GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
V-ATPase_G - Vacuolar (H)-ATPase G subunit
Pfam: PF03179 (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: CL0255
Length: 105
Sequences: 1966
Seq/Len: 18.72
HH_delta: 0.111 (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
33_Q37_E0.741232.531
18_E22_E0.68822.350
43_E47_A0.632852.161
54_K58_A0.606552.071
31_L34_A0.587912.008
21_E25_K0.534741.826
7_Q11_E0.514491.757
40_K44_E0.503941.721
72_E76_E0.492061.680
42_I45_F0.47431.620
85_S89_N0.463521.583
31_L35_K0.456661.559
82_I89_N0.456191.558
55_E59_E0.451951.543
38_A42_I0.448121.530
28_E32_K0.443641.515
39_E43_E0.437351.494
46_R50_E0.433651.481
47_A51_E0.43351.480
25_K29_Q0.431011.472
77_E81_E0.420051.434
51_E55_E0.413871.413
11_E15_E0.406061.387
72_E75_T0.405411.384
29_Q33_Q0.404741.382
48_E51_E0.403841.379
22_E26_E0.39361.344
42_I46_R0.390611.334
54_K57_E0.386611.320
15_E18_E0.385451.316
63_E67_E0.38381.311
45_F53_F0.373411.275
96_M100_R0.372041.270
36_E40_K0.371261.268
70_E74_E0.365641.249
89_N92_K0.363391.241
28_E31_L0.362931.239
7_Q10_L0.360681.232
44_E48_E0.357541.221
21_E24_R0.351591.201
49_A53_F0.3491.192
57_E61_E0.346291.183
37_E41_E0.343671.174
80_E84_K0.340931.164
17_Q21_E0.3361.147
32_K36_E0.330931.130
91_D95_D0.330931.130
8_Q11_E0.322331.101
68_A71_L0.321531.098
50_E54_K0.319641.092
30_R33_Q0.318581.088
30_R35_K0.3171.083
56_K59_E0.316791.082
53_F64_A0.315171.076
87_S91_D0.31351.071
14_K17_Q0.308911.055
25_K28_E0.302051.031
47_A50_E0.300911.028
92_K96_M0.297721.017
11_E14_K0.28790.983
33_Q36_E0.2850.973
35_K39_E0.279220.954
53_F60_A0.2760.943
51_E54_K0.267570.914
62_G66_Q0.264220.902
37_E40_K0.26250.896
59_E63_E0.260230.889
74_E77_E0.259320.886
40_K43_E0.257550.880
16_A20_V0.256980.878
22_E25_K0.256890.877
76_E80_E0.254790.870
10_L14_K0.254120.868
53_F57_E0.25110.857
30_R34_A0.246980.843
18_E21_E0.246370.841
64_A68_A0.244160.834
46_R52_E0.2420.826
68_A72_E0.238630.815
27_R97_L0.233260.797
60_A64_A0.232050.792
12_A16_A0.2320.792
90_K93_V0.230480.787
14_K18_E0.228810.781
94_V98_L0.226150.772
8_Q13_E0.223850.764
36_E39_E0.223080.762
27_R31_L0.222290.759
18_E25_K0.215540.736
8_Q15_E0.215190.735
96_M101_V0.214220.732
52_E56_K0.213990.731
70_E73_K0.213450.729
94_V97_L0.213290.728
66_Q81_E0.211690.723
96_M99_S0.209550.716
20_V75_T0.207240.708
58_A62_G0.206390.705
16_A19_I0.204810.699
41_E45_F0.201260.687
27_R35_K0.200710.685
60_A68_A0.197380.674
83_K90_K0.197280.674
13_E75_T0.197280.674
45_F49_A0.197230.674
27_R34_A0.19620.670
15_E19_I0.194370.664
8_Q12_A0.194310.664
74_E78_K0.19250.657
61_E64_A0.191480.654
69_E80_E0.190970.652
43_E46_R0.190930.652
69_E73_K0.189710.648
72_E80_E0.186630.637
77_E83_K0.18540.633
23_A27_R0.184110.629
23_A79_I0.18320.626
30_R38_A0.182120.622
75_T90_K0.181680.620
49_A60_A0.181510.620
20_V23_A0.180850.618
21_E28_E0.179550.613
10_L13_E0.179350.612
59_E62_G0.17880.611
50_E56_K0.178170.608
63_E66_Q0.17680.604
14_K22_E0.176330.602
26_E30_R0.176290.602
56_K60_A0.175480.599
65_E76_E0.175340.599
93_V97_L0.174820.597
9_L41_E0.174230.595
57_E60_A0.173340.592
71_L78_K0.173180.591
34_A38_A0.173130.591
67_E70_E0.171890.587
34_A97_L0.171460.586
69_E72_E0.171180.585
43_E50_E0.170880.584
26_E29_Q0.169470.579
73_K76_E0.167620.572
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
4efaG199.10.111
2dm9A0.98196.70.553
1l2pA0.58196.60.557
2k6iA0.41995.10.614
3v6iA0.961992.10.659
3v6iA0.990591.30.666
1l2pA0.581880.687
2dm9A0.895287.40.691
4efaE0.990584.30.703
2kk7A0.428681.80.711

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