GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CBM49 - Carbohydrate binding domain CBM49
Pfam: PF09478 (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: CL0203
Length: 80
Sequences: 1301
Seq/Len: 16.26
HH_delta: 0.35 (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
20_Q78_I1.13494.053
68_K71_Q0.839062.997
47_I52_K0.776792.774
50_L60_L0.768352.744
51_D61_P0.703952.514
24_T74_T0.655252.340
48_W76_G0.596892.132
46_S78_I0.590542.109
22_D74_T0.590212.108
23_V75_F0.57692.060
6_T22_D0.51131.826
5_Q77_Y0.506481.809
61_P64_Q0.464981.661
41_D57_T0.454141.622
67_I73_F0.453971.621
33_I67_I0.451471.612
47_I50_L0.423791.514
9_N20_Q0.423181.511
39_S57_T0.40011.429
34_K65_P0.398821.424
8_V22_D0.391991.400
52_K75_F0.376561.345
21_Y77_Y0.367421.312
53_V56_N0.366061.307
10_S13_E0.333491.191
6_T24_T0.330961.182
3_I38_I0.328771.174
7_L10_S0.326231.165
30_S69_P0.32351.155
8_V20_Q0.319041.139
36_L64_Q0.310741.110
40_I58_Y0.303581.084
62_S65_P0.292891.046
35_S65_P0.288211.029
28_N69_P0.287541.027
25_I38_I0.284471.016
4_T26_T0.281591.006
67_I71_Q0.280791.003
43_L53_V0.267880.957
40_I75_F0.267640.956
11_W48_W0.265720.949
53_V58_Y0.257390.919
34_K66_T0.249560.891
21_Y36_L0.247120.883
5_Q40_I0.244870.875
47_I75_F0.244230.872
64_Q73_F0.244140.872
47_I60_L0.232510.830
42_N77_Y0.227410.812
7_L21_Y0.227040.811
31_K66_T0.224950.803
50_L58_Y0.220650.788
31_K59_T0.217720.778
24_T72_S0.210790.753
32_P68_K0.210740.753
38_I73_F0.209680.749
27_N69_P0.201550.720
36_L50_L0.200230.715
9_N22_D0.19540.698
26_T72_S0.192830.689
42_N46_S0.186460.666
50_L75_F0.185630.663
23_V36_L0.181290.647
31_K69_P0.178610.638
29_G32_P0.177050.632
27_N67_I0.172640.617
54_S57_T0.171690.613
5_Q21_Y0.171620.613
26_T70_G0.169560.606
8_V24_T0.169540.606
22_D78_I0.168720.603
40_I43_L0.167960.600
11_W76_G0.167860.600
23_V77_Y0.167810.599
63_Y76_G0.167220.597
3_I27_N0.167160.597
61_P65_P0.166420.594
37_K59_T0.166150.593
13_E62_S0.166130.593
60_L65_P0.160970.575
4_T33_I0.160370.573
20_Q49_G0.157690.563
47_I51_D0.157590.563
40_I56_N0.157290.562
20_Q76_G0.156790.560
42_N56_N0.156530.559
46_S66_T0.155810.556
40_I52_K0.155050.554
6_T28_N0.154990.554
11_W49_G0.154050.550
49_G52_K0.153440.548
44_Y54_S0.151690.542
27_N38_I0.148230.529
25_I67_I0.146940.525
14_N40_I0.145330.519
30_S51_D0.142680.510
31_K45_G0.140090.500
26_T67_I0.138040.493
21_Y38_I0.138030.493
38_I75_F0.137620.492
44_Y57_T0.137370.491
44_Y53_V0.137050.489
32_P70_G0.135550.484
49_G76_G0.135510.484
4_T54_S0.133840.478
14_N48_W0.133470.477
12_T46_S0.133360.476
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
3icgA0.9599.10.35
3ndzE0.95990.378
1exgA0.937598.90.397
1e5bA0.812597.70.598
2cwrA0.8597.70.6
1hehC0.812597.30.635
1c7sA0.9591.90.751
1yewA0.966.10.812
3rfrA0.87557.90.821
2g30A0.837548.40.83

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