GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Complex1_30kDa - Respiratory-chain NADH dehydrogenase 30 Kd subunit
Pfam: PF00329 (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: 103
Sequences: 1762
Seq/Len: 17.11
HH_delta: 0.008 (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
55_E82_E1.038424.160
3_A59_I1.003944.022
57_P82_E0.638912.560
3_A45_V0.62932.521
4_K8_D0.545782.187
3_A34_F0.540912.167
59_I66_A0.494931.983
28_F79_I0.494291.980
67_D84_H0.478141.916
14_L66_A0.47731.912
73_I81_F0.444491.781
30_V81_F0.426561.709
18_T31_V0.422851.694
19_A77_F0.416031.667
84_H87_L0.403171.615
17_I32_Y0.395481.584
29_E48_K0.394571.581
30_V56_I0.391361.568
55_E80_R0.385721.545
19_A73_I0.383441.536
34_F59_I0.379211.519
93_P96_W0.361311.448
57_P83_G0.353521.416
50_P54_P0.34791.394
22_Y29_E0.340641.365
32_Y59_I0.339861.362
14_L17_I0.33621.347
74_Y87_L0.332011.330
18_T33_H0.330851.326
12_A37_D0.330441.324
3_A63_F0.329481.320
36_S39_D0.320561.284
35_A42_L0.318551.276
47_V56_I0.317891.274
75_D89_R0.314931.262
10_G38_G0.294011.178
68_W90_L0.281.122
64_P67_D0.279141.118
13_R37_D0.268941.077
56_I81_F0.265641.064
5_F9_E0.264711.061
21_D27_R0.258751.037
58_S61_P0.258641.036
14_L65_A0.255021.022
71_R85_P0.249661.000
35_A40_G0.247740.993
2_V5_F0.247460.991
6_L43_V0.246330.987
50_P53_N0.246020.986
16_T69_Y0.240710.964
17_I30_V0.239010.958
5_F8_D0.238830.957
13_R65_A0.237420.951
74_Y84_H0.236690.948
18_T44_R0.232740.932
29_E46_K0.227260.910
60_T66_A0.225780.905
23_P27_R0.224350.899
92_L96_W0.22420.898
19_A30_V0.224190.898
4_K61_P0.222670.892
69_Y91_L0.220630.884
77_F101_L0.220420.883
65_A69_Y0.217380.871
76_M92_L0.216810.869
23_P28_F0.210430.843
76_M91_L0.205720.824
23_P79_I0.205530.823
33_H44_R0.204770.820
89_R96_W0.2030.813
11_G41_T0.20270.812
44_R77_F0.201990.809
20_V31_V0.201960.809
74_Y80_R0.201160.806
23_P26_G0.200350.803
68_W73_I0.200230.802
69_Y73_I0.199450.799
19_A79_I0.197380.791
74_Y81_F0.19660.788
4_K62_I0.196210.786
75_D92_L0.196070.786
9_E50_P0.194710.780
32_Y85_P0.190880.765
99_H102_R0.18940.759
35_A92_L0.187780.752
18_T73_I0.18770.752
75_D90_L0.187560.751
58_S65_A0.186890.749
18_T69_Y0.186280.746
12_A38_G0.185140.742
10_G39_D0.184980.741
34_F63_F0.184110.738
87_L90_L0.183130.734
59_I63_F0.181760.728
60_T85_P0.18060.724
21_D102_R0.180490.723
26_G29_E0.180250.722
23_P49_V0.180060.721
49_V54_P0.179630.720
27_R50_P0.178560.715
10_G36_S0.178470.715
34_F62_I0.178210.714
92_L95_D0.176550.707
11_G36_S0.176220.706
4_K38_G0.17340.695
58_S70_E0.172690.692
16_T77_F0.172190.690
74_Y91_L0.171410.687
5_F41_T0.170580.683
60_T84_H0.169290.678
77_F103_K0.168340.674
39_D53_N0.164530.659
22_Y27_R0.164350.658
63_F81_F0.164120.658
70_E84_H0.163810.656
26_G48_K0.161970.649
75_D99_H0.161070.645
78_G100_P0.160470.643
31_V44_R0.160340.642
65_A75_D0.160280.642
2_V18_T0.159870.640
50_P55_E0.159410.639
10_G13_R0.158540.635
5_F52_E0.158190.634
68_W84_H0.157960.633
74_Y98_G0.15790.633
15_V35_A0.157330.630
2_V9_E0.155720.624
71_R88_R0.15440.619
20_V29_E0.15420.618
2_V10_G0.153530.615
89_R95_D0.153430.615
76_M99_H0.153110.613
12_A64_P0.152690.612
24_E27_R0.151680.608
60_T67_D0.151260.606
57_P61_P0.150960.605
17_I66_A0.150860.604
41_T45_V0.150050.601
36_S40_G0.149620.599
6_L34_F0.149450.599
35_A44_R0.149210.598
15_V41_T0.148960.597
53_N80_R0.148810.596
4_K9_E0.14840.595
47_V57_P0.148380.594
71_R87_L0.147480.591
93_P101_L0.146690.588
13_R63_F0.145390.582
37_D40_G0.145180.582
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
3i9v511000.008
3mcrA0.864199.90.186
4gyiA0.98069.40.927
1dlwA0.62148.70.929
1jg5A0.29137.40.931
2bmmA0.66026.50.932
3f8lA0.53460.933
2kscA0.63115.70.934
1ji8A0.82524.90.936
3f8mA0.5344.90.936

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