GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Phage_antitermQ - Phage antitermination protein Q
Pfam: PF06530 (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: CL0123
Length: 125
Sequences: 4195
Seq/Len: 33.56
HH_delta: 0.433 (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
81_K96_R1.184483.309
67_E105_F1.117273.121
10_R32_K1.002892.801
66_E69_D1.001742.798
98_R101_R0.908752.538
93_G96_R0.825522.306
79_W87_K0.802652.242
82_R86_R0.710311.984
64_D105_F0.680621.901
99_L103_E0.639631.787
90_C95_I0.631381.764
96_R99_L0.625631.748
82_R92_E0.624691.745
73_L84_I0.583141.629
72_I77_Y0.543841.519
67_E101_R0.539961.508
45_C52_L0.533081.489
53_I76_V0.52461.465
15_V30_G0.520431.454
97_K100_Q0.512441.431
74_Y99_L0.512221.431
73_L87_K0.508261.420
94_K98_R0.505961.413
16_R19_R0.499111.394
77_Y87_K0.495091.383
33_G38_S0.493121.377
71_L102_A0.484371.353
93_G97_K0.476261.330
53_I68_Y0.469831.312
26_P29_A0.46541.300
73_L79_W0.454451.269
92_E96_R0.446051.246
68_Y72_I0.443791.240
73_L78_G0.441831.234
14_W37_S0.433891.212
54_D57_V0.414441.158
30_G40_K0.413381.155
69_D73_L0.410131.146
47_D52_L0.405331.132
80_S83_Q0.404931.131
29_A33_G0.40451.130
73_L88_L0.403331.127
22_V26_P0.401181.121
90_C98_R0.39721.110
66_E90_C0.395841.106
79_W83_Q0.372961.042
28_A32_K0.372941.042
73_L77_Y0.364971.020
52_L61_K0.360111.006
34_V37_S0.359271.004
13_A16_R0.35070.980
85_A92_E0.348770.974
93_G100_Q0.347460.971
64_D67_E0.347080.970
74_Y102_A0.346610.968
94_K100_Q0.337680.943
83_Q86_R0.329290.920
85_A95_I0.328960.919
41_S45_C0.32360.904
49_D52_L0.316250.883
85_A88_L0.314170.878
31_F35_L0.313210.875
15_V34_V0.310450.867
90_C94_K0.308280.861
53_I60_L0.305550.854
12_G16_R0.301130.841
94_K97_K0.301030.841
66_E98_R0.297960.832
91_S94_K0.295210.825
41_S48_D0.292720.818
22_V27_I0.288060.805
44_S62_K0.286520.800
29_A32_K0.285880.799
97_K101_R0.285330.797
45_C54_D0.285040.796
101_R104_G0.284590.795
69_D72_I0.28320.791
98_R104_G0.283030.791
55_R72_I0.283020.791
29_A36_P0.282250.788
40_K99_L0.279960.782
70_L102_A0.278880.779
70_L98_R0.278020.777
70_L84_I0.274410.767
81_K98_R0.271450.758
58_A61_K0.266470.744
81_K103_E0.265730.742
17_S22_V0.265680.742
47_D51_L0.260990.729
65_P69_D0.258950.723
19_R27_I0.258850.723
33_G37_S0.257810.720
81_K99_L0.254130.710
90_C100_Q0.250530.700
48_D76_V0.249850.698
63_R105_F0.247150.690
16_R102_A0.24540.685
45_C48_D0.2450.684
85_A90_C0.241740.675
70_L74_Y0.240530.672
82_R90_C0.240430.672
46_S76_V0.237980.665
14_W39_S0.231010.645
39_S47_D0.230580.644
88_L98_R0.229760.642
53_I72_I0.22920.640
14_W34_V0.229060.640
33_G36_P0.228220.638
63_R102_A0.227820.636
17_S26_P0.227750.636
26_P33_G0.227730.636
60_L71_L0.227040.634
13_A19_R0.225090.629
41_S44_S0.223680.625
71_L103_E0.220910.617
100_Q103_E0.220050.615
74_Y81_K0.219090.612
17_S30_G0.218940.612
70_L88_L0.217190.607
66_E88_L0.214810.600
25_S28_A0.214280.599
15_V37_S0.211550.591
44_S56_C0.211010.589
46_S49_D0.210670.588
18_G45_C0.210360.588
15_V19_R0.209540.585
40_K47_D0.208360.582
91_S98_R0.208140.581
80_S95_I0.207680.580
85_A91_S0.206390.577
100_Q104_G0.205660.574
81_K92_E0.204350.571
99_L102_A0.203090.567
62_K68_Y0.201160.562
23_D93_G0.200050.559
74_Y79_W0.199090.556
17_S27_I0.198260.554
96_R103_E0.198020.553
79_W86_R0.197470.552
24_Y27_I0.196790.550
55_R59_R0.195980.547
18_G22_V0.19520.545
20_S37_S0.19510.545
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
4gvpA0.97699.30.433
3kloA0.98499.20.467
3c3wA0.97699.20.473
1a04A0.96899.20.479
4hyeA0.91299.20.48
1yioA0.936990.52
1kgsA0.95298.90.533
1ys7A0.93698.90.54
1p2fA0.92898.90.544
3q9sA0.92898.90.544

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