GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FeoA - FeoA domain
Pfam: PF04023 (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: CL0206
Length: 74
Sequences: 2640
Seq/Len: 35.68
HH_delta: 0.012 (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
6_L12_A2.051415.065
7_P10_E1.029052.541
14_I70_I0.970962.397
11_R38_E0.869862.148
13_R73_E0.864862.135
4_S68_E0.864222.134
40_T54_K0.856412.115
37_S56_D0.824962.037
15_V73_E0.818322.020
13_R38_E0.817292.018
11_R40_T0.808511.996
63_S66_I0.787781.945
42_I59_R0.718341.774
52_V59_R0.698771.725
2_P71_F0.613391.514
26_R30_D0.611221.509
51_V67_A0.59531.470
12_A72_V0.586191.447
25_L29_A0.581921.437
18_S71_F0.580371.433
2_P5_E0.552171.363
12_A39_I0.548431.354
54_K59_R0.522021.289
6_L10_E0.50261.241
41_V51_V0.502141.240
34_T56_D0.493651.219
27_R31_L0.491871.214
65_E69_K0.478041.180
14_I33_L0.472541.167
6_L41_V0.458281.132
16_R71_F0.441591.090
6_L72_V0.439521.085
17_I29_A0.43811.082
18_S69_K0.434051.072
43_R52_V0.426261.052
42_I54_K0.42611.052
39_I53_I0.404610.999
41_V53_I0.394130.973
33_L60_I0.391740.967
64_R68_E0.390940.965
58_S61_A0.387130.956
29_A35_P0.383390.947
62_L67_A0.376820.930
8_P43_R0.376710.930
54_K57_G0.365320.902
15_V71_F0.340790.841
45_N63_S0.333620.824
24_L66_I0.332660.821
8_P44_K0.329940.815
55_V58_S0.328670.812
46_P49_G0.324190.800
49_G63_S0.323890.800
52_V61_A0.323330.798
50_P63_S0.32150.794
44_K64_R0.319860.790
19_D69_K0.315910.780
50_P64_R0.308470.762
33_L37_S0.302170.746
33_L53_I0.294260.727
30_D58_S0.292920.723
28_L33_L0.286120.706
65_E68_E0.278880.689
45_N52_V0.269890.666
15_V18_S0.257310.635
37_S55_V0.256660.634
7_P44_K0.254390.628
16_R19_D0.252990.625
27_R30_D0.248290.613
51_V64_R0.2460.607
32_G70_I0.245790.607
19_D24_L0.242740.599
53_I60_I0.240220.593
2_P68_E0.237760.587
25_L35_P0.237160.586
14_I39_I0.235950.583
41_V59_R0.229770.567
29_A34_T0.228040.563
5_E68_E0.227230.561
27_R63_S0.226950.560
30_D56_D0.225850.558
33_L55_V0.222880.550
44_K51_V0.22060.545
19_D25_L0.219070.541
27_R32_G0.218870.540
31_L61_A0.218010.538
5_E71_F0.217030.536
33_L62_L0.217030.536
48_G64_R0.216890.536
32_G60_I0.216350.534
56_D59_R0.216240.534
44_K48_G0.213380.527
28_L66_I0.211890.523
14_I37_S0.210150.519
24_L30_D0.209680.518
3_L33_L0.205870.508
17_I27_R0.204720.505
30_D52_V0.197340.487
25_L48_G0.196940.486
45_N50_P0.19660.485
3_L53_I0.194510.480
22_P69_K0.188660.466
31_L58_S0.188240.465
32_G58_S0.186670.461
8_P40_T0.185810.459
5_E46_P0.185490.458
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
2k5lA0.986599.40.012
2k5fA0.986599.40.013
2k4yA0.986599.40.017
2k5iA0.986599.40.022
3mhxA199.40.022
3hrsA0.986599.40.04
3e19A0.97399.30.059
2h3jA0.97399.30.059
2lx9A0.959599.30.092
2gcxA0.959599.20.099

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