NUOI - ECOLI - GREMLIN Contacts

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NUOI - NADH-quinone oxidoreductase subunit I

UniProt:	P0AFD6	Sequences: MTLKELLVGFGTQVRSIWMIGLHAFAKRETRMYPEEPVYLPPRYRGRIVLTRDPDGEERCVACNLCAVACPVGCISLQKAETKDGRWYPEFFRINFSRCIFCGLCEEACPTTAIQLTPDFEMGEYKRQDLVYEKEDLLISGPGKYPEYNFYRMAGMAIDGKDKGEAENEAKPIDVKSLLP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12089
Length:	180 (147)
Sequences:	1027 (465)
Seq/√Len:	38.4

ECOLI - NUOI HYFH HYCF
HALSA - Q9HRL7
SULSO - Q980H1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_A	108_A	3.809	1.00
106_E	116_L	3.706	1.00
126_K	129_D	3.304	1.00
13_Q	17_I	3.174	1.00
11_G	15_R	2.977	1.00
21_G	24_A	2.921	1.00
40_L	120_F	2.788	1.00
80_A	90_E	2.574	1.00
62_A	79_K	2.463	1.00
106_E	114_I	2.376	1.00
121_E	130_L	2.345	1.00
15_R	18_W	2.258	0.99
78_Q	91_F	2.199	0.99
32_M	35_E	2.116	0.99
16_S	20_I	2.089	0.99
64_N	77_L	2.059	0.99
61_V	111_T	2.032	0.99
37_P	121_E	1.970	0.99
108_A	113_A	1.822	0.98
133_E	136_D	1.820	0.98
14_V	18_W	1.811	0.98
72_V	100_I	1.705	0.96
147_E	151_Y	1.701	0.96
97_S	130_L	1.695	0.96
96_F	101_F	1.602	0.95
124_E	129_D	1.587	0.95
47_R	119_D	1.558	0.94
9_G	12_T	1.520	0.93
50_L	134_K	1.513	0.93
61_V	115_Q	1.495	0.93
94_I	107_E	1.454	0.92
79_K	87_W	1.377	0.89
37_P	120_F	1.374	0.89
23_H	26_A	1.356	0.88
12_T	15_R	1.351	0.88
82_T	86_R	1.288	0.86
149_N	153_M	1.254	0.84
140_S	144_K	1.243	0.84
32_M	36_E	1.237	0.83
72_V	92_F	1.227	0.83
65_L	68_V	1.224	0.83
47_R	101_F	1.220	0.82
13_Q	16_S	1.219	0.82
124_E	130_L	1.216	0.82
96_F	132_Y	1.187	0.81
58_E	134_K	1.176	0.80
61_V	64_N	1.173	0.80
105_C	109_C	1.166	0.79
10_F	14_V	1.157	0.79
50_L	114_I	1.153	0.79
86_R	97_S	1.151	0.79
47_R	124_E	1.150	0.78
78_Q	90_E	1.149	0.78
48_I	96_F	1.147	0.78
146_P	149_N	1.137	0.78
74_C	100_I	1.130	0.77
42_P	118_P	1.129	0.77
89_P	92_F	1.115	0.76
50_L	113_A	1.108	0.76
10_F	13_Q	1.100	0.75
50_L	137_L	1.095	0.75
22_L	152_R	1.087	0.74
80_A	88_Y	1.083	0.74
79_K	89_P	1.083	0.74
67_A	76_S	1.058	0.72
24_A	146_P	1.043	0.71
53_D	61_V	1.032	0.70
150_F	153_M	1.018	0.69
151_Y	155_G	1.017	0.69
20_I	29_E	1.015	0.69
134_K	137_L	0.997	0.68
53_D	56_G	0.993	0.67
68_V	106_E	0.990	0.67
52_R	58_E	0.981	0.66
64_N	68_V	0.981	0.66
94_I	100_I	0.979	0.66
75_I	95_N	0.973	0.66
99_C	105_C	0.972	0.66
48_I	94_I	0.966	0.65
149_N	154_A	0.959	0.65
135_E	138_L	0.957	0.65
33_Y	121_E	0.955	0.64
62_A	89_P	0.953	0.64
65_L	69_A	0.951	0.64
56_G	139_I	0.941	0.63
67_A	77_L	0.926	0.62
40_L	44_Y	0.915	0.61
38_V	120_F	0.912	0.61
67_A	96_F	0.910	0.61
44_Y	69_A	0.904	0.60
75_I	114_I	0.896	0.59
75_I	113_A	0.895	0.59
100_I	107_E	0.892	0.59
16_S	19_M	0.889	0.59
23_H	92_F	0.886	0.59
123_G	130_L	0.874	0.57
126_K	133_E	0.866	0.57
76_S	91_F	0.858	0.56
96_F	106_E	0.855	0.56
47_R	117_T	0.854	0.56
10_F	131_V	0.850	0.55
21_G	25_F	0.840	0.54
53_D	59_R	0.824	0.53
43_R	51_T	0.819	0.53
65_L	134_K	0.813	0.52
48_I	119_D	0.807	0.52
74_C	96_F	0.802	0.51
18_W	22_L	0.799	0.51
69_A	104_L	0.799	0.51
