GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PRD - PRD domain
Pfam: PF00874 (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: CL0166
Length: 89
Sequences: 4059
Seq/Len: 45.61
HH_delta: -0.074 (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
10_K61_E1.054763.099
67_E73_T0.926412.722
55_E87_E0.884312.599
60_K79_I0.712152.093
63_C79_I0.704892.071
8_E14_Q0.689292.025
59_A83_A0.650451.911
32_E36_N0.603741.774
7_I86_F0.603591.774
6_E65_R0.593911.745
45_I80_A0.593041.743
26_H85_H0.590771.736
2_Q69_R0.571991.681
49_K56_Y0.569551.674
3_I62_I0.54341.597
49_K76_D0.526131.546
33_R78_E0.524721.542
6_E61_E0.483181.420
55_E59_A0.469671.380
57_Q60_K0.461711.357
11_L58_I0.452281.329
60_K76_D0.445451.309
47_E51_K0.438221.288
59_A62_I0.434751.278
59_A79_I0.412241.211
34_L75_P0.409771.204
6_E10_K0.408511.200
45_I49_K0.406291.194
55_E83_A0.403161.185
57_Q61_E0.396131.164
28_S32_E0.393751.157
33_R40_I0.383811.128
60_K64_E0.376561.107
60_K63_C0.374021.099
79_I83_A0.372231.094
15_F86_F0.372171.094
5_N9_Q0.367871.081
62_I86_F0.367451.080
20_L24_I0.367161.079
56_Y60_K0.362641.066
75_P78_E0.357581.051
2_Q65_R0.353961.040
37_G72_I0.3481.023
30_M74_L0.347611.021
31_L35_K0.347211.020
30_M34_L0.345511.015
7_I11_L0.343921.011
76_D79_I0.342561.007
7_I58_I0.33760.992
41_E77_D0.337170.991
48_I52_Y0.331880.975
69_R72_I0.325710.957
18_E22_N0.316440.930
54_K57_Q0.314620.925
56_Y83_A0.311380.915
55_E86_F0.311170.914
64_E67_E0.31110.914
33_R37_G0.306640.901
22_N26_H0.302810.890
49_K60_K0.301390.886
61_E64_E0.298750.878
48_I80_A0.296970.873
59_A86_F0.296510.871
25_I29_I0.295890.869
80_A83_A0.295440.868
24_I28_S0.282610.830
5_N8_E0.280840.825
19_F29_I0.280770.825
56_Y76_D0.280710.825
19_F23_L0.275790.810
22_N88_S0.274440.806
18_E88_S0.274370.806
26_H30_M0.272990.802
78_E81_Y0.272050.799
44_L48_I0.271960.799
64_E68_K0.27010.794
26_H81_Y0.269910.793
3_I65_R0.266870.784
63_C74_L0.266160.782
43_P77_D0.265190.779
42_N80_A0.260920.767
45_I77_D0.25920.762
46_E49_K0.256440.754
46_E50_E0.253930.746
62_I65_R0.252920.743
16_D51_K0.252830.743
47_E50_E0.252450.742
31_L72_I0.251310.738
65_R69_R0.251190.738
42_N77_D0.249040.732
8_E20_L0.245960.723
25_I85_H0.24590.723
59_A63_C0.244980.720
42_N45_I0.243780.716
45_I56_Y0.242040.711
9_Q12_G0.236030.694
29_I32_E0.233750.687
48_I56_Y0.233640.687
41_E44_L0.232560.683
6_E9_Q0.231550.680
8_E12_G0.230810.678
42_N48_I0.228740.672
30_M40_I0.227150.667
6_E68_K0.227120.667
22_N85_H0.227010.667
39_E75_P0.226350.665
25_I28_S0.226240.665
53_P57_Q0.224340.659
64_E73_T0.222640.654
10_K54_K0.222260.653
28_S88_S0.221860.652
45_I76_D0.221820.652
34_L74_L0.219030.644
67_E74_L0.218660.643
17_D21_N0.218130.641
45_I81_Y0.216120.635
18_E21_N0.216050.635
19_F26_H0.215990.635
9_Q68_K0.215440.633
44_L84_L0.21540.633
56_Y80_A0.214360.630
52_Y87_E0.214190.629
18_E87_E0.213580.628
10_K58_I0.21320.626
26_H78_E0.212530.625
38_I42_N0.211510.622
11_L54_K0.210770.619
44_L50_E0.20990.617
11_L14_Q0.209160.615
23_L82_L0.208110.612
18_E85_H0.206680.607
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
3rioA199-0.074
3ufeA198.80.026
1h99A198.80.038
1h99A198.70.054
3nufA0.943896.70.443
3sqnA0.932696.20.481
3sqnA0.898995.80.498
3nw0A0.932616.90.773
3d5pA0.51693.90.827
3d9wA0.41573.70.828

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