DHSC - BACSU - GREMLIN Contacts

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DHSC - Succinate dehydrogenase cytochrome b558 subunit

UniProt:	P08064	Sequences: MSGNREFYFRRLHSLLGVIPVGIFLIQHLVVNQFAARGAEAFNSAAHFMDSLPFRYALEIFIIFLPLIYHAVYGVYIAFTAKNNAGQYSYMRNWLFVLQRVTGIITLIFVSWHVWETRIAAQMGAEVNFDMMANILSSPAMLGFYIVGVLSTIFHFSNGLWSFAVTWGITVTPRSQRISTYVTLIIFVALSYVGLKAIFAFV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	202 (198)
Sequences:	279 (181)
Seq/√Len:	12.9

BACSU - DHSC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
142_L	198_I	4.328	1.00
83_N	96_F	3.806	0.99
68_I	72_V	3.530	0.99
106_T	110_V	3.186	0.98
144_F	147_V	3.079	0.97
106_T	152_T	3.026	0.97
91_M	95_L	2.844	0.95
162_S	165_V	2.775	0.94
21_V	67_L	2.629	0.93
150_L	195_L	2.588	0.92
27_Q	49_M	2.498	0.91
18_V	160_L	2.480	0.90
57_A	61_F	2.474	0.90
190_L	193_V	2.335	0.87
75_V	104_I	2.309	0.87
164_A	169_I	2.173	0.83
150_L	191_S	2.113	0.81
27_Q	31_V	2.086	0.80
77_I	81_A	2.083	0.80
105_I	147_V	2.017	0.78
127_V	131_M	2.014	0.78
136_L	142_L	1.989	0.77
48_F	58_L	1.945	0.75
21_V	110_V	1.944	0.75
160_L	183_T	1.864	0.72
164_A	179_S	1.863	0.72
36_A	196_K	1.839	0.71
67_L	110_V	1.799	0.69
39_A	129_F	1.782	0.68
170_T	179_S	1.751	0.67
179_S	183_T	1.745	0.67
142_L	146_I	1.733	0.66
107_L	152_T	1.725	0.66
67_L	186_I	1.716	0.65
69_Y	94_W	1.708	0.65
11_R	33_Q	1.685	0.64
160_L	164_A	1.680	0.64
56_Y	60_I	1.646	0.62
188_V	197_A	1.631	0.61
81_A	96_F	1.595	0.59
141_M	144_F	1.521	0.56
96_F	106_T	1.513	0.55
83_N	97_V	1.503	0.55
56_Y	64_F	1.498	0.55
127_V	182_V	1.487	0.54
18_V	26_I	1.462	0.53
195_L	199_F	1.427	0.51
35_A	200_A	1.403	0.50
146_I	198_I	1.392	0.49
47_H	50_D	1.381	0.48
64_F	171_V	1.354	0.47
23_I	62_I	1.335	0.46
121_A	131_M	1.327	0.46
7_F	11_R	1.325	0.46
55_R	121_A	1.322	0.45
46_A	49_M	1.322	0.45
31_V	46_A	1.322	0.45
85_A	97_V	1.311	0.45
78_A	124_G	1.307	0.45
88_Y	188_V	1.302	0.44
121_A	127_V	1.284	0.43
112_W	135_I	1.283	0.43
97_V	101_V	1.276	0.43
47_H	51_S	1.245	0.41
34_F	55_R	1.242	0.41
23_I	69_Y	1.218	0.40
119_I	123_M	1.187	0.39
140_A	147_V	1.185	0.38
27_Q	34_F	1.165	0.38
69_Y	114_V	1.148	0.37
138_S	169_I	1.147	0.37
15_L	19_I	1.143	0.36
103_G	117_T	1.143	0.36
27_Q	157_S	1.140	0.36
146_I	195_L	1.136	0.36
197_A	200_A	1.130	0.36
26_I	198_I	1.128	0.36
130_D	133_A	1.122	0.35
142_L	199_F	1.112	0.35
58_L	61_F	1.108	0.35
67_L	190_L	1.104	0.35
116_E	141_M	1.090	0.34
136_L	149_V	1.085	0.34
115_W	120_A	1.084	0.34
156_F	186_I	1.082	0.34
41_A	157_S	1.066	0.33
4_N	72_V	1.065	0.33
85_A	102_T	1.062	0.33
124_G	131_M	1.060	0.33
54_F	197_A	1.048	0.32
