GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GFO_IDH_MocA - Oxidoreductase family NAD-binding Rossmann fold
Pfam: PF01408 (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: 120
Sequences: 33812
Seq/Len: 281.77
HH_delta: -0.075 (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
4_G63_V2.535032.504
2_R27_E2.44512.415
55_E81_K2.265262.238
80_K108_A2.109262.083
36_P40_E2.106522.081
76_A104_E1.997131.973
76_A80_K1.988671.964
35_D38_R1.951731.928
80_K84_E1.934291.911
4_G57_L1.903531.880
53_D56_E1.887461.864
107_E111_E1.748721.727
2_R64_D1.686571.666
108_A112_K1.677391.657
88_H115_K1.662781.642
19_L67_I1.626811.607
76_A101_E1.601491.582
40_E44_E1.587111.568
8_A31_V1.587031.568
70_T78_I1.58351.564
2_R29_V1.575531.556
84_E108_A1.568951.550
106_V110_K1.510941.492
74_S78_I1.466711.449
108_A111_E1.449861.432
3_V26_F1.428211.411
80_K104_E1.412441.395
51_Y56_E1.392941.376
103_E107_E1.378261.361
98_T101_E1.376081.359
104_E108_A1.338431.322
84_E112_K1.332541.316
15_H67_I1.315961.300
55_E59_A1.294911.279
17_R21_R1.219641.205
3_V65_A1.20221.187
109_A114_V1.195981.181
88_H114_V1.183211.169
97_L101_E1.163571.149
52_T56_E1.154931.141
79_A91_V1.145391.131
22_S25_D1.136161.122
63_V87_K1.135881.122
36_P52_T1.125061.111
36_P39_A1.105881.092
83_L114_V1.092451.079
41_A45_K1.091141.078
70_T74_S1.082761.070
29_V63_V1.080971.068
38_R41_A1.075841.063
3_V67_I1.067851.055
81_K85_A1.063591.051
11_I69_A1.05981.047
37_E40_E1.058671.046
103_E106_V1.044381.032
77_E81_K1.039761.027
101_E104_E1.032171.020
13_R45_K1.024251.012
83_L112_K1.021221.009
79_A105_L1.01621.004
104_E107_E1.013891.001
5_I16_L1.008590.996
18_A21_R1.003780.991
13_R41_A1.00030.988
14_R17_R0.996730.985
4_G66_V0.995150.983
57_L63_V0.991480.979
4_G32_C0.977240.965
37_E41_A0.976650.965
18_A22_S0.972260.960
81_K84_E0.967770.956
54_L81_K0.962780.951
33_D39_A0.951840.940
5_I67_I0.941280.930
107_E110_K0.94110.930
74_S77_E0.939440.928
39_A43_A0.929450.918
99_L103_E0.927750.916
109_A116_V0.91820.907
58_L82_A0.916860.906
83_L109_A0.911880.901
41_A44_E0.909780.899
56_E59_A0.90680.896
15_H69_A0.895050.884
59_A85_A0.889320.878
96_A102_A0.884880.874
32_C54_L0.884010.873
12_G17_R0.876990.866
29_V62_D0.876360.866
39_A50_V0.869890.859
40_E43_A0.868670.858
2_R62_D0.866130.856
3_V19_L0.86360.853
100_E104_E0.853910.843
66_V82_A0.852420.842
33_D38_R0.844880.835
8_A33_D0.822290.812
96_A105_L0.820940.811
95_L102_A0.81810.808
8_A16_L0.811220.801
102_A106_V0.800390.791
62_D87_K0.800060.790
51_Y57_L0.799290.790
68_I79_A0.768660.759
100_E103_E0.767380.758
92_E95_L0.761820.752
78_I81_K0.761130.752
12_G69_A0.760090.751
86_G112_K0.755390.746
9_G12_G0.75140.742
77_E104_E0.749190.740
12_G16_L0.747730.739
84_E111_E0.744560.735
13_R17_R0.739930.731
10_S72_P0.73880.730
14_R18_A0.72920.720
88_H92_E0.728640.720
58_L85_A0.72740.719
6_I32_C0.726170.717
54_L78_I0.724660.716
10_S14_R0.720270.711
77_E80_K0.711640.703
54_L58_L0.708280.700
106_V109_A0.69690.688
5_I15_H0.691730.683
87_K114_V0.684320.676
83_L108_A0.679010.671
38_R42_F0.677250.669
29_V51_Y0.676740.668
2_R63_V0.676020.668
13_R46_Y0.672120.664
27_E49_P0.671930.664
6_I78_I0.66950.661
79_A89_V0.660430.652
17_R45_K0.646070.638
6_I70_T0.645340.637
71_P74_S0.642110.634
42_F45_K0.641710.634
82_A87_K0.637230.629
95_L116_V0.633640.626
29_V49_P0.631610.624
11_I14_R0.631320.624
72_P75_H0.628690.621
91_V95_L0.625640.618
35_D40_E0.62170.614
6_I68_I0.618370.611
5_I28_V0.617350.610
96_A101_E0.615880.608
43_A50_V0.615420.608
20_L49_P0.60740.600
69_A92_E0.603380.596
65_A88_H0.602970.596
17_R46_Y0.602420.595
68_I71_P0.600190.593
36_P50_V0.598970.592
9_G69_A0.597440.590
39_A52_T0.593980.587
6_I66_V0.592860.586
91_V116_V0.592470.585
22_S26_F0.586410.579
70_T75_H0.583590.576
11_I72_P0.582690.576
68_I78_I0.582150.575
2_R28_V0.568650.562
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
4fb5A199.8-0.075
4gqaA199.8-0.065
4h3vA0.991799.8-0.035
3rc1A0.991799.8-0.028
3moiA0.991799.8-0.023
3db2A0.991799.8-0.022
1zh8A199.8-0.021
3ec7A199.8-0.019
3q2iA199.8-0.017
3ohsX199.8-0.013

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