GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FixP_N - N-terminal domain of cytochrome oxidase-cbb3 FixP
Pfam: PF14715 (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: 51
Sequences: 527
Seq/Len: 10.33
HH_delta: 0.038 (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
3_D18_N0.581022.603
9_E13_I0.486972.182
20_L24_W0.460072.061
39_L45_L0.444671.992
39_L44_G0.387671.737
5_T14_R0.371161.663
10_W17_D0.369781.657
10_W13_I0.365661.638
37_G49_Q0.329081.474
9_E14_R0.319711.432
29_Y32_I0.316211.417
26_W30_G0.310011.389
22_R26_W0.295781.325
2_G16_L0.294341.319
32_I36_V0.288351.292
36_V40_V0.288221.291
47_N50_G0.278771.249
44_G50_G0.271351.216
28_F32_I0.248961.115
20_L23_W0.244821.097
39_L46_G0.242131.085
13_I17_D0.241181.081
27_L46_G0.238751.070
16_L25_L0.236991.062
37_G41_L0.233481.046
26_W34_F0.230261.032
20_L28_F0.224321.005
11_D23_W0.218460.979
9_E12_G0.217640.975
18_N38_Y0.211760.949
11_D28_F0.209880.940
30_G33_V0.209420.938
27_L31_T0.199110.892
30_G40_V0.198430.889
8_H23_W0.195260.875
6_T22_R0.194140.870
6_T19_P0.193380.866
7_G43_P0.190160.852
27_L39_L0.185260.830
30_G49_Q0.183160.821
7_G14_R0.181840.815
8_H15_E0.18140.813
12_G17_D0.180560.809
35_A39_L0.179080.802
10_W22_R0.175080.784
7_G19_P0.174290.781
12_G25_L0.172610.773
14_R25_L0.170860.765
37_G48_W0.165560.742
6_T27_L0.162020.726
11_D18_N0.161670.724
34_F38_Y0.160050.717
2_G49_Q0.159650.715
29_Y37_G0.158790.711
7_G44_G0.158320.709
4_E17_D0.157840.707
10_W46_G0.156470.701
25_L31_T0.156380.701
28_F31_T0.152540.683
37_G47_N0.152060.681
36_V47_N0.150860.676
44_G47_N0.150240.673
27_L35_A0.149560.670
8_H16_L0.147550.661
13_I44_G0.145170.650
19_P43_P0.14390.645
20_L31_T0.141170.632
40_V48_W0.138880.622
29_Y33_V0.13860.621
40_V47_N0.138340.620
11_D42_Y0.137920.618
15_E42_Y0.137820.617
20_L35_A0.137650.617
28_F39_L0.136880.613
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
3mk7C199.70.038
1jb0A19.10.885
3vx6A0.94128.10.888
3tlwA0.88246.60.892
4gslA0.92165.60.896
1n3hA15.30.896
2j7aC0.74514.70.898
1jb0B14.10.901
3mn8A0.50984.10.902
4aw6A13.70.904

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