GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
BolA - BolA-like protein
Pfam: PF01722 (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: 76
Sequences: 1705
Seq/Len: 22.43
HH_delta: -0.007 (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
42_K50_L1.07952.752
42_K46_K0.999872.549
16_E31_K0.799492.038
14_E31_K0.780491.990
40_E74_E0.729821.860
37_D40_E0.726451.852
56_K60_K0.692931.766
33_I71_Y0.682581.740
59_I63_I0.656881.675
37_D73_P0.652011.662
12_E33_I0.647341.650
8_P11_L0.640331.632
52_Y59_I0.608381.551
33_I69_K0.598381.525
43_S46_K0.588981.501
45_I49_R0.583821.488
46_K49_R0.580551.480
34_I70_T0.547621.396
15_D27_G0.533281.359
13_V32_I0.526821.343
55_L66_L0.517781.320
31_K69_K0.515661.315
49_R53_K0.506321.291
10_H33_I0.495531.263
5_A54_A0.483571.233
47_R70_T0.4741.208
6_L50_L0.473871.208
16_E67_S0.463071.180
35_V72_T0.462441.179
7_P38_E0.461321.176
57_D60_K0.44341.130
38_E42_K0.443181.130
29_H65_A0.432781.103
53_K56_K0.429311.094
6_L34_I0.426271.087
15_D26_G0.402371.026
58_E62_G0.387670.988
48_H68_I0.383560.978
44_R47_R0.37980.968
45_I52_Y0.37380.953
3_K7_P0.370670.945
40_E72_T0.369840.943
31_K67_S0.363740.927
32_I66_L0.363610.927
35_V71_Y0.360440.919
52_Y56_K0.345480.881
50_L54_A0.336060.857
15_D25_G0.334930.854
29_H52_Y0.327920.836
6_L54_A0.323730.825
17_S26_G0.321630.820
29_H67_S0.319730.815
4_A40_E0.317880.810
9_T37_D0.317660.810
9_T73_P0.31280.797
16_E29_H0.310440.791
48_H66_L0.309220.788
2_L6_L0.306680.782
63_I66_L0.305320.778
57_D61_D0.30050.766
5_A38_E0.300170.765
49_R52_Y0.299760.764
13_V30_F0.295660.754
28_S63_I0.294060.750
29_H66_L0.289080.737
50_L53_K0.287450.733
10_H35_V0.284760.726
3_K11_L0.279760.713
59_I66_L0.273630.698
3_K8_P0.273370.697
29_H63_I0.267320.681
38_E50_L0.264270.674
14_E33_I0.258050.658
58_E61_D0.256650.654
40_E73_P0.255730.652
10_H46_K0.255310.651
39_F70_T0.251820.642
15_D45_I0.251140.640
11_L60_K0.245850.627
5_A9_T0.23580.601
8_P36_S0.233630.596
15_D30_F0.23340.595
59_I62_G0.232970.594
32_I37_D0.232770.593
33_I72_T0.230870.589
45_I67_S0.23040.587
39_F50_L0.229360.585
2_L28_S0.228820.583
3_K9_T0.225420.575
17_S28_S0.223120.569
35_V39_F0.21760.555
53_K57_D0.216460.552
47_R65_A0.214390.547
2_L32_I0.212880.543
33_I37_D0.212290.541
56_K62_G0.208190.531
36_S48_H0.205050.523
34_I51_V0.199630.509
13_V41_G0.198480.506
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
2dhmA199.9-0.007
1v60A199.9-0.003
3o2eA0.907999.90.11
2kdnA0.907999.90.116
1v9jA0.921199.90.118
1ny8A0.868499.90.153
3tr3A0.881699.90.16
1xs3A0.881699.90.168
2kz0A0.828999.80.212
1ylqA0.907977.70.854

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