GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Lumazine_bd_2 - Putative lumazine-binding
Pfam: PF12893 (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: 116
Sequences: 6026
Seq/Len: 51.95
HH_delta: 0.091 (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
21_D24_K1.820533.939
104_T107_G1.171322.534
102_V111_V1.089652.357
15_D19_N0.987532.137
30_H111_V0.968232.095
29_F33_A0.967262.093
31_P48_I0.960542.078
26_R52_I0.951942.060
16_G24_K0.945842.046
9_T101_L0.91611.982
47_P50_E0.891591.929
12_D24_K0.806091.744
24_K27_S0.802481.736
33_A51_F0.739861.601
34_R112_S0.717811.553
103_K108_W0.702851.521
88_Y95_F0.695761.505
8_A12_D0.679811.471
82_A108_W0.671091.452
80_D103_K0.670911.452
22_S26_R0.668221.446
7_E11_Q0.643961.393
104_T109_K0.642991.391
30_H104_T0.639761.384
47_P51_F0.639051.383
53_A57_S0.638111.381
86_V99_F0.62881.360
18_Y68_R0.621551.345
29_F113_K0.611671.323
12_D28_A0.608341.316
49_E53_A0.603721.306
77_I82_A0.581741.259
16_G28_A0.56841.230
53_A56_K0.554511.200
52_I56_K0.549561.189
98_Y112_S0.544071.177
48_I52_I0.538351.165
13_Y25_L0.533891.155
6_I82_A0.532581.152
30_H109_K0.531121.149
73_L86_V0.530351.147
17_L25_L0.521871.129
23_E52_I0.516731.118
26_R48_I0.508131.099
100_T112_S0.503121.089
81_V102_V0.502961.088
50_E53_A0.500551.083
23_E26_R0.489041.058
84_A101_L0.487531.055
83_S98_Y0.486631.053
72_I87_E0.48481.049
7_E73_L0.481451.042
71_S89_E0.478651.036
86_V97_D0.477611.033
13_Y29_F0.473221.024
101_L110_I0.473011.023
11_Q15_D0.469411.016
13_Y28_A0.466611.010
16_G21_D0.465571.007
5_A103_K0.463221.002
10_V86_V0.45630.987
30_H102_V0.455870.986
99_F113_K0.455560.986
69_K89_E0.453060.980
78_D81_V0.450880.975
49_E52_I0.449640.973
46_M50_E0.449260.972
29_F51_F0.435920.943
83_S100_T0.435380.942
85_K98_Y0.430620.932
26_R49_E0.42320.916
84_A99_F0.419780.908
71_S87_E0.418920.906
104_T111_V0.416870.902
97_D113_K0.409730.886
10_V101_L0.399220.864
6_I75_I0.398140.861
10_V84_A0.395210.855
99_F110_I0.390630.845
78_D83_S0.389890.844
51_F55_V0.387890.839
48_I51_F0.387120.838
12_D16_G0.383740.830
81_V100_T0.383710.830
76_D83_S0.3710.803
14_F70_E0.370450.801
22_S56_K0.367810.796
75_I82_A0.356070.770
75_I84_A0.353480.765
5_A9_T0.351040.759
9_T110_I0.347970.753
25_L55_V0.345040.747
85_K96_V0.344290.745
74_S85_K0.340410.736
23_E27_S0.339730.735
15_D74_S0.339110.734
18_Y67_E0.335810.727
6_I9_T0.335510.726
12_D27_S0.333750.722
9_T28_A0.333520.722
95_F99_F0.332870.720
15_D18_Y0.332760.720
58_R63_P0.330830.716
22_S25_L0.328680.711
9_T12_D0.327050.708
27_S109_K0.325920.705
31_P109_K0.325230.704
10_V99_F0.325010.703
36_Q112_S0.320680.694
25_L28_A0.314190.680
55_V58_R0.313670.679
32_D111_V0.313330.678
13_Y17_L0.307480.665
17_L90_F0.305210.660
19_N24_K0.305190.660
6_I108_W0.303750.657
16_G27_S0.301050.651
80_D102_V0.298980.647
23_E56_K0.296340.641
36_Q44_R0.292370.633
12_D107_G0.290810.629
6_I101_L0.290220.628
14_F18_Y0.289690.627
29_F110_I0.2890.625
14_F88_Y0.288310.624
88_Y97_D0.286870.621
30_H33_A0.285420.618
86_V113_K0.285110.617
17_L68_R0.281940.610
87_E96_V0.279820.605
5_A8_A0.279710.605
10_V110_I0.276420.598
73_L87_E0.276370.598
89_E94_W0.274160.593
7_E10_V0.273230.591
103_K107_G0.271620.588
11_Q14_F0.262320.568
45_T50_E0.261790.566
35_L113_K0.258430.559
45_T48_I0.257060.556
12_D15_D0.255730.553
51_F54_R0.255590.553
14_F99_F0.252740.547
48_I109_K0.25230.546
8_A11_Q0.252210.546
24_K28_A0.250620.542
27_S107_G0.242230.524
14_F17_L0.239310.518
34_R46_M0.236280.511
69_K91_P0.233630.505
16_G19_N0.233570.505
10_V113_K0.232990.504
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
3f7sA0.991499.50.091
3h51A0.965599.40.157
3cnxA0.974199.40.168
3hx8A0.965599.40.174
3bb9A0.965599.40.174
3gzrA0.982899.40.175
2ux0A199.40.183
3fkaA0.974199.30.196
3cu3A0.982899.30.197
3gwrA0.974199.30.203

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