14_V	139_I	0.785	0.50
50_L	122_M	0.777	0.49
24_A	27_K	0.776	0.49
129_D	133_E	0.775	0.49
24_A	28_R	0.772	0.48
93_R	133_E	0.767	0.48
31_R	38_V	0.764	0.48
152_R	155_G	0.759	0.47
15_R	21_G	0.757	0.47
149_N	152_R	0.755	0.47
49_V	115_Q	0.749	0.46
132_Y	136_D	0.748	0.46
94_I	116_L	0.748	0.46
94_I	98_R	0.743	0.46
59_R	113_A	0.743	0.46
64_N	111_T	0.740	0.45
96_F	114_I	0.738	0.45
77_L	93_R	0.738	0.45
68_V	108_A	0.734	0.45
77_L	92_F	0.732	0.45
43_R	114_I	0.721	0.44
32_M	37_P	0.720	0.44
36_E	39_Y	0.719	0.44
95_N	98_R	0.719	0.44
21_G	28_R	0.711	0.43
94_I	110_P	0.702	0.42
148_Y	151_Y	0.701	0.42
82_T	85_G	0.698	0.42
62_A	84_D	0.698	0.42
15_R	19_M	0.696	0.42
62_A	81_E	0.691	0.41
60_C	63_C	0.689	0.41
60_C	66_C	0.689	0.41
63_C	66_C	0.689	0.41
66_C	70_C	0.689	0.41
63_C	70_C	0.689	0.41
60_C	70_C	0.689	0.41
103_G	106_E	0.688	0.41
66_C	102_C	0.685	0.41
70_C	102_C	0.685	0.41
63_C	102_C	0.685	0.41
60_C	102_C	0.685	0.41
48_I	117_T	0.683	0.40
48_I	72_V	0.679	0.40
98_R	119_D	0.676	0.40
31_R	140_S	0.669	0.39
14_V	128_Q	0.666	0.39
78_Q	95_N	0.661	0.39
94_I	135_E	0.655	0.38
112_T	118_P	0.655	0.38
12_T	100_I	0.655	0.38
22_L	147_E	0.654	0.38
68_V	89_P	0.653	0.38
102_C	105_C	0.647	0.37
20_I	24_A	0.644	0.37
39_Y	128_Q	0.641	0.37
9_G	86_R	0.636	0.36
65_L	98_R	0.635	0.36
132_Y	140_S	0.634	0.36
22_L	29_E	0.631	0.36
124_E	132_Y	0.628	0.36
81_E	89_P	0.612	0.35
70_C	99_C	0.608	0.34
66_C	99_C	0.608	0.34
63_C	99_C	0.608	0.34
60_C	99_C	0.608	0.34
147_E	150_F	0.607	0.34
64_N	67_A	0.605	0.34
93_R	106_E	0.603	0.34
99_C	102_C	0.603	0.34
75_I	94_I	0.601	0.34
66_C	109_C	0.590	0.33
70_C	109_C	0.590	0.33
63_C	109_C	0.590	0.33
60_C	109_C	0.590	0.33
73_G	101_F	0.589	0.33
26_A	42_P	0.586	0.32
102_C	109_C	0.582	0.32
43_R	57_E	0.576	0.32
65_L	103_G	0.574	0.31
67_A	75_I	0.573	0.31
16_S	92_F	0.571	0.31
29_E	32_M	0.571	0.31
129_D	136_D	0.569	0.31
78_Q	84_D	0.568	0.31
41_P	101_F	0.567	0.31
86_R	89_P	0.562	0.31
99_C	110_P	0.560	0.30
11_G	18_W	0.558	0.30
95_N	112_T	0.558	0.30
22_L	26_A	0.557	0.30
76_S	82_T	0.555	0.30
77_L	95_N	0.549	0.30
61_V	92_F	0.547	0.29
51_T	58_E	0.542	0.29
83_K	152_R	0.535	0.29
57_E	106_E	0.534	0.28
86_R	95_N	0.531	0.28
149_N	155_G	0.526	0.28
125_Y	135_E	0.523	0.28
74_C	89_P	0.522	0.28
26_A	32_M	0.522	0.28
104_L	120_F	0.521	0.28
18_W	24_A	0.520	0.27
29_E	79_K	0.519	0.27
77_L	112_T	0.519	0.27
52_R	56_G	0.517	0.27
18_W	26_A	0.512	0.27
91_F	133_E	0.503	0.26
108_A	120_F	0.502	0.26
47_R	96_F	0.500	0.26

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
3i9v9	1	0.7833	100	0.546	Contact Map
5c4iB	1	0.6	99.5	0.737	Contact Map
1gteA	4	0.6389	99.5	0.738	Contact Map
1xerA	2	0.5389	99.4	0.752	Contact Map
2c42A	2	0.9222	99.4	0.754	Contact Map
4omfG	2	0.6111	99.3	0.762	Contact Map
1jb0C	1	0.4444	99.3	0.762	Contact Map
2gmhA	1	0.6778	99.3	0.763	Contact Map
3i9v3	1	0.8333	99.3	0.764	Contact Map
2fgoA	1	0.4167	99.3	0.768	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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