GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PAP2 - PAP2 superfamily
Pfam: PF01569 (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: CL0525
Length: 129
Sequences: 6207
Seq/Len: 48.12
HH_delta: 0.182 (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
25_R104_S1.320493.136
60_A110_I1.138712.704
51_F108_A1.112732.643
16_N57_A1.085782.579
109_G113_G1.024152.432
64_F117_A1.012732.405
92_A110_I0.977822.322
24_G49_N0.976062.318
50_S105_D0.917672.179
55_H101_H0.802521.906
68_Y121_Y0.790981.879
12_A57_A0.785611.866
56_A92_A0.760711.807
8_A61_A0.750931.783
11_L116_I0.742121.763
20_K54_G0.735581.747
60_A88_A0.730671.735
63_A88_A0.708861.684
96_V106_V0.680321.616
12_A61_A0.664561.578
50_S102_F0.645361.533
27_R95_R0.641511.524
113_G117_A0.638471.516
56_A109_G0.631921.501
60_A92_A0.610381.450
102_F105_D0.591421.405
16_N54_G0.581891.382
19_L23_F0.579561.376
94_S98_L0.544141.292
96_V103_F0.517591.229
64_F114_I0.513211.219
59_A91_V0.51261.217
52_P112_L0.501951.192
92_A106_V0.501581.191
95_R101_H0.486851.156
25_R102_F0.48471.151
12_A116_I0.484621.151
56_A106_V0.479911.140
52_P108_A0.471251.119
18_V22_I0.468911.114
67_A71_G0.460191.093
23_F51_F0.456881.085
93_L97_Y0.448541.065
21_W49_N0.440831.047
15_L112_L0.4321.026
19_L52_P0.428371.017
63_A87_L0.419310.996
32_I35_Y0.41860.994
68_Y117_A0.417920.993
54_G101_H0.403130.957
64_F68_Y0.391930.931
56_A60_A0.389720.926
17_N21_W0.38510.915
67_A85_I0.384670.914
55_H94_S0.383440.911
13_A17_N0.382930.909
61_A117_A0.381650.906
95_R100_A0.381510.906
107_I111_L0.373590.887
64_F113_G0.372920.886
53_S101_H0.371920.883
61_A65_F0.364940.867
70_L74_G0.364080.865
112_L116_I0.362340.861
103_F107_I0.35930.853
51_F105_D0.354210.841
57_A116_I0.353680.840
20_K27_R0.350060.831
63_A67_A0.349430.830
9_L13_A0.348750.828
64_F85_I0.348370.827
25_R50_S0.343950.817
114_I118_Y0.342990.815
68_Y118_Y0.341090.810
59_A88_A0.339110.805
72_S75_W0.338860.805
8_A117_A0.335090.796
20_K56_A0.332940.791
25_R105_D0.331440.787
29_F33_P0.32920.782
57_A109_G0.32820.779
65_F69_Y0.328170.779
56_A110_I0.325230.772
72_S76_I0.324550.771
88_A110_I0.32420.770
115_L118_Y0.319940.760
27_R50_S0.318730.757
31_Y34_N0.317280.754
71_G75_W0.317240.753
52_P55_H0.314140.746
35_Y38_Y0.313550.745
66_L84_A0.311170.739
59_A62_F0.303890.722
73_R76_I0.303450.721
91_V94_S0.301670.716
95_R106_V0.301150.715
100_A103_F0.296580.704
12_A16_N0.295790.702
14_I17_N0.295480.702
50_S95_R0.293930.698
11_L14_I0.293880.698
21_W24_G0.292530.695
60_A117_A0.289250.687
60_A64_F0.28750.683
31_Y35_Y0.282540.671
116_I120_F0.28210.670
29_F100_A0.280850.667
108_A111_L0.279940.665
99_G103_F0.279560.664
63_A85_I0.279360.663
71_G76_I0.278060.660
14_I18_V0.273770.650
90_L94_S0.2710.644
15_L52_P0.270580.643
49_N98_L0.270540.643
60_A114_I0.269110.639
9_L62_F0.267440.635
71_G74_G0.267050.634
54_G58_I0.264980.629
69_Y73_R0.26430.628
84_A88_A0.264120.627
59_A63_A0.262820.624
9_L12_A0.261710.622
34_N38_Y0.26170.622
20_K101_H0.259920.617
53_S106_V0.257390.611
75_W86_V0.256560.609
15_L91_V0.254490.604
26_P30_F0.253940.603
117_A121_Y0.253590.602
19_L22_I0.253520.602
17_N58_I0.252860.601
13_A58_I0.251120.596
26_P48_F0.251090.596
53_S56_A0.250740.595
16_N112_L0.250320.594
56_A59_A0.24980.593
33_P37_L0.248550.590
57_A112_L0.247080.587
70_L83_L0.246380.585
111_L114_I0.244930.582
30_F48_F0.242710.576
67_A84_A0.241560.574
9_L58_I0.239940.570
115_L119_L0.23770.565
28_P105_D0.237330.564
111_L115_L0.236720.562
99_G102_F0.234580.557
30_F102_F0.234280.556
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
2ipbA0.945799.60.182
1d2tA0.945799.60.183
1qi9A199.30.329
3bb0A199.20.367
1up8A199.20.385
4b19A0.23268.30.893
2losA0.72877.10.896
2looA0.65894.70.904
3j1zP0.8453.90.908
2lx0A0.22483.80.908

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