Q9HRK1 - HALSA - GREMLIN Contacts

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Q9HRK1 - Cytochrome c oxidase subunit III

UniProt:	Q9HRK1	Sequences: MSVADDSTDDHGHHLPAVEDWPKGFGEASWWPFITAIGAAGFYIGAALYVLGRGESALVGPMVGPGVFIASTFAFLAGLYGWVYHAFVAAYWSNDGGGSTALRWGMIGFLGSEIATFGAGFAYYFFIRAGTQWSTAASAIPDGFLGSLVVVNTAILVVSSFTLHFAHVALRKGNRSRFLALLVSTLVLGVVFIGGQVYEYYEFIAHEGFTLSGGLFESAFFGLTGLHGLHVTMGAVLIGIIMVRGLRGQYSADRHTSVSTVSMYWHFVDIVWIFLVVVLYAGSVA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	285 (251)
Sequences:	2714 (1290)
Seq/√Len:	81.4

ECOLI - CYOC
BACSU - QOX3 COX3
HALSA - Q9HRK1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
256_T	260_T	4.278	1.00
115_A	118_G	4.230	1.00
178_F	245_G	4.050	1.00
35_T	78_G	3.794	1.00
183_V	242_M	3.642	1.00
38_G	74_A	3.625	1.00
258_V	262_S	3.275	1.00
116_T	226_L	3.150	1.00
45_G	71_S	3.046	1.00
162_T	184_S	2.939	1.00
175_R	248_G	2.865	1.00
165_F	181_L	2.833	1.00
38_G	75_F	2.714	1.00
123_Y	219_A	2.474	1.00
193_I	232_T	2.364	1.00
179_L	246_L	2.313	1.00
166_A	245_G	2.305	1.00
34_I	78_G	2.292	1.00
127_I	215_L	2.252	1.00
174_N	177_R	2.233	1.00
163_L	238_I	2.208	1.00
239_G	243_V	2.202	1.00
223_L	279_L	2.200	1.00
90_A	102_L	2.181	1.00
175_R	179_L	2.145	1.00
35_T	79_L	2.095	1.00
125_F	278_V	2.085	1.00
162_T	185_T	2.004	1.00
166_A	178_F	1.977	1.00
140_I	144_F	1.961	1.00
75_F	79_L	1.930	1.00
155_I	195_G	1.882	1.00
42_F	75_F	1.879	1.00
41_G	71_S	1.840	1.00
229_L	233_M	1.800	1.00
241_I	261_V	1.796	1.00
173_G	252_A	1.781	1.00
190_V	239_G	1.776	1.00
45_G	67_V	1.693	1.00
232_T	236_V	1.683	1.00
235_A	239_G	1.675	1.00
237_L	261_V	1.652	1.00
194_G	198_Y	1.634	1.00
154_A	158_V	1.629	1.00
148_L	195_G	1.622	1.00
111_G	115_A	1.582	1.00
91_Y	249_Q	1.565	1.00
242_M	246_L	1.558	1.00
148_L	198_Y	1.555	1.00
163_L	166_A	1.549	1.00
186_L	239_G	1.540	0.99
76_L	80_Y	1.526	0.99
166_A	258_V	1.525	0.99
179_L	242_M	1.520	0.99
84_Y	88_V	1.520	0.99
106_M	110_L	1.504	0.99
170_L	178_F	1.501	0.99
278_V	283_S	1.488	0.99
197_V	201_Y	1.455	0.99
193_I	235_A	1.450	0.99
190_V	232_T	1.439	0.99
176_S	180_A	1.427	0.99
191_V	195_G	1.409	0.99
186_L	235_A	1.382	0.99
166_A	181_L	1.375	0.99
170_L	258_V	1.369	0.99
169_A	181_L	1.369	0.99
186_L	242_M	1.368	0.99
164_H	167_H	1.348	0.99
111_G	114_I	1.345	0.99
190_V	194_G	1.343	0.99
41_G	74_A	1.317	0.98
183_V	187_V	1.312	0.98
83_V	237_L	1.301	0.98
240_I	243_V	1.299	0.98
190_V	235_A	1.292	0.98
81_G	84_Y	1.280	0.98
77_A	81_G	1.273	0.98
99_S	103_R	1.273	0.98
182_L	245_G	1.261	0.98
127_I	219_A	1.256	0.98
194_G	197_V	1.246	0.98
40_A	43_Y	1.232	0.98
49_Y	65_P	1.225	0.97
222_G	229_L	1.224	0.97
157_V	273_I	1.223	0.97
