GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF336 - Domain of unknown function (DUF336)
Pfam: PF03928 (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: 132
Sequences: 1335
Seq/Len: 10.11
HH_delta: 0.014 (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
12_G39_A0.653123.241
18_E21_E0.645323.202
29_A54_A0.606983.012
9_W41_A0.480762.385
27_S40_F0.443442.200
29_A37_L0.432462.146
69_L122_H0.389471.932
9_W16_V0.38671.919
18_E123_A0.380381.887
26_V124_I0.371961.846
18_E22_R0.345281.713
3_L38_L0.344961.712
37_L40_F0.341171.693
52_D55_Q0.339311.684
29_A40_F0.33361.655
98_G112_G0.331351.644
67_S100_P0.319061.583
126_V130_A0.317241.574
116_G120_E0.306721.522
68_S98_G0.306281.520
102_R107_V0.300821.493
49_D64_F0.298261.480
49_D63_R0.296831.473
56_R91_D0.294841.463
95_L118_G0.294571.462
53_W114_S0.288951.434
15_A128_A0.284371.411
11_L128_A0.284241.410
29_A55_Q0.283651.407
99_V122_H0.283161.405
59_Y63_R0.283061.404
31_V110_A0.271061.345
11_L101_I0.270661.343
96_G122_H0.268611.333
37_L55_Q0.264151.311
40_F51_I0.263481.307
19_A26_V0.263421.307
113_V125_A0.261741.299
4_T7_D0.260391.292
15_A28_I0.258511.283
27_S50_S0.25821.281
13_D17_E0.255481.268
101_I129_V0.252031.251
20_R43_M0.25171.249
16_V41_A0.251491.248
15_A111_I0.248311.232
16_V28_I0.246041.221
22_R123_A0.240731.194
9_W13_D0.23491.166
30_V39_A0.234681.164
24_L116_G0.232511.154
32_D42_R0.232351.153
58_A112_G0.231691.150
122_H126_V0.223741.110
11_L111_I0.222621.105
45_G106_G0.220731.095
10_K13_D0.219191.088
6_E10_K0.215711.070
14_A131_A0.214441.064
59_Y91_D0.213311.058
25_P45_G0.212971.057
5_L41_A0.212491.054
15_A113_V0.209831.041
64_F71_L0.20981.041
26_V115_G0.208641.035
73_E76_Q0.206391.024
49_D53_W0.205611.020
68_S72_G0.198460.985
56_R93_V0.198240.984
8_A39_A0.198070.983
46_A50_S0.197630.981
98_G110_A0.196640.976
12_G41_A0.194290.964
54_A112_G0.193950.962
62_A110_A0.193730.961
19_A43_M0.193420.960
72_G76_Q0.193260.959
99_V125_A0.191920.952
60_T68_S0.190930.947
16_V20_R0.189840.942
7_D10_K0.189660.941
67_S99_V0.188810.937
75_L82_F0.187950.933
19_A124_I0.187080.928
22_R127_A0.186990.928
11_L14_A0.186020.923
69_L99_V0.183080.908
55_Q59_Y0.183010.908
57_K114_S0.179960.893
69_L96_G0.179960.893
127_A131_A0.177250.879
96_G118_G0.176880.878
68_S71_L0.17590.873
37_L51_I0.175290.870
47_P50_S0.174060.864
10_K14_A0.173030.859
77_P82_F0.171870.853
127_A130_A0.170830.848
65_G102_R0.170480.846
70_A74_R0.170030.844
53_W93_V0.168620.837
26_V116_G0.166550.826
103_V106_G0.166090.824
15_A124_I0.165170.820
68_S94_A0.165020.819
71_L94_A0.163790.813
120_E123_A0.16320.810
57_K115_G0.162740.807
13_D41_A0.160890.798
30_V101_I0.160410.796
102_R105_G0.159460.791
6_E13_D0.15910.789
17_E21_E0.158920.789
38_L44_D0.158530.787
5_L8_A0.15810.784
5_L44_D0.158010.784
27_S51_I0.15780.783
128_A131_A0.157610.782
15_A125_A0.155960.774
66_R74_R0.155490.772
119_E123_A0.155430.771
14_A17_E0.155040.769
11_L129_V0.154310.766
52_D56_R0.153910.764
34_G42_R0.150330.746
81_L84_S0.150220.745
22_R104_D0.149560.742
3_L7_D0.148690.738
99_V126_V0.148680.738
31_V58_A0.148270.736
75_L84_S0.147840.734
33_A48_P0.146470.727
24_L120_E0.146330.726
29_A112_G0.144970.719
16_V43_M0.143490.712
14_A127_A0.142260.706
117_T120_E0.142080.705
69_L73_E0.142060.705
26_V50_S0.141340.701
99_V129_V0.141270.701
82_F85_I0.141020.700
10_K21_E0.140710.698
103_V108_I0.139610.693
63_R68_S0.139590.693
6_E20_R0.139360.691
13_D16_V0.139050.690
98_G125_A0.137770.684
32_D58_A0.137730.683
40_F55_Q0.136420.677
26_V113_V0.136320.676
18_E127_A0.135730.673
25_P116_G0.134110.665
47_P64_F0.133540.663
93_V114_S0.133350.662
29_A51_I0.133330.662
14_A18_E0.13330.661
83_G94_A0.132740.659
58_A98_G0.131670.653
72_G75_L0.131480.652
12_G30_V0.131340.652
4_T8_A0.13070.649
48_P63_R0.130590.648
79_G85_I0.129880.644
62_A65_G0.12980.644
5_L9_W0.12970.644
95_L114_S0.129150.641
70_A73_E0.128940.640
100_P129_V0.128770.639
53_W95_L0.128320.637
76_Q82_F0.128010.635
31_V60_T0.127510.633
25_P33_A0.127360.632
85_I94_A0.12710.631
5_L38_L0.126850.629
17_E104_D0.126160.626
50_S116_G0.125590.623
57_K121_D0.125430.622
121_D125_A0.124950.620
115_G121_D0.124460.618
8_A30_V0.124450.617
42_R46_A0.124350.617
14_A128_A0.124160.616
21_E123_A0.123810.614
60_T71_L0.123420.612
81_L118_G0.12340.612
67_S129_V0.123250.612
47_P53_W0.122850.610
114_S121_D0.122560.608
7_D103_V0.122460.608
8_A38_L0.122410.607
20_R30_V0.121710.604
37_L109_G0.12170.604
99_V111_I0.121430.603
22_R116_G0.121190.601
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
2a2lA11000.014
3fpwA0.96211000.04
3mmhA0.901585.40.879
1iruJ0.333382.90.882
1rypJ0.333380.80.885
1rypM0.333380.50.885
1iruM0.333380.30.885
3trcA0.931880.20.885
1mkmA0.94773.90.891
4g3wA0.969769.90.894

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