GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4148 - Domain of unknown function (DUF4148)
Pfam: PF13663 (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: 58
Sequences: 276
Seq/Len: 4.76
HH_delta: 0.831 (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
23_Q27_E0.514242.858
27_E31_A0.505682.811
53_Q57_A0.384012.134
7_P10_A0.321511.787
33_A56_L0.314191.746
27_E30_Q0.311071.729
26_A33_A0.288881.606
26_A30_Q0.276771.538
49_A54_A0.264841.472
5_A8_A0.262881.461
7_P13_Q0.253711.410
28_L36_Y0.250091.390
32_E38_P0.240631.337
25_R29_A0.229161.274
5_A10_A0.228651.271
54_A57_A0.215541.198
34_A54_A0.213581.187
4_L7_P0.211091.173
40_G48_D0.204881.139
31_A36_Y0.202941.128
39_S42_S0.202471.125
36_Y52_A0.200341.113
40_G43_D0.199991.112
28_L32_E0.199111.107
38_P48_D0.186931.039
49_A53_Q0.179190.996
29_A57_A0.179030.995
50_Q54_A0.175480.975
30_Q56_L0.174940.972
44_S48_D0.174820.972
4_L43_D0.174410.969
19_L41_E0.170940.950
32_E48_D0.170720.949
34_A56_L0.169930.944
29_A33_A0.163820.911
29_A32_E0.161210.896
30_Q55_R0.160050.890
29_A41_E0.156190.868
25_R50_Q0.155960.867
7_P33_A0.155240.863
10_A42_S0.154550.859
31_A49_A0.152050.845
49_A52_A0.151650.843
5_A23_Q0.150380.836
37_L40_G0.150070.834
14_A42_S0.148350.825
25_R33_A0.1440.800
40_G44_S0.141340.786
11_F22_A0.140170.779
43_D56_L0.13920.774
28_L46_P0.135080.751
7_P12_A0.134890.750
6_A27_E0.13260.737
7_P18_P0.131330.730
44_S47_D0.128840.716
6_A50_Q0.128060.712
9_A47_D0.128030.712
39_S51_A0.124420.692
31_A46_P0.122010.678
13_Q55_R0.12020.668
28_L35_G0.119470.664
36_Y45_Y0.116920.650
6_A22_A0.116770.649
26_A56_L0.115570.642
36_Y50_Q0.115530.642
52_A55_R0.111070.617
11_F45_Y0.110110.612
49_A55_R0.110060.612
28_L45_Y0.109640.609
20_T39_S0.109560.609
38_P53_Q0.108970.606
50_Q55_R0.108560.603
25_R36_Y0.108550.603
52_A56_L0.108480.603
25_R49_A0.108050.601
44_S57_A0.107260.596
33_A41_E0.107080.595
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
2jnaA0.965552.30.831
2nocA0.982820.80.862
1g6uA0.655216.10.868
3nnfA0.93111.50.877
3go6A0.62077.50.885
3qphA160.89
3kmlA0.87935.70.892
3pdmP0.87935.20.894
3g20A0.948350.894
2b0tA0.79314.30.897
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