NUOB - ECOLI - GREMLIN Contacts

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NUOB - NADH-quinone oxidoreductase subunit B

UniProt:	P0AFC7	Sequences: MDYTLTRIDPNGENDRYPLQKQEIVTDPLEQEVNKNVFMGKLNDMVNWGRKNSIWPYNFGLSCCYVEMVTSFTAVHDVARFGAEVLRASPRQADLMVVAGTCFTKMAPVIQRLYDQMLEPKWVISMGACANSGGMYDIYSVVQGVDKFIPVDVYIPGCPPRPEAYMQALMLLQESIGKERRPLSWVVGDQGVYRANMQSERERKRGERIAVTNLRTPDEI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12083
Length:	220 (171)
Sequences:	444 (133)
Seq/√Len:	10.2

ECOLI - NUOB HYFI HYCG
HALSA - Q9HRM0
SULSO - Q7LXP2 Q97ZA8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
114_Y	123_V	5.174	1.00
60_G	65_Y	5.163	1.00
167_Q	171_L	3.257	0.96
109_V	143_Q	3.000	0.93
128_A	168_A	2.753	0.90
68_M	165_Y	2.664	0.88
122_W	131_N	2.523	0.85
125_S	131_N	2.515	0.85
41_K	44_D	2.507	0.84
155_I	168_A	2.377	0.81
61_L	68_M	2.309	0.79
79_A	83_A	2.032	0.69
97_V	126_M	1.984	0.67
54_I	176_I	1.960	0.66
71_S	166_M	1.907	0.64
99_A	145_V	1.860	0.62
85_V	89_S	1.787	0.59
93_A	121_K	1.763	0.58
73_T	78_V	1.761	0.58
101_T	164_A	1.744	0.57
83_A	173_Q	1.725	0.56
75_V	175_S	1.712	0.55
132_S	161_R	1.689	0.54
128_A	131_N	1.658	0.53
88_A	145_V	1.644	0.52
75_V	163_E	1.577	0.49
101_T	107_A	1.505	0.46
192_V	195_A	1.479	0.45
47_N	89_S	1.464	0.44
135_M	143_Q	1.449	0.43
81_F	161_R	1.410	0.42
40_G	89_S	1.376	0.40
33_V	43_N	1.370	0.40
74_A	78_V	1.344	0.39
61_L	102_C	1.342	0.38
59_F	173_Q	1.339	0.38
128_A	155_I	1.314	0.37
121_K	155_I	1.303	0.37
131_N	136_Y	1.299	0.37
144_G	151_V	1.299	0.37
44_D	174_E	1.296	0.36
75_V	111_Q	1.294	0.36
189_D	193_Y	1.287	0.36
65_Y	103_F	1.286	0.36
97_V	165_Y	1.279	0.36
71_S	78_V	1.276	0.36
95_L	156_P	1.267	0.35
92_Q	116_Q	1.228	0.34
32_E	95_L	1.221	0.33
58_N	86_L	1.207	0.33
65_Y	72_F	1.204	0.33
140_S	143_Q	1.195	0.32
37_V	153_V	1.194	0.32
105_K	126_M	1.183	0.32
37_V	113_L	1.180	0.32
58_N	65_Y	1.174	0.31
122_W	140_S	1.173	0.31
25_V	28_P	1.170	0.31
51_K	177_G	1.157	0.31
128_A	141_V	1.155	0.31
111_Q	115_D	1.148	0.30
73_T	125_S	1.148	0.30
102_C	145_V	1.145	0.30
57_Y	93_A	1.141	0.30
56_P	106_M	1.133	0.30
96_M	99_A	1.117	0.29
113_L	131_N	1.113	0.29
139_Y	151_V	1.113	0.29
52_N	122_W	1.105	0.29
108_P	142_V	1.097	0.28
105_K	117_M	1.093	0.28
43_N	175_S	1.084	0.28
128_A	136_Y	1.081	0.28
90_P	100_G	1.060	0.27
81_F	170_M	1.052	0.27
