GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OsmC - OsmC-like protein
Pfam: PF02566 (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: 100
Sequences: 3599
Seq/Len: 35.99
HH_delta: 0.066 (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
71_E75_E1.400623.524
75_E79_E1.252523.151
56_S96_E1.064722.679
69_D73_E1.026282.582
58_H98_E0.981752.470
17_A42_V0.889782.239
31_R80_R0.877252.207
43_E60_R0.816972.056
21_A40_V0.801662.017
41_E62_T0.78541.976
45_E58_H0.774311.948
39_E62_T0.752071.892
73_E76_E0.747841.882
36_E64_K0.744341.873
69_D72_E0.721481.815
76_E80_R0.709751.786
28_A35_L0.69791.756
21_A38_L0.687711.730
65_S74_L0.66741.679
12_L91_L0.658151.656
43_E58_H0.646061.626
37_D64_K0.641081.613
33_I73_E0.625991.575
12_L15_A0.623911.570
26_M30_K0.586231.475
15_A87_V0.576871.451
60_R98_E0.568651.431
23_T27_V0.546921.376
45_E56_S0.545581.373
79_E83_K0.52861.330
7_N10_E0.499391.257
31_R73_E0.493831.243
19_C85_C0.488581.229
27_V80_R0.479951.208
27_V84_R0.474621.194
13_L44_G0.470161.183
41_E60_R0.462871.165
80_R84_R0.449811.132
73_E77_L0.431751.086
72_E75_E0.430241.083
31_R76_E0.429831.082
76_E79_E0.42821.077
12_L87_V0.428181.077
24_L81_A0.426611.073
6_P14_A0.419971.057
36_E66_D0.419761.056
40_V59_L0.418971.054
20_F61_I0.406741.023
13_L57_I0.402831.014
90_T95_I0.394910.994
9_E87_V0.386620.973
56_S98_E0.383250.964
20_F59_L0.382170.962
16_L59_L0.35220.886
12_L90_T0.351710.885
44_G54_F0.343810.865
85_C88_S0.340410.857
8_P19_C0.340260.856
42_V57_I0.339080.853
65_S68_D0.336530.847
63_V74_L0.334470.842
17_A40_V0.331580.834
90_T93_N0.331110.833
16_L91_L0.328230.826
21_A25_R0.326450.821
80_R83_K0.320740.807
34_D66_D0.320140.806
23_T85_C0.319790.805
24_L77_L0.319350.804
48_P51_P0.317240.798
6_P10_E0.308960.777
68_D73_E0.308410.776
82_E97_V0.308070.775
13_L42_V0.306530.771
20_F88_S0.304210.765
44_G57_I0.303770.764
47_D52_R0.299050.752
9_E46_L0.299020.752
72_E76_E0.298710.752
89_N92_R0.29750.749
49_E52_R0.293680.739
37_D40_V0.290520.731
6_P11_L0.288640.726
28_A77_L0.287710.724
30_K80_R0.286030.720
51_P89_N0.284840.717
18_S21_A0.284230.715
27_V77_L0.282290.710
56_S94_G0.28030.705
90_T94_G0.267430.673
9_E86_P0.266350.670
20_F78_L0.265660.668
69_D74_L0.2650.667
12_L16_L0.264890.666
26_M29_E0.260050.654
77_L80_R0.259990.654
82_E85_C0.258720.651
82_E88_S0.258620.651
27_V30_K0.258350.650
9_E90_T0.254540.640
43_E62_T0.251090.632
22_M26_M0.250580.630
74_L78_L0.249350.627
23_T84_R0.249050.627
25_R29_E0.247620.623
24_L78_L0.244660.616
47_D55_E0.239070.602
20_F23_T0.237330.597
28_A33_I0.235660.593
84_R89_N0.234220.589
9_E22_M0.233520.588
54_F90_T0.231070.581
3_G7_N0.230620.580
34_D67_G0.230230.579
30_K84_R0.230050.579
57_I91_L0.227990.574
41_E45_E0.22790.573
91_L94_G0.226180.569
16_L86_P0.226080.569
11_L14_A0.225530.567
88_S92_R0.225220.567
40_V61_I0.224080.564
42_V59_L0.223790.563
68_D74_L0.221430.557
23_T86_P0.221260.557
75_E78_L0.22060.555
87_V90_T0.22030.554
14_A17_A0.220090.554
35_L65_S0.219670.553
66_D71_E0.219580.552
23_T26_M0.219460.552
44_G59_L0.217490.547
52_R89_N0.216530.545
22_M87_V0.216460.545
39_E60_R0.216020.544
38_L63_V0.21550.542
39_E64_K0.214750.540
22_M25_R0.21370.538
29_E34_D0.213690.538
88_S97_V0.212650.535
15_A23_T0.212420.534
47_D56_S0.209850.528
23_T30_K0.209150.526
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
2onfA0.9999.80.066
1vlaA199.80.083
1ml8A0.9899.80.084
2oplA0.9899.80.094
3cjeA0.9899.80.099
2d7vA199.80.1
1qwiA0.9999.70.106
1nyeA0.9999.70.108
2e8eA0.9799.70.108
2pn2A0.9699.70.117

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