GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1214 - Protein of unknown function (DUF1214)
Pfam: PF06742 (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. )
Clan: CL0528
Length: 103
Sequences: 1041
Seq/Len: 10.11
HH_delta: 0.187 (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
64_D68_S0.791614.863
64_D70_T0.594793.654
28_T70_T0.537613.303
38_G99_F0.355242.182
20_D90_A0.342852.106
58_R61_I0.301461.852
46_D49_G0.273321.679
78_P83_W0.262621.613
26_V72_T0.262261.611
43_T51_L0.256621.577
20_D23_R0.252911.554
21_G67_G0.248381.526
74_S83_W0.235051.444
34_A37_A0.232451.428
75_P85_T0.232361.428
28_T64_D0.231651.423
75_P87_P0.216961.333
44_L85_T0.20741.274
73_L85_T0.202881.246
43_T96_R0.200961.235
7_Y41_S0.200931.234
6_V11_F0.200891.234
54_N59_Y0.199151.223
77_P80_G0.192771.184
8_F97_L0.188671.159
72_T83_W0.186451.145
29_I34_A0.184371.133
51_L59_Y0.18391.130
41_S100_P0.182641.122
59_Y62_N0.182541.121
4_D99_F0.18151.115
73_L93_L0.181271.114
56_L84_L0.180941.112
8_F95_V0.180271.108
13_D35_P0.180091.106
5_A98_Y0.179581.103
10_A19_L0.179191.101
76_E87_P0.178861.099
12_V18_Y0.177031.088
13_D19_L0.176671.085
7_Y96_R0.175871.080
58_R63_S0.175491.078
60_S63_S0.17461.073
46_D52_V0.173161.064
52_V86_P0.172211.058
49_G92_N0.170121.045
46_D92_N0.16951.041
34_A69_F0.169461.041
30_P33_A0.168341.034
13_D25_Y0.16781.031
58_R62_N0.166991.026
42_V61_I0.165961.020
41_S45_Y0.157760.969
26_V29_I0.156440.961
32_G65_A0.1550.952
40_W100_P0.154220.947
67_G96_R0.153430.943
45_Y98_Y0.152750.938
24_T76_E0.152720.938
4_D70_T0.150480.924
47_A92_N0.150460.924
66_D82_N0.14870.914
71_I93_L0.147860.908
44_L73_L0.145830.896
54_N61_I0.145670.895
56_L59_Y0.144480.888
26_V70_T0.143470.881
63_S69_F0.139460.857
44_L56_L0.137630.846
50_G87_P0.137430.844
39_F45_Y0.13740.844
35_P40_W0.137270.843
10_A95_V0.137050.842
52_V75_P0.136280.837
37_A97_L0.135050.830
19_L93_L0.132020.811
4_D56_L0.131430.807
58_R84_L0.131230.806
15_D87_P0.130920.804
17_E30_P0.130310.801
9_T92_N0.129280.794
76_E80_G0.128630.790
9_T73_L0.128520.790
42_V51_L0.128130.787
36_P97_L0.127910.786
49_G94_I0.127610.784
25_Y35_P0.127340.782
25_Y78_P0.127270.782
28_T34_A0.127190.781
37_A99_F0.125220.769
69_F95_V0.124580.765
57_N60_S0.123610.759
4_D60_S0.122660.754
5_A41_S0.122510.753
91_F98_Y0.122220.751
13_D91_F0.121290.745
45_Y100_P0.120430.740
28_T68_S0.119920.737
49_G99_F0.119110.732
30_P69_F0.11830.727
16_G27_L0.116780.717
6_V97_L0.116750.717
19_L91_F0.116330.715
24_T94_I0.115620.710
5_A8_F0.115050.707
35_P84_L0.114210.702
56_L79_G0.113830.699
44_L93_L0.113580.698
29_I32_G0.112840.693
17_E76_E0.112670.692
4_D26_V0.112150.689
5_A39_F0.111620.686
48_D91_F0.111510.685
8_F52_V0.110590.679
23_R37_A0.110490.679
16_G77_P0.110250.677
5_A43_T0.108880.669
27_L42_V0.108670.668
44_L52_V0.108510.667
18_Y38_G0.108430.666
11_F53_P0.108290.665
4_D57_N0.10810.664
50_G54_N0.107920.663
27_L71_I0.107070.658
33_A65_A0.106860.657
38_G41_S0.106380.654
74_S77_P0.106350.653
14_S26_V0.105840.650
22_N90_A0.10580.650
73_L84_L0.105650.649
19_L23_R0.105220.646
24_T87_P0.105060.645
12_V24_T0.104410.641
46_D65_A0.104170.640
85_T90_A0.103850.638
12_V19_L0.103670.637
76_E83_W0.103520.636
10_A93_L0.103470.636
42_V93_L0.103250.634
74_S78_P0.103170.634
49_G60_S0.102890.632
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
3u07A0.980699.80.187
2p3yA0.990399.80.192
2bumA0.941718.90.898
3t63M0.93216.50.9
2xsuA0.893214.50.903
2bumB0.941714.40.903
3llpA0.980610.80.908
3o5uA0.89329.30.91
2xwxA0.86418.30.912
2vldA0.81556.10.917

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