GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Reductase_C - Reductase C-terminal
Pfam: PF14759 (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: 85
Sequences: 1391
Seq/Len: 16.36
HH_delta: 0.176 (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
28_D31_S0.708142.840
26_R76_D0.595582.388
21_D40_R0.576682.313
47_A59_A0.522672.096
70_D73_R0.516852.073
49_S56_L0.471861.892
52_R55_D0.466951.873
38_Y48_V0.460521.847
22_E71_P0.440741.767
27_G34_F0.434291.742
23_V36_A0.432271.733
39_L74_L0.370291.485
5_D10_R0.366951.471
22_E42_G0.359321.441
12_Q53_P0.357091.432
33_K52_R0.338391.357
1_W5_D0.326661.310
17_P20_A0.325451.305
20_A38_Y0.323791.298
13_I48_V0.312971.255
3_W12_Q0.311251.248
1_W10_R0.30941.241
17_P48_V0.306811.230
25_V29_P0.297771.194
42_G72_A0.296591.189
71_P75_A0.295861.186
14_A56_L0.292791.174
37_F74_L0.292331.172
39_L44_L0.291511.169
14_A63_I0.289561.161
10_R57_R0.284231.140
10_R53_P0.27471.102
37_F62_L0.271391.088
35_V55_D0.265391.064
63_I66_G0.264361.060
3_W11_I0.263681.057
3_W10_R0.262141.051
3_W49_S0.259731.042
17_P46_A0.256011.027
24_V75_A0.254431.020
12_Q49_S0.252021.011
35_V49_S0.252011.011
17_P45_V0.250751.006
13_I46_A0.247590.993
73_R76_D0.246390.988
9_V51_N0.245790.986
1_W38_Y0.242340.972
7_Y12_Q0.2320.930
35_V52_R0.230340.924
25_V34_F0.229130.919
9_V32_G0.228620.917
25_V36_A0.22790.914
69_V74_L0.226430.908
54_R57_R0.220690.885
38_Y46_A0.21820.875
60_R64_A0.216870.870
56_L60_R0.214370.860
4_S57_R0.213780.857
19_G45_V0.212860.854
10_R48_V0.21070.845
2_F13_I0.210120.843
44_L63_I0.209650.841
3_W6_Q0.207410.832
37_F44_L0.206920.830
1_W48_V0.202340.811
5_D12_Q0.201980.810
18_G41_D0.200550.804
21_D41_D0.199840.801
43_R66_G0.199760.801
55_D58_A0.199680.801
43_R68_R0.197560.792
14_A47_A0.196830.789
48_V54_R0.195870.785
6_Q11_I0.194890.782
43_R67_A0.194670.781
12_Q57_R0.194250.779
13_I36_A0.191960.770
63_I67_A0.191120.766
42_G71_P0.189940.762
44_L69_V0.189920.762
69_V77_P0.183550.736
2_F9_V0.183450.736
53_P57_R0.183440.736
12_Q60_R0.181290.727
20_A23_V0.179530.720
66_G75_A0.178760.717
6_Q12_Q0.178410.715
41_D76_D0.178330.715
22_E25_V0.177070.710
24_V27_G0.176350.707
18_G31_S0.172780.693
24_V39_L0.170790.685
7_Y10_R0.170230.683
14_A17_P0.169540.680
9_V50_V0.168290.675
45_V66_G0.167260.671
8_G51_N0.166430.667
20_A45_V0.165560.664
13_I49_S0.165520.664
61_R65_A0.161440.647
72_A75_A0.161230.647
3_W48_V0.16070.644
6_Q10_R0.160570.644
37_F59_A0.16040.643
3_W54_R0.159120.638
1_W60_R0.158270.635
29_P61_R0.156410.627
47_A56_L0.156370.627
1_W13_I0.156150.626
13_I17_P0.155640.624
22_E39_L0.155160.622
30_E70_D0.154730.620
57_R63_I0.154270.619
67_A72_A0.153340.615
73_R77_P0.152810.613
22_E40_R0.152520.612
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
3lxdA199.60.176
3fg2P199.60.179
3ef6A199.50.231
1q1rA199.10.409
2gqwA0.9882990.424
1m6iA0.964798.90.443
3kljA0.917698.80.47
1xhcA0.717696.50.709
1v59A0.9647850.799
3cgbA0.9765820.806

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