_A0.150060.739
21_L24_A0.149380.735
42_H83_T0.148810.733
51_K94_E0.148670.732
8_T39_V0.148490.731
85_L90_L0.148460.731
25_N28_A0.147530.726
48_L78_I0.14710.724
18_K116_G0.1450.714
72_E115_E0.144210.710
39_V67_L0.14220.700
90_L95_D0.142110.700
23_L110_A0.142080.700
6_I42_H0.141680.698
104_S108_E0.141680.698
4_F38_V0.141540.697
4_F109_L0.141410.696
58_E73_A0.141190.695
47_K90_L0.140520.692
4_F7_V0.140250.691
19_I23_L0.139680.688
80_V85_L0.139310.686
68_K74_G0.13760.677
38_V117_Y0.137530.677
112_L117_Y0.137090.675
18_K51_K0.136680.673
74_G77_K0.136610.673
71_K99_V0.136530.672
22_R26_A0.136390.671
46_V88_R0.136070.670
5_F40_F0.135510.667
8_T78_I0.135160.665
42_H84_C0.134220.661
35_H59_G0.134170.661
72_E93_K0.13260.653
81_C84_C0.132070.650
28_A70_L0.130380.642
19_I61_P0.130330.642
24_A39_V0.130280.641
50_L80_V0.130260.641
91_D115_E0.129850.639
42_H119_V0.129650.638
22_R30_M0.129430.637
17_A63_L0.128670.633
85_L96_L0.128370.632
59_G62_P0.128280.632
24_A31_G0.127960.630
26_A106_M0.127920.630
79_Y102_V0.127820.629
65_E73_A0.127750.629
49_A84_C0.127360.627
41_F48_L0.127330.627
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
3mc3A0.950899.80.153
2d1pA0.950899.70.168
1jx7A0.934499.70.18
2d1pB0.95999.70.195
2hy5B0.950899.70.195
2hy5A0.942699.70.198
2qs7A0.934499.60.259
3pnxA0.934499.60.274
2pd2A0.885299.50.315
2fb6A0.893499.50.317

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