GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ldh_1_N - lactatemalate dehydrogenase NAD binding domain
Pfam: PF00056 (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: 141
Sequences: 69501
Seq/Len: 492.91
HH_delta: 0.151 (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
8_A31_L3.524482.575
88_L96_K3.474492.539
92_E96_K3.291992.406
3_V72_I3.264662.386
88_L92_E3.175442.320
75_I116_V3.142312.296
59_I62_G2.950212.156
64_Y104_K2.94172.150
2_K28_E2.871482.098
36_E40_E2.687841.964
19_L23_Q2.647551.935
32_I55_S2.609861.907
14_S18_L2.534361.852
9_A33_D2.274451.662
3_V20_L2.251451.645
96_K100_E2.242861.639
2_K30_V2.237961.635
55_S62_G2.129521.556
35_N38_K2.111051.543
60_T100_E2.089711.527
91_L95_A2.089131.527
73_V105_I2.044031.494
30_V70_A2.028971.483
99_K103_K1.979421.446
14_S42_E1.89831.387
3_V25_L1.845551.349
73_V101_I1.815281.326
25_L72_I1.790251.308
19_L22_Q1.786341.305
5_I17_A1.777831.299
14_S45_D1.764061.289
62_G65_E1.757091.284
18_L45_D1.753181.281
76_T117_V1.747921.277
67_L105_I1.710911.250
63_D101_I1.703111.245
4_A70_A1.701311.243
17_A31_L1.692261.237
74_V117_V1.667631.219
36_E54_P1.652241.207
32_I66_A1.64041.199
79_V93_A1.610741.177
96_K99_K1.596671.167
60_T64_Y1.59021.162
64_Y107_K1.588941.161
18_L22_Q1.584841.158
15_T18_L1.55841.139
20_L25_L1.552981.135
86_S89_D1.548051.131
39_A52_P1.532981.120
10_G38_K1.529951.118
40_E44_L1.527781.116
65_E68_K1.522891.113
64_Y68_K1.508351.102
100_E104_K1.498431.095
40_E43_A1.481621.083
30_V53_L1.475491.078
10_G14_S1.454961.063
15_T19_L1.444231.055
104_K107_K1.441671.053
16_L74_V1.440511.053
60_T103_K1.428551.044
30_V51_A1.423631.040
91_L96_K1.422271.039
83_P86_S1.413211.033
16_L76_T1.395751.020
55_S66_A1.376861.006
98_V116_V1.317380.963
87_R96_K1.301620.951
38_K41_G1.300660.950
79_V89_D1.297460.948
98_V102_A1.290560.943
28_E49_A1.286570.940
28_E51_A1.283050.938
61_S65_E1.279350.935
75_I102_A1.253650.916
41_G45_D1.238640.905
100_E103_K1.225590.896
65_E69_D1.214950.888
12_V16_L1.212940.886
37_D40_E1.209740.884
87_R90_L1.200540.877
58_R92_E1.164940.851
81_R89_D1.162830.850
41_G44_L1.158740.847
75_I101_I1.135550.830
42_E45_D1.128490.825
87_R99_K1.117490.817
78_G94_N1.114080.814
67_L70_A1.113610.814
8_A17_A1.108550.810
33_D39_A1.104180.807
37_D41_G1.102510.806
30_V69_D1.099550.803
56_P59_I1.087040.794
6_I75_I1.085660.793
105_I109_A1.076760.787
58_R89_D1.075520.786
103_K107_K1.072980.784
43_A47_S1.070370.782
102_A106_A1.069130.781
75_I98_V1.06890.781
77_A97_I1.062490.776
44_L47_S1.05570.771
42_E46_L1.052190.769
93_A97_I1.049940.767
2_K71_D1.042780.762
10_G35_N1.042110.762
104_K108_Y1.041340.761
102_A105_I1.041210.761
4_A32_I1.033350.755
53_L69_D1.029960.753
43_A52_P1.029050.752
4_A67_L1.024790.749
98_V101_I1.020590.746
14_S41_G1.005580.735
105_I108_Y0.99470.727
6_I77_A0.994530.727
103_K106_A0.993420.726
55_S63_D0.991530.725
31_L50_S0.985940.720
58_R93_A0.983190.718
63_D100_E0.982030.718
16_L20_L0.978690.715
72_I113_I0.975890.713
25_L28_E0.97520.713
61_S64_Y0.974650.712
72_I115_I0.959380.701
57_V97_I0.955020.698
68_K108_Y0.951640.695
113_I117_V0.95110.695
39_A43_A0.950160.694
62_G66_A0.927310.678
95_A99_K0.926150.677
10_G33_D0.921260.673
63_D104_K0.918850.671
47_S50_S0.914530.668
85_M89_D0.913390.667
102_A116_V0.912390.667
6_I101_I0.908460.664
2_K70_A0.906080.662
102_A114_V0.897360.656
4_A66_A0.890330.651
79_V90_L0.883070.645
89_D92_E0.869880.636
18_L21_A0.869420.635
21_A29_I0.868670.635
106_A109_A0.860790.629
6_I76_T0.857380.627
17_A21_A0.851020.622
63_D66_A0.846110.618
16_L19_L0.84160.615
9_A35_N0.838470.613
101_I105_I0.837050.612
9_A34_I0.826550.604
60_T104_K0.82430.602
86_S90_L0.821830.601
89_D93_A0.813620.595
33_D36_E0.807420.590
4_A73_V0.806360.589
13_G76_T0.794120.580
32_I62_G0.787760.576
57_V77_A0.784230.573
81_R86_S0.782620.572
94_N119_N0.78210.572
73_V114_V0.780720.570
20_L72_I0.775980.567
21_A46_L0.77180.564
53_L66_A0.74930.548
90_L94_N0.74860.547
87_R91_L0.743220.543
85_M90_L0.741890.542
18_L46_L0.74150.542
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
1hyeA0.992999.70.151
1b8pA199.70.153
1o6zA0.992999.70.159
1y7tA199.70.174
2x0jA0.992999.70.174
3fi9A0.992999.60.186
5mdhA199.60.191
3nepX0.992999.60.191
3vkuA0.985899.60.195
3pqeA0.992999.60.199

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