GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YMF19 - Plant ATP synthase F0
Pfam: PF02326 (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: 86
Sequences: 1085
Seq/Len: 12.62
HH_delta: 0.702 (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
46_S50_S0.580922.220
68_K72_N0.557282.129
47_S51_S0.548022.094
36_R40_L0.533272.038
54_K58_E0.531712.032
53_S57_S0.492741.883
39_K42_S0.414381.583
64_V68_K0.407511.557
44_L48_S0.405231.548
57_S61_K0.402941.540
43_K47_S0.400641.531
51_S54_K0.399421.526
61_K65_S0.386021.475
65_S68_K0.364371.392
24_I28_N0.36151.381
39_K43_K0.353711.352
64_V67_D0.352071.345
45_S49_I0.347821.329
25_F29_F0.345481.320
58_E61_K0.325271.243
65_S69_L0.316421.209
63_S67_D0.315661.206
11_Q15_L0.30771.176
57_S60_S0.306671.172
51_S55_L0.295171.128
59_S63_S0.295171.128
56_N60_S0.29381.123
15_L18_F0.293411.121
59_S69_L0.293351.121
67_D71_S0.289911.108
20_F24_I0.287371.098
24_I27_V0.287081.097
66_Y69_L0.28251.079
12_Y15_L0.27961.068
50_S54_K0.279251.067
54_K57_S0.275061.051
43_K46_S0.272941.043
19_F23_Y0.264321.010
61_K64_V0.264311.010
68_K71_S0.255810.977
27_V31_L0.255720.977
42_S46_S0.255450.976
9_F17_I0.2520.963
15_L23_Y0.249950.955
60_S64_V0.243920.932
18_F31_L0.238970.913
15_L33_K0.238850.913
16_L20_F0.236420.903
14_W26_L0.235550.900
39_K52_K0.219850.840
13_F17_I0.218270.834
29_F33_K0.217640.832
62_L66_Y0.215590.824
11_Q14_W0.213140.814
58_E63_S0.211220.807
40_L43_K0.211070.807
13_F16_L0.210480.804
30_I34_I0.207860.794
27_V32_P0.205790.786
19_F41_R0.204890.783
51_S58_E0.203930.779
69_L72_N0.198890.760
53_S60_S0.196730.752
9_F12_Y0.196560.751
64_V71_S0.194630.744
55_L66_Y0.194430.743
26_L31_L0.193370.739
49_I52_K0.19290.737
23_Y27_V0.19180.733
57_S64_V0.189930.726
58_E62_L0.189890.726
12_Y16_L0.185090.707
15_L26_L0.184940.707
52_K56_N0.184280.704
62_L65_S0.184170.704
11_Q23_Y0.183360.701
50_S53_S0.18310.700
14_W23_Y0.18060.690
39_K46_S0.178640.683
9_F18_F0.177240.677
48_S56_N0.176840.676
63_S66_Y0.17680.676
64_V72_N0.175690.671
25_F59_S0.174910.668
40_L44_L0.174830.668
22_F58_E0.173910.665
52_K55_L0.172580.659
22_F27_V0.172310.658
27_V30_I0.171820.657
12_Y23_Y0.17070.652
39_K44_L0.168560.644
41_R52_K0.16740.640
60_S63_S0.166310.635
15_L29_F0.165370.632
20_F43_K0.162330.620
33_K38_L0.162270.620
26_L33_K0.161090.616
13_F23_Y0.160560.614
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
1b9uA0.3953970.702
2khkA0.581495.90.741
2oarA0.848882.30.817
2clyA174.90.828
2rddB0.430231.90.868
3hzqA0.418626.60.873
4i9wA0.68620.20.879
2yiuB0.476720.80.879
2ksdA0.779119.10.881
2f95B115.60.885
If you are interested in a protein containing this domain,
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