GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ATP-synt_ab_C - ATP synthase alphabeta chain C terminal domain
Pfam: PF00306 (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: 113
Sequences: 3327
Seq/Len: 29.44
HH_delta: 0.347 (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
87_E90_K1.100932.912
5_G8_K1.058442.800
74_A80_F0.986882.611
74_A79_K0.921912.439
39_R81_D0.913912.418
78_G81_D0.858692.272
90_K94_K0.816512.160
84_P87_E0.799062.114
6_Q9_L0.765932.026
43_I75_I0.746081.974
13_Q16_E0.737861.952
38_E41_R0.712011.884
6_Q77_R0.707681.872
3_V73_Y0.70161.856
31_D35_L0.690511.827
45_E48_K0.674761.785
55_V96_I0.624621.652
73_Y77_R0.607931.608
70_D74_A0.607511.607
3_V69_I0.60221.593
6_Q76_L0.602191.593
93_T97_E0.550071.455
50_N53_D0.536821.420
15_R18_E0.525871.391
80_F98_K0.513111.357
70_D95_D0.487561.290
39_R78_G0.482111.275
10_I76_L0.48151.274
91_I97_E0.470161.244
38_E42_R0.459621.216
34_K38_E0.459081.214
16_E86_E0.450121.191
7_L47_L0.448991.188
15_R44_R0.443421.173
65_L69_I0.443321.173
9_L13_Q0.437471.157
46_F75_I0.428051.132
83_I98_K0.421221.114
35_L81_D0.40741.078
74_A98_K0.406231.075
2_K6_Q0.400661.060
10_I43_I0.386441.022
80_F83_I0.385761.021
42_R85_E0.380281.006
41_R85_E0.374590.991
14_Y44_R0.364370.964
50_N89_E0.355650.941
45_E89_E0.355020.939
6_Q10_I0.353660.936
32_E36_I0.353350.935
80_F91_I0.352220.932
53_D93_T0.3440.910
94_K97_E0.341780.904
85_E97_E0.340080.900
83_I87_E0.339690.899
45_E86_E0.339540.898
92_E96_I0.33940.898
71_L96_I0.332670.880
5_G9_L0.326070.863
50_N93_T0.325930.862
24_V37_L0.322440.853
31_D34_K0.318750.843
4_A9_L0.316640.838
2_K73_Y0.313640.830
37_L41_R0.31150.824
46_F71_L0.294780.780
11_L43_I0.290510.769
14_Y18_E0.289310.765
83_I97_E0.281480.745
17_L21_V0.278440.737
74_A95_D0.276820.732
6_Q73_Y0.274330.726
83_I91_I0.273920.725
93_T98_K0.26830.710
67_E70_D0.264890.701
69_I73_Y0.2630.696
33_D79_K0.260530.689
24_V27_D0.260240.688
71_L92_E0.258920.685
5_G26_S0.255020.675
29_L34_K0.253350.670
17_L36_I0.25220.667
80_F88_L0.246770.653
2_K66_E0.245490.649
18_E44_R0.244720.647
14_Y40_G0.244010.646
16_E22_Q0.23990.635
91_I95_D0.238620.631
25_G34_K0.237420.628
1_K10_I0.23740.628
89_E96_I0.236160.625
21_V51_A0.235760.624
25_G36_I0.234680.621
26_S34_K0.231370.612
35_L50_N0.23080.611
82_D98_K0.230010.608
21_V40_G0.229190.606
10_I34_K0.225650.597
91_I96_I0.224140.593
14_Y41_R0.223840.592
36_I98_K0.223570.591
31_D86_E0.223350.591
41_R50_N0.221340.586
21_V24_V0.220930.584
13_Q36_I0.220510.583
8_K22_Q0.22020.583
66_E70_D0.219420.580
14_Y24_V0.219350.580
54_P72_F0.21930.580
72_F75_I0.219210.580
41_R45_E0.218550.578
2_K9_L0.21750.575
67_E96_I0.217260.575
4_A47_L0.214480.567
42_R88_L0.211910.561
14_Y37_L0.210420.557
22_Q33_D0.209160.553
13_Q52_F0.209130.553
12_A20_F0.208810.552
32_E35_L0.207640.549
70_D93_T0.207540.549
71_L75_I0.207430.549
87_E91_I0.206980.548
34_K82_D0.206390.546
15_R92_E0.203490.538
43_I46_F0.202440.536
37_L40_G0.202140.535
39_R43_I0.199590.528
43_I76_L0.199460.528
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
3oaaA0.911599.70.347
2ck3A0.911599.60.37
2qe7A0.911599.60.373
2r9vA0.911599.60.373
1fx0B0.964699.60.375
1fx0A0.911599.60.375
2ck3D0.955899.60.394
1skyE0.946999.60.407
3mfyA0.902799.50.452
3vr4A0.920499.40.458

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