GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glyco_hydro_2 - Glycosyl hydrolases family 2
Pfam: PF00703 (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: 110
Sequences: 3305
Seq/Len: 30.05
HH_delta: 0.165 (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
77_K85_Y1.080723.040
39_R92_E0.999782.812
43_F90_E0.87412.459
77_K83_D0.824892.320
80_S83_D0.822612.314
41_R92_E0.786512.212
40_V91_V0.780162.195
92_E102_S0.739752.081
88_T106_R0.726182.043
41_R90_E0.691441.945
42_L107_F0.689271.939
18_A109_F0.65891.853
6_V91_V0.639211.798
73_I76_P0.62531.759
23_E68_T0.619071.741
89_L107_F0.618791.741
21_S68_T0.616151.733
94_D99_V0.610921.719
12_L78_L0.607331.708
88_T104_E0.588131.654
90_E102_S0.586031.649
90_E104_E0.585841.648
92_E99_V0.554941.561
19_K70_T0.554781.561
45_P85_Y0.554651.560
73_I109_F0.553391.557
10_P109_F0.547281.540
43_F49_K0.509031.432
41_R49_K0.505491.422
80_S84_P0.471011.325
6_V103_I0.468731.319
40_V89_L0.464951.308
39_R94_D0.458741.290
36_V93_L0.455541.281
86_L106_R0.450461.267
9_T23_E0.447011.257
94_D98_E0.44121.241
21_S70_T0.440381.239
49_K52_T0.429481.208
6_V105_T0.428881.206
8_V89_L0.425821.198
17_S72_E0.410421.155
43_F88_T0.408571.149
99_V102_S0.401271.129
13_D78_L0.392941.105
23_E66_R0.381171.072
8_V107_F0.381021.072
47_G50_V0.379111.066
44_D48_K0.373191.050
40_V69_L0.37281.049
42_L89_L0.372761.049
10_P107_F0.372181.047
37_T54_S0.364251.025
19_K72_E0.35821.008
44_D77_K0.357571.006
95_D100_L0.355411.000
8_V105_T0.353240.994
51_V71_I0.350150.985
4_E27_R0.337020.948
93_L100_L0.333250.937
14_D17_S0.330580.930
41_R52_T0.330280.929
17_S74_P0.327340.921
38_V91_V0.325160.915
44_D88_T0.31540.887
24_V69_L0.315230.887
4_E25_E0.314320.884
8_V22_V0.313660.882
20_V109_F0.310520.873
44_D47_G0.310460.873
25_E66_R0.309420.870
9_T21_S0.304010.855
76_P109_F0.301720.849
20_V107_F0.298050.838
39_R54_S0.295880.832
18_A76_P0.295180.830
11_D21_S0.291440.820
44_D50_V0.284120.799
37_T94_D0.282750.795
7_F23_E0.278860.784
10_P18_A0.277370.780
12_L109_F0.275360.775
10_P20_V0.265190.746
57_V67_I0.260590.733
12_L76_P0.259620.730
81_P84_P0.259250.729
10_P13_D0.252590.711
2_H93_L0.249960.703
17_S78_L0.249910.703
81_P103_I0.248620.699
88_T91_V0.243130.684
39_R52_T0.242370.682
6_V24_V0.242290.682
10_P82_E0.239370.673
12_L18_A0.237090.667
91_V105_T0.234860.661
38_V93_L0.234310.659
11_D14_D0.234150.659
69_L91_V0.232940.655
103_I106_R0.232470.654
3_I24_V0.232160.653
44_D85_Y0.230360.648
22_V40_V0.229450.645
24_V38_V0.22540.634
3_I91_V0.223140.628
45_P77_K0.222810.627
77_K87_Y0.218830.616
13_D17_S0.21580.607
2_H101_D0.214260.603
93_L101_D0.212620.598
42_L73_I0.211360.595
101_D104_E0.207840.585
75_N98_E0.207550.584
81_P101_D0.205340.578
95_D98_E0.20530.578
29_E96_D0.20370.573
22_V69_L0.202040.568
76_P87_Y0.201310.566
30_S95_D0.198960.560
20_V71_I0.197960.557
43_F47_G0.195370.550
24_V101_D0.192330.541
11_D19_K0.189260.532
38_V67_I0.189240.532
6_V10_P0.1890.532
24_V40_V0.188070.529
3_I6_V0.188040.529
101_D105_T0.187510.527
11_D18_A0.187420.527
13_D16_D0.184430.519
5_D9_T0.183950.517
94_D97_G0.183170.515
2_H27_R0.182530.513
97_G100_L0.18190.512
81_P105_T0.1810.509
43_F66_R0.179590.505
7_F25_E0.17840.502
4_E105_T0.177770.500
14_D52_T0.177550.499
86_L108_G0.175980.495
24_V27_R0.175860.495
81_P107_F0.175650.494
2_H26_V0.174110.490
39_R74_P0.172450.485
6_V101_D0.169610.477
5_D12_L0.168750.475
12_L16_D0.16870.475
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
3fn9A0.990999.60.165
3gm8A0.963699.60.172
3cmgA0.972799.60.186
2je8A0.981899.60.196
1jz7A0.972799.50.213
3bgaA0.954599.50.215
3obaA0.963699.50.23
2vzsA0.945599.50.243
3hn3A0.854599.40.274
3lpfA0.827399.30.301

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