GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4143 - Domain of unknown function (DUF4143)
Pfam: PF13635 (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: CL0236
Length: 90
Sequences: 1084
Seq/Len: 12.04
HH_delta: 0.74 (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
48_A74_F0.579033.051
51_L74_F0.47942.526
47_V87_V0.449052.366
50_E53_K0.413472.178
66_D70_Q0.394192.077
22_N42_L0.344621.816
48_A61_L0.339971.791
39_K89_Y0.339911.791
48_A87_V0.33481.764
72_V84_P0.33231.751
49_Q53_K0.312821.648
45_N49_Q0.292291.540
71_E88_K0.289721.526
19_G50_E0.285911.506
60_E77_E0.267181.408
75_V84_P0.264411.393
21_L42_L0.262121.381
77_E82_I0.25351.336
27_I36_L0.231431.219
18_P45_N0.229331.208
62_Y77_E0.22841.203
46_F50_E0.227641.199
43_F87_V0.227431.198
64_W70_Q0.218961.154
78_N81_R0.216451.140
55_L84_P0.215951.138
64_W84_P0.210851.111
28_S31_D0.210241.108
76_I85_I0.20911.102
35_N38_E0.206761.089
22_N28_S0.204581.078
18_P22_N0.203611.073
47_V85_I0.203531.072
74_F87_V0.195041.028
23_A36_L0.193781.021
52_L61_L0.193191.018
66_D69_G0.192691.015
58_G62_Y0.190741.005
65_R69_G0.187170.986
40_G88_K0.186010.980
18_P49_Q0.184430.972
51_L76_I0.1830.964
55_L59_Y0.178790.942
17_D71_E0.176680.931
19_G40_G0.173090.912
40_G44_E0.169580.893
21_L89_Y0.169390.892
26_G37_D0.169050.891
20_L72_V0.168520.888
35_N66_D0.165740.873
23_A35_N0.164780.868
20_L24_L0.159030.838
45_N48_A0.158750.836
19_G49_Q0.158710.836
22_N25_L0.156210.823
19_G46_F0.155570.820
54_R82_I0.155540.819
21_L39_K0.153250.807
59_Y83_I0.150340.792
41_A63_Y0.149890.790
24_L30_Q0.147450.777
63_Y76_I0.147220.776
55_L63_Y0.146990.774
72_V75_V0.14550.767
51_L64_W0.145280.765
25_L90_G0.144010.759
17_D88_K0.141750.747
29_S52_L0.141290.744
41_A80_G0.140960.743
29_S32_L0.140870.742
55_L62_Y0.140830.742
30_Q53_K0.140260.739
48_A64_W0.13990.737
55_L58_G0.138630.730
63_Y74_F0.138550.730
78_N83_I0.138480.730
28_S36_L0.13790.727
71_E86_E0.136790.721
53_K62_Y0.13580.715
19_G45_N0.135580.714
31_D42_L0.135280.713
44_E86_E0.134520.709
67_K90_G0.134260.707
61_L74_F0.132510.698
53_K58_G0.132370.697
59_Y76_I0.132080.696
55_L61_L0.130710.689
47_V58_G0.130510.688
55_L60_E0.12970.683
29_S33_L0.129040.680
54_R78_N0.127860.674
85_I88_K0.127690.673
18_P90_G0.126760.668
19_G70_Q0.126540.667
64_W85_I0.12650.666
73_D86_E0.126490.666
22_N45_N0.125590.662
18_P32_L0.125240.660
43_F65_R0.124970.658
50_E54_R0.124830.658
39_K69_G0.12470.657
31_D34_N0.123630.651
35_N75_V0.123050.648
31_D81_R0.122930.648
18_P41_A0.121460.640
30_Q70_Q0.120460.635
50_E77_E0.11950.630
43_F64_W0.118710.625
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
1hh1A0.697.20.74
1gefA0.5444970.748
2eo0A0.622296.70.759
3fovA0.755696.70.76
1y88A0.688996.70.761
1ob8A0.566796.60.762
2wcwA0.588996.20.774
1xmxA0.966795.10.794
2ostA0.686.60.836
3dnxA0.6778650.864
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0712 seconds.