CYOD - ECOLI - GREMLIN Contacts

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CYOD - Cytochrome bo(3) ubiquinol oxidase subunit 4

UniProt:	P0ABJ6	Sequences: MSHSTDHSGASHGSVKTYMTGFILSIILTVIPFWMVMTGAASPAVILGTILAMAVVQVLVHLVCFLHMNTKSDEGWNMTAFVFTVLIIAILVVGSIWIMWNLNYNMMMH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10181
Length:	109 (102)
Sequences:	732 (512)
Seq/√Len:	50.7

ECOLI - CYOD
BACSU - QOX4

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_V	19_M	3.669	1.00
32_P	50_I	2.766	1.00
83_F	87_I	2.765	1.00
25_S	61_H	2.497	1.00
32_P	53_M	2.282	1.00
41_A	45_V	2.073	1.00
41_A	46_I	2.007	1.00
90_I	94_G	1.984	1.00
51_L	95_S	1.931	0.99
58_V	61_H	1.926	0.99
13_G	17_T	1.917	0.99
23_I	27_I	1.841	0.99
19_M	23_I	1.840	0.99
60_V	106_M	1.809	0.99
101_N	105_N	1.780	0.99
34_W	38_T	1.730	0.99
9_G	72_S	1.722	0.99
87_I	91_L	1.713	0.99
102_L	105_N	1.704	0.99
35_M	41_A	1.652	0.98
71_K	74_E	1.565	0.97
94_G	102_L	1.547	0.97
90_I	93_V	1.522	0.97
45_V	49_T	1.500	0.97
17_T	64_C	1.500	0.97
61_H	80_A	1.474	0.96
85_V	89_A	1.461	0.96
34_W	74_E	1.377	0.95
71_K	75_G	1.303	0.93
96_I	99_M	1.300	0.93
33_F	66_L	1.297	0.93
48_G	52_A	1.274	0.92
42_S	45_V	1.268	0.92
94_G	99_M	1.246	0.91
27_I	31_I	1.243	0.91
71_K	78_M	1.241	0.91
78_M	86_L	1.231	0.91
75_G	101_N	1.217	0.90
42_S	48_G	1.209	0.90
94_G	101_N	1.203	0.90
95_S	103_N	1.200	0.89
51_L	96_I	1.197	0.89
76_W	90_I	1.196	0.89
62_L	98_I	1.185	0.89
26_I	30_V	1.168	0.88
23_I	68_M	1.159	0.88
88_I	92_V	1.118	0.86
61_H	66_L	1.109	0.85
11_S	17_T	1.101	0.85
62_L	68_M	1.084	0.84
55_V	58_V	1.082	0.84
82_V	85_V	1.045	0.82
54_A	98_I	1.026	0.81
35_M	46_I	1.013	0.80
99_M	102_L	1.012	0.80
62_L	81_F	1.011	0.80
93_V	100_W	0.990	0.78
91_L	95_S	0.973	0.77
27_I	56_V	0.971	0.77
88_I	105_N	0.943	0.75
46_I	50_I	0.936	0.74
47_L	86_L	0.923	0.73
72_S	76_W	0.894	0.71
31_I	53_M	0.875	0.69
55_V	59_L	0.868	0.68
34_W	96_I	0.864	0.68
83_F	90_I	0.863	0.68
89_A	104_Y	0.861	0.68
24_L	84_T	0.860	0.68
75_G	78_M	0.854	0.67
72_S	77_N	0.847	0.66
51_L	92_V	0.843	0.66
55_V	92_V	0.826	0.64
66_L	106_M	0.808	0.63
69_N	72_S	0.803	0.62
38_T	54_A	0.802	0.62
10_A	13_G	0.798	0.62
97_W	103_N	0.797	0.62
79_T	91_L	0.796	0.62
49_T	53_M	0.795	0.61
36_V	39_G	0.791	0.61
78_M	99_M	0.783	0.60
59_L	81_F	0.764	0.58
35_M	40_A	0.760	0.58
76_W	99_M	0.759	0.58
12_H	16_K	0.755	0.57
87_I	90_I	0.748	0.57
10_A	16_K	0.740	0.56
39_G	51_L	0.737	0.56
49_T	54_A	0.732	0.55
10_A	50_I	0.723	0.54
56_V	59_L	0.722	0.54
39_G	97_W	0.722	0.54
61_H	91_L	0.722	0.54
95_S	98_I	0.712	0.53
17_T	27_I	0.708	0.53
75_G	88_I	0.703	0.52
87_I	96_I	0.703	0.52
96_I	100_W	0.695	0.51
75_G	80_A	0.690	0.51
26_I	47_L	0.688	0.51
88_I	102_L	0.687	0.51
98_I	102_L	0.678	0.50
31_I	97_W	0.677	0.49
22_F	64_C	0.675	0.49
12_H	29_T	0.665	0.48
49_T	104_Y	0.664	0.48
15_V	47_L	0.655	0.47
99_M	104_Y	0.651	0.47
44_A	48_G	0.644	0.46
6_D	10_A	0.643	0.46
79_T	87_I	0.642	0.46
90_I	102_L	0.642	0.46
74_E	78_M	0.638	0.45
25_S	54_A	0.635	0.45
15_V	86_L	0.631	0.45
7_H	11_S	0.626	0.44
13_G	25_S	0.625	0.44
83_F	102_L	0.623	0.44
76_W	105_N	0.617	0.43
100_W	104_Y	0.615	0.43
23_I	48_G	0.614	0.43
63_V	105_N	0.611	0.43
43_P	62_L	0.607	0.42
27_I	72_S	0.604	0.42
34_W	40_A	0.599	0.42
16_K	31_I	0.593	0.41
35_M	53_M	0.586	0.40
51_L	77_N	0.582	0.40
63_V	99_M	0.577	0.39
52_A	55_V	0.569	0.39
17_T	43_P	0.568	0.38
7_H	10_A	0.568	0.38
26_I	55_V	0.555	0.37
101_N	104_Y	0.553	0.37
44_A	51_L	0.551	0.37
32_P	97_W	0.548	0.37
37_M	98_I	0.546	0.36
32_P	61_H	0.538	0.36
42_S	69_N	0.537	0.35
29_T	57_Q	0.535	0.35
14_S	85_V	0.534	0.35
43_P	50_I	0.532	0.35
19_M	83_F	0.527	0.35
6_D	11_S	0.526	0.34
70_T	85_V	0.516	0.34
22_F	68_M	0.515	0.33
81_F	84_T	0.514	0.33
73_D	88_I	0.512	0.33
50_I	95_S	0.511	0.33
86_L	89_A	0.501	0.32
6_D	86_L	0.501	0.32
94_G	98_I	0.500	0.32

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
2ksrA	1	0.8349	11.9	0.935	Contact Map
2bg9A	1	0.8899	10.9	0.936	Contact Map
4g1uA	2	0.4587	5	0.945	Contact Map
4njnA	4	0.5413	4.2	0.947	Contact Map
2oarA	7	0.789	3.8	0.948	Contact Map
4xtrG	1	0.1927	3.6	0.949	Contact Map
3rlbA	1	0.8532	3.5	0.949	Contact Map
4od4A	1	0.8073	3.3	0.95	Contact Map
2lx0A	1	0.2936	3	0.951	Contact Map
4aq5A	1	0.5413	2.8	0.952	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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