GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3447 - Domain of unknown function (DUF3447)
Pfam: PF11929 (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: CL0465
Length: 76
Sequences: 1090
Seq/Len: 14.34
HH_delta: 0.746 (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
11_E32_D0.41562.262
24_I27_K0.370412.016
28_K71_R0.364711.985
11_E35_C0.357291.945
63_D66_K0.333651.816
10_L35_C0.314041.709
69_N72_A0.310721.691
39_A48_A0.292071.590
8_K11_E0.285431.554
62_S66_K0.284241.547
62_S65_L0.26721.454
45_N75_Y0.265341.444
37_E63_D0.26191.426
19_F47_I0.260671.419
36_L48_A0.2511.366
58_K63_D0.241711.316
63_D67_Y0.240421.309
49_D75_Y0.239441.303
34_D37_E0.238441.298
29_N32_D0.237531.293
10_L26_L0.217231.182
8_K66_K0.21161.152
26_L54_N0.208711.136
10_L31_P0.206841.126
70_L73_F0.206181.122
2_N11_E0.205381.118
48_A64_C0.204361.112
28_K56_N0.204191.111
34_D66_K0.203161.106
47_I50_W0.202761.104
39_A51_L0.201631.097
40_I59_I0.201531.097
2_N65_L0.201231.095
4_K29_N0.197141.073
17_G22_I0.196141.068
17_G47_I0.195441.064
16_G21_I0.194351.058
44_N47_I0.187281.019
7_K11_E0.187171.019
9_T25_C0.184541.004
7_K34_D0.184171.002
23_N27_K0.183260.997
10_L30_K0.181760.989
16_G34_D0.180410.982
16_G71_R0.17780.968
11_E38_Y0.176820.962
43_H67_Y0.175080.953
17_G49_D0.174280.949
59_I64_C0.173970.947
2_N62_S0.173690.945
7_K32_D0.173560.945
5_I25_C0.170170.926
35_C38_Y0.169450.922
8_K12_Y0.169180.921
33_N37_E0.167560.912
61_I73_F0.163510.890
60_S65_L0.160520.874
7_K29_N0.160190.872
45_N48_A0.159420.868
14_I47_I0.158130.861
50_W55_Y0.157970.860
6_T9_T0.156680.853
27_K47_I0.156260.851
7_K33_N0.156010.849
14_I44_N0.155880.848
9_T42_S0.155270.845
58_K61_I0.154430.841
58_K62_S0.154390.840
7_K62_S0.153870.838
49_D71_R0.15320.834
34_D60_S0.152160.828
8_K58_K0.149510.814
4_K7_K0.147550.803
2_N28_K0.147050.800
52_I56_N0.146890.800
60_S63_D0.145830.794
54_N61_I0.14560.792
14_I17_G0.145370.791
12_Y38_Y0.145110.790
33_N52_I0.144110.784
7_K58_K0.142860.778
49_D54_N0.142850.778
8_K34_D0.140950.767
23_N50_W0.140720.766
36_L57_L0.140310.764
20_E68_Y0.138660.755
37_E66_K0.137940.751
67_Y72_A0.137730.750
8_K33_N0.135760.739
8_K65_L0.135150.736
2_N7_K0.134870.734
27_K54_N0.13440.732
9_T24_I0.133620.727
30_K33_N0.132950.724
62_S68_Y0.13220.720
69_N74_F0.132040.719
64_C72_A0.13170.717
44_N48_A0.129350.704
8_K19_F0.128250.698
4_K28_K0.127390.693
56_N72_A0.126340.688
71_R75_Y0.126050.686
15_I42_S0.125920.685
34_D65_L0.125770.685
37_E62_S0.125770.685
10_L25_C0.12530.682
4_K34_D0.124990.680
3_A58_K0.124950.680
4_K30_K0.124870.680
8_K62_S0.124710.679
2_N63_D0.12410.675
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
2dznA0.947494.90.746
1n11A193.80.76
2f8yA193.70.76
4duiA0.973793.60.762
3keaA0.986893.30.764
4hbdA0.763293.30.764
1n11A193.20.765
2ajaA0.986893.20.765
3b7bA1930.767
2f8yA0.9868930.767
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