GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DAGK_prokar - Prokaryotic diacylglycerol kinase
Pfam: PF01219 (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: 104
Sequences: 1158
Seq/Len: 11.13
HH_delta: -0.015 (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
66_V77_A0.862813.482
6_R78_K0.735232.967
55_A58_L0.724282.923
11_A57_L0.722722.916
12_F22_L0.599282.418
68_L77_A0.528992.135
50_F94_F0.520212.099
25_A49_I0.478411.930
55_A91_A0.459471.854
38_S41_E0.438761.770
57_L83_I0.435191.756
41_E102_I0.43351.749
8_L86_A0.425831.718
9_K13_R0.42551.717
76_L80_A0.419281.692
32_A42_W0.410511.656
65_L80_A0.402171.623
12_F23_V0.385281.555
37_L102_I0.382381.543
44_L48_A0.361811.460
54_I91_A0.352741.423
52_V88_V0.346561.398
21_H88_V0.342531.382
4_A85_A0.341031.376
51_L91_A0.33871.367
36_G42_W0.331271.337
3_Y6_R0.330021.332
64_R79_R0.323761.306
52_V95_A0.309731.250
20_I24_A0.295571.193
17_N20_I0.29521.191
47_L94_F0.292721.181
22_L53_L0.291621.177
60_T83_I0.290441.172
57_L90_V0.289691.169
17_N21_H0.2881.162
60_T79_R0.282591.140
18_F53_L0.281721.137
18_F21_H0.281041.134
57_L86_A0.279021.126
29_L49_I0.274931.109
11_A83_I0.270971.093
55_A87_A0.270031.090
15_E64_R0.269521.088
14_T79_R0.269441.087
61_A80_A0.267511.079
11_A18_F0.266441.075
53_L90_V0.261821.056
10_F15_E0.260391.051
40_W44_L0.251991.017
69_V77_A0.251551.015
70_S74_H0.247160.997
15_E19_R0.243990.985
28_V95_A0.243750.984
46_I94_F0.243090.981
51_L54_I0.242830.980
4_A17_N0.241920.976
66_V80_A0.239440.966
1_F89_L0.237540.958
50_F90_V0.237530.958
70_S78_K0.231210.933
45_L48_A0.229120.925
37_L42_W0.226660.915
39_P101_I0.218290.881
50_F97_I0.217490.878
4_A20_I0.215710.870
60_T64_R0.213660.862
5_L9_K0.21320.860
39_P102_I0.213110.860
10_F79_R0.212470.857
1_F5_L0.211590.854
65_L69_V0.210560.850
10_F83_I0.21030.849
93_I97_I0.208420.841
88_V95_A0.207720.838
70_S77_A0.206130.832
18_F57_L0.204630.826
67_D81_K0.203210.820
64_R83_I0.20130.812
39_P43_A0.201020.811
89_L93_I0.200990.811
59_N63_E0.200910.811
86_A89_L0.200540.809
63_E81_K0.200290.808
97_I101_I0.199650.806
10_F14_T0.199110.803
31_A35_L0.198820.802
48_A95_A0.197790.798
44_L94_F0.192850.778
33_F101_I0.191160.771
37_L45_L0.191130.771
92_A96_V0.190540.769
65_L77_A0.188030.759
61_A69_V0.185660.749
25_A28_V0.184540.745
59_N81_K0.184250.743
14_T60_T0.183450.740
58_L87_A0.182440.736
48_A98_V0.18190.734
16_R19_R0.181610.733
29_L33_F0.181560.733
35_L103_F0.178950.722
80_A84_A0.178780.721
24_A92_A0.178690.721
2_R6_R0.176380.712
5_L89_L0.175940.710
40_W47_L0.175890.710
1_F20_I0.175590.709
40_W43_A0.174560.704
61_A87_A0.17250.696
21_H92_A0.172420.696
28_V49_I0.171510.692
21_H52_V0.170710.689
26_V29_L0.170690.689
54_I58_L0.169040.682
30_I33_F0.16880.681
68_L84_A0.167750.677
32_A45_L0.167470.676
5_L102_I0.16660.672
21_H85_A0.166260.671
65_L71_P0.166020.670
63_E82_D0.165690.669
24_A95_A0.163660.660
69_V76_L0.162390.655
52_V91_A0.162340.655
27_L31_A0.161390.651
3_Y17_N0.161150.650
68_L80_A0.160790.649
25_A52_V0.160780.649
3_Y10_F0.160710.648
43_A98_V0.159650.644
30_I34_F0.159340.643
55_A92_A0.157990.638
28_V31_A0.157530.636
20_I85_A0.157520.636
47_L73_Y0.156280.631
17_N77_A0.155960.629
12_F28_V0.155380.627
15_E82_D0.155290.627
17_N85_A0.153980.621
51_L98_V0.153350.619
47_L102_I0.152770.616
75_P79_R0.151470.611
17_N60_T0.150650.608
4_A92_A0.150270.606
31_A103_F0.149490.603
85_A92_A0.149060.601
9_K26_V0.149060.601
59_N82_D0.148740.600
15_E80_A0.148740.600
97_I100_L0.148670.600
9_K29_L0.147740.596
51_L64_R0.147010.593
84_A87_A0.146980.593
95_A99_G0.146350.591
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
3ze3A1100-0.015
2kdcA1100-0.011
1rh5B0.490480.931
4b03D0.54815.10.936
1zoyC0.326950.937
2wwbB0.46154.70.937
2lckA0.63464.30.938
2wdqC0.42313.60.941
2l1tA0.33653.40.941
1pi7A0.25963.30.942

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