GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DAP_epimerase - Diaminopimelate epimerase
Pfam: PF01678 (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: CL0288
Length: 121
Sequences: 4801
Seq/Len: 39.68
HH_delta: 0.066 (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
90_E103_E1.495843.538
57_R65_E1.37993.263
44_N72_G1.315563.111
92_T99_I1.193222.822
53_D94_E1.161022.746
55_R94_E1.155382.732
94_E99_I1.131292.675
78_A82_E0.919612.175
47_E55_R0.863632.042
21_D24_D0.808021.911
69_C72_G0.795611.882
65_E96_P0.790571.870
90_E101_R0.778951.842
76_A91_V0.77771.839
92_T101_R0.772131.826
53_D92_T0.724061.712
13_F46_V0.72391.712
54_I93_V0.677261.602
31_I43_V0.676181.599
44_N56_M0.651571.541
51_D88_K0.649861.537
46_V75_C0.623481.475
67_L96_P0.595751.409
16_D47_E0.571491.352
50_D53_D0.5361.268
49_S55_R0.527971.249
79_Y87_G0.525251.242
52_A99_I0.522751.236
49_S94_E0.521161.233
12_I43_V0.519691.229
10_D34_R0.514191.216
68_A100_L0.503751.191
55_R96_P0.503691.191
13_F84_G0.503551.191
20_E23_L0.496471.174
24_D27_L0.466821.104
46_V76_A0.460231.088
73_C93_V0.459921.088
23_L27_L0.446051.055
44_N58_I0.442171.046
58_I69_C0.433351.025
56_M95_T0.430151.017
89_D106_E0.404040.956
59_F65_E0.399320.944
7_N58_I0.398020.941
28_A43_V0.3940.932
68_A97_G0.393290.930
77_A81_L0.385910.913
12_I31_I0.382840.905
18_E48_I0.381150.901
13_F79_Y0.38070.900
46_V54_I0.380680.900
45_F59_F0.380670.900
54_I75_C0.380670.900
10_D31_I0.377990.894
16_D19_E0.376390.890
58_I66_T0.373970.884
49_S52_A0.373780.884
9_H71_N0.371170.878
93_V102_V0.367450.869
17_R48_I0.364030.861
79_Y83_G0.363430.860
9_H69_C0.360020.851
76_A93_V0.358080.847
67_L97_G0.35770.846
89_D104_V0.357190.845
17_R47_E0.356840.844
28_A59_F0.354920.839
44_N75_C0.354050.837
74_R78_A0.353640.836
44_N69_C0.350640.829
9_H74_R0.344440.815
36_F43_V0.343710.813
14_V43_V0.342310.810
81_L104_V0.339410.803
73_C76_A0.339270.802
58_I72_G0.337940.799
74_R80_L0.334320.791
53_D88_K0.333860.790
52_A92_T0.328390.777
49_S53_D0.323680.765
60_N68_A0.322650.763
3_K78_A0.321260.760
76_A80_L0.314810.745
27_L31_I0.312530.739
9_H58_I0.310790.735
27_L30_A0.309420.732
53_D99_I0.309330.732
9_H66_T0.30650.725
11_V78_A0.302070.714
97_G100_L0.298770.707
24_D30_A0.295030.698
33_D36_F0.287640.680
73_C102_V0.281720.666
95_T98_G0.279630.661
77_A104_V0.27590.652
6_G75_C0.2750.650
19_E23_L0.274840.650
28_A32_C0.27460.649
10_D69_C0.274480.649
78_A81_L0.272860.645
32_C59_F0.27280.645
52_A88_K0.271990.643
50_D87_G0.271730.643
9_H72_G0.270360.639
81_L84_G0.266420.630
56_M68_A0.265820.629
3_K64_S0.264080.625
56_M75_C0.260690.617
9_H60_N0.260280.616
95_T100_L0.260050.615
80_L89_D0.259970.615
60_N71_N0.249720.591
66_T72_G0.248780.588
16_D45_F0.247980.586
22_D29_R0.247660.586
60_N64_S0.247390.585
60_N63_G0.24650.583
4_M32_C0.246190.582
49_S92_T0.245880.581
7_N98_G0.245730.581
20_E27_L0.244910.579
62_D66_T0.243860.577
58_I68_A0.243110.575
54_I80_L0.243070.575
58_I100_L0.243050.575
4_M8_P0.239820.567
23_L28_A0.238680.564
18_E49_S0.235570.557
18_E21_D0.234850.555
74_R79_Y0.234120.554
20_E105_D0.234070.554
52_A94_E0.234060.554
4_M7_N0.233870.553
5_H64_S0.23180.548
68_A95_T0.231130.547
9_H75_C0.2310.546
5_H36_F0.230590.545
8_P33_D0.230580.545
18_E83_G0.230550.545
24_D57_R0.22870.541
43_V71_N0.226920.537
60_N66_T0.226610.536
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
3fveA199.90.066
3ejxA0.991799.90.079
2gkeA0.991799.80.248
2otnA199.80.248
3ednA0.933999.80.26
3ejxA0.966999.80.263
1qyaA0.925699.70.325
1u0kA0.925699.70.328
1xubA0.909199.70.333
1s7jA0.892699.70.339

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