GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ClpB_D2-small - C-terminal D2-small domain of ClpB protein
Pfam: PF10431 (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: 81
Sequences: 6919
Seq/Len: 85.42
HH_delta: 0.266 (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
3_E40_E2.417583.568
7_E36_D2.35553.477
11_D35_V2.319193.423
2_S5_D2.123153.134
67_A72_K1.809442.671
3_E36_D1.757612.594
8_K12_L1.616692.386
15_K18_N1.499112.213
37_Y41_K1.450882.141
37_Y40_E1.405912.075
7_E32_D1.26241.863
13_Q16_K1.222061.804
41_K59_E1.101151.625
22_K27_E1.071941.582
38_L55_I1.068481.577
19_E22_K0.995771.470
62_P66_D0.968281.429
32_D36_D0.901151.330
66_D70_S0.882671.303
55_I59_E0.880551.300
18_N22_K0.870771.285
37_Y59_E0.861971.272
67_A70_S0.821491.212
7_E35_V0.818461.208
13_Q53_R0.808141.193
18_N27_E0.806871.191
14_L30_F0.793341.171
41_K55_I0.790051.166
5_D8_K0.756091.116
11_D32_D0.712941.052
3_E7_E0.692671.022
41_K44_D0.689631.018
42_G55_I0.681831.006
36_D40_E0.672460.993
4_E36_D0.669740.988
30_F34_V0.664050.980
7_E11_D0.660040.974
17_L61_E0.659710.974
8_K11_D0.658330.972
10_A35_V0.657760.971
42_G52_L0.652790.963
31_D34_V0.64670.954
4_E7_E0.627280.926
1_L6_L0.61580.909
38_L59_E0.603980.891
10_A39_A0.600930.887
30_F35_V0.589760.870
15_K19_E0.581480.858
63_P67_A0.567110.837
18_N28_L0.564560.833
59_E63_P0.563630.832
14_L56_I0.559170.825
14_L18_N0.556470.821
6_L43_Y0.538580.795
13_Q17_L0.536790.792
6_L39_A0.524130.774
7_E39_A0.521440.770
11_D18_N0.508870.751
17_L56_I0.499640.737
10_A52_L0.496010.732
16_K19_E0.489270.722
10_A56_I0.484660.715
57_E61_E0.472530.697
15_K22_K0.472380.697
38_L56_I0.466970.689
53_R57_E0.456580.674
30_F60_I0.456380.674
47_Y58_R0.453030.669
47_Y54_R0.45170.667
13_Q61_E0.448150.661
20_R61_E0.437580.646
67_A71_G0.432570.638
11_D15_K0.422330.623
61_E65_A0.414040.611
18_N21_L0.406590.600
44_D51_P0.39660.585
34_V60_I0.383620.566
17_L20_R0.374360.553
32_D35_V0.370650.547
42_G47_Y0.36930.545
53_R62_P0.363250.536
3_E43_Y0.35450.523
42_G51_P0.354360.523
61_E66_D0.351620.519
12_L53_R0.350990.518
16_K25_G0.350770.518
14_L34_V0.349620.516
34_V37_Y0.348540.514
26_I68_I0.34030.502
55_I61_E0.339370.501
53_R61_E0.33580.496
61_E64_L0.335320.495
6_L10_A0.333390.492
13_Q52_L0.333310.492
56_I59_E0.33270.491
55_I62_P0.329810.487
14_L35_V0.329580.486
16_K20_R0.328830.485
21_L24_K0.327860.484
1_L9_I0.32670.482
4_E8_K0.325140.480
51_P62_P0.320650.473
47_Y51_P0.317530.469
29_E32_D0.31010.458
18_N30_F0.307440.454
28_L34_V0.303110.447
54_R60_I0.302160.446
21_L26_I0.301450.445
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
3pxiA199.20.266
1r6bX199.10.287
1qvrA199.10.306
4fcwA198.60.426
3hwsA0.96398.40.461
1g41A0.950698.20.504
1um8A0.9506980.535
1ofhA0.950696.60.65
3m6aA0.9136950.698
1qzmA0.913684.10.768

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