GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CBM_48 - Carbohydrate-binding module 48 (Isoamylase N-terminal domain)
Pfam: PF02922 (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: CL0369
Length: 85
Sequences: 4523
Seq/Len: 53.21
HH_delta: 0.02 (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
12_G54_T1.429262.719
42_M53_V1.300082.473
67_K79_E1.06542.027
24_S41_P1.063862.024
69_R79_E1.059152.015
28_V79_E0.992041.887
6_Y13_V0.970171.846
25_V70_I0.948221.804
24_S71_D0.944631.797
28_V69_R0.906571.725
71_D77_T0.904231.720
26_E41_P0.861921.640
72_G78_P0.846261.610
23_K71_D0.837221.593
16_R52_E0.830171.579
26_E69_R0.826781.573
2_L50_V0.815451.551
15_F68_Y0.808731.539
23_K73_D0.804011.530
4_A13_V0.79211.507
7_T54_T0.771961.469
20_P49_G0.734531.397
16_R50_V0.700281.332
26_E71_D0.682891.299
81_V85_A0.681361.296
7_T14_T0.668221.271
66_Y82_D0.667081.269
69_R77_T0.663361.262
37_A69_R0.663121.262
26_E39_E0.65031.237
15_F27_L0.632891.204
14_T52_E0.628451.196
40_Y53_V0.627651.194
4_A15_F0.603811.149
17_V25_V0.594981.132
30_Y65_Y0.580911.105
70_I80_V0.579891.103
55_V59_L0.576211.096
13_V59_L0.573611.091
42_M68_Y0.558031.062
72_G76_E0.55671.059
14_T54_T0.551271.049
22_A51_W0.547681.042
39_E69_R0.534431.017
17_V70_I0.524190.997
40_Y55_V0.520070.989
47_D52_E0.507670.966
46_D49_G0.495120.942
29_L40_Y0.485950.925
2_L84_Y0.473610.901
28_V39_E0.472160.898
15_F66_Y0.450070.856
46_D52_E0.44690.850
28_V67_K0.439660.836
19_A25_V0.433810.825
17_V68_Y0.429380.817
5_H14_T0.427110.813
17_V80_V0.415850.791
4_A68_Y0.413080.786
45_K48_D0.410710.781
27_L42_M0.404420.769
4_A66_Y0.400940.763
45_K52_E0.395710.753
27_L53_V0.385430.733
32_N40_Y0.384960.732
6_Y60_P0.374020.712
19_A22_A0.373150.710
21_N72_G0.370280.704
9_D12_G0.368120.700
7_T12_G0.365520.695
25_V42_M0.365020.694
48_D84_Y0.35680.679
43_T53_V0.351490.669
18_W50_V0.351050.668
28_V32_N0.346620.659
73_D76_E0.337540.642
22_A70_I0.329810.627
70_I78_P0.329280.626
55_V58_D0.329070.626
37_A65_Y0.323460.615
2_L16_R0.322260.613
17_V27_L0.319470.608
71_D76_E0.319210.607
2_L5_H0.316540.602
71_D74_D0.313890.597
43_T52_E0.311110.592
26_E38_E0.309910.590
15_F59_L0.309250.588
13_V60_P0.305470.581
17_V82_D0.29960.570
6_Y21_N0.29850.568
33_G48_D0.294650.561
24_S43_T0.293850.559
18_W49_G0.289030.550
19_A68_Y0.284480.541
6_Y9_D0.28240.537
67_K81_V0.282230.537
23_K74_D0.281960.536
53_V56_P0.281650.536
21_N73_D0.280650.534
19_A70_I0.278550.530
5_H84_Y0.277840.529
9_D14_T0.274390.522
65_Y81_V0.272510.518
19_A49_G0.262610.500
21_N80_V0.261620.498
68_Y84_Y0.260360.495
8_E54_T0.258850.492
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
3k1dA0.964799.50.02
4aioA0.941299.50.025
3amlA0.941299.50.037
1m7xA0.964799.40.066
2fhfA0.952999.40.071
2e8yA0.917699.40.094
3fawA0.952999.40.099
2wskA0.929499.30.104
2wanA0.929499.30.105
2vr5A0.941299.30.11

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