GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF423 - Protein of unknown function (DUF423)
Pfam: PF04241 (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: 89
Sequences: 792
Seq/Len: 8.9
HH_delta: 0.89 (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_Q0.690233.646
29_Q70_Y0.586863.100
35_A58_F0.515472.723
11_K17_E0.427492.258
64_L82_P0.377571.994
21_W69_L0.377381.993
6_G22_F0.373711.974
3_G28_Y0.338741.789
31_I34_L0.331381.750
22_F25_A0.320551.693
68_S84_T0.305811.615
39_L58_F0.304671.609
17_E20_E0.292131.543
82_P86_I0.273131.443
14_L19_L0.273021.442
18_Q21_W0.267141.411
14_L73_A0.259551.371
26_V29_Q0.255061.347
35_A38_A0.250771.325
21_W72_L0.246471.302
7_A24_T0.245941.299
72_L81_G0.239071.263
27_Q31_I0.23721.253
72_L84_T0.235321.243
25_A73_A0.227461.201
79_S82_P0.226821.198
31_I36_L0.222961.178
32_H62_T0.222031.173
53_L56_W0.218131.152
5_F9_G0.217321.148
69_L75_T0.215561.139
6_G29_Q0.204411.080
54_A57_L0.202961.072
2_L7_A0.197851.045
38_A41_L0.196981.040
4_A8_H0.193681.023
5_F68_S0.19341.022
5_F69_L0.19251.017
27_Q30_F0.190411.006
39_L55_G0.188970.998
33_A62_T0.188410.995
56_W60_L0.186170.983
84_T89_M0.186090.983
30_F34_L0.184470.974
6_G9_G0.184270.973
11_K66_S0.183870.971
3_G6_G0.182190.962
10_L74_L0.182040.962
39_L51_L0.181780.960
32_H67_G0.18160.959
5_F28_Y0.181320.958
49_R53_L0.178410.942
80_L83_I0.176660.933
69_L82_P0.174740.923
68_S72_L0.170740.902
73_A77_P0.168990.893
22_F29_Q0.168420.890
57_L60_L0.168280.889
22_F34_L0.165380.874
1_A9_G0.164220.867
37_L40_G0.162310.857
34_L84_T0.160690.849
22_F27_Q0.160420.847
62_T66_S0.159830.844
33_A38_A0.158690.838
41_L47_S0.158220.836
29_Q62_T0.156360.826
37_L44_Q0.154790.818
18_Q73_A0.152820.807
43_A51_L0.152210.804
3_G10_L0.152150.804
32_H58_F0.151720.801
26_V33_A0.149950.792
28_Y68_S0.149210.788
18_Q25_A0.148760.786
8_H85_P0.148320.783
10_L22_F0.14810.782
82_P89_M0.147370.778
60_L71_Y0.14640.773
24_T84_T0.146320.773
20_E23_Q0.145230.767
64_L86_I0.145090.766
41_L44_Q0.144980.766
42_L57_L0.14430.762
71_Y75_T0.144190.762
9_G14_L0.143990.761
33_A48_S0.143770.759
18_Q76_G0.143640.759
23_Q31_I0.143090.756
25_A66_S0.142580.753
62_T70_Y0.142440.752
6_G28_Y0.142090.751
63_L74_L0.142010.750
30_F86_I0.1420.750
49_R60_L0.141290.746
3_G8_H0.141120.745
15_S43_A0.140560.742
79_S86_I0.13870.733
41_L48_S0.13840.731
48_S54_A0.13840.731
81_G89_M0.13830.731
72_L80_L0.137690.727
43_A59_L0.135930.718
9_G74_L0.135870.718
75_T83_I0.135170.714
25_A37_L0.133710.706
10_L28_Y0.133320.704
49_R52_R0.133070.703
47_S51_L0.133020.703
13_Q47_S0.131660.695
71_Y77_P0.131610.695
50_L80_L0.131180.693
85_P88_G0.129980.687
65_F85_P0.12940.684
40_G44_Q0.12840.678
72_L82_P0.127850.675
27_Q43_A0.127610.674
15_S18_Q0.127390.673
5_F81_G0.126720.669
4_A10_L0.12530.662
69_L72_L0.125080.661
24_T28_Y0.125060.661
21_W82_P0.124910.660
18_Q78_K0.124650.658
23_Q26_V0.124590.658
13_Q43_A0.124280.656
30_F35_A0.124050.655
24_T69_L0.123960.655
21_W73_A0.121270.641
16_P20_E0.121210.640
13_Q16_P0.121180.640
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
1v54K0.539327.70.89
2y69K0.8098.80.911
1rz2A0.53932.10.933
1z1nX0.505620.934
1larA0.52811.50.938
3s3eA0.49441.50.938
3ux4A0.4271.50.938
3b9wA0.85391.40.938
2bzlA0.50561.40.939
3qe7A0.84271.30.939
If you are interested in a protein containing this domain,
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