GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4129 - Domain of unknown function (DUF4129)
Pfam: PF13559 (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: 72
Sequences: 1010
Seq/Len: 14.03
HH_delta: 0.754 (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
21_E29_R0.860054.468
24_R48_E0.765583.977
22_T25_E0.500632.601
3_Y44_T0.443812.306
42_E64_R0.344621.790
6_L40_L0.307321.597
49_R61_E0.291231.513
50_A53_G0.282721.469
23_P51_R0.275451.431
31_A41_E0.266711.386
27_A44_T0.2551.325
17_R21_E0.253011.314
43_L69_L0.251481.307
65_A69_L0.24721.284
59_A63_Q0.246681.282
17_R26_Y0.245461.275
3_Y7_L0.239351.244
7_L26_Y0.239341.243
30_L34_G0.238111.237
58_S61_E0.229541.193
21_E26_Y0.229231.191
12_R67_E0.228051.185
28_R32_Q0.220431.145
28_R56_P0.215121.118
46_L65_A0.214371.114
17_R47_Y0.211381.098
64_R67_E0.208561.084
7_L17_R0.197881.028
63_Q67_E0.19421.009
47_Y51_R0.192771.002
43_L65_A0.190230.988
20_S25_E0.189870.986
23_P48_E0.189170.983
50_A57_P0.189040.982
6_L10_L0.188150.978
41_E60_E0.186590.969
56_P63_Q0.1860.966
38_E63_Q0.185970.966
65_A68_A0.180710.939
23_P40_L0.175250.910
23_P47_Y0.173730.903
57_P62_F0.173410.901
6_L69_L0.165080.858
4_R23_P0.164220.853
62_F69_L0.163750.851
27_A31_A0.162950.847
28_R31_A0.162640.845
25_E47_Y0.161740.840
6_L62_F0.158220.822
42_E46_L0.157820.820
15_I30_L0.156590.814
14_G21_E0.156440.813
16_P26_Y0.154490.803
22_T44_T0.154320.802
54_G58_S0.154220.801
48_E68_A0.154010.800
7_L22_T0.152080.790
61_E64_R0.151970.790
30_L43_L0.151540.787
23_P44_T0.150270.781
26_Y47_Y0.150190.780
47_Y50_A0.14930.776
22_T50_A0.148890.774
4_R57_P0.147280.765
58_S64_R0.144750.752
40_L44_T0.143990.748
21_E25_E0.143110.744
28_R38_E0.142150.739
14_G30_L0.141920.737
31_A45_R0.141430.735
5_A8_R0.140780.731
47_Y53_G0.140480.730
32_Q45_R0.139940.727
7_L23_P0.139690.726
60_E64_R0.138710.721
28_R41_E0.137380.714
31_A34_G0.136670.710
34_G37_A0.136120.707
52_Y57_P0.135560.704
7_L52_Y0.134690.700
15_I21_E0.134450.699
48_E51_R0.134010.696
49_R54_G0.133710.695
38_E60_E0.13370.695
23_P52_Y0.133110.692
10_L34_G0.133070.691
5_A13_R0.132410.688
28_R59_A0.132330.688
8_R52_Y0.13190.685
39_A63_Q0.129630.673
14_G23_P0.129360.672
3_Y6_L0.129290.672
2_L43_L0.128840.669
18_R21_E0.12880.669
42_E68_A0.128650.668
12_R64_R0.128410.667
62_F66_R0.128010.665
2_L40_L0.127270.661
39_A43_L0.127150.661
41_E56_P0.126910.659
38_E41_E0.126770.659
2_L6_L0.126250.656
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
1o3uA0.986160.30.754
1wolA0.958358.90.756
2hsbA153.70.764
1ufbA0.986151.10.767
3cuqB0.986119.60.811
1w7pD0.9583190.812
4glxA0.597217.30.816
1zauA0.722215.20.82
3pefA0.6806150.82
2noxA0.87513.30.824
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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