GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PucR - Purine catabolism regulatory protein-like family
Pfam: PF07905 (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: 123
Sequences: 1387
Seq/Len: 11.28
HH_delta: 0.483 (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
89_E93_E0.594313.114
95_A102_L0.534942.803
13_K104_E0.501212.626
45_L75_G0.457482.397
16_A96_D0.436342.287
16_A20_G0.423972.222
61_L90_E0.411342.156
16_A95_A0.409482.146
66_R97_E0.381011.997
17_G20_G0.37741.978
93_E97_E0.372451.952
57_D60_E0.369551.937
105_I111_F0.359841.886
14_L103_I0.307821.613
66_R94_L0.307431.611
78_I87_I0.298611.565
31_M46_V0.293191.536
12_A103_I0.287041.504
45_L77_G0.285221.495
20_G23_R0.283161.484
92_I102_L0.277611.455
76_L100_L0.27431.437
20_G96_D0.266721.398
19_N99_G0.264861.388
62_R90_E0.262451.375
94_L97_E0.257851.351
79_K111_F0.25341.328
15_V104_E0.252321.322
93_E96_D0.250331.312
80_T104_E0.246651.293
36_P46_V0.244951.284
62_R93_E0.240441.260
66_R98_L0.240261.259
14_L21_L0.238061.248
63_E67_E0.230281.207
27_W116_R0.217821.141
68_L73_A0.215681.130
18_E96_D0.208351.092
92_I96_D0.206131.080
47_L118_V0.204081.069
115_T118_V0.20211.059
105_I109_V0.201521.056
94_L98_L0.200281.050
21_L24_P0.197291.034
32_E51_Y0.196981.032
46_V73_A0.196131.028
41_R116_R0.193761.015
27_W115_T0.193351.013
33_A36_P0.183240.960
57_D63_E0.181860.953
13_K106_P0.181350.950
68_L76_L0.179330.940
44_E74_A0.179260.939
58_E90_E0.17740.930
40_L73_A0.175920.922
77_G105_I0.172640.905
67_E70_E0.172510.904
62_R66_R0.171480.899
40_L109_V0.167420.877
29_H79_K0.164930.864
69_A76_L0.163520.857
16_A101_P0.161460.846
14_L115_T0.161040.844
86_E89_E0.159370.835
16_A23_R0.158910.833
81_G104_E0.157790.827
47_L77_G0.157680.826
65_I91_I0.157430.825
35_D52_A0.157310.824
48_T111_F0.156120.818
15_V108_E0.154590.810
110_P113_D0.154240.808
73_A76_L0.154040.807
51_Y79_K0.15340.804
16_A19_N0.15280.801
27_W114_I0.152470.799
59_E62_R0.152010.797
69_A98_L0.151520.794
81_G106_P0.151050.792
15_V96_D0.150680.790
38_D42_G0.149520.784
17_G101_P0.149310.782
40_L46_V0.14910.781
33_A79_K0.149080.781
79_K105_I0.148350.777
59_E93_E0.148190.777
58_E62_R0.147620.774
66_R70_E0.147420.773
47_L79_K0.146730.769
29_H100_L0.146270.766
32_E46_V0.146110.766
17_G21_L0.145340.762
89_E92_I0.14530.761
89_E107_W0.145230.761
30_V61_L0.144240.756
16_A102_L0.144190.756
41_R113_D0.143740.753
65_I88_P0.142920.749
23_R74_A0.142190.745
31_M36_P0.141250.740
38_D54_R0.140980.739
45_L59_E0.140440.736
65_I69_A0.140410.736
63_E97_E0.139780.732
52_A109_V0.139550.731
26_R116_R0.139540.731
35_D48_T0.139470.731
14_L25_V0.138440.725
34_P64_F0.138020.723
70_E89_E0.137610.721
17_G23_R0.137280.719
14_L17_G0.137260.719
49_T105_I0.136980.718
41_R87_I0.135950.712
36_P79_K0.135830.712
36_P67_E0.135760.711
88_P91_I0.135680.711
44_E49_T0.135510.710
14_L20_G0.135480.710
12_A111_F0.135450.710
12_A105_I0.13490.707
25_V102_L0.134640.706
29_H112_S0.133890.702
18_E101_P0.133860.701
49_T75_G0.133840.701
27_W44_E0.133410.699
62_R94_L0.133170.698
47_L112_S0.133150.698
29_H40_L0.132620.695
58_E89_E0.132550.695
39_W79_K0.132520.694
80_T87_I0.132320.693
49_T52_A0.132320.693
18_E106_P0.131760.690
33_A112_S0.131560.689
41_R49_T0.131560.689
31_M40_L0.131270.688
52_A73_A0.130940.686
27_W43_G0.13040.683
41_R114_I0.129680.680
34_P39_W0.12930.678
55_D71_K0.129010.676
59_E63_E0.128990.676
17_G96_D0.128820.675
52_A69_A0.12810.671
32_E81_G0.127760.669
31_M64_F0.126190.661
62_R91_I0.125880.660
26_R77_G0.125770.659
13_K58_E0.125730.659
22_D26_R0.125680.659
45_L103_I0.125090.656
18_E62_R0.125060.655
39_W110_P0.124510.652
20_G101_P0.12430.651
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
1knxA0.93599.30.483
1ko7A0.93599.10.526
2iojA0.869998.60.612
3l2bA0.87895.30.794
4ggiA0.894384.90.843
3nvtA0.926877.90.853
1g8mA0.837459.70.87
2qkfA0.74858.80.871
3dnjA0.691157.90.872
4ahqA0.967556.10.873

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