GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Hepsin-SRCR - Hepsin SRCR
Pfam: PF09272 (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: CL0550
Length: 110
Sequences: 1743
Seq/Len: 15.85
HH_delta: 0.205 (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
33_N36_V0.979023.848
93_R96_F0.815973.207
28_C91_C0.732832.880
30_S95_R0.681212.678
32_S97_L0.607792.389
14_L40_S0.58732.308
78_Y81_R0.550582.164
14_L97_L0.537432.112
34_A49_A0.525162.064
70_C87_S0.466011.832
79_A82_L0.450431.770
71_V83_L0.447621.759
23_T68_F0.436761.717
6_Q24_W0.427571.681
72_D90_D0.397431.562
73_E84_E0.393591.547
26_L96_F0.390911.536
31_R73_E0.383571.508
75_R81_R0.380131.494
14_L99_T0.374971.474
26_L93_R0.372461.464
29_S95_R0.36541.436
18_D21_E0.363991.431
69_F93_R0.358121.408
32_S40_S0.351911.383
75_R78_Y0.34631.361
32_S36_V0.344361.354
55_L59_T0.337241.326
34_A38_G0.328991.293
39_L75_R0.326271.282
57_V60_A0.324751.276
69_F96_F0.32331.271
38_G49_A0.316191.243
6_Q15_M0.299661.178
77_P81_R0.297571.170
77_P80_R0.29391.155
14_L27_L0.291171.144
30_S90_D0.290551.142
36_V39_L0.289891.139
56_D59_T0.286321.125
18_D86_L0.272251.070
43_E50_V0.267041.050
73_E90_D0.260031.022
84_E88_V0.256081.007
32_S37_A0.255851.006
7_V10_A0.252920.994
38_G48_R0.251020.987
54_E58_R0.249870.982
13_R96_F0.244780.962
90_D95_R0.244440.961
43_E79_A0.24160.950
35_R38_G0.232320.913
85_V88_V0.230580.906
51_S100_I0.230230.905
6_Q9_P0.226850.892
13_R26_L0.217120.853
15_M24_W0.216120.849
5_V40_S0.214740.844
12_Q15_M0.213790.840
88_V92_P0.213630.840
16_V27_L0.209540.824
17_F43_E0.209280.823
30_S72_D0.203760.801
43_E47_L0.201350.791
59_T64_G0.199920.786
70_C86_L0.198950.782
51_S55_L0.198640.781
23_T31_R0.197420.776
43_E77_P0.196040.771
88_V94_G0.195420.768
55_L58_R0.193460.760
31_R82_L0.19310.759
38_G99_T0.192890.758
29_S98_A0.192690.757
28_C45_G0.192640.757
79_A86_L0.185270.728
12_Q81_R0.18140.713
72_D95_R0.180930.711
72_D89_C0.180210.708
23_T66_S0.179880.707
76_L80_R0.179690.706
48_R102_Q0.179210.704
17_F50_V0.179160.704
69_F89_C0.17910.704
17_F21_E0.178870.703
65_T69_F0.175130.688
35_R76_L0.174620.686
24_W91_C0.173990.684
35_R102_Q0.172940.680
5_V43_E0.172880.680
72_D87_S0.17120.673
40_S78_Y0.170610.671
5_V79_A0.170470.670
17_F68_F0.169650.667
33_N97_L0.16910.665
67_G93_R0.168950.664
34_A50_V0.167940.660
58_R64_G0.16780.660
46_F79_A0.166780.656
51_S80_R0.164310.646
50_V100_I0.162780.640
31_R86_L0.162250.638
23_T50_V0.161190.634
47_L102_Q0.161090.633
11_D46_F0.159830.628
37_A97_L0.159250.626
26_L65_T0.158780.624
37_A49_A0.158750.624
39_L42_E0.158290.622
97_L101_C0.157760.620
16_V22_G0.157630.620
55_L100_I0.15720.618
11_D76_L0.157070.617
69_F73_E0.157050.617
46_F86_L0.156820.616
7_V15_M0.155260.610
41_C45_G0.15490.609
46_F50_V0.153790.604
23_T38_G0.153530.603
5_V11_D0.153450.603
50_V102_Q0.151440.595
27_L78_Y0.150810.593
74_G79_A0.149630.588
60_A100_I0.149440.587
21_E80_R0.148820.585
57_V82_L0.148810.585
37_A54_E0.146860.577
32_S99_T0.146550.576
74_G77_P0.146130.574
38_G84_E0.145660.573
9_P64_G0.145520.572
40_S44_M0.145280.571
30_S91_C0.144880.569
67_G96_F0.144540.568
26_L69_F0.144330.567
51_S76_L0.144310.567
73_E88_V0.144240.567
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
1by2A0.936499.80.205
2oyaA0.845599.80.217
1z8gA0.981899.80.227
2ja4A0.836499.70.252
2jopA0.836499.70.259
2xrcA0.927399.60.321
2orwA0.336428.80.888
2j9rA0.336411.30.906
2xocA0.809190.91
3ttcA0.46366.10.917

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