GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
COX2_TM - Cytochrome C oxidase subunit II transmembrane domain
Pfam: PF02790 (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: 84
Sequences: 4401
Seq/Len: 52.39
HH_delta: 0.068 (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_V77_L0.747642.672
25_D29_I0.501151.791
72_I76_F0.495461.771
32_I36_V0.477041.705
25_D28_M0.4761.701
61_K65_I0.472131.687
39_F42_L0.414451.481
74_L80_P0.40851.460
53_N56_F0.408261.459
31_M35_F0.376611.346
33_F40_Y0.375831.343
29_I33_F0.369441.320
26_F40_Y0.367041.312
64_I68_I0.364751.304
12_P21_D0.364491.303
43_I47_F0.363091.298
12_P17_M0.356321.273
68_I72_I0.356281.273
15_P18_E0.352971.261
26_F76_F0.342731.225
11_D15_P0.340781.218
70_P81_S0.337881.208
55_F58_H0.336931.204
7_L10_Q0.335291.198
63_E67_T0.32641.167
43_I46_L0.325091.162
39_F43_I0.320541.146
40_Y44_Y0.316241.130
34_I38_V0.315951.129
65_I69_I0.315641.128
18_E22_W0.312411.117
73_I76_F0.31241.116
34_I81_S0.310561.110
58_H75_L0.308541.103
21_D25_D0.305861.093
47_F51_F0.300241.073
12_P18_E0.297091.062
69_I73_I0.296031.058
30_I37_F0.293931.050
22_W76_F0.291831.043
44_Y48_N0.291191.041
56_F59_N0.28981.036
26_F71_A0.288891.032
35_F39_F0.287571.028
66_W70_P0.283981.015
26_F30_I0.283891.015
17_M20_M0.277610.992
17_M21_D0.273750.978
6_Q12_P0.273730.978
6_Q10_Q0.273380.977
48_N51_F0.272460.974
23_L27_V0.271840.972
50_K53_N0.264010.944
66_W74_L0.263680.942
58_H71_A0.259460.927
6_Q64_I0.259430.927
58_H73_I0.258960.926
24_H28_M0.258380.923
24_H78_A0.257080.919
9_F21_D0.253960.908
36_V40_Y0.251860.900
12_P22_W0.251080.897
47_F52_P0.247970.886
26_F33_F0.245410.877
6_Q37_F0.244140.873
62_L66_W0.243090.869
74_L78_A0.243030.869
57_N64_I0.242810.868
8_N73_I0.242680.867
19_E35_F0.242060.865
31_M77_L0.237330.848
34_I73_I0.236390.845
75_L79_F0.235840.843
36_V47_F0.235440.841
37_F69_I0.232750.832
60_N64_I0.232130.830
65_I70_P0.23110.826
74_L81_S0.231090.826
11_D21_D0.230590.824
22_W25_D0.228770.818
63_E70_P0.228270.816
19_E83_K0.227910.815
57_N60_N0.227510.813
24_H80_P0.227460.813
55_F59_N0.227040.811
55_F68_I0.226760.810
32_I43_I0.225420.806
22_W75_L0.225170.805
42_L77_L0.225050.804
37_F41_F0.223690.799
22_W73_I0.220520.788
24_H34_I0.217130.776
15_P19_E0.216850.775
45_F48_N0.215240.769
16_M31_M0.21380.764
55_F79_F0.211810.757
53_N59_N0.20940.748
47_F56_F0.209060.747
16_M19_E0.209060.747
36_V44_Y0.208680.746
57_N62_L0.207580.742
51_F75_L0.206110.737
44_Y79_F0.205560.735
23_L81_S0.204150.730
19_E22_W0.204020.729
20_M26_F0.20270.724
39_F47_F0.202530.724
33_F36_V0.202150.722
26_F80_P0.201820.721
23_L77_L0.201340.720
26_F83_K0.201030.718
19_E38_V0.200180.715
9_F25_D0.199570.713
30_I69_I0.198380.709
38_V44_Y0.196380.702
21_D24_H0.194790.696
44_Y62_L0.194440.695
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
3hb3B199.70.068
1v54B0.988199.70.072
2gsmB199.70.074
2yevB199.40.234
1fftB199.30.27
3j1zP0.904814.30.868
3h90A0.90488.50.88
2iubA0.53577.10.884
4i0uA0.53575.50.89
4ev6A0.53574.50.894

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