GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Lumazine_bd - Lumazine-binding domain
Pfam: PF12870 (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: CL0051
Length: 111
Sequences: 3589
Seq/Len: 32.33
HH_delta: 0.293 (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
24_D27_K1.254184.331
104_E107_K0.84962.934
104_E109_K0.611422.111
19_A27_K0.574261.983
27_K30_A0.571561.974
19_A24_D0.564741.950
83_V101_L0.55651.922
12_V101_L0.551341.904
87_I95_K0.549011.896
7_S10_E0.527721.822
18_D22_N0.500011.727
19_A31_Y0.496921.716
79_D103_K0.483861.671
15_N31_Y0.478031.651
9_P101_L0.475121.641
32_L36_S0.469631.622
11_E15_N0.469531.621
84_T98_T0.43711.509
33_S109_K0.433441.497
51_K55_S0.4271.474
15_N27_K0.423361.462
16_F28_A0.416111.437
10_E14_K0.415431.434
74_E81_A0.40141.386
25_Y29_Y0.381431.317
33_S104_E0.38141.317
81_A108_W0.380471.314
9_P72_V0.377621.304
14_K18_D0.373021.288
45_D48_Q0.372121.285
75_N78_G0.371761.284
13_V99_V0.370721.280
16_F31_Y0.367291.268
47_E51_K0.367051.267
13_V83_V0.36641.265
16_F32_L0.365311.261
20_L28_A0.361681.249
45_D49_F0.360611.245
9_P81_A0.360231.244
21_K65_G0.350391.210
46_F49_F0.343461.186
13_V101_L0.330611.142
80_T100_P0.3151.088
34_P104_E0.311991.077
72_V81_A0.309811.070
85_V97_F0.300061.036
17_F87_I0.295961.022
85_V99_V0.295681.021
7_S11_E0.295241.019
72_V83_V0.29291.011
86_K96_T0.287860.994
34_P46_F0.287180.992
13_V85_V0.286750.990
26_E30_A0.279810.966
101_L110_V0.278120.960
69_I86_K0.27790.960
82_T100_P0.277640.959
9_P12_V0.277590.959
16_F20_L0.27530.951
16_F99_V0.274750.949
68_K88_T0.272630.941
9_P108_W0.272370.940
16_F85_V0.26690.922
74_E78_G0.263710.911
99_V110_V0.26220.905
13_V110_V0.25950.896
20_L99_V0.257480.889
32_L110_V0.256930.887
17_F20_L0.256620.886
12_V110_V0.255170.881
49_F53_F0.254260.878
13_V16_F0.250560.865
87_I97_F0.250550.865
17_F21_K0.249190.860
12_V31_Y0.248030.856
75_N100_P0.247380.854
47_E54_A0.245410.847
103_K108_W0.242570.838
75_N80_T0.238310.823
46_F50_E0.237680.821
33_S102_V0.237070.819
40_E85_V0.232130.802
26_E29_Y0.229770.793
49_F52_Q0.229360.792
48_Q51_K0.228230.788
29_Y46_F0.228080.788
9_P83_V0.227880.787
28_A38_E0.22440.775
89_Y94_E0.223120.770
70_V85_V0.222530.768
35_E38_E0.222170.767
32_L38_E0.222090.767
15_N18_D0.220050.760
33_S36_S0.217260.750
11_E14_K0.216150.746
80_T102_V0.214890.742
75_N82_T0.21430.740
73_E82_T0.213110.736
97_F101_L0.205670.710
45_D50_E0.205380.709
17_F67_I0.204670.707
83_V110_V0.204020.704
67_I85_V0.203450.703
52_Q56_E0.203370.702
31_Y109_K0.202930.701
28_A50_E0.200270.692
50_E54_A0.198410.685
39_P43_K0.196590.679
8_T12_V0.19370.669
101_L108_W0.191710.662
68_K82_T0.189860.656
32_L46_F0.189810.655
14_K70_V0.189210.653
12_V15_N0.188250.650
14_K67_I0.185970.642
8_T11_E0.185590.641
17_F99_V0.185370.640
24_D30_A0.184740.638
19_A28_A0.184440.637
37_R43_K0.181750.628
84_T96_T0.181450.627
28_A31_Y0.180910.625
16_F97_F0.179750.621
69_I72_V0.179110.618
53_F56_E0.178570.617
16_F87_I0.178410.616
66_S88_T0.177630.613
19_A30_A0.177510.613
56_E60_K0.175970.608
34_P109_K0.175780.607
25_Y28_A0.175470.606
38_E89_Y0.175220.605
10_E70_V0.1750.604
83_V97_F0.17430.602
68_K86_K0.173310.598
100_P104_E0.173180.598
56_E59_K0.172820.597
18_D21_K0.172240.595
82_T98_T0.171640.593
40_E60_K0.170220.588
29_Y50_E0.169410.585
87_I99_V0.169390.585
23_G53_F0.169080.584
36_S54_A0.168780.583
89_Y95_K0.168110.580
41_K85_V0.166480.575
51_K54_A0.166250.574
23_G85_V0.165880.573
82_T93_K0.165880.573
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
3k7cA0.991990.293
3gzrA0.96498.70.372
3dukA0.945998.70.378
3fkaA0.95598.60.391
3h51A0.98298.50.407
3hx8A0.97398.50.409
3bb9A0.98298.50.409
3blzA0.95598.50.409
3f7sA0.97398.50.416
3b7cA0.97398.40.431

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