GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NAD_Gly3P_dh_N - NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
Pfam: PF01210 (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: CL0063
Length: 157
Sequences: 10705
Seq/Len: 68.18
HH_delta: 0.069 (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
32_E36_E1.681983.421
3_A70_A1.560243.173
1_K24_E1.409322.866
84_E88_Q1.243832.530
62_D65_E1.227952.497
7_A27_L1.152582.344
7_A29_G1.075592.187
36_E40_E1.072752.182
24_E58_K1.014082.062
2_I18_L1.000152.034
77_V85_V0.992162.018
29_G35_I0.917511.866
33_E36_E0.888951.808
35_I59_A0.888461.807
87_E121_I0.886961.804
76_A102_A0.881131.792
64_E92_Y0.87581.781
24_E56_N0.86851.766
1_K26_T0.856711.742
39_N59_A0.855311.739
3_A66_A0.8171.662
19_A57_I0.812271.652
26_T69_D0.797511.622
15_A27_L0.789211.605
16_A20_D0.786021.599
113_L116_E0.778731.584
93_L97_Q0.774861.576
32_E61_T0.761371.548
31_D34_Q0.759081.544
28_W63_L0.732991.491
26_T58_K0.716391.457
84_E87_E0.702741.429
136_A139_I0.682971.389
88_Q91_P0.667431.357
26_T60_T0.665221.353
36_E39_N0.645261.312
2_I23_H0.643721.309
90_A112_L0.633351.288
73_I97_Q0.630031.281
1_K69_D0.625691.272
72_I98_I0.623561.268
5_I63_L0.620561.262
52_K55_E0.599131.218
38_I59_A0.595131.210
94_K97_Q0.587471.195
81_A106_F0.587311.194
62_D66_A0.581851.183
37_E40_E0.579091.178
83_R87_E0.575391.170
4_V15_A0.561851.143
83_R107_E0.561151.141
64_E88_Q0.556861.132
112_L120_E0.556291.131
87_E91_P0.549651.118
90_A111_L0.547271.113
44_N48_L0.540741.100
16_A54_P0.539481.097
1_K71_D0.533461.085
71_D94_K0.53071.079
2_I72_I0.522491.063
5_I85_V0.52061.059
60_T65_E0.519431.056
10_W139_I0.519191.056
122_L125_P0.516261.050
83_R113_L0.513521.044
39_N58_K0.512511.042
3_A67_L0.512351.042
17_L21_N0.512331.042
5_I28_W0.510761.039
29_G34_Q0.507151.031
87_E117_V0.499171.015
35_I39_N0.495421.008
71_D96_G0.488910.994
60_T66_A0.487840.992
63_L88_Q0.486770.990
20_D53_L0.482990.982
69_D94_K0.482910.982
115_S136_A0.482910.982
115_S119_E0.482060.980
34_Q37_E0.480210.977
38_I82_H0.474530.965
14_L102_A0.470630.957
98_I101_S0.468660.953
65_E68_E0.468260.952
18_L74_I0.467510.951
37_E45_P0.465780.947
35_I61_T0.464480.945
7_A15_A0.463580.943
73_I93_L0.463190.942
131_S137_E0.462830.941
7_A38_I0.458390.932
64_E68_E0.456440.928
43_Q52_K0.453360.922
88_Q92_Y0.452450.920
28_W60_T0.446440.908
131_S140_A0.44040.896
3_A73_I0.438140.891
45_P48_L0.430470.875
83_R110_T0.426150.867
43_Q50_G0.425360.865
101_S108_P0.422040.858
58_K65_E0.417580.849
3_A26_T0.413690.841
26_T70_A0.413690.841
33_E37_E0.40820.830
83_R117_V0.408190.830
28_W88_Q0.405240.824
37_E41_T0.404360.822
72_I100_I0.401610.817
93_L99_I0.395370.804
96_G128_A0.394230.802
10_W102_A0.393060.799
74_I102_A0.392450.798
70_A73_I0.391650.797
52_K56_N0.387260.788
44_N53_L0.387060.787
38_I42_R0.385320.784
86_L99_I0.385160.783
15_A25_V0.38320.779
79_S114_L0.382480.778
8_G11_G0.381280.775
28_W66_A0.380540.774
4_V25_V0.378290.769
22_G25_V0.373180.759
40_E43_Q0.372680.758
114_L117_V0.372630.758
63_L67_L0.371370.755
68_E94_K0.370140.753
67_L70_A0.368860.750
86_L89_L0.36540.743
30_R34_Q0.364480.741
75_I82_H0.363950.740
85_V88_Q0.363490.739
66_A69_D0.361050.734
43_Q108_P0.359170.730
19_A56_N0.358920.730
112_L116_E0.35740.727
30_R84_E0.3560.724
5_I89_L0.352660.717
41_T45_P0.350980.714
81_A84_E0.34930.710
12_T37_E0.343350.698
121_I125_P0.340850.693
117_V121_I0.340560.693
79_S103_T0.337150.686
10_W14_L0.334380.680
51_I55_E0.334190.680
82_H103_T0.333890.679
113_L117_V0.330540.672
116_E119_E0.328720.669
14_L17_L0.327230.665
67_L89_L0.325620.662
18_L23_H0.325270.662
27_L59_A0.325090.661
74_I100_I0.324170.659
3_A60_T0.323640.658
135_F139_I0.323620.658
4_V14_L0.3230.657
17_L20_D0.322780.656
4_V76_A0.322270.655
31_D35_I0.320970.653
16_A44_N0.320750.652
121_I124_I0.320660.652
80_Q84_E0.318450.648
28_W61_T0.315860.642
53_L56_N0.315660.642
48_L51_I0.315470.642
115_S134_S0.314130.639
116_E120_E0.313550.638
7_A11_G0.312420.635
5_I75_I0.312310.635
78_P81_A0.311560.634
67_L97_Q0.309850.630
103_T106_F0.309180.629
81_A85_V0.308880.628
65_E69_D0.30880.628
102_A106_F0.307060.624
39_N43_Q0.306660.624
14_L76_A0.305890.622
105_G120_E0.305120.621
75_I86_L0.301580.613
132_G135_F0.301050.612
68_E92_Y0.300960.612
37_E43_Q0.300470.611
3_A28_W0.29850.607
5_I73_I0.298180.606
67_L73_I0.297770.606
1_K68_E0.297620.605
42_R46_K0.297110.604
9_N12_T0.293260.596
42_R45_P0.292440.595
14_L18_L0.29220.594
12_T44_N0.290430.591
111_L114_L0.288820.587
108_P111_L0.287230.584
63_L92_Y0.286460.583
42_R55_E0.285520.581
30_R59_A0.283570.577
107_E110_T0.283030.576
30_R88_Q0.282730.575
122_L126_R0.281990.573
101_S104_K0.281840.573
118_I139_I0.279690.569
73_I99_I0.279180.568
114_L118_I0.278950.567
11_G15_A0.278860.567
100_I118_I0.278120.566
75_I118_I0.277640.565
115_S127_I0.277530.564
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
4fgwA0.993699.90.069
3k96A0.993699.90.097
4a7pA0.987399.80.221
1yj8A0.993699.80.226
1evyA199.80.234
1x0vA0.993699.80.251
1z82A0.94999.80.266
3gg2A0.987399.80.27
2y0cA0.987399.70.291
1txgA0.974599.70.31

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