GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
2-Hacid_dh - D-isomer specific 2-hydroxyacid dehydrogenase catalytic domain
Pfam: PF00389 (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: CL0325
Length: 133
Sequences: 2773
Seq/Len: 20.85
HH_delta: 0.388 (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
52_A81_E1.026152.778
52_A56_E0.993822.691
29_E53_E0.978832.650
28_S31_E0.925322.505
40_D62_K0.863412.338
55_L64_I0.808072.188
13_E17_E0.799452.164
22_E39_A0.795582.154
9_D13_E0.792592.146
79_A86_V0.789592.138
78_A81_E0.779572.111
22_E35_R0.760492.059
41_A63_L0.73341.986
52_A78_A0.710341.923
33_A53_E0.696811.887
56_E82_R0.695981.884
12_I16_E0.689421.867
2_L39_A0.660711.789
29_E51_T0.655181.774
38_D60_N0.641821.738
29_E33_A0.628151.701
77_E81_E0.617351.671
56_E78_A0.610711.653
74_I79_A0.587151.590
66_T74_I0.570981.546
55_L79_A0.568991.540
42_I50_L0.548741.486
63_L87_T0.545641.477
13_E16_E0.537241.455
55_L82_R0.517371.401
68_G73_N0.514351.393
1_I19_F0.514131.392
40_D60_N0.510391.382
33_A54_V0.502961.362
10_E13_E0.482891.307
30_E34_E0.469971.272
31_E35_R0.464411.257
33_A57_A0.459541.244
59_P82_R0.449331.217
91_G94_A0.447281.211
78_A82_R0.43031.165
24_C35_R0.424241.149
74_I86_V0.422471.144
65_S87_T0.422031.143
34_E37_K0.413271.119
51_T54_V0.410511.111
37_K59_P0.405771.099
31_E34_E0.39861.079
52_A75_D0.390151.056
55_L84_I0.388031.051
1_I15_L0.378531.025
89_V92_Y0.375661.017
64_I79_A0.369561.001
58_A61_L0.364080.986
53_E56_E0.363760.985
75_D78_A0.363010.983
76_L80_K0.362450.981
93_N96_A0.357720.968
24_C27_P0.357170.967
30_E53_E0.350790.950
71_V76_L0.346460.938
66_T73_N0.339160.918
36_L58_A0.335980.910
52_A82_R0.325640.882
37_K57_A0.321340.870
77_E80_K0.320520.868
38_D59_P0.317930.861
9_D16_E0.30940.838
9_D23_F0.306210.829
68_G74_I0.305620.827
55_L78_A0.305520.827
89_V93_N0.300050.812
7_L11_E0.298690.809
35_R39_A0.2950.799
4_T48_T0.294680.798
93_N100_H0.290720.787
16_E23_F0.285240.772
96_A99_E0.279670.757
6_P47_G0.276620.749
3_I21_V0.276520.749
22_E38_D0.275650.746
3_I12_I0.264380.716
45_G67_A0.263180.713
63_L69_A0.262490.711
36_L42_I0.261070.707
34_E57_A0.259890.704
41_A65_S0.25980.703
93_N97_V0.258250.699
43_I67_A0.256820.695
33_A37_K0.253920.687
63_L85_P0.251870.682
2_L35_R0.251340.680
41_A62_K0.249280.675
32_L36_L0.24750.670
66_T72_D0.247080.669
32_L42_I0.247010.669
95_E99_E0.246620.668
33_A36_L0.246110.666
47_G69_A0.245410.664
64_I84_I0.241410.654
65_S93_N0.239890.649
35_R38_D0.239070.647
69_A96_A0.238970.647
16_E20_E0.23760.643
24_C28_S0.23520.637
61_L99_E0.235130.637
92_Y100_H0.234310.634
58_A84_I0.230570.624
87_T97_V0.22870.619
14_R17_E0.226180.612
80_K85_P0.22370.606
44_V68_G0.223410.605
14_R18_G0.223260.604
71_V85_P0.222370.602
93_N99_E0.220970.598
50_L54_V0.219290.594
69_A101_A0.218130.591
11_E14_R0.21790.590
94_A97_V0.216510.586
24_C39_A0.213930.579
6_P25_D0.213510.578
79_A90_P0.213190.577
2_L27_P0.213160.577
69_A93_N0.212740.576
45_G68_G0.208770.565
1_I41_A0.20840.564
10_E14_R0.207330.561
27_P31_E0.206360.559
5_D48_T0.205420.556
12_I23_F0.205270.556
44_V74_I0.201960.547
7_L43_I0.196870.533
48_T67_A0.195910.530
17_E20_E0.19410.526
5_D50_L0.194050.525
45_G99_E0.193930.525
40_D64_I0.193340.523
25_D28_S0.193090.523
43_I96_A0.192790.522
3_I15_L0.192330.521
89_V94_A0.191890.520
45_G71_V0.190810.517
36_L54_V0.19030.515
70_G88_N0.189970.514
56_E81_E0.189930.514
46_S68_G0.186090.504
9_D12_I0.184990.501
90_P94_A0.184670.500
89_V98_A0.18460.500
49_P72_D0.184350.499
19_F24_C0.183050.496
70_G97_V0.181960.493
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
4dgsA199.80.388
1ygyA199.80.401
3k5pA199.80.404
1sc6A199.80.406
4g2nA199.80.406
4e5nA199.80.415
2g76A199.70.431
2d0iA199.70.439
1wwkA199.70.439
2yq5A0.98599.70.44

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