GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CBM_6 - Carbohydrate binding module (family 6)
Pfam: PF03422 (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: CL0202
Length: 125
Sequences: 1662
Seq/Len: 13.3
HH_delta: 0.067 (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
67_D102_H1.1555.119
25_V34_I0.571712.534
35_E105_Y0.555642.462
40_D101_K0.53632.377
52_R120_Y0.458152.030
33_W105_Y0.447411.983
53_Y79_L0.429761.905
106_L118_I0.428341.898
50_T122_Q0.419811.861
46_T96_K0.408941.812
28_I108_F0.403591.789
36_Y121_F0.391531.735
65_R107_V0.390551.731
98_P102_H0.39041.730
41_V97_L0.384721.705
37_N103_T0.362381.606
50_T124_T0.355011.573
41_V47_Y0.340291.508
50_T92_S0.339971.507
50_T90_T0.339231.503
48_T92_S0.328451.456
18_D119_D0.319091.414
63_E109_N0.316191.401
60_G116_F0.313861.391
44_A98_P0.313491.389
36_Y106_L0.312411.385
47_Y97_L0.311961.383
80_P91_V0.308621.368
26_G85_W0.304981.352
58_G81_P0.30241.340
65_R73_L0.296381.314
65_R105_Y0.293791.302
51_I77_V0.28711.272
53_Y91_V0.286731.271
52_R90_T0.28611.268
52_R119_D0.283551.257
66_I102_H0.278051.232
35_E103_T0.275741.222
13_I23_Y0.274181.215
65_R68_G0.26191.161
63_E107_V0.252021.117
63_E73_L0.250411.110
62_I116_F0.247291.096
61_T78_S0.245571.088
14_E24_V0.241761.071
49_L121_F0.239921.063
14_E117_N0.238151.055
54_A88_W0.235131.042
61_T76_T0.235111.042
56_G85_W0.233711.036
16_D119_D0.230361.021
29_E32_D0.229281.016
77_V93_V0.22751.008
63_E76_T0.226881.005
42_P47_Y0.226171.002
24_V117_N0.225150.998
51_I79_L0.2250.997
37_N101_K0.218430.968
84_G87_T0.217310.963
73_L107_V0.214930.953
12_Y27_Y0.213470.946
28_I116_F0.211040.935
88_W117_N0.209730.929
9_G12_Y0.207580.920
11_V32_D0.206520.915
16_D24_V0.206440.915
64_L95_V0.203250.901
108_F116_F0.202810.899
51_I62_I0.199690.885
55_N81_P0.198510.880
15_T23_Y0.19770.876
52_R88_W0.19760.876
41_V44_A0.197130.874
30_N109_N0.196020.869
49_L64_L0.193780.859
48_T124_T0.192620.854
67_D98_P0.192380.853
34_I118_I0.191720.850
54_A83_G0.191220.847
43_E98_P0.189420.839
45_G97_L0.188420.835
47_Y123_F0.18830.835
41_V99_A0.187960.833
82_T90_T0.186890.828
64_L104_I0.186620.827
54_A117_N0.185160.821
85_W117_N0.182660.810
42_P45_G0.180760.801
39_V121_F0.179930.797
27_Y86_D0.179720.796
46_T94_S0.178120.789
24_V86_D0.177880.788
33_W37_N0.177190.785
41_V45_G0.17660.783
24_V27_Y0.176580.783
54_A82_T0.174990.776
44_A99_A0.173760.770
83_G87_T0.173230.768
62_I108_F0.172450.764
75_G93_V0.172170.763
68_G105_Y0.1710.758
56_G116_F0.170520.756
41_V66_I0.169640.752
43_E46_T0.168960.749
25_V28_I0.167670.743
90_T122_Q0.167260.741
12_Y32_D0.166830.739
106_L121_F0.166250.737
49_L93_V0.163550.725
36_Y39_V0.16220.719
10_G13_I0.162060.718
27_Y32_D0.16190.718
26_G117_N0.16140.715
39_V104_I0.160990.713
86_D119_D0.160430.711
27_Y117_N0.159480.707
49_L123_F0.15590.691
51_I93_V0.155620.690
73_L104_I0.154850.686
22_G27_Y0.154770.686
74_I104_I0.154430.684
43_E96_K0.153970.682
14_E17_N0.153210.679
79_L82_T0.150720.668
62_I79_L0.149960.665
23_Y37_N0.148710.659
24_V88_W0.147930.656
48_T94_S0.147670.654
54_A84_G0.147280.653
40_D99_A0.147180.652
45_G100_G0.147150.652
55_N85_W0.145420.644
90_T120_Y0.144670.641
55_N59_G0.144420.640
65_R109_N0.144370.640
66_I98_P0.143750.637
30_N73_L0.143140.634
63_E112_D0.142150.630
80_P89_Q0.139170.617
112_D116_F0.139060.616
65_R76_T0.136890.607
41_V123_F0.136860.607
61_T110_G0.136710.606
93_V121_F0.136280.604
51_I121_F0.136260.604
25_V39_V0.1360.603
34_I63_E0.135830.602
51_I96_K0.13570.601
74_I89_Q0.135590.601
30_N112_D0.134210.595
10_G18_D0.133190.590
48_T91_V0.132970.589
44_A47_Y0.132590.588
10_G32_D0.132320.586
30_N61_T0.131910.585
14_E84_G0.131580.583
66_I123_F0.131430.582
12_Y16_D0.131170.581
62_I112_D0.131160.581
66_I104_I0.131070.581
77_V80_P0.131040.581
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
1uxzA0.96899.80.067
1w9sA0.99299.80.087
2v4vA0.97699.80.089
1uy4A0.95299.80.099
1uxxX0.9699.80.108
1od3A0.95299.80.108
2cdpA0.98499.80.112
4kmqA0.9699.80.121
3c7fA0.99299.80.126
2y8kA0.94499.80.142

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