GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Shikimate_DH - Shikimate quinate 5-dehydrogenase
Pfam: PF01488 (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: CL0063
Length: 135
Sequences: 13553
Seq/Len: 100.39
HH_delta: 0.282 (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
16_L76_A1.655232.609
15_V31_L1.590142.507
46_P50_E1.58472.498
14_R40_T1.539222.426
15_V36_A1.516012.390
20_A41_I1.498952.363
91_T94_M1.416952.234
30_A34_L1.381132.177
14_R37_K1.380262.176
25_R29_A1.315142.073
15_V78_I1.276342.012
29_A55_E1.146511.807
50_E54_E1.115111.758
14_R75_E1.111991.753
17_V28_A1.073991.693
45_T48_R1.056431.665
12_G36_A1.029781.623
70_E117_E1.005931.586
25_R52_L0.982071.548
25_R55_E0.970611.530
43_N49_A0.954171.504
51_A55_E0.921721.453
30_A33_A0.907521.431
105_V109_A0.877731.384
50_E53_A0.873251.377
26_A30_A0.871271.373
31_L36_A0.836271.318
26_A29_A0.835481.317
23_A27_V0.834051.315
96_K109_A0.827581.305
47_E50_E0.816141.287
14_R77_D0.796391.255
96_K105_V0.785351.238
68_D71_E0.784261.236
36_A78_I0.754581.190
13_K77_D0.753641.188
40_T76_A0.742621.171
15_V80_I0.737991.163
92_E96_K0.724951.143
28_A41_I0.709411.118
28_A39_I0.698241.101
29_A33_A0.697631.100
42_V61_I0.69211.091
104_L108_L0.688631.086
51_A54_E0.680871.073
95_L98_A0.677671.068
31_L80_I0.668711.054
27_V82_A0.668411.054
53_A57_G0.663071.045
40_T73_L0.658731.038
76_A114_I0.654411.032
81_N111_P0.653961.031
114_I118_V0.643651.015
13_K78_I0.640241.009
25_R51_A0.63981.009
70_E94_M0.624770.985
18_I42_V0.62050.978
104_L107_D0.591790.933
79_V110_V0.582290.918
113_D116_P0.579610.914
110_V113_D0.579320.913
16_L42_V0.55960.882
115_D119_A0.559530.882
66_L109_A0.557040.878
48_R51_A0.556970.878
65_P68_D0.553240.872
54_E57_G0.551150.869
20_A52_L0.54690.862
20_A43_N0.546870.862
76_A79_V0.545220.859
107_D111_P0.54290.856
13_K36_A0.539610.851
28_A56_F0.53780.848
47_E51_A0.53730.847
41_I53_A0.531750.838
49_A53_A0.527550.832
93_E97_K0.515210.812
53_A56_F0.512640.808
16_L72_A0.508370.801
70_E97_K0.504470.795
14_R74_Q0.497510.784
52_L56_F0.497290.784
68_D72_A0.497290.784
93_E98_A0.497210.784
27_V30_A0.494830.780
72_A76_A0.489410.771
21_G43_N0.489350.771
92_E109_A0.485410.765
18_I81_N0.483920.763
70_E73_L0.483730.763
92_E112_R0.482320.760
28_A32_A0.478120.754
17_V80_I0.471610.743
27_V80_I0.471210.743
16_L79_V0.469840.741
66_L92_E0.469590.740
57_G60_N0.468880.739
87_M98_A0.468620.739
109_A113_D0.468110.738
21_G48_R0.468030.738
12_G37_K0.463750.731
56_F59_V0.462680.729
24_A82_A0.461990.728
46_P49_A0.461010.727
40_T72_A0.460660.726
32_A56_F0.460610.726
31_L78_I0.458470.723
85_S98_A0.457670.721
89_I109_A0.456030.719
111_P115_D0.454370.716
116_P120_E0.45040.710
20_A42_V0.447920.706
117_E120_E0.446210.703
104_L109_A0.44510.702
17_V31_L0.444910.701
114_I117_E0.444470.701
29_A32_A0.444430.701
43_N48_R0.442580.698
14_R73_L0.440440.694
93_E96_K0.438880.692
23_A26_A0.435930.687
115_D118_V0.431570.680
40_T75_E0.431490.680
16_L69_L0.429650.677
21_G25_R0.425520.671
111_P116_P0.420040.662
69_L73_L0.419810.662
67_E71_E0.418720.660
14_R76_A0.417910.659
18_I83_T0.41720.658
45_T49_A0.413250.651
37_K73_L0.409180.645
76_A117_E0.408780.644
95_L105_V0.408530.644
70_E120_E0.404030.637
52_L55_E0.39540.623
94_M97_K0.393940.621
81_N110_V0.390640.616
56_F60_N0.387120.610
79_V114_I0.381860.602
116_P119_A0.381650.602
74_Q97_K0.380590.600
17_V27_V0.380530.600
46_P60_N0.380210.599
22_G25_R0.378570.597
90_I94_M0.375630.592
32_A59_V0.372460.587
66_L112_R0.371150.585
37_K40_T0.370640.584
17_V24_A0.370530.584
23_A82_A0.368440.581
29_A59_V0.365910.577
73_L76_A0.364030.574
70_E74_Q0.361470.570
18_I79_V0.35980.567
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
1gpjA0.977899.60.282
3oj0A0.896399.50.311
3hdjA0.933399.30.383
1omoA0.933399.30.403
3jyoA0.970499.20.416
1x7dA0.948199.20.418
2eggA0.955699.20.427
1edzA0.940799.20.431
2i99A0.948199.20.432
3pwzA0.955699.20.434

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