GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CBS - CBS domain
Pfam: PF00571 (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: 57
Sequences: 35313
Seq/Len: 619.53
HH_delta: -0.109 (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
16_D20_E2.492382.392
13_S16_D2.481272.382
14_P43_V2.469442.370
11_T36_V2.362112.267
12_V33_L2.204232.116
10_I28_N1.891731.816
37_D41_K1.846221.772
12_V16_D1.799391.727
16_D24_I1.735581.666
12_V35_V1.730731.661
31_S48_R1.70641.638
34_P42_L1.628731.563
13_S38_E1.586421.523
14_P37_D1.550351.488
12_V21_A1.525271.464
47_S50_D1.48861.429
48_R52_L1.476381.417
25_M33_L1.441991.384
17_S20_E1.414511.358
37_D43_V1.347361.293
24_I28_N1.312511.260
32_R45_I1.251481.201
20_E24_I1.244481.195
2_G5_M1.210421.162
19_E23_E1.172211.125
10_I24_I1.167031.120
1_V5_M1.13711.091
30_I33_L1.103361.059
21_A33_L1.075461.032
11_T40_G1.041841.000
10_I30_I1.035490.994
23_E27_K1.025730.985
6_T30_I1.00720.967
20_E23_E1.005380.965
14_P38_E1.002170.962
24_I27_K0.972440.933
36_V40_G0.954830.916
31_S49_S0.951340.913
32_R47_S0.894190.858
46_I51_L0.892210.856
45_I50_D0.86060.826
13_S37_D0.856460.822
21_A46_I0.84330.809
49_S53_K0.841650.808
31_S47_S0.84140.808
22_L26_R0.826080.793
22_L51_L0.80930.777
22_L52_L0.805380.773
23_E26_R0.803160.771
32_R48_R0.800140.768
21_A25_M0.764910.734
22_L48_R0.757380.727
13_S36_V0.752590.722
49_S52_L0.743420.714
18_L51_L0.724690.696
35_V43_V0.710770.682
15_D38_E0.705470.677
30_I34_P0.696080.668
12_V24_I0.675370.648
18_L54_A0.646880.621
16_D21_A0.63770.612
32_R49_S0.62930.604
26_R52_L0.624770.600
26_R48_R0.623060.598
50_D53_K0.604050.580
36_V39_D0.576940.554
9_P34_P0.568170.545
49_S54_A0.552280.530
36_V42_L0.548240.526
36_V43_V0.538240.517
25_M51_L0.52480.504
25_M48_R0.51210.492
26_R53_K0.504080.484
2_G7_P0.497440.477
6_T10_I0.496240.476
1_V4_I0.491550.472
18_L21_A0.481610.462
18_L46_I0.480.461
32_R52_L0.473920.455
6_T9_P0.462260.444
32_R50_D0.460310.442
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
4esyA198.2-0.109
3orgA0.982598.1-0.098
3kxrA198-0.079
2zy9A198-0.077
4esyA0.982598-0.076
3l2bA198-0.074
2yzqA198-0.074
3orgA198-0.067
2ouxA198-0.066
2yvyA198-0.064

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