89_S	119_E	1.044	0.26
132_S	143_Q	1.037	0.26
68_M	185_W	1.037	0.26
33_V	37_V	1.034	0.26
45_M	195_A	1.033	0.26
48_W	113_L	1.022	0.26
42_L	121_K	1.020	0.26
189_D	195_A	1.018	0.26
58_N	88_A	1.018	0.26
117_M	123_V	1.012	0.25
76_H	121_K	1.012	0.25
133_G	139_Y	1.012	0.25
95_L	165_Y	1.009	0.25
163_E	173_Q	1.006	0.25
61_L	131_N	1.005	0.25
146_D	154_Y	0.985	0.24
62_S	86_L	0.981	0.24
57_Y	66_V	0.974	0.24
66_V	102_C	0.971	0.24
70_T	162_P	0.966	0.24
47_N	175_S	0.966	0.24
68_M	86_L	0.965	0.24
47_N	57_Y	0.963	0.24
79_A	85_V	0.961	0.24
74_A	88_A	0.960	0.24
62_S	69_V	0.956	0.23
74_A	186_V	0.953	0.23
76_H	166_M	0.949	0.23
64_C	159_P	0.948	0.23
98_V	130_A	0.941	0.23
122_W	143_Q	0.941	0.23
42_L	49_G	0.940	0.23
129_C	133_G	0.937	0.23
86_L	165_Y	0.935	0.23
61_L	65_Y	0.935	0.23
75_V	87_R	0.925	0.22
34_N	185_W	0.919	0.22
88_A	93_A	0.918	0.22
122_W	130_A	0.915	0.22
113_L	124_I	0.908	0.22
114_Y	151_V	0.907	0.22
135_M	162_P	0.904	0.22
49_G	52_N	0.903	0.22
164_A	168_A	0.899	0.22
78_V	83_A	0.899	0.22
177_G	188_G	0.899	0.22
33_V	36_N	0.898	0.22
52_N	79_A	0.895	0.21
104_T	137_D	0.892	0.21
42_L	46_V	0.886	0.21
106_M	159_P	0.882	0.21
71_S	187_V	0.868	0.21
116_Q	120_P	0.864	0.21
58_N	137_D	0.861	0.20
40_G	54_I	0.860	0.20
45_M	76_H	0.853	0.20
96_M	149_I	0.845	0.20
104_T	110_I	0.836	0.20
141_V	164_A	0.830	0.20
136_Y	147_K	0.826	0.19
93_A	145_V	0.825	0.19
31_Q	74_A	0.817	0.19
34_N	168_A	0.808	0.19
25_V	29_L	0.802	0.19
68_M	125_S	0.790	0.18
69_V	104_T	0.787	0.18
112_R	115_D	0.786	0.18
41_K	46_V	0.784	0.18
153_V	162_P	0.783	0.18
129_C	150_P	0.783	0.18
78_V	110_I	0.780	0.18
133_G	152_D	0.779	0.18
115_D	170_M	0.779	0.18
45_M	176_I	0.778	0.18
85_V	112_R	0.774	0.18
42_L	119_E	0.772	0.18
24_I	27_D	0.770	0.18
125_S	128_A	0.765	0.18
38_F	166_M	0.761	0.18
107_A	111_Q	0.759	0.18
62_S	96_M	0.757	0.17
30_E	38_F	0.757	0.17
99_A	165_Y	0.754	0.17
155_I	173_Q	0.744	0.17
129_C	152_D	0.735	0.17
89_S	106_M	0.734	0.17
74_A	86_L	0.731	0.17
42_L	57_Y	0.730	0.17
117_M	133_G	0.729	0.17
133_G	150_P	0.729	0.17
62_S	101_T	0.727	0.17
136_Y	156_P	0.724	0.17
72_F	97_V	0.720	0.17
73_T	135_M	0.718	0.16
166_M	180_R	0.717	0.16
38_F	43_N	0.715	0.16
39_M	179_E	0.710	0.16
35_K	193_Y	0.707	0.16
116_Q	155_I	0.707	0.16
123_V	151_V	0.707	0.16
26_T	33_V	0.707	0.16
149_I	180_R	0.705	0.16