179_L	245_G	1.221	0.97
266_H	269_D	1.219	0.97
34_I	74_A	1.214	0.97
158_V	161_F	1.203	0.97
165_F	177_R	1.194	0.97
223_L	226_L	1.191	0.97
169_A	177_R	1.183	0.97
114_I	271_V	1.172	0.97
182_L	238_I	1.169	0.97
87_F	249_Q	1.162	0.96
99_S	254_R	1.147	0.96
227_H	230_H	1.142	0.96
122_A	126_F	1.134	0.96
177_R	181_L	1.127	0.96
198_Y	202_E	1.125	0.96
244_R	249_Q	1.109	0.95
163_L	182_L	1.109	0.95
69_I	73_F	1.102	0.95
85_H	88_V	1.099	0.95
120_G	222_G	1.089	0.95
277_V	281_A	1.085	0.95
74_A	78_G	1.079	0.95
223_L	275_L	1.074	0.95
243_V	247_R	1.068	0.94
38_G	71_S	1.067	0.94
131_T	135_T	1.063	0.94
35_T	39_A	1.055	0.94
98_G	160_S	1.040	0.94
162_T	188_L	1.026	0.93
131_T	136_A	1.023	0.93
166_A	182_L	1.020	0.93
48_L	53_R	1.016	0.93
79_L	83_V	1.008	0.92
65_P	68_F	1.004	0.92
41_G	67_V	1.003	0.92
180_A	183_V	0.995	0.92
34_I	37_I	0.978	0.91
241_I	257_S	0.978	0.91
43_Y	47_A	0.973	0.91
49_Y	68_F	0.971	0.91
76_L	79_L	0.966	0.91
279_L	283_S	0.960	0.90
120_G	223_L	0.952	0.90
164_H	259_S	0.946	0.90
181_L	184_S	0.939	0.89
106_M	256_T	0.935	0.89
182_L	242_M	0.925	0.89
234_G	265_W	0.921	0.89
91_Y	254_R	0.919	0.88
98_G	101_A	0.916	0.88
44_I	48_L	0.911	0.88
46_A	50_V	0.909	0.88
244_R	250_Y	0.907	0.88
141_P	144_F	0.903	0.88
273_I	277_V	0.902	0.87
183_V	246_L	0.899	0.87
94_N	98_G	0.889	0.87
171_R	259_S	0.887	0.87
83_V	86_A	0.885	0.86
160_S	164_H	0.883	0.86
95_D	98_G	0.883	0.86
50_V	211_L	0.881	0.86
211_L	217_E	0.880	0.86
218_S	222_G	0.874	0.86
231_V	268_V	0.873	0.86
167_H	259_S	0.867	0.85
139_A	144_F	0.866	0.85
66_G	70_A	0.866	0.85
265_W	272_W	0.866	0.85
19_E	154_A	0.863	0.85
46_A	49_Y	0.853	0.84
29_S	32_P	0.851	0.84
163_L	262_S	0.848	0.84
154_A	278_V	0.844	0.84
138_S	142_D	0.843	0.84
231_V	234_G	0.843	0.84
103_R	119_A	0.841	0.84
90_A	254_R	0.840	0.83
222_G	226_L	0.838	0.83
140_I	143_G	0.828	0.83
133_W	137_A	0.824	0.82
203_F	208_G	0.813	0.81
140_I	145_L	0.813	0.81
150_V	168_V	0.806	0.81
31_W	85_H	0.805	0.81
164_H	168_V	0.799	0.80
46_A	68_F	0.797	0.80
155_I	191_V	0.795	0.80
157_V	161_F	0.795	0.80
151_V	195_G	0.794	0.80
96_G	100_T	0.791	0.80
269_D	272_W	0.787	0.79
264_Y	280_Y	0.787	0.79
31_W	81_G	0.785	0.79
129_A	282_G	0.783	0.79
133_W	136_A	0.780	0.79
36_A	41_G	0.779	0.79
214_G	217_E	0.778	0.79
80_Y	87_F	0.769	0.78
238_I	241_I	0.767	0.78
134_S	139_A	0.766	0.77
106_M	128_R	0.765	0.77
265_W	268_V	0.763	0.77
126_F	130_G	0.760	0.77
72_T	229_L	0.759	0.77
100_T	104_W	0.758	0.77
264_Y	267_F	0.755	0.76
117_F	192_F	0.753	0.76
135_T	138_S	0.750	0.76
201_Y	208_G	0.748	0.76
182_L	258_V	0.740	0.75
165_F	169_A	0.740	0.75
20_D	198_Y	0.738	0.75
172_K	262_S	0.737	0.75
