GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Smr - Smr domain
Pfam: PF01713 (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: 83
Sequences: 1835
Seq/Len: 22.11
HH_delta: 0.08 (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
6_L14_A0.920113.302
8_V48_A0.77072.766
18_F30_L0.614432.205
15_L32_I0.592382.126
50_R67_D0.557842.002
34_T78_T0.526651.890
17_E21_E0.518641.861
22_A30_L0.517651.858
29_E81_Y0.504251.810
36_K76_G0.470741.689
72_D79_I0.457261.641
64_A81_Y0.43521.562
15_L49_V0.425851.528
3_L49_V0.422451.516
68_A77_A0.415921.493
31_R79_I0.414361.487
67_D75_S0.393551.412
31_R77_A0.39071.402
68_A72_D0.387081.389
3_L15_L0.377091.353
66_R81_Y0.369621.326
22_A27_I0.367571.319
6_L10_E0.366841.317
12_L52_W0.366821.316
14_A17_E0.365581.312
32_I80_V0.356061.278
5_G11_A0.352011.263
23_R61_E0.3511.260
46_K67_D0.344161.235
19_L30_L0.339171.217
68_A74_N0.338221.214
12_L48_A0.336171.206
66_R72_D0.326991.174
50_R57_Y0.317821.141
66_R69_E0.316541.136
63_L81_Y0.310351.114
11_A45_L0.30011.077
36_K75_S0.297861.069
22_A82_L0.278180.998
33_I76_G0.277190.995
69_E72_D0.271250.973
57_Y83_K0.264920.951
8_V11_A0.261810.940
4_H78_T0.26050.935
20_D61_E0.25870.928
37_G45_L0.252150.905
20_D24_Q0.251150.901
34_T50_R0.250110.898
21_E26_G0.249920.897
53_L80_V0.247530.888
53_L62_V0.24720.887
8_V47_R0.243080.872
7_T10_E0.240770.864
63_L83_K0.237070.851
19_L59_Y0.236760.850
57_Y65_Y0.236060.847
13_R17_E0.234740.842
47_R51_R0.233670.839
46_K50_R0.232360.834
51_R60_E0.226530.813
32_I49_V0.222260.798
15_L52_W0.221040.793
28_R82_L0.220590.792
7_T11_A0.219720.789
1_I18_F0.21970.788
30_L82_L0.217180.779
9_E12_L0.215880.775
27_I51_R0.213390.766
22_A26_G0.210540.756
77_A80_V0.20890.750
71_E74_N0.204260.733
16_E52_W0.204050.732
7_T49_V0.20380.731
21_E31_R0.203460.730
36_K45_L0.196610.706
65_Y78_T0.195570.702
32_I53_L0.192710.692
27_I30_L0.192490.691
1_I32_I0.191610.688
8_V44_V0.190610.684
28_R47_R0.189770.681
2_D76_G0.188860.678
21_E25_R0.188760.677
50_R65_Y0.188030.675
12_L58_Q0.186690.670
30_L80_V0.185740.667
23_R83_K0.184910.664
1_I46_K0.182320.654
2_D36_K0.181480.651
9_E28_R0.177980.639
9_E26_G0.177290.636
45_L74_N0.177220.636
52_W62_V0.173760.624
7_T70_P0.173380.622
21_E28_R0.172080.618
36_K67_D0.171060.614
16_E20_D0.170650.612
17_E20_D0.170410.612
51_R58_Q0.170020.610
13_R64_A0.16950.608
4_H77_A0.169320.608
34_T65_Y0.169310.608
33_I36_K0.169120.607
1_I36_K0.168480.605
6_L11_A0.168320.604
1_I14_A0.165960.596
8_V12_L0.165880.595
30_L50_R0.165730.595
27_I70_P0.165470.594
4_H36_K0.163580.587
42_G60_E0.162520.583
47_R50_R0.161130.578
2_D5_G0.159750.573
47_R57_Y0.15930.572
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
3qd7X0.963999.80.08
2zqeA0.915799.70.131
3fauA0.879599.60.216
2vkcA0.879599.60.235
2d9iA0.879599.60.237
3lubA0.915773.20.831
1v7zA0.975945.20.857
3lvjC0.807237.40.864
3hz7A0.819337.10.864
3no4A0.975936.90.864

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