GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DHquinase_II - Dehydroquinase class II
Pfam: PF01220 (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. )
Length: 140
Sequences: 1476
Seq/Len: 10.54
HH_delta: -0.017 (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
7_N31_E0.907482.770
80_T114_V0.864582.639
48_F59_W0.848852.591
69_G138_L0.818322.497
37_T136_E0.754772.304
100_I128_A0.7132.176
41_L139_V0.680082.076
52_H58_D0.671512.049
30_I128_A0.651821.989
85_R118_V0.644631.967
56_L84_I0.621751.898
60_I91_I0.596211.820
43_V139_V0.587091.792
31_E47_F0.575711.757
126_F130_G0.562741.717
71_I98_V0.558611.705
33_K132_L0.551361.683
2_K44_E0.548081.673
25_T128_A0.542111.654
85_R89_K0.536851.638
13_L90_A0.528341.612
116_S122_V0.522691.595
121_G126_F0.520691.589
129_D132_L0.511261.560
89_K118_V0.511141.560
28_E31_E0.510241.557
82_I114_V0.493111.505
38_A45_V0.491631.500
52_H55_E0.490191.496
21_I101_S0.48571.482
16_K64_R0.484861.480
74_P115_I0.478971.462
104_H124_S0.469861.434
37_T132_L0.467371.426
126_F133_L0.465721.421
25_T33_K0.464711.418
6_I56_L0.46331.414
48_F55_E0.461471.408
85_R117_P0.454621.387
31_E35_K0.445111.358
4_L67_V0.441451.347
5_V47_F0.439591.342
55_E58_D0.434571.326
71_I134_A0.433121.322
59_W62_E0.432931.321
132_L136_E0.427381.304
50_S77_Y0.425791.299
77_Y83_A0.42421.295
60_I84_I0.421841.287
13_L64_R0.421461.286
7_N47_F0.420521.283
60_I70_I0.420471.283
18_E89_K0.416781.272
71_I135_L0.403031.230
126_F137_A0.400271.222
129_D133_L0.395321.206
27_L31_E0.392671.198
76_A82_I0.382441.167
102_N121_G0.380791.162
88_L95_V0.37821.154
34_C45_V0.371941.135
30_I100_I0.36761.122
72_I88_L0.365411.115
32_Q36_E0.35861.094
12_N51_N0.348971.065
95_V115_I0.347571.061
27_L30_I0.347461.060
103_I122_V0.346651.058
105_A120_V0.345831.055
25_T29_D0.345211.054
95_V119_A0.344981.053
34_C135_L0.341691.043
6_I48_F0.340551.039
55_E59_W0.338991.035
89_K117_P0.335561.024
57_I76_A0.332791.016
37_T40_E0.329471.006
33_K37_T0.326950.998
133_L137_A0.325560.994
57_I61_H0.324990.992
29_D32_Q0.32390.989
3_I135_L0.323680.988
96_V137_A0.319230.974
102_N126_F0.318340.972
26_T29_D0.317270.968
37_T41_L0.31210.953
3_I43_V0.311180.950
108_E112_H0.310780.948
51_N58_D0.309680.945
41_L136_E0.306930.937
13_L65_D0.305930.934
96_V126_F0.305610.933
61_H87_A0.303530.926
79_H110_R0.302920.924
78_T103_I0.30260.924
50_S56_L0.301860.921
41_L135_L0.298810.912
56_L77_Y0.297550.908
4_L59_W0.292750.893
77_Y84_I0.292470.893
104_H122_V0.291910.891
76_A83_A0.290830.888
36_E39_A0.289120.882
70_I91_I0.288860.882
62_E66_D0.288370.880
91_I95_V0.280290.855
2_K46_E0.278840.851
40_E136_E0.278470.850
129_D136_E0.276340.843
75_G115_I0.275540.841
36_E40_E0.273950.836
5_V34_C0.273440.835
16_K65_D0.271860.830
114_V119_A0.271320.828
12_N61_H0.268990.821
130_G134_A0.266240.813
103_I124_S0.263080.803
95_V120_V0.261650.799
54_G77_Y0.26160.798
18_E90_A0.260280.794
123_I126_F0.260030.794
5_V31_E0.255120.779
63_A66_D0.254910.778
11_L27_L0.254760.778
103_I130_G0.254020.775
9_P77_Y0.253960.775
39_A44_E0.250210.764
28_E35_K0.25010.763
46_E66_D0.250070.763
70_I95_V0.24860.759
34_C71_I0.244530.746
82_I109_F0.243470.743
57_I83_A0.24110.736
11_L100_I0.240380.734
64_R92_S0.23720.724
35_K39_A0.236820.723
96_V138_L0.235250.718
13_L16_K0.232850.711
88_L115_I0.232370.709
28_E32_Q0.232290.709
79_H109_F0.229420.700
78_T113_S0.228370.697
74_P78_T0.227360.694
13_L61_H0.226970.693
108_E111_H0.226810.692
6_I72_I0.226680.692
21_I24_T0.226610.692
112_H116_S0.224760.686
27_L47_F0.224690.686
38_A71_I0.224530.685
121_G137_A0.223040.681
74_P130_G0.22250.679
121_G133_L0.221160.675
43_V68_D0.219390.670
59_W63_A0.219120.669
4_L63_A0.21860.667
20_E24_T0.216440.661
34_C132_L0.214550.655
100_I130_G0.213790.652
77_Y80_T0.213370.651
34_C37_T0.212110.647
6_I50_S0.212050.647
60_I88_L0.20960.640
60_I87_A0.205810.628
33_K128_A0.204820.625
107_E110_R0.204660.625
104_H116_S0.204370.624
70_I93_I0.203590.621
115_I119_A0.200810.613
32_Q35_K0.196010.598
17_R22_Y0.195780.598
88_L119_A0.195330.596
2_K43_V0.192870.589
59_W67_V0.192860.589
111_H124_S0.191250.584
35_K44_E0.191240.584
38_A135_L0.189790.579
90_A95_V0.18810.574
18_E85_R0.187350.572
45_V135_L0.185560.566
57_I74_P0.184420.563
11_L14_L0.183080.559
18_E21_I0.18210.556
123_I130_G0.181660.554
16_K92_S0.17990.549
15_G23_G0.179110.547
48_F62_E0.178210.544
57_I84_I0.178060.543
98_V134_A0.176940.540
102_N112_H0.176930.540
123_I133_L0.176770.539
35_K45_V0.176390.538
76_A79_H0.175880.537
14_L18_E0.175620.536
75_G90_A0.172890.528
76_A100_I0.171840.524
14_L100_I0.171390.523
84_I87_A0.170940.522
129_D137_A0.170530.520
96_V134_A0.169150.516
80_T83_A0.168180.513
58_D61_H0.167530.511
63_A70_I0.167390.511
39_A42_G0.167180.510
38_A47_F0.167150.510
71_I138_L0.166610.508
3_I138_L0.165370.505
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
3n8kA1100-0.017
1gtzA1100-0.016
2c4wA1100-0.014
3lwzA1100-0.011
1uqrA1100-0.006
1gqoA1100-0.003
3u80A1100-0.002
1h05A1100-0.002
2uygA0.99291000.001
3kipA11000.002

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