GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ETF - Electron transfer flavoprotein domain
Pfam: PF01012 (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: CL0039
Length: 164
Sequences: 3592
Seq/Len: 21.9
HH_delta: 0.007 (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
34_E61_K1.066423.490
23_A26_R0.952643.117
36_T63_Y0.838562.744
123_D134_T0.795992.605
24_A35_V0.779822.552
84_E87_K0.751462.459
106_A156_T0.715832.342
83_A87_K0.687762.251
96_F106_A0.585971.917
132_V145_T0.576761.887
25_R29_E0.574051.878
79_A112_R0.56721.856
65_I81_A0.555051.816
37_A53_A0.550071.800
86_I94_V0.544791.783
118_V146_V0.538061.761
36_T91_P0.530091.735
44_E66_D0.527441.726
21_L59_A0.51981.701
134_T143_V0.51471.684
23_A162_F0.511271.673
36_T61_K0.509961.669
13_L49_A0.481981.577
121_V133_V0.480461.572
28_A60_D0.470291.539
121_V155_V0.47021.539
122_T134_T0.445471.458
20_A95_L0.441381.444
146_V153_A0.440561.442
38_V85_L0.432921.417
74_D77_A0.42791.400
19_E160_G0.423931.387
39_V46_A0.421861.380
25_R57_Y0.411871.348
37_A59_A0.408911.338
34_E60_D0.407621.334
96_F109_L0.405011.325
99_T104_D0.396241.297
157_V161_A0.394361.290
84_E88_E0.393111.286
25_R60_D0.387231.267
45_E48_E0.381031.247
42_P45_E0.377871.237
125_E132_V0.376731.233
36_T60_D0.375131.228
80_D84_E0.374561.226
125_E134_T0.370951.214
67_D70_L0.370921.214
83_A109_L0.369111.208
83_A112_R0.369061.208
110_A117_L0.366371.199
63_Y85_L0.363111.188
44_E48_E0.356511.167
38_V82_L0.354461.160
65_I85_L0.353831.158
35_V59_A0.351131.149
13_L18_L0.350461.147
93_L153_A0.342821.122
79_A109_L0.342341.120
128_D147_R0.34091.116
137_V140_G0.340451.114
20_A97_G0.337751.105
94_V115_A0.334241.094
70_L81_A0.333681.092
14_N17_S0.332991.090
75_P104_D0.332341.088
120_D158_R0.329421.078
18_L57_Y0.328151.074
135_R142_V0.325641.066
23_A123_D0.325481.065
47_A64_H0.324941.063
82_L109_L0.324191.061
127_E132_V0.323331.058
108_R112_R0.321461.052
115_A154_V0.319711.046
54_L62_V0.318331.042
137_V142_V0.314871.030
27_L95_L0.314561.029
87_K90_G0.31251.023
122_T143_V0.301170.986
78_Y105_L0.299680.981
87_K113_L0.299040.979
82_L105_L0.29860.977
113_L154_V0.295680.968
13_L53_A0.295120.966
136_P158_R0.294530.964
95_L155_V0.294450.964
42_P46_A0.292970.959
79_A108_R0.291540.954
24_A95_L0.289950.949
73_Y78_Y0.289750.948
42_P66_D0.287090.939
11_G45_E0.284840.932
16_V19_E0.283520.928
116_P153_A0.282570.925
16_V97_G0.28240.924
73_Y81_A0.280450.918
25_R35_V0.279250.914
139_G160_G0.278120.910
118_V133_V0.278080.910
86_I113_L0.27770.909
86_I91_P0.274410.898
40_L78_Y0.27440.898
68_P71_A0.271360.888
53_A57_Y0.270920.887
40_L81_A0.270770.886
86_I109_L0.26980.883
98_S120_D0.269110.881
124_L133_V0.266320.871
129_G147_R0.263180.861
44_E47_A0.261960.857
134_T141_K0.259710.850
83_A113_L0.259390.849
92_D129_G0.257870.844
117_L156_T0.257340.842
12_R49_A0.25560.836
73_Y104_D0.25230.826
46_A49_A0.248820.814
133_V153_A0.247080.809
80_D112_R0.247020.808
46_A64_H0.244870.801
75_P108_R0.244020.799
132_V143_V0.243980.798
96_F156_T0.240210.786
103_R120_D0.237340.777
17_S37_A0.234960.769
22_E26_R0.234730.768
45_E49_A0.234710.768
61_K89_E0.233440.764
121_V124_L0.230320.754
122_T136_P0.228650.748
40_L82_L0.228640.748
127_E145_T0.227670.745
85_L89_E0.225290.737
148_L153_A0.224950.736
16_V98_S0.223880.733
101_F104_D0.220640.722
22_E164_P0.215790.706
98_S158_R0.214840.703
95_L157_V0.214530.702
63_Y89_E0.212590.696
76_E80_D0.212550.696
86_I154_V0.212240.695
109_L154_V0.211250.691
121_V157_V0.211150.691
109_L112_R0.211040.691
117_L154_V0.210970.690
124_L155_V0.21040.688
69_A72_E0.208810.683
133_V155_V0.207610.679
22_E25_R0.207090.678
107_P156_T0.205030.671
36_T89_E0.204690.670
98_S159_P0.202470.663
15_P124_L0.201330.659
12_R46_A0.201240.659
73_Y77_A0.198670.650
26_R123_D0.198610.650
135_R140_G0.198020.648
118_V148_L0.195480.640
126_V132_V0.195180.639
103_R119_T0.194850.638
42_P68_P0.194160.635
108_R111_A0.19310.632
67_D72_E0.191020.625
118_V153_A0.190490.623
44_E64_H0.190180.622
128_D153_A0.189990.622
19_E158_R0.188730.618
57_Y164_P0.188610.617
75_P103_R0.188460.617
78_Y101_F0.186970.612
136_P140_G0.185450.607
23_A157_V0.18510.606
81_A85_L0.184270.603
23_A161_A0.18380.601
87_K91_P0.183780.601
39_V64_H0.183090.599
17_S142_V0.182940.599
120_D135_R0.18280.598
21_L39_V0.18260.598
93_L155_V0.181720.595
15_P164_P0.17960.588
18_L164_P0.179590.588
110_A154_V0.179520.587
42_P57_Y0.179020.586
47_A62_V0.178160.583
129_G132_V0.177970.582
55_A62_V0.177310.580
47_A54_L0.177210.580
18_L49_A0.176520.578
118_V144_A0.176280.577
42_P71_A0.175360.574
107_P117_L0.175330.574
25_R28_A0.174950.572
15_P101_F0.174640.571
98_S139_G0.173460.568
138_Y142_V0.173360.567
40_L73_Y0.173310.567
111_A115_A0.171810.562
48_E55_A0.171190.560
60_D63_Y0.169570.555
42_P49_A0.169520.555
119_T156_T0.168280.551
91_P115_A0.167890.549
73_Y105_L0.167610.548
83_A86_I0.167130.547
16_V159_P0.166620.545
62_V120_D0.16630.544
86_I115_A0.165870.543
92_D155_V0.165030.540
98_S104_D0.164960.540
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
3ih5A0.98171000.007
1o97D0.96341000.055
1efvA0.94511000.079
1efpA0.92681000.121
1o97C0.97561000.173
1efpB0.963499.90.204
1efvB0.963499.90.205
3fetA0.835499.90.255
3tnjA0.68991.10.866
3fdxA0.713489.70.87

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