GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CBM_20 - Starch binding domain
Pfam: PF00686 (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: 96
Sequences: 1003
Seq/Len: 10.45
HH_delta: 0.051 (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
78_E83_R0.684873.291
31_D34_K0.608572.925
65_K82_N0.579092.783
63_E82_N0.562352.702
38_L52_A0.499032.398
40_W48_P0.498842.397
19_Y69_K0.466172.240
5_T53_T0.45932.207
24_C62_F0.383461.843
12_T15_G0.35661.714
59_G87_V0.353521.699
23_S63_E0.336641.618
18_V68_I0.318831.532
30_W65_K0.315571.516
70_D74_N0.308911.484
23_S62_F0.30291.456
35_A67_V0.300611.445
12_T18_V0.300441.444
13_Q16_E0.298961.437
19_Y35_A0.297331.429
22_G27_L0.296471.425
20_I52_A0.290691.397
19_Y67_V0.281571.353
15_G40_W0.275391.323
16_E70_D0.270831.301
78_E82_N0.261271.256
30_W82_N0.25141.208
17_S37_P0.250961.206
3_S53_T0.234811.128
7_R51_S0.231571.113
25_P29_N0.23021.106
21_V67_V0.229711.104
23_S29_N0.226531.089
16_E68_I0.223251.073
36_V52_A0.221741.066
11_Q48_P0.216161.039
12_T16_E0.209721.008
21_V77_W0.209441.006
62_F85_L0.207440.997
8_V15_G0.206810.994
12_T40_W0.204190.981
3_S55_D0.197410.949
10_Y14_P0.196620.945
41_N51_S0.193150.928
65_K78_E0.191730.921
49_I70_D0.191720.921
12_T48_P0.19140.920
61_P86_T0.190680.916
19_Y37_P0.189780.912
4_V59_G0.186830.898
24_C29_N0.184250.885
56_L87_V0.183770.883
9_N49_I0.182510.877
10_Y68_I0.180520.867
14_P40_W0.17810.856
20_I83_R0.169080.813
68_I76_I0.168070.808
25_P28_G0.168040.808
7_R49_I0.167870.807
63_E77_W0.166850.802
6_F66_Y0.163020.783
6_F54_V0.161230.775
40_W68_I0.161170.775
57_P60_T0.159610.767
22_G28_G0.157420.756
73_G80_G0.15740.756
8_V18_V0.156390.752
5_T51_S0.153070.736
50_W77_W0.151820.730
20_I37_P0.150220.722
18_V38_L0.149280.717
31_D68_I0.149220.717
35_A69_K0.149190.717
72_D87_V0.146450.704
30_W78_E0.145760.700
33_K72_D0.145580.700
36_V67_V0.145230.698
12_T50_W0.145010.697
61_P84_V0.144580.695
68_I77_W0.14240.684
54_V58_A0.140870.677
41_N49_I0.140670.676
69_K73_G0.13940.670
10_Y18_V0.138950.668
58_A78_E0.138550.666
49_I66_Y0.138160.664
67_V75_V0.13680.657
58_A81_E0.136180.654
13_Q71_A0.135520.651
19_Y68_I0.135220.650
73_G87_V0.134860.648
10_Y54_V0.134350.646
32_P56_L0.132840.638
17_S70_D0.132350.636
10_Y48_P0.132190.635
65_K80_G0.130990.629
6_F76_I0.130710.628
67_V77_W0.129270.621
53_T69_K0.129030.620
3_S58_A0.128870.619
6_F20_I0.128560.618
8_V11_Q0.128310.617
81_E84_V0.128270.616
58_A88_P0.127680.614
10_Y84_V0.127590.613
7_R53_T0.126360.607
33_K69_K0.125670.604
41_N48_P0.125660.604
55_D58_A0.125560.603
24_C87_V0.125080.601
27_L62_F0.125050.601
25_P71_A0.124680.599
9_N40_W0.124120.596
12_T68_I0.124010.596
9_N48_P0.123560.594
28_G70_D0.123320.593
29_N86_T0.122720.590
65_K81_E0.12220.587
12_T17_S0.121890.586
54_V88_P0.120580.579
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
1cygA0.989699.90.051
2vn4A199.90.053
3bmvA0.979299.90.066
1d3cA0.979299.90.069
1ac0A199.80.087
1qhoA0.958399.80.092
1vemA0.947999.80.101
1gcyA0.968899.80.11
2z0bA0.989699.80.135
2laaA0.843898.30.613

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