65_Y	176_I	0.702	0.16
73_T	167_Q	0.695	0.16
47_N	121_K	0.695	0.16
59_F	155_I	0.686	0.16
169_L	184_S	0.685	0.16
35_K	175_S	0.684	0.16
103_F	138_I	0.681	0.16
65_Y	69_V	0.681	0.16
95_L	124_I	0.678	0.15
125_S	141_V	0.677	0.15
66_V	110_I	0.672	0.15
128_A	164_A	0.672	0.15
111_Q	149_I	0.672	0.15
58_N	72_F	0.670	0.15
73_T	171_L	0.663	0.15
58_N	69_V	0.659	0.15
117_M	120_P	0.657	0.15
114_Y	146_D	0.649	0.15
144_G	154_Y	0.649	0.15
91_R	100_G	0.647	0.15
48_W	103_F	0.644	0.15
62_S	65_Y	0.643	0.15
120_P	123_V	0.641	0.15
183_L	187_V	0.631	0.14
104_T	162_P	0.620	0.14
135_M	138_I	0.614	0.14
101_T	168_A	0.614	0.14
101_T	141_V	0.613	0.14
43_N	188_G	0.610	0.14
24_I	29_L	0.608	0.14
30_E	34_N	0.606	0.14
94_D	99_A	0.602	0.14
190_Q	195_A	0.600	0.14
30_E	33_V	0.594	0.14
54_I	177_G	0.592	0.14
114_Y	144_G	0.589	0.13
80_R	100_G	0.589	0.13
78_V	166_M	0.582	0.13
50_R	75_V	0.581	0.13
89_S	92_Q	0.578	0.13
72_F	86_L	0.576	0.13
80_R	90_P	0.576	0.13
104_T	117_M	0.574	0.13
93_A	155_I	0.572	0.13
144_G	150_P	0.569	0.13
50_R	87_R	0.568	0.13
54_I	124_I	0.567	0.13
56_P	86_L	0.565	0.13
43_N	92_Q	0.562	0.13
83_A	169_L	0.555	0.13
113_L	145_V	0.553	0.13
131_N	141_V	0.552	0.13
61_L	128_A	0.549	0.13
138_I	143_Q	0.547	0.13
183_L	188_G	0.544	0.12
102_C	106_M	0.532	0.12
92_Q	149_I	0.530	0.12
145_V	151_V	0.530	0.12
130_A	139_Y	0.526	0.12
45_M	54_I	0.525	0.12
171_L	174_E	0.524	0.12
144_G	159_P	0.523	0.12
98_V	187_V	0.523	0.12
69_V	113_L	0.523	0.12
48_W	87_R	0.520	0.12
40_G	97_V	0.517	0.12
110_I	145_V	0.515	0.12
54_I	95_L	0.515	0.12
88_A	115_D	0.513	0.12
57_Y	69_V	0.509	0.12
72_F	137_D	0.508	0.12
101_T	140_S	0.508	0.12
50_R	76_H	0.508	0.12
167_Q	178_K	0.507	0.12
155_I	161_R	0.506	0.12
82_G	90_P	0.502	0.12
118_L	170_M	0.502	0.12
56_P	126_M	0.502	0.12
126_M	142_V	0.500	0.12

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
3i9v6	1	0.6591	100	0.432	Contact Map
1h2aS	1	0.7727	100	0.625	Contact Map
2wpnA	1	0.7773	100	0.636	Contact Map
3ayxB	2	0.7545	100	0.641	Contact Map
4uqlA	1	0.7636	100	0.65	Contact Map
4ue3S	2	0.7591	100	0.65	Contact Map
3ze9A	1	0.7545	100	0.66	Contact Map
3myrA	3	0.7591	100	0.661	Contact Map
1yq9A	2	0.7636	100	0.665	Contact Map
4u9hS	1	0.7636	100	0.666	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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