GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FR47 - FR47-like protein
Pfam: PF08445 (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: CL0257
Length: 86
Sequences: 25223
Seq/Len: 293.29
HH_delta: 0.083 (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
47_A77_F2.834142.911
40_S75_L2.70662.780
59_L72_Y2.084782.141
40_S74_K2.065552.122
69_I73_E1.95012.003
33_H36_R1.841231.891
45_A48_R1.840931.891
45_A49_E1.783451.832
73_E79_E1.777571.826
61_V69_I1.731911.779
70_R73_E1.668981.714
43_V75_L1.581781.625
44_A75_L1.55421.596
69_I79_E1.515741.557
30_L33_H1.500431.541
49_E53_R1.497961.539
68_S72_Y1.452881.492
40_S44_A1.430991.470
43_V72_Y1.402331.440
38_L41_A1.288021.323
49_E52_E1.285461.320
41_A45_A1.256671.291
65_N68_S1.244561.278
39_G71_L1.226491.260
71_L75_L1.149861.181
66_E69_I1.121581.152
24_I43_V1.114041.144
48_R52_E1.103031.133
29_T39_G1.101411.131
31_P34_R1.097511.127
34_R67_A1.085991.116
61_V72_Y1.064271.093
29_T34_R1.046571.075
61_V65_N1.034151.062
29_T38_L1.024861.053
37_G40_S1.023991.052
27_V43_V1.02261.050
47_A51_L1.014821.042
23_E60_Y1.011661.039
13_V46_L0.996761.024
43_V77_F0.991471.018
44_A48_R0.972240.999
41_A44_A0.970440.997
23_E58_F0.968950.995
22_G55_K0.954690.981
29_T42_L0.935060.960
33_H38_L0.930340.956
10_V14_A0.921570.947
72_Y77_F0.899950.924
11_A15_W0.892450.917
66_E70_R0.878540.902
44_A47_A0.862440.886
22_G50_L0.861910.885
61_V68_S0.845540.869
11_A16_I0.843910.867
12_L15_W0.83210.855
27_V39_G0.829690.852
27_V72_Y0.816890.839
10_V16_I0.813980.836
25_G28_Y0.785240.807
47_A75_L0.782260.804
70_R74_K0.763460.784
11_A29_T0.761870.783
23_E26_G0.756220.777
43_V47_A0.75340.774
67_A70_R0.752280.773
62_D65_N0.751550.772
48_R51_L0.750780.771
11_A14_A0.748290.769
42_L45_A0.742720.763
50_L55_K0.741690.762
59_L77_F0.731550.751
68_S71_L0.729710.750
10_V15_W0.678870.697
23_E62_D0.677710.696
46_L50_L0.662740.681
25_G60_Y0.661160.679
51_L54_G0.641710.659
59_L68_S0.634420.652
40_S71_L0.619330.636
28_Y62_D0.613690.630
47_A57_P0.611230.628
35_R67_A0.610940.628
16_I46_L0.608670.625
50_L57_P0.606570.623
15_W28_Y0.59220.608
27_V71_L0.590750.607
37_G41_A0.588020.604
65_N69_I0.581330.597
39_G43_V0.580840.597
10_V13_V0.556290.571
43_V71_L0.550560.566
14_A18_R0.547780.563
26_G65_N0.544720.560
11_A32_E0.543950.559
10_V33_H0.542920.558
17_I23_E0.542560.557
13_V42_L0.539610.554
51_L55_K0.536520.551
28_Y68_S0.53320.548
26_G62_D0.531410.546
24_I27_V0.513020.527
21_D25_G0.511750.526
27_V46_L0.506840.521
16_I23_E0.496310.510
38_L42_L0.495920.509
15_W25_G0.491650.505
15_W22_G0.488360.502
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
3ec4A199.20.083
1tiqA199.20.099
4e2aA199.10.108
1u6mA199.10.122
2pdoA199.10.127
1wwzA199.10.128
4evyA199.10.136
3kkwA199.10.136
3fixA199.10.137
3c26A199.10.138

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