89_S	162_S	1.026	0.31
16_L	165_V	1.024	0.31
27_Q	30_V	1.021	0.31
18_V	48_F	1.011	0.30
16_L	162_S	1.006	0.30
193_V	197_A	1.005	0.30
105_I	151_S	0.997	0.30
8_Y	195_L	0.989	0.29
140_A	144_F	0.988	0.29
76_Y	174_R	0.986	0.29
105_I	152_T	0.982	0.29
18_V	164_A	0.982	0.29
90_Y	110_V	0.961	0.28
5_R	8_Y	0.958	0.28
60_I	65_L	0.957	0.28
29_L	81_A	0.957	0.28
146_I	169_I	0.950	0.28
57_A	185_I	0.946	0.28
71_A	78_A	0.945	0.28
46_A	55_R	0.941	0.27
130_D	134_N	0.936	0.27
110_V	189_A	0.933	0.27
27_Q	55_R	0.931	0.27
191_S	195_L	0.924	0.27
87_Q	94_W	0.924	0.27
39_A	69_Y	0.922	0.27
61_F	64_F	0.913	0.26
83_N	90_Y	0.911	0.26
16_L	132_M	0.908	0.26
98_L	119_I	0.906	0.26
92_R	176_Q	0.903	0.26
75_V	179_S	0.888	0.25
31_V	49_M	0.884	0.25
124_G	127_V	0.884	0.25
62_I	110_V	0.877	0.25
33_Q	88_Y	0.874	0.25
117_T	132_M	0.872	0.25
94_W	138_S	0.861	0.24
98_L	154_F	0.853	0.24
107_L	174_R	0.851	0.24
118_R	122_Q	0.846	0.24
192_Y	196_K	0.840	0.23
82_K	102_T	0.832	0.23
105_I	156_F	0.831	0.23
21_V	25_L	0.826	0.23
37_R	41_A	0.821	0.23
108_I	111_S	0.818	0.23
107_L	111_S	0.815	0.22
68_I	164_A	0.813	0.22
42_F	137_S	0.807	0.22
38_G	164_A	0.805	0.22
96_F	178_I	0.798	0.22
60_I	156_F	0.794	0.22
31_V	42_F	0.786	0.21
69_Y	72_V	0.786	0.21
157_S	186_I	0.784	0.21
153_I	157_S	0.781	0.21
11_R	182_V	0.775	0.21
56_Y	108_I	0.774	0.21
157_S	185_I	0.774	0.21
183_T	186_I	0.774	0.21
25_L	156_F	0.774	0.21
16_L	35_A	0.772	0.21
102_T	106_T	0.771	0.21
47_H	195_L	0.769	0.21
119_I	125_A	0.769	0.21
26_I	152_T	0.761	0.21
94_W	98_L	0.760	0.21
27_Q	172_T	0.756	0.20
23_I	60_I	0.756	0.20
104_I	185_I	0.755	0.20
27_Q	33_Q	0.754	0.20
71_A	94_W	0.753	0.20
89_S	154_F	0.752	0.20
78_A	81_A	0.751	0.20
10_R	13_H	0.750	0.20
26_I	30_V	0.749	0.20
40_E	48_F	0.745	0.20
22_G	102_T	0.743	0.20
11_R	123_M	0.742	0.20
141_M	151_S	0.742	0.20
27_Q	52_L	0.727	0.19
32_N	93_N	0.724	0.19
8_Y	127_V	0.717	0.19
56_Y	175_S	0.715	0.19
67_L	160_L	0.714	0.19
42_F	89_S	0.710	0.19
166_T	193_V	0.710	0.19
46_A	171_V	0.710	0.19
112_W	132_M	0.708	0.19
71_A	177_R	0.705	0.19
120_A	193_V	0.702	0.19
40_E	124_G	0.697	0.18
27_Q	62_I	0.696	0.18
65_L	123_M	0.696	0.18
90_Y	182_V	0.695	0.18
6_E	186_I	0.689	0.18
46_A	107_L	0.689	0.18
12_L	186_I	0.682	0.18
50_D	128_N	0.681	0.18
102_T	152_T	0.675	0.18
101_V	105_I	0.673	0.18
106_T	156_F	0.671	0.18
110_V	154_F	0.663	0.17
81_A	184_L	0.662	0.17
78_A	86_G	0.661	0.17
30_V	34_F	0.661	0.17
6_E	190_L	0.658	0.17
172_T	188_V	0.656	0.17
44_S	60_I	0.652	0.17
8_Y	42_F	0.651	0.17
97_V	151_S	0.649	0.17
181_Y	186_I	0.648	0.17
143_G	150_L	0.647	0.17
33_Q	196_K	0.647	0.17
11_R	107_L	0.647	0.17
