GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MttA_Hcf106 - mttAHcf106 family
Pfam: PF02416 (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: 53
Sequences: 2419
Seq/Len: 45.64
HH_delta: 0.031 (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
2_G5_E1.333863.108
1_I5_E1.076012.507
26_A30_G0.895322.086
34_R38_K0.797211.858
17_F25_L0.76131.774
13_A19_P0.690591.609
21_K24_E0.630311.469
1_I6_L0.60251.404
27_R35_E0.580671.353
43_A46_E0.565521.318
41_N44_K0.5141.198
41_N45_E0.506741.181
5_E9_I0.505311.177
3_F7_L0.504321.175
19_P23_P0.489091.140
35_E38_K0.481521.122
28_S32_A0.480241.119
40_I43_A0.476341.110
27_R31_K0.473961.104
37_K40_I0.47371.104
24_E28_S0.473191.103
16_L19_P0.470821.097
30_G34_R0.451371.052
5_E8_I0.451211.051
23_P31_K0.442081.030
25_L29_L0.427380.996
31_K35_E0.421570.982
12_V16_L0.421340.982
42_E45_E0.405590.945
29_L32_A0.396330.923
3_F6_L0.395050.920
27_R43_A0.389580.908
20_K24_E0.382920.892
4_P7_L0.379660.885
32_A36_F0.37780.880
38_K41_N0.372970.869
33_I36_F0.368830.859
8_I12_V0.363880.848
22_L26_A0.360090.839
6_L9_I0.354340.826
38_K43_A0.350910.818
6_L10_L0.350710.817
11_V14_L0.348530.812
31_K38_K0.334170.779
39_A43_A0.334030.778
35_E39_A0.331730.773
38_K42_E0.329260.767
36_F39_A0.326680.761
2_G6_L0.322820.752
13_A17_F0.310290.723
38_K45_E0.309820.722
26_A32_A0.307580.717
34_R40_I0.30360.707
35_E40_I0.301620.703
14_L19_P0.300680.701
31_K39_A0.288760.673
15_L20_K0.286380.667
34_R42_E0.285670.666
5_E12_V0.281880.657
10_L13_A0.279730.652
17_F26_A0.272910.636
17_F36_F0.270290.630
26_A35_E0.268330.625
30_G35_E0.265040.618
24_E31_K0.264370.616
7_L45_E0.262470.612
23_P27_R0.262290.611
2_G9_I0.260230.606
19_P28_S0.257540.600
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
2l16A199.40.031
2lzrA0.981199.20.127
1mhsA141.60.798
4dpoA122.30.823
2j69A0.962318.50.829
1gp7A0.9057160.834
1oqwA0.981113.30.84
2hi2A0.981111.70.843
1lq9A111.60.843
4i9wA110.50.847

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