GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4177 - Domain of unknown function (DUF4177)
Pfam: PF13783 (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: 61
Sequences: 342
Seq/Len: 5.61
HH_delta: 0.777 (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
35_E59_K0.815964.361
3_E60_R0.478412.557
1_K31_K0.33881.811
23_E27_N0.331371.771
21_D24_E0.328731.757
5_K29_Y0.325011.737
7_V29_Y0.296591.585
37_V59_K0.276051.475
2_W59_K0.264461.413
5_K23_E0.261251.396
38_S54_Y0.254481.360
36_L58_F0.243061.299
2_W61_E0.236971.267
5_K32_E0.235251.257
30_G59_K0.232341.242
40_I54_Y0.231481.237
21_D39_I0.221631.185
5_K28_E0.196741.052
22_L40_I0.196591.051
22_L57_I0.194931.042
6_V23_E0.191341.023
26_L30_G0.19041.018
2_W30_G0.189371.012
7_V58_F0.185720.993
6_V55_V0.180390.964
50_G54_Y0.179770.961
40_I57_I0.177470.949
6_V26_L0.175650.939
28_E32_E0.166940.892
26_L55_V0.166430.890
1_K30_G0.162270.867
25_I37_V0.160220.856
25_I29_Y0.159440.852
9_V58_F0.157640.843
40_I50_G0.154590.826
34_W60_R0.154030.823
29_Y58_F0.145780.779
36_L56_L0.14260.762
28_E60_R0.141180.755
24_E31_K0.13990.748
10_P50_G0.139630.746
38_S42_P0.139460.745
38_S59_K0.135220.723
42_P53_G0.134560.719
2_W29_Y0.134040.716
6_V30_G0.132860.710
28_E50_G0.131930.705
11_T52_E0.130450.697
11_T53_G0.128050.684
50_G53_G0.127410.681
10_P57_I0.127230.680
11_T21_D0.126680.677
9_V53_G0.125830.673
7_V21_D0.125220.669
10_P41_P0.124970.668
39_I56_L0.124610.666
30_G35_E0.122110.653
9_V39_I0.121360.649
50_G60_R0.121250.648
39_I57_I0.120810.646
36_L53_G0.120410.644
29_Y32_E0.119650.640
1_K61_E0.118640.634
24_E37_V0.117920.630
8_E39_I0.117640.629
20_E24_E0.116530.623
2_W35_E0.115070.615
4_Y35_E0.11460.613
9_V42_P0.11440.611
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
1qb3A0.967270.80.777
3qy2A0.9672690.78
1pucA0.9672670.782
1cksA0.852565.90.784
1jg5A0.672145.50.808
3drxA0.8525150.847
2psoA113.90.849
1ln1A0.655713.30.85
3vusA113.20.85
4f9dA111.40.854
If you are interested in a protein containing this domain,
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