GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NAD_binding_1 - Oxidoreductase NAD-binding domain
Pfam: PF00175 (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: CL0091
Length: 109
Sequences: 10266
Seq/Len: 94.18
HH_delta: 0.085 (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
42_R46_E1.536672.848
4_G100_P1.433952.658
3_A11_F1.316942.441
33_A39_L1.285122.382
16_R44_E1.216592.255
28_T57_H1.163642.157
47_A51_E1.104822.048
77_D81_E0.990851.836
35_T38_D0.980881.818
3_A31_Y0.965371.789
2_I103_M0.962191.783
6_T9_A0.923441.711
32_G103_M0.919521.704
1_L11_F0.910551.688
39_L42_R0.884491.639
12_L44_E0.878371.628
39_L60_Y0.844481.565
8_I29_L0.841961.560
102_P106_A0.839751.556
2_I107_V0.825321.530
78_L81_E0.816931.514
4_G103_M0.812341.506
1_L14_M0.788851.462
97_I104_M0.770531.428
12_L16_R0.769021.425
36_P42_R0.758721.406
31_Y40_L0.749861.390
97_I107_V0.748421.387
46_E49_A0.741351.374
15_L27_V0.733641.360
28_T59_V0.717261.329
3_A29_L0.699561.296
14_M96_Y0.689311.277
101_P105_K0.685251.270
41_F44_E0.666711.236
71_F82_D0.661551.226
12_L41_F0.652421.209
36_P64_P0.65241.209
6_T40_L0.641871.190
19_L52_Y0.636171.179
15_L45_L0.630591.169
32_G75_V0.613571.137
1_L15_L0.604231.120
74_R102_P0.604091.120
76_T79_L0.6011.114
11_F29_L0.595341.103
19_L48_L0.58531.085
26_K57_H0.582241.079
2_I30_F0.580551.076
18_L27_V0.569851.056
30_F82_D0.569851.056
19_L51_E0.566521.050
17_Y20_E0.559431.037
46_E50_Q0.557921.034
15_L29_L0.543621.007
44_E47_A0.541.001
89_D92_D0.535940.993
75_V79_L0.527390.977
77_D80_L0.522580.968
8_I31_Y0.515340.955
16_R48_L0.515160.955
104_M107_V0.513740.952
1_L27_V0.513710.952
43_D47_A0.50710.940
44_E48_L0.494980.917
42_R58_V0.486620.902
13_S17_Y0.486610.902
80_L83_L0.478580.887
105_K108_R0.476410.883
98_C104_M0.475750.882
50_Q53_P0.47530.881
43_D46_E0.472750.876
102_P105_K0.469380.870
8_I45_L0.462580.857
32_G73_G0.462310.857
59_V71_F0.45280.839
90_P93_T0.450390.835
73_G78_L0.446630.828
74_R106_A0.446420.827
82_D85_P0.443980.823
49_A56_F0.441120.818
10_P98_C0.438250.812
19_L27_V0.434460.805
1_L96_Y0.432760.802
32_G61_V0.432210.801
29_L56_F0.429930.797
4_G102_P0.429250.796
47_A50_Q0.42370.785
11_F14_M0.416510.772
101_P104_M0.415470.770
12_L45_L0.41210.764
89_D93_T0.410880.761
97_I108_R0.409090.758
2_I95_V0.407710.756
63_S74_R0.407710.756
15_L48_L0.405480.751
17_Y23_D0.405460.751
8_I41_F0.396150.734
62_S65_D0.392010.727
33_A60_Y0.388640.720
28_T93_T0.38770.719
34_R38_D0.381220.707
66_D72_K0.378240.701
57_H60_Y0.377190.699
29_L49_A0.374840.695
34_R74_R0.365350.677
57_H61_V0.361730.670
49_A52_Y0.359490.666
39_L45_L0.355740.659
95_V107_V0.355250.658
49_A53_P0.353830.656
32_G74_R0.351970.652
33_A38_D0.351660.652
34_R62_S0.350190.649
12_L48_L0.345390.640
71_F78_L0.344420.638
5_G10_P0.342550.635
30_F59_V0.340610.631
10_P13_S0.338470.627
20_E51_E0.338460.627
16_R19_L0.337070.625
18_L25_R0.336160.623
14_M104_M0.332030.615
11_F15_L0.324810.602
45_L48_L0.323080.599
77_D106_A0.322790.598
28_T92_D0.322430.598
103_M106_A0.321120.595
5_G98_C0.315620.585
8_I12_L0.310940.576
49_A54_N0.310450.575
64_P67_G0.310090.575
7_G10_P0.310020.575
29_L45_L0.309810.574
4_G32_G0.308130.571
30_F79_L0.306390.568
80_L84_L0.304920.565
30_F75_V0.304480.564
15_L56_F0.303890.563
33_A40_L0.30370.563
2_I97_I0.303070.562
65_D73_G0.302460.561
100_P104_M0.301380.559
78_L82_D0.300160.556
48_L52_Y0.299370.555
42_R60_Y0.298340.553
26_K91_D0.295380.547
9_A13_S0.294690.546
97_I101_P0.294310.545
5_G8_I0.293260.543
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
3jqqA199.70.085
2b5oA199.70.107
1umkA0.981799.70.116
3vo2A199.70.117
1krhA0.954199.60.124
2cndA0.981799.60.126
1fnbA199.60.126
1fdrA199.60.127
3lo8A199.60.13
2r6hA0.990899.60.13

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