GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ACT_6 - ACT domain
Pfam: PF13740 (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: CL0070
Length: 76
Sequences: 11169
Seq/Len: 146.96
HH_delta: 0.084 (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
26_H61_A2.111863.401
21_G25_E1.619692.609
23_L28_C1.603062.582
59_E63_E1.402772.259
17_A21_G1.37632.217
22_V61_A1.171051.886
9_G15_I1.142181.840
26_H57_R1.119761.803
31_E49_S0.988321.592
25_E61_A0.986041.588
56_E60_S0.983211.584
22_V26_H0.911071.467
7_V19_V0.882551.421
4_V47_L0.876521.412
22_V25_E0.863721.391
55_L59_E0.844721.360
6_T45_I0.827041.332
16_V33_S0.822371.324
61_A64_E0.807481.301
60_S64_E0.799611.288
17_A24_A0.767441.236
16_V20_T0.750651.209
12_R18_A0.736051.185
22_V65_L0.713171.149
33_S46_M0.706351.138
18_A21_G0.705361.136
57_R60_S0.704641.135
11_D14_G0.698621.125
56_E59_E0.691061.113
18_A65_L0.676261.089
35_Q44_L0.6741.086
12_R15_I0.673611.085
22_V62_L0.66481.071
57_R61_A0.657121.058
50_I54_S0.648081.044
54_S57_R0.64571.040
20_T30_I0.627571.011
5_I48_V0.59650.961
29_N49_S0.591650.953
32_D47_L0.590770.951
36_A39_G0.559850.902
60_S63_E0.533630.859
18_A22_V0.532030.857
13_P27_G0.531710.856
15_I18_A0.516420.832
34_R47_L0.508460.819
4_V45_I0.506850.816
23_L48_V0.501010.807
8_V41_R0.499440.804
11_D29_N0.494340.796
17_A20_T0.481760.776
20_T23_L0.47870.771
8_V43_T0.477340.769
9_G44_L0.466060.751
21_G24_A0.463430.746
33_S37_V0.46190.744
9_G33_S0.452820.729
14_G29_N0.434580.700
52_E55_L0.430830.694
7_V46_M0.429770.692
32_D35_Q0.428720.690
43_T47_L0.421160.678
28_C50_I0.421150.678
36_A45_I0.41870.674
61_A65_L0.417230.672
38_L43_T0.417160.672
53_D56_E0.410520.661
51_P54_S0.404420.651
23_L58_L0.398760.642
15_I65_L0.396210.638
28_C54_S0.394910.636
38_L45_I0.394210.635
20_T24_A0.393510.634
9_G16_V0.384750.620
28_C58_L0.383190.617
6_T43_T0.382920.617
20_T46_M0.381770.615
35_Q46_M0.378020.609
19_V46_M0.375970.606
17_A47_L0.371080.598
39_G42_F0.361040.581
9_G42_F0.348350.561
53_D57_R0.347760.560
35_Q42_F0.341250.550
38_L41_R0.338110.545
44_L48_V0.332130.535
41_R45_I0.331730.534
16_V23_L0.330730.533
34_R38_L0.327440.527
30_I50_I0.325360.524
4_V38_L0.324980.523
5_I59_E0.321980.519
4_V29_N0.31820.512
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
3p96A198.50.084
3louA198.40.11
3nrbA198.40.118
3o1lA198.30.124
3obiA198.30.127
3n0vA198.30.128
1zpvA198.30.129
2nyiA0.986898.30.151
1u8sA198.20.158
2nyiA198.10.187

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