GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AP2 - AP2 domain
Pfam: PF00847 (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: CL0081
Length: 56
Sequences: 1665
Seq/Len: 29.73
HH_delta: 0.216 (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
43_K47_I0.893822.385
46_A50_R0.878262.343
49_A52_E0.742511.981
47_I50_R0.699191.865
8_W15_W0.681031.817
48_E51_K0.658631.757
18_Q30_R0.657581.754
38_F41_E0.639771.707
3_Y39_E0.583691.557
44_R48_E0.581261.551
16_R32_S0.579571.546
37_G41_E0.569921.520
36_F45_A0.568481.517
7_S18_Q0.556171.484
2_G39_E0.537571.434
32_S35_K0.517851.382
9_D16_R0.46691.246
33_V49_A0.448581.197
43_K46_A0.426451.138
39_E43_K0.421251.124
20_R30_R0.411241.097
21_V31_F0.399531.066
44_R47_I0.381261.017
7_S16_R0.374170.998
14_R37_G0.362520.967
7_S32_S0.361870.965
12_R35_K0.354140.945
16_R35_K0.347420.927
12_R19_I0.34560.922
16_R21_V0.335570.895
9_D35_K0.319660.853
17_A41_E0.319490.852
33_V45_A0.315840.843
8_W13_G0.308280.822
3_Y43_K0.303540.810
40_E44_R0.301350.804
22_W28_R0.298450.796
7_S30_R0.287540.767
34_G45_A0.286780.765
9_D18_Q0.28630.764
16_R20_R0.280860.749
36_F42_A0.273250.729
19_I46_A0.272990.728
9_D14_R0.269470.719
43_K50_R0.268450.716
50_R54_E0.266910.712
10_K16_R0.265540.708
48_E52_E0.265270.708
10_K14_R0.258610.690
29_K52_E0.256520.684
29_K51_K0.256390.684
28_R53_L0.255660.682
31_F52_E0.253030.675
14_R34_G0.25080.669
2_G29_K0.249010.664
12_R30_R0.247850.661
9_D32_S0.246020.656
30_R35_K0.245250.654
2_G15_W0.245130.654
39_E46_A0.245090.654
18_Q32_S0.244510.652
12_R20_R0.24410.651
47_I51_K0.242990.648
21_V29_K0.242640.647
2_G52_E0.240140.641
17_A46_A0.239960.640
20_R35_K0.238330.636
8_W12_R0.236810.632
5_G17_A0.235470.628
10_K54_E0.23470.626
3_Y47_I0.232030.619
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
1gccA0.946498.50.216
3igmB0.946498.20.289
1u3eM0.87568.60.713
3jtzA0.946462.40.723
1z1bA0.857161.90.724
3ju0A0.946454.30.736
3zl9A0.87517.90.793
4bgpA0.875170.795
4j1jD0.87516.70.796
3zlaA0.87516.30.797

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