GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4160 - Domain of unknown function (DUF4160)
Pfam: PF13711 (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: 66
Sequences: 454
Seq/Len: 6.88
HH_delta: 0.862 (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
19_V54_I0.537473.207
57_N60_E0.386562.307
13_D16_P0.38262.283
46_E52_E0.319331.906
17_P61_L0.316851.891
1_G23_Y0.316161.887
28_A42_L0.3011.796
44_R48_R0.297411.775
17_P62_L0.293741.753
31_W34_P0.268061.600
30_I51_L0.265681.585
43_P46_E0.263091.570
59_E63_E0.244611.460
30_I47_L0.242981.450
58_Q62_L0.23221.386
35_L54_I0.223471.334
56_E60_E0.209471.250
32_L61_L0.208021.241
5_Y22_R0.202021.206
26_F43_P0.195391.166
16_P29_K0.194991.164
21_V28_A0.187731.120
4_I53_W0.183771.097
13_D29_K0.179731.073
23_Y53_W0.1771.056
35_L51_L0.173691.036
32_L62_L0.171571.024
31_W36_E0.170811.019
14_H43_P0.169391.011
50_I53_W0.161990.967
49_K60_E0.161650.965
28_A37_V0.161170.962
1_G25_G0.159090.949
47_L55_E0.157960.943
15_E32_L0.157960.943
6_F61_L0.15540.927
23_Y43_P0.150750.900
43_P60_E0.149130.890
49_K56_E0.147950.883
59_E62_L0.14740.880
23_Y26_F0.147350.879
2_I21_V0.145920.871
58_Q61_L0.144140.860
21_V49_K0.143610.857
35_L38_N0.141390.844
6_F12_N0.140680.840
47_L51_L0.140180.837
5_Y8_S0.140050.836
17_P37_V0.139280.831
36_E45_K0.1380.824
48_R57_N0.13680.816
2_I23_Y0.136530.815
52_E55_E0.13620.813
31_W38_N0.135870.811
12_N36_E0.134650.804
48_R55_E0.132960.793
38_N47_L0.129950.775
22_R27_E0.129610.773
20_H45_K0.1290.770
15_E29_K0.127830.763
27_E44_R0.127550.761
8_S32_L0.127250.759
53_W61_L0.127160.759
1_G24_G0.125270.748
52_E56_E0.125220.747
34_P47_L0.124610.744
21_V30_I0.12380.739
33_E59_E0.123750.738
17_P58_Q0.123190.735
41_F44_R0.122430.731
21_V42_L0.122320.730
35_L59_E0.121580.726
55_E63_E0.121390.724
22_R44_R0.121250.724
62_L66_N0.12060.720
54_I58_Q0.120440.719
33_E55_E0.119930.716
12_N62_L0.118910.710
5_Y27_E0.118770.709
5_Y54_I0.118710.708
42_L50_I0.117270.700
1_G49_K0.117110.699
55_E58_Q0.11710.699
22_R66_N0.116170.693
24_G39_E0.115560.690
50_I64_E0.114320.682
49_K52_E0.112880.674
7_Y39_E0.111310.664
29_K47_L0.110820.661
40_G43_P0.110650.660
33_E62_L0.109710.655
15_E31_W0.109470.653
26_F30_I0.109360.653
22_R63_E0.109310.652
14_H31_W0.109080.651
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
2bnlA0.348527.70.862
3dljA0.484818.10.873
3pmdA0.409117.80.874
3qyhA0.984815.70.876
2dl6A0.878813.90.879
1m55A0.878812.60.882
4akgA0.848512.50.882
3ksvA0.878812.40.882
2cycA0.954511.50.884
1ykuA0.363611.10.884
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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