GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2513 - Hypothetical protein (DUF2513)
Pfam: PF10711 (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: 102
Sequences: 11272
Seq/Len: 110.51
HH_delta: 0.292 (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
53_S68_R1.394252.404
51_E68_R1.379662.379
45_D52_G1.242142.142
55_S66_I1.089831.880
35_E38_A1.024591.767
33_S36_E0.979961.690
35_E39_Y0.969811.673
32_Y36_E0.93631.615
70_T73_G0.9131.575
82_D85_V0.883421.524
25_E28_E0.874081.507
38_A42_K0.86571.493
32_Y37_I0.852311.470
77_L81_R0.829151.430
13_E29_I0.826371.425
41_L67_K0.813441.403
69_L73_G0.805711.390
36_E39_Y0.779631.345
49_L72_S0.748731.291
15_E77_L0.735461.268
79_A82_D0.72561.251
19_D68_R0.717141.237
16_E29_I0.712911.229
85_V88_K0.696481.201
51_E70_T0.69551.199
14_I69_L0.678621.170
15_E81_R0.675681.165
40_H43_L0.674711.164
10_I40_H0.673131.161
36_E40_H0.665711.148
27_D37_I0.665511.148
75_D78_D0.662731.143
15_E69_L0.656991.133
12_L15_E0.645231.113
74_H78_D0.642041.107
12_L16_E0.639111.102
14_I50_I0.637671.100
52_G67_K0.625061.078
33_S39_Y0.618991.067
48_G72_S0.616711.064
72_S75_D0.593291.023
11_L14_I0.58931.016
34_K38_A0.586291.011
71_W75_D0.580591.001
75_D79_A0.571930.986
42_K46_E0.564790.974
39_Y43_L0.560560.967
74_H77_L0.555620.958
27_D34_K0.548220.945
38_A52_G0.547950.945
17_N29_I0.545030.940
71_W74_H0.541170.933
20_P25_E0.533040.919
87_N91_D0.532890.919
26_E37_I0.517930.893
25_E29_I0.515250.889
73_G76_F0.509250.878
45_D50_I0.508690.877
18_P53_S0.504230.870
82_D88_K0.503230.868
43_L47_A0.500990.864
78_D82_D0.500630.863
17_N20_P0.485150.837
13_E30_D0.483230.833
18_P68_R0.483120.833
41_L50_I0.482830.833
86_W90_K0.480790.829
91_D95_S0.475890.821
42_K45_D0.469150.809
18_P21_P0.465150.802
86_W89_T0.462890.798
72_S76_F0.460270.794
56_G66_I0.459360.792
13_E17_N0.456060.787
11_L15_E0.450060.776
26_E29_I0.443030.764
39_Y42_K0.441260.761
89_T93_I0.436060.752
22_N38_A0.428570.739
40_H47_A0.427670.738
13_E19_D0.427580.737
79_A92_K0.427070.737
88_K92_K0.42080.726
91_D94_A0.41960.724
10_I37_I0.419380.723
38_A67_K0.418080.721
51_E54_V0.417910.721
92_K95_S0.414360.715
49_L76_F0.412760.712
13_E26_E0.412740.712
73_G77_L0.412230.711
20_P66_I0.411210.709
34_K43_L0.409490.706
54_V57_T0.406550.701
69_L74_H0.403360.696
21_P37_I0.398010.686
89_T92_K0.396450.684
45_D51_E0.393320.678
14_I19_D0.392190.676
76_F79_A0.385070.664
32_Y40_H0.38250.660
10_I26_E0.38020.656
27_D41_L0.379490.654
15_E74_H0.377840.652
68_R74_H0.377620.651
92_K96_K0.376460.649
33_S37_I0.372760.643
21_P41_L0.372150.642
37_I41_L0.36890.636
30_D36_E0.368720.636
34_K54_V0.367560.634
50_I57_T0.367310.633
53_S56_G0.362980.626
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
4aikA0.931498.80.292
4em2A0.931498.80.303
3g3zA0.931498.80.312
4g9yA0.931498.70.318
3k0lA0.931498.70.318
4fhtA0.931498.70.318
3e6mA0.931498.70.319
3echA0.931498.70.321
1hsjA0.843198.70.322
3oopA0.931498.70.322

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