68_I	198_I	0.644	0.17
54_F	82_K	0.644	0.17
22_G	25_L	0.641	0.17
62_I	94_W	0.638	0.17
12_L	177_R	0.637	0.17
97_V	104_I	0.637	0.17
72_V	105_I	0.629	0.16
23_I	27_Q	0.628	0.16
57_A	171_V	0.628	0.16
9_F	88_Y	0.623	0.16
79_F	115_W	0.621	0.16
120_A	123_M	0.619	0.16
102_T	151_S	0.617	0.16
47_H	149_V	0.613	0.16
89_S	116_E	0.612	0.16
65_L	149_V	0.609	0.16
55_R	152_T	0.607	0.16
134_N	153_I	0.606	0.16
112_W	173_P	0.605	0.16
77_I	150_L	0.605	0.16
47_H	104_I	0.604	0.16
62_I	172_T	0.603	0.16
184_L	188_V	0.601	0.16
21_V	95_L	0.600	0.16
120_A	129_F	0.599	0.16
33_Q	165_V	0.599	0.16
156_F	172_T	0.599	0.16
89_S	165_V	0.599	0.16
107_L	147_V	0.598	0.16
142_L	197_A	0.596	0.16
72_V	180_T	0.591	0.15
86_G	89_S	0.590	0.15
69_Y	87_Q	0.586	0.15
65_L	75_V	0.586	0.15
44_S	188_V	0.585	0.15
160_L	186_I	0.583	0.15
56_Y	111_S	0.579	0.15
134_N	192_Y	0.578	0.15
23_I	125_A	0.576	0.15
189_A	193_V	0.575	0.15
13_H	17_G	0.570	0.15
137_S	153_I	0.566	0.15
36_A	41_A	0.566	0.15
96_F	187_F	0.565	0.15
56_Y	193_V	0.564	0.15
90_Y	97_V	0.563	0.15
80_T	188_V	0.563	0.15
80_T	108_I	0.559	0.15
87_Q	154_F	0.559	0.15
123_M	190_L	0.555	0.14
117_T	120_A	0.555	0.14
154_F	158_N	0.551	0.14
7_F	26_I	0.551	0.14
61_F	186_I	0.550	0.14
39_A	133_A	0.548	0.14
4_N	90_Y	0.544	0.14
184_L	198_I	0.540	0.14
54_F	96_F	0.538	0.14
129_F	175_S	0.536	0.14
43_N	171_V	0.536	0.14
131_M	192_Y	0.535	0.14
95_L	104_I	0.534	0.14
141_M	147_V	0.533	0.14
91_M	96_F	0.533	0.14
85_A	178_I	0.531	0.14
64_F	182_V	0.530	0.14
132_M	166_T	0.528	0.14
5_R	181_Y	0.525	0.14
27_Q	42_F	0.524	0.14
116_E	165_V	0.524	0.14
101_V	104_I	0.522	0.14
50_D	193_V	0.522	0.14
21_V	39_A	0.522	0.14
104_I	170_T	0.521	0.14
55_R	189_A	0.517	0.13
64_F	111_S	0.514	0.13
43_N	127_V	0.514	0.13
112_W	141_M	0.514	0.13
54_F	129_F	0.513	0.13
143_G	146_I	0.513	0.13
6_E	193_V	0.513	0.13
53_P	163_F	0.513	0.13
176_Q	201_F	0.510	0.13
16_L	120_A	0.509	0.13
35_A	165_V	0.506	0.13
132_M	182_V	0.506	0.13
149_V	199_F	0.505	0.13
146_I	189_A	0.503	0.13
85_A	123_M	0.502	0.13
121_A	180_T	0.501	0.13
18_V	175_S	0.500	0.13

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
2bs2C	2	0.9752	100	0.575	Contact Map
2wdqC	1	0.5743	99.5	0.832	Contact Map
2wdqD	2	0.5149	99.4	0.84	Contact Map
1zoyC	1	0.5644	99.2	0.855	Contact Map
2h88C	2	0.5693	99.2	0.855	Contact Map
4ytpC	1	0.6535	99.2	0.856	Contact Map
4ysxC	1	0.6436	98.8	0.876	Contact Map
2h88D	1	0.4208	67.8	0.954	Contact Map
4ysxD	1	0.5495	36.6	0.962	Contact Map
1kf6C	1	0.5495	29.8	0.964	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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