GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ETF_alpha - Electron transfer flavoprotein FAD-binding domain
Pfam: PF00766 (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: CL0085
Length: 86
Sequences: 1243
Seq/Len: 14.45
HH_delta: -0.102 (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_E65_K1.077113.515
12_A72_I1.033383.372
10_V62_V0.768032.506
49_I53_R0.716692.339
13_G23_F0.713872.330
39_A49_I0.692652.260
67_Y78_H0.60681.980
24_E27_E0.593521.937
3_D6_E0.579031.890
10_V38_G0.573221.871
24_E28_E0.572981.870
28_E32_A0.532831.739
13_G26_I0.529131.727
26_I70_F0.512271.672
12_A69_A0.507941.658
27_E37_V0.505551.650
40_S72_I0.487531.591
63_A84_D0.459381.499
65_K86_K0.449541.467
4_L10_V0.444941.452
62_V82_I0.440821.439
29_L33_L0.440361.437
50_P53_R0.438351.430
9_V35_A0.431331.408
44_V54_Q0.428861.400
69_A78_H0.424031.384
69_A72_I0.416021.358
5_E60_K0.413621.350
12_A55_I0.409081.335
17_V26_I0.406371.326
64_P85_S0.405861.324
82_I85_S0.40321.316
39_A43_V0.397751.298
23_F37_V0.391031.276
31_E34_G0.385531.258
27_E31_E0.362621.183
25_L28_E0.35771.167
39_A44_V0.352361.150
19_S22_N0.348591.138
38_G55_I0.347221.133
11_V29_L0.330181.077
45_D54_Q0.31071.014
4_L38_G0.30550.997
52_E63_A0.303740.991
16_G22_N0.296510.968
22_N25_L0.293010.956
23_F43_V0.288330.941
9_V65_K0.284680.929
12_A40_S0.284080.927
18_G22_N0.280790.916
10_V36_A0.275690.900
30_A37_V0.273520.893
19_S48_W0.269860.881
75_A86_K0.264650.864
57_Q80_A0.259440.847
47_G54_Q0.258050.842
17_V22_N0.256240.836
79_L83_K0.254170.829
13_G17_V0.251580.821
4_L86_K0.24950.814
63_A83_K0.246430.804
42_P80_A0.245470.801
26_I37_V0.241060.787
16_G40_S0.240690.785
55_I69_A0.238750.779
13_G43_V0.234340.765
29_L66_L0.230510.752
36_A53_R0.230360.752
55_I82_I0.227510.742
27_E49_I0.225580.736
2_V36_A0.225560.736
12_A62_V0.223160.728
20_K49_I0.222980.728
5_E22_N0.220.718
38_G53_R0.215540.703
18_G29_L0.215440.703
58_S76_I0.213910.698
16_G25_L0.209570.684
25_L70_F0.208140.679
40_S80_A0.207850.678
23_F26_I0.206160.673
32_A76_I0.201070.656
22_N28_E0.200340.654
6_E68_I0.199970.653
5_E68_I0.199760.652
10_V53_R0.196260.640
12_A78_H0.195870.639
36_A50_P0.19310.630
47_G57_Q0.192710.629
79_L82_I0.190930.623
5_E9_V0.190580.622
16_G48_W0.190060.620
17_V25_L0.18860.615
26_I32_A0.18780.613
24_E34_G0.18770.613
51_R55_I0.186780.610
6_E63_A0.18630.608
13_G70_F0.18560.606
25_L32_A0.185160.604
56_G59_G0.1850.604
67_Y72_I0.183750.600
51_R63_A0.183410.599
61_T76_I0.1830.597
8_E86_K0.182870.597
11_V37_V0.182580.596
41_R45_D0.18240.595
71_G74_G0.181820.593
3_D60_K0.181780.593
18_G25_L0.180570.589
4_L60_K0.17950.586
4_L64_P0.177380.579
15_R45_D0.175820.574
33_L68_I0.174960.571
63_A66_L0.174880.571
49_I61_T0.174370.569
20_K24_E0.173910.568
21_E31_E0.173480.566
83_K86_K0.173030.565
42_P46_A0.173010.565
15_R42_P0.170640.557
11_V33_L0.169690.554
36_A63_A0.168640.550
79_L84_D0.168310.549
20_K50_P0.168290.549
35_A48_W0.167720.547
43_V48_W0.167560.547
29_L32_A0.165670.541
13_G49_I0.164560.537
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
1efpA1100-0.102
1efvA1100-0.101
1o97D1100-0.095
1t9bA0.953584.20.879
2ihtA0.965180.50.884
1ozhA0.965178.80.886
2wvgA0.976776.50.888
3cf4G0.976775.50.889
2nxwA0.976775.40.889
2pgnA0.976771.90.892

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