GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2726 - Protein of unknown function (DUF2726)
Pfam: PF10881 (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: 126
Sequences: 618
Seq/Len: 4.9
HH_delta: 0.506 (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
77_D106_R0.41593.269
94_D106_R0.360782.836
81_H90_D0.335792.640
58_V97_L0.279732.199
9_E90_D0.266452.095
77_D94_D0.249661.963
75_E93_K0.246821.940
31_R34_D0.238911.878
78_G81_H0.218321.716
17_E25_R0.218161.715
29_Q57_H0.214911.689
94_D98_K0.205471.615
61_V70_P0.194381.528
12_F76_L0.186981.470
73_V97_L0.186171.463
107_I121_D0.184561.451
56_K93_K0.178981.407
58_V73_V0.17841.402
75_E81_H0.178111.400
16_L74_I0.176061.384
94_D104_L0.173551.364
75_E90_D0.171181.346
59_D75_E0.169451.332
9_E75_E0.169031.329
29_Q75_E0.168371.324
84_E88_E0.162451.277
32_L93_K0.155541.223
77_D81_H0.154721.216
91_E95_R0.150761.185
35_L61_V0.149611.176
9_E29_Q0.146851.154
114_S117_E0.144851.139
97_L102_I0.143531.128
27_F63_C0.143411.127
16_L70_P0.14251.120
34_D56_K0.139851.099
35_L58_V0.139841.099
10_R14_K0.139261.095
32_L58_V0.138081.085
61_V102_I0.137221.079
78_G93_K0.134141.054
95_R98_K0.132171.039
36_L100_A0.131941.037
36_L97_L0.131151.031
12_F107_I0.13021.024
77_D90_D0.129561.018
20_L74_I0.129541.018
75_E78_G0.128621.011
81_H109_P0.127090.999
20_L62_V0.126330.993
13_Y17_E0.125660.988
81_H93_K0.125350.985
33_S55_Q0.125310.985
13_Y26_V0.124540.979
60_F63_C0.124520.979
31_R53_I0.123910.974
11_A15_A0.12190.958
29_Q81_H0.12080.950
79_S82_D0.120730.949
59_D81_H0.12060.948
56_K96_V0.120130.944
58_V103_P0.119660.941
13_Y25_R0.119550.940
111_D114_S0.119230.937
72_A103_P0.118910.935
93_K104_L0.118740.933
26_V61_V0.116220.914
78_G86_R0.115290.906
98_K115_V0.113890.895
15_A18_E0.112520.885
24_Y72_A0.109460.860
57_H63_C0.109420.860
30_V79_S0.109180.858
70_P102_I0.108420.852
22_D62_V0.107650.846
32_L97_L0.107340.844
85_K91_E0.107210.843
87_Q117_E0.10680.840
83_Q87_Q0.105620.830
72_A93_K0.105610.830
9_E77_D0.105070.826
16_L122_L0.104280.820
116_E119_R0.104230.819
59_D78_G0.103350.812
14_K25_R0.102470.806
6_T9_E0.101990.802
19_A63_C0.101470.798
73_V93_K0.100690.792
116_E120_R0.100240.788
30_V64_D0.100190.788
32_L56_K0.100190.788
10_R22_D0.099950.786
115_V119_R0.099780.784
34_D57_H0.099650.783
75_E106_R0.099510.782
29_Q78_G0.098950.778
64_D110_K0.098750.776
37_R107_I0.098640.775
23_D101_G0.098490.774
85_K119_R0.098420.774
54_N117_E0.097520.767
12_F60_F0.097480.766
60_F70_P0.097170.764
6_T80_S0.096270.757
59_D106_R0.095910.754
24_Y85_K0.095650.752
56_K86_R0.095640.752
8_Q118_L0.095570.751
24_Y111_D0.095560.751
33_S53_I0.094140.740
14_K118_L0.093310.734
55_Q72_A0.092870.730
70_P107_I0.092310.726
64_D69_R0.092090.724
75_E104_L0.092010.723
62_V96_V0.091910.723
31_R92_F0.091550.720
26_V62_V0.091430.719
31_R54_N0.09140.718
59_D90_D0.091250.717
73_V102_I0.091110.716
26_V69_R0.090690.713
17_E26_V0.090670.713
53_I96_V0.08980.706
35_L122_L0.089620.705
20_L71_V0.089610.704
12_F23_D0.088990.700
58_V61_V0.088970.699
64_D100_A0.088270.694
10_R68_G0.087870.691
57_H92_F0.087540.688
19_A37_R0.087510.688
87_Q95_R0.087380.687
6_T109_P0.086920.683
8_Q12_F0.086550.680
80_S86_R0.086530.680
19_A107_I0.086270.678
9_E68_G0.085570.673
95_R108_S0.085540.672
36_L54_N0.085450.672
13_Y62_V0.085220.670
57_H104_L0.084730.666
72_A100_A0.084480.664
22_D26_V0.084290.663
30_V61_V0.08390.660
13_Y61_V0.083830.659
74_I77_D0.083690.658
79_S117_E0.083270.655
6_T12_F0.083150.654
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
3hrlA0.769899.20.506
3r3pA0.75499.20.525
1cw0A0.761998.80.596
1vsrA0.738198.70.601
1t0fA0.976279.70.855
3o3mA0.968362.80.872
3h1tA0.952457.90.875
3kc2A0.555639.80.887
4aklA0.785738.30.888
1zjjA0.452433.10.892
If you are interested in a protein containing this domain,
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