GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PP-binding - Phosphopantetheine attachment site
Pfam: PF00550 (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: CL0314
Length: 67
Sequences: 19041
Seq/Len: 284.19
HH_delta: -0.117 (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
2_Q44_E2.787582.760
21_D61_R2.577222.551
59_T62_D2.198522.176
19_D22_T1.935471.916
20_P61_R1.933821.914
57_H66_Y1.817961.800
6_I40_E1.813781.796
30_D33_D1.806011.788
53_D66_Y1.761771.744
7_I29_L1.670711.654
23_D58_P1.629421.613
50_P53_D1.623061.607
4_R8_A1.615071.599
4_R20_P1.589391.573
9_E40_E1.562511.547
24_F29_L1.515171.500
42_E48_K1.482691.468
2_Q6_I1.430291.416
57_H62_D1.412221.398
40_E44_E1.388061.374
38_V42_E1.384721.371
23_D26_D1.375711.362
6_I9_E1.369181.355
2_Q5_E1.29861.286
7_I60_I1.24941.237
29_L33_D1.217651.205
11_L29_L1.202991.191
3_L64_A1.200741.189
6_I44_E1.176561.165
10_V40_E1.158581.147
5_E44_E1.114551.103
7_I37_L1.077161.066
4_R60_I1.046261.036
8_A17_E1.041731.031
2_Q45_F0.992210.982
13_V16_E0.987870.978
7_I63_L0.982540.973
61_R65_E0.979980.970
20_P60_I0.973370.964
4_R18_I0.957560.948
58_P62_D0.957410.948
62_D65_E0.951860.942
34_A38_V0.939680.930
60_I64_A0.936550.927
22_T27_L0.936290.927
36_E40_E0.907780.899
33_D36_E0.904750.896
35_I51_P0.904430.895
20_P64_A0.903920.895
53_D57_H0.816580.808
3_L41_L0.806210.798
6_I37_L0.80150.793
10_V36_E0.792760.785
25_F34_A0.779880.772
13_V17_E0.771440.764
39_S43_E0.754890.747
53_D56_E0.73620.729
31_S35_I0.720780.714
52_S56_E0.716050.709
8_A16_E0.708160.701
39_S55_F0.704910.698
35_I39_S0.704120.697
8_A13_V0.703550.696
3_L60_I0.702450.695
40_E43_E0.697490.690
36_E39_S0.691570.685
41_L67_I0.67360.667
8_A18_I0.670650.664
24_F63_L0.657540.651
6_I10_V0.656710.650
34_A54_L0.65440.648
5_E9_E0.645220.639
42_E47_I0.638780.632
10_V37_L0.633310.627
29_L34_A0.6250.619
34_A55_F0.620610.614
37_L63_L0.603980.598
25_F55_F0.598950.593
22_T26_D0.597420.591
47_I67_I0.596410.590
21_D59_T0.591710.586
6_I41_L0.59110.585
38_V52_S0.580660.575
34_A51_P0.574390.569
10_V33_D0.573660.568
5_E8_A0.569890.564
9_E44_E0.567640.562
18_I60_I0.552080.547
52_S55_F0.541680.536
38_V51_P0.53740.532
41_L45_F0.534030.529
61_R64_A0.533250.528
41_L47_I0.523320.518
37_L41_L0.518860.514
37_L54_L0.518820.514
25_F39_S0.504030.499
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
2kjsA198.6-0.117
2l22A198.6-0.114
2lteA198.5-0.088
4i4dA0.970198.5-0.088
2vsqA0.970198.5-0.087
2cq8A0.970198.5-0.086
4dg8A0.970198.5-0.083
3tejA0.970198.5-0.082
1dnyA0.970198.5-0.077
4dxeH198.5-0.075

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