GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FAD_binding_6 - Oxidoreductase FAD-binding domain
Pfam: PF00970 (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: CL0076
Length: 99
Sequences: 9725
Seq/Len: 98.23
HH_delta: 0.079 (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
9_E15_K2.009912.971
5_V20_K1.929162.852
18_R62_Y1.862612.754
18_R64_E1.811562.678
3_K87_E1.804252.667
83_K86_D1.80212.664
6_E18_R1.767262.613
16_I64_E1.758132.599
10_L16_I1.714192.534
7_I15_K1.695632.507
3_K20_K1.412352.088
36_V65_F1.373732.031
37_S50_P1.323881.957
39_R89_E1.320821.953
8_E16_I1.319861.951
6_E84_P1.283411.897
2_A90_I1.265161.870
5_V62_Y1.25471.855
54_A66_A1.146511.695
69_R80_H1.115591.649
2_A19_F1.089341.610
16_I66_A1.087191.607
34_Q95_G1.083361.602
19_F65_F1.034071.529
4_V82_L1.007541.490
69_R77_R1.006691.488
55_S64_E0.916171.354
7_I17_F0.902591.334
17_F79_L0.881491.303
7_I83_K0.869331.285
36_V53_P0.866891.282
8_E18_R0.819451.211
39_R48_S0.787921.165
91_R94_Y0.775391.146
38_V65_F0.763681.129
36_V90_I0.760181.124
13_D68_K0.75261.113
37_S91_R0.75121.111
73_G76_S0.744921.101
7_I84_P0.733281.084
20_K62_Y0.731531.081
4_V19_F0.730811.080
3_K22_P0.713861.055
2_A21_L0.70871.048
49_R75_V0.705631.043
4_V17_F0.688021.017
77_R81_Q0.685961.014
11_S14_V0.683521.011
15_K80_H0.669770.990
31_K34_Q0.644910.953
40_V75_V0.641220.948
14_V66_A0.614210.908
35_F95_G0.600510.888
78_Y82_L0.566480.837
17_F67_I0.566290.837
70_Y73_G0.54770.810
57_P60_K0.544890.806
79_L82_L0.541830.801
48_S91_R0.539360.797
69_R81_Q0.535480.792
51_Y76_S0.522680.773
5_V18_R0.518580.767
82_L86_D0.512870.758
67_I79_L0.503890.745
9_E12_P0.501290.741
10_L66_A0.498590.737
77_R80_H0.49270.728
39_R91_R0.49220.728
75_V79_L0.490360.725
32_P57_P0.489730.724
59_D62_Y0.482280.713
30_F56_S0.478080.707
41_P78_Y0.477790.706
6_E62_Y0.476950.705
78_Y81_Q0.47490.702
14_V68_K0.471970.698
21_L27_K0.465290.688
67_I80_H0.463830.686
7_I67_I0.46360.685
6_E16_I0.461850.683
37_S48_S0.461340.682
30_F53_P0.454240.672
37_S94_Y0.450420.666
47_V75_V0.447670.662
27_K63_L0.438110.648
41_P46_Q0.434460.642
47_V74_R0.434190.642
50_P94_Y0.434150.642
2_A63_L0.432690.640
15_K69_R0.431880.638
74_R77_R0.426270.630
42_I45_K0.424990.628
37_S49_R0.423810.627
28_L92_G0.409780.606
45_K74_R0.405920.600
4_V7_I0.401870.594
22_P87_E0.38750.573
13_D70_Y0.376220.556
63_L90_I0.37550.555
42_I74_R0.373220.552
21_L63_L0.372680.551
33_G95_G0.372370.551
51_Y78_Y0.371280.549
56_S59_D0.369610.546
40_V78_Y0.368050.544
42_I46_Q0.367430.543
70_Y76_S0.364270.539
39_R75_V0.363940.538
38_V79_L0.360050.532
54_A64_E0.356190.527
35_F50_P0.350920.519
38_V88_V0.349320.516
42_I47_V0.347190.513
74_R78_Y0.345130.510
79_L88_V0.343850.508
36_V91_R0.339710.502
20_K61_G0.336610.498
82_L88_V0.335270.496
40_V47_V0.33380.493
56_S60_K0.332060.491
50_P96_N0.329470.487
9_E69_R0.328450.486
33_G52_S0.326110.482
27_K30_F0.323970.479
2_A88_V0.323930.479
2_A22_P0.32330.478
53_P63_L0.322660.477
21_L28_L0.322190.476
17_F80_H0.318750.471
38_V90_I0.318560.471
13_D69_R0.318510.471
55_S62_Y0.316220.467
35_F73_G0.31270.462
2_A27_K0.311670.461
41_P45_K0.310650.459
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
2eixA199.70.079
1umkA199.70.087
1ep3B0.979899.60.102
1gvhA0.989999.60.106
2piaA0.969799.60.111
2cndA199.60.113
1cqxA0.989999.60.123
1krhA0.969799.60.127
4fk8A0.959699.60.13
2r6hA0.989999.60.134

Page generated in 0.0341 seconds.