GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1450 - Protein of unknown function (DUF1450)
Pfam: PF07293 (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: 78
Sequences: 3202
Seq/Len: 41.05
HH_delta: 0.31 (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
22_K65_L1.353173.050
36_C40_C0.905942.042
22_K61_A0.82921.869
22_K25_K0.794271.790
24_E31_V0.766131.727
60_T63_E0.765861.726
49_A59_E0.712361.605
54_E71_K0.711481.603
23_L49_A0.709251.598
4_I32_I0.698871.575
23_L64_L0.687231.549
20_Y24_E0.677151.526
5_V51_V0.672691.516
4_I30_D0.670361.511
7_F20_Y0.655671.478
59_E67_K0.642781.449
66_E70_E0.633431.428
8_C11_N0.626361.412
11_N40_C0.617691.392
56_V67_K0.608711.372
20_Y33_E0.605371.364
9_V33_E0.590841.332
19_V64_L0.587751.325
50_L53_G0.561291.265
18_Q21_E0.553071.246
65_L69_K0.553011.246
39_Y48_F0.552231.245
37_L50_L0.548451.236
21_E25_K0.526781.187
21_E24_E0.518161.168
10_S38_S0.512691.155
6_E32_I0.512381.155
50_L55_I0.495761.117
12_L35_G0.478441.078
8_C40_C0.475511.072
6_E50_L0.463131.044
56_V71_K0.461381.040
17_D21_E0.449151.012
11_N36_C0.442450.997
14_S46_K0.43750.986
6_E34_Y0.436890.985
39_Y57_A0.429630.968
7_F49_A0.419080.944
37_L48_F0.417280.940
22_K64_L0.403440.909
8_C46_K0.403020.908
19_V61_A0.391270.882
37_L55_I0.382660.862
11_N46_K0.371150.836
10_S13_A0.363480.819
18_Q61_A0.360870.813
51_V71_K0.358120.807
56_V59_E0.354460.799
22_K62_E0.346160.780
48_F55_I0.343290.774
12_L17_D0.343240.774
12_L41_G0.340190.767
15_G18_Q0.339430.765
26_D30_D0.339260.765
10_S35_G0.339080.764
13_A35_G0.326560.736
8_C36_C0.325560.734
10_S41_G0.323290.729
52_N71_K0.319560.720
9_V48_F0.319290.720
67_K71_K0.312970.705
9_V35_G0.312950.705
63_E66_E0.311070.701
10_S46_K0.310710.700
9_V41_G0.308680.696
17_D33_E0.294130.663
12_L16_T0.291570.657
6_E52_N0.291350.657
7_F31_V0.288170.649
23_L31_V0.284190.640
21_E65_L0.282460.637
29_I56_V0.277530.625
5_V53_G0.275020.620
66_E69_K0.274220.618
34_Y37_L0.273920.617
39_Y55_I0.271820.613
25_K61_A0.26720.602
59_E63_E0.265610.599
10_S14_S0.263240.593
54_E70_E0.261960.590
49_A56_V0.258480.583
9_V20_Y0.257110.579
9_V17_D0.252990.570
7_F16_T0.252290.569
20_Y31_V0.251550.567
12_L46_K0.244980.552
33_E37_L0.242530.547
29_I68_I0.240470.542
5_V67_K0.240190.541
41_G57_A0.238760.538
48_F57_A0.23770.536
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
1m2dA0.961599.30.31
2auvA0.871899.30.318
3i9v20.961599.30.332
1egoA0.897440.80.851
3qqcA135.80.855
1t3qA0.948729.80.861
3ic4A0.85924.30.866
3ba3A0.820524.50.866
4fiwA0.846220.80.87
1rm6C0.935920.80.87

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