GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AIG2_2 - AIG2-like family
Pfam: PF13772 (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: CL0278
Length: 83
Sequences: 1236
Seq/Len: 14.89
HH_delta: 0.112 (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
18_D30_R0.593443.039
18_D48_Y0.567782.908
14_L30_R0.538372.757
3_W76_P0.535242.741
34_T42_P0.432872.217
35_V45_A0.407612.087
6_L35_V0.396952.033
61_R65_L0.387721.986
34_T44_E0.3751.920
29_R51_N0.363511.862
6_L45_A0.330981.695
58_P69_G0.29941.533
77_A81_E0.290761.489
21_E28_Y0.280371.436
33_V47_T0.279131.429
30_R48_Y0.277271.420
5_V73_H0.254591.304
36_S42_P0.250341.282
18_D22_G0.249681.279
60_D64_D0.239351.226
65_L68_R0.223191.143
37_T41_K0.220931.131
59_S66_I0.219861.126
71_R81_E0.217421.113
32_E44_E0.209871.075
2_V66_I0.207021.060
20_Y59_S0.20691.060
70_A75_L0.200871.029
70_A80_V0.191870.983
30_R46_F0.1890.968
2_V79_Y0.188030.963
29_R49_V0.186820.957
8_E52_P0.186530.955
37_T43_V0.185380.949
17_L48_Y0.179890.921
7_Y20_Y0.179780.921
22_G30_R0.177410.909
28_Y48_Y0.177070.907
67_L78_E0.177020.907
65_L69_G0.176710.905
2_V70_A0.176650.905
20_Y27_A0.176420.903
31_I45_A0.174650.894
39_D42_P0.174460.893
65_L72_E0.174160.892
22_G48_Y0.172870.885
40_G43_V0.171610.879
49_V63_L0.171150.876
64_D68_R0.170760.874
61_R64_D0.170730.874
61_R66_I0.170340.872
69_G72_E0.169750.869
58_P75_L0.169290.867
27_A50_A0.167550.858
68_R72_E0.167360.857
10_S13_D0.167080.856
64_D67_L0.167060.856
38_A44_E0.1670.855
36_S40_G0.165820.849
37_T42_P0.165810.849
71_R80_V0.163630.838
12_E42_P0.16320.836
78_E81_E0.16310.835
23_V59_S0.161140.825
66_I69_G0.1580.809
6_L37_T0.157880.809
58_P70_A0.157440.806
71_R78_E0.15660.802
5_V72_E0.152690.782
19_R22_G0.152690.782
24_P28_Y0.15160.776
14_L18_D0.150560.771
59_S65_L0.150380.770
77_A80_V0.150280.770
70_A79_Y0.150220.769
4_G75_L0.15020.769
47_T65_L0.148810.762
14_L65_L0.148250.759
55_E78_E0.147340.755
15_E41_K0.147130.753
70_A77_A0.147130.753
24_P27_A0.146530.750
16_S72_E0.145110.743
22_G27_A0.144920.742
54_P59_S0.144810.742
67_L80_V0.144660.741
28_Y62_Y0.143920.737
74_G77_A0.143730.736
76_P81_E0.143630.736
18_D28_Y0.143520.735
13_D16_S0.143310.734
50_A65_L0.142610.730
45_A49_V0.141710.726
67_L73_H0.141460.724
43_V75_L0.141180.723
23_V79_Y0.140610.720
50_A53_K0.138930.711
50_A66_I0.138520.709
14_L48_Y0.137470.704
16_S22_G0.137360.703
12_E15_E0.137050.702
67_L71_R0.13690.701
12_E55_E0.136610.700
15_E64_D0.136190.697
9_L13_D0.134880.691
7_Y50_A0.134320.688
15_E24_P0.133880.686
16_S53_K0.132920.681
12_E36_S0.13210.677
42_P74_G0.131470.673
32_E48_Y0.131420.673
67_L76_P0.130370.668
36_S64_D0.130180.667
39_D43_V0.128820.660
20_Y48_Y0.128550.658
23_V62_Y0.128450.658
50_A59_S0.127660.654
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
3cryA199.60.112
2qikA0.98899.60.154
1vkbA0.951899.40.267
3judA0.951898.70.461
2g0qA0.951898.40.521
1xhsA0.831398.30.527
2jqvA0.963998.30.533
2qikA0.879598.30.537
1v30A0.807298.20.546
tr|CX0.867547.80.837

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