GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ATP-synt_C - ATP synthase subunit C
Pfam: PF00137 (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: 66
Sequences: 2265
Seq/Len: 34.32
HH_delta: 0.028 (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
27_A30_G1.214343.804
25_G45_G1.024883.211
13_A56_G0.690342.163
16_G20_G0.507751.591
6_A64_L0.491081.538
21_Q51_A0.466541.462
32_I41_K0.464541.455
19_I23_I0.454671.424
28_A42_M0.454211.423
23_I26_S0.443761.390
25_G46_A0.438641.374
28_A38_L0.431371.351
7_G11_G0.424511.330
4_L8_L0.418041.310
51_A55_Y0.415051.300
10_V56_G0.403371.264
21_Q49_I0.402121.260
54_I58_V0.394131.235
58_V61_L0.388081.216
10_V60_A0.387991.215
17_S21_Q0.387931.215
24_A55_Y0.387541.214
31_A38_L0.371561.164
24_A49_I0.37051.161
28_A32_I0.369571.158
14_A53_G0.355351.113
21_Q52_L0.350471.098
49_I53_G0.347471.089
5_G9_A0.342991.075
5_G20_G0.337431.057
29_I41_K0.335461.051
16_G19_I0.323551.014
15_I18_A0.322281.010
29_I42_M0.321291.007
23_I27_A0.316170.990
52_L55_Y0.315250.988
17_S53_G0.314280.985
34_R37_E0.309850.971
49_I52_L0.309080.968
42_M46_A0.300730.942
21_Q46_A0.295460.926
8_L12_L0.291530.913
12_L15_I0.284910.893
47_A51_A0.283040.887
33_A38_L0.281490.882
55_Y58_V0.276710.867
45_G50_E0.274210.859
21_Q25_G0.272140.853
39_F43_L0.27180.851
33_A41_K0.268780.842
8_L15_I0.267930.839
3_Y34_R0.264130.827
40_T44_I0.262220.821
21_Q50_E0.262150.821
50_E53_G0.260990.818
19_I22_G0.256010.802
58_V62_L0.254110.796
54_I57_L0.253320.794
2_A13_A0.252220.790
5_G24_A0.246160.771
29_I40_T0.246010.771
20_G49_I0.244220.765
30_G34_R0.243670.763
44_I48_F0.240260.753
11_G18_A0.239660.751
5_G16_G0.238750.748
26_S30_G0.237270.743
2_A62_L0.235750.739
30_G35_Q0.232880.730
25_G49_I0.23160.726
28_A41_K0.23120.724
52_L57_L0.229230.718
20_G36_P0.228030.714
2_A63_L0.227880.714
14_A58_V0.227530.713
24_A42_M0.226980.711
48_F51_A0.224210.702
31_A34_R0.221080.693
46_A52_L0.220270.690
14_A17_S0.218250.684
32_I42_M0.217850.682
28_A43_L0.217490.681
36_P47_A0.216470.678
61_L64_L0.216450.678
10_V59_V0.216030.677
2_A58_V0.215630.676
8_L11_G0.215310.675
3_Y7_G0.214220.671
21_Q48_F0.214090.671
4_L7_G0.211980.664
4_L34_R0.209510.656
46_A50_E0.208790.654
56_G60_A0.20850.653
45_G49_I0.207390.650
24_A45_G0.20680.648
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
2bl2A199.30.028
2bl2A199.20.042
2xquA199.20.046
1wu0A199.20.053
2x2vA0.984899.20.078
2wgmA0.984899.20.081
3zk1A0.984899.10.091
1a91A199.10.099
2xndJ0.969799.10.108
4f4sA0.9848990.136

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