GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1998 - Domain of unknown function (DUF1998)
Pfam: PF09369 (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: 84
Sequences: 973
Seq/Len: 11.58
HH_delta: 0.858 (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
5_A71_L0.431022.428
80_C83_C0.377732.128
68_L72_E0.370442.087
9_A70_L0.336131.894
57_R62_E0.32691.842
5_A67_A0.310171.747
76_C80_C0.294271.658
76_C83_C0.28741.619
13_F62_E0.284751.604
16_C20_E0.266651.502
4_H7_R0.263041.482
55_F79_G0.260821.469
3_A7_R0.258241.455
25_I29_P0.251091.415
10_A54_L0.24561.384
69_E72_E0.243871.374
2_L38_I0.242931.369
17_D70_L0.240921.357
13_F66_R0.240131.353
2_L64_L0.238671.345
1_S84_L0.23791.340
23_F26_Y0.234391.321
17_D39_F0.234361.320
79_G84_L0.218321.230
3_A23_F0.217171.223
3_A43_T0.212961.200
60_F64_L0.210921.188
69_E73_E0.209591.181
56_E61_E0.2011.132
9_A67_A0.198261.117
66_R69_E0.194491.096
7_R23_F0.19331.089
22_G43_T0.190221.072
15_G48_A0.189841.070
33_Q56_E0.188871.064
65_R69_E0.18721.055
33_Q62_E0.185031.042
61_E65_R0.182631.029
8_R11_P0.181391.022
6_L73_E0.180761.018
41_Y74_C0.180681.018
42_D47_G0.179721.013
1_S79_G0.173190.976
22_G41_Y0.170610.961
6_L67_A0.168090.947
53_R57_R0.167860.946
9_A63_L0.167390.943
23_F29_P0.167270.942
14_L51_A0.165370.932
62_E66_R0.165280.931
10_A36_P0.165150.930
33_Q37_R0.163320.920
29_P34_G0.162130.913
56_E78_D0.160490.904
16_C48_A0.159980.901
42_D45_P0.159620.899
56_E72_E0.158940.895
62_E65_R0.158880.895
57_R61_E0.157960.890
42_D51_A0.156440.881
2_L84_L0.156080.879
4_H15_G0.155120.874
3_A39_F0.154140.868
25_I28_R0.153910.867
38_I64_L0.153070.862
65_R72_E0.153040.862
10_A21_I0.152040.857
45_P74_C0.149210.841
19_S72_E0.147550.831
21_I43_T0.146550.826
66_R75_D0.145890.822
33_Q75_D0.145790.821
47_G76_C0.145450.819
6_L69_E0.145320.819
21_I51_A0.144970.817
3_A25_I0.143790.810
22_G54_L0.142960.805
4_H71_L0.142370.802
22_G40_L0.137990.777
11_P79_G0.137620.775
53_R60_F0.137510.775
7_R40_L0.136790.771
45_P53_R0.136630.770
65_R73_E0.136520.769
21_I53_R0.13530.762
14_L20_E0.135290.762
23_F41_Y0.1350.761
57_R60_F0.134150.756
7_R26_Y0.134110.756
28_R33_Q0.133790.754
6_L40_L0.132910.749
1_S81_P0.132470.746
12_L66_R0.131860.743
56_E73_E0.131640.742
26_Y39_F0.131460.741
61_E72_E0.131250.739
47_G80_C0.131180.739
12_L82_S0.131080.738
47_G71_L0.130920.738
54_L63_L0.13080.737
65_R75_D0.127870.720
34_G60_F0.127820.720
47_G83_C0.127340.717
2_L71_L0.127120.716
7_R43_T0.126680.714
4_H16_C0.126560.713
66_R70_L0.126390.712
10_A50_Y0.126010.710
54_L57_R0.125420.707
74_C81_P0.125240.706
34_G61_E0.125230.706
5_A48_A0.125010.704
57_R68_L0.12310.694
46_G81_P0.122370.689
38_I60_F0.121970.687
34_G70_L0.121960.687
56_E65_R0.121840.686
55_F61_E0.121750.686
20_E79_G0.121520.685
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
3h0gC0.785742.40.858
1twfC0.726231.20.868
2jadA0.9167240.874
3zywA0.857116.90.882
3ipzA0.809512.30.889
3m20A0.547612.30.889
1hfoA0.476210.40.892
3ry0A0.571410.30.892
2x4kA0.51199.80.894
3ej9A0.69059.70.894
If you are interested in a protein containing this domain,
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