192_F	227_H	0.736	0.75
97_G	100_T	0.736	0.75
70_A	74_A	0.736	0.75
272_W	280_Y	0.736	0.75
21_W	24_G	0.736	0.75
146_G	276_V	0.733	0.74
30_W	85_H	0.732	0.74
136_A	139_A	0.726	0.74
124_Y	128_R	0.724	0.73
196_Q	200_Y	0.724	0.73
65_P	69_I	0.717	0.73
37_I	41_G	0.716	0.73
110_L	263_M	0.715	0.72
211_L	222_G	0.715	0.72
192_F	230_H	0.715	0.72
37_I	78_G	0.705	0.71
42_F	46_A	0.705	0.71
244_R	257_S	0.704	0.71
116_T	120_G	0.700	0.71
268_V	272_W	0.698	0.71
139_A	143_G	0.697	0.71
154_A	189_G	0.697	0.71
160_S	281_A	0.695	0.70
152_N	275_L	0.694	0.70
170_L	262_S	0.691	0.70
25_F	50_V	0.691	0.70
159_S	269_D	0.683	0.69
270_I	275_L	0.682	0.69
264_Y	268_V	0.681	0.69
173_G	194_G	0.676	0.68
39_A	43_Y	0.676	0.68
268_V	271_V	0.673	0.68
85_H	89_A	0.671	0.68
192_F	199_E	0.670	0.68
245_G	250_Y	0.665	0.67
106_M	185_T	0.665	0.67
66_G	69_I	0.664	0.67
79_L	233_M	0.663	0.67
236_V	240_I	0.662	0.67
200_Y	224_T	0.659	0.66
231_V	265_W	0.657	0.66
48_L	67_V	0.655	0.66
123_Y	283_S	0.653	0.66
21_W	25_F	0.652	0.65
266_H	272_W	0.648	0.65
223_L	274_F	0.646	0.65
125_F	274_F	0.645	0.65
102_L	256_T	0.645	0.65
70_A	183_V	0.644	0.64
132_Q	135_T	0.643	0.64
46_A	189_G	0.642	0.64
180_A	184_S	0.642	0.64
135_T	143_G	0.640	0.64
34_I	81_G	0.640	0.64
28_A	161_F	0.639	0.64
148_L	155_I	0.638	0.64
256_T	262_S	0.636	0.63
199_E	230_H	0.636	0.63
164_H	262_S	0.633	0.63
189_G	234_G	0.632	0.63
82_W	89_A	0.631	0.63
137_A	142_D	0.627	0.62
41_G	44_I	0.626	0.62
247_R	277_V	0.626	0.62
262_S	273_I	0.625	0.62
216_F	279_L	0.625	0.62
83_V	88_V	0.624	0.62
48_L	66_G	0.624	0.62
99_S	256_T	0.624	0.62
47_A	52_G	0.619	0.61
53_R	64_G	0.618	0.61
49_Y	103_R	0.616	0.61
189_G	265_W	0.615	0.61
269_D	275_L	0.613	0.61
119_A	125_F	0.612	0.61
156_L	192_F	0.611	0.60
20_D	49_Y	0.610	0.60
33_F	37_I	0.610	0.60
20_D	158_V	0.607	0.60
106_M	120_G	0.607	0.60
131_T	134_S	0.606	0.60
132_Q	154_A	0.603	0.59
195_G	281_A	0.602	0.59
42_F	65_P	0.598	0.59
163_L	239_G	0.596	0.59
26_G	30_W	0.595	0.58
107_I	111_G	0.594	0.58
230_H	264_Y	0.592	0.58
30_W	84_Y	0.589	0.58
86_A	102_L	0.588	0.57
230_H	234_G	0.587	0.57
232_T	235_A	0.587	0.57
138_S	215_L	0.587	0.57
94_N	102_L	0.585	0.57
179_L	183_V	0.585	0.57
106_M	162_T	0.579	0.56
159_S	268_V	0.576	0.56
210_T	218_S	0.575	0.56
155_I	188_L	0.575	0.56
173_G	190_V	0.575	0.56
234_G	267_F	0.575	0.56
35_T	38_G	0.570	0.55
66_G	74_A	0.569	0.55
243_V	246_L	0.568	0.55
29_S	85_H	0.565	0.55
245_G	248_G	0.564	0.54
220_F	228_G	0.563	0.54
238_I	261_V	0.562	0.54
44_I	47_A	0.562	0.54
24_G	101_A	0.562	0.54
209_F	216_F	0.561	0.54
157_V	181_L	0.558	0.54
24_G	105_G	0.557	0.53
52_G	64_G	0.555	0.53
228_G	231_V	0.555	0.53
87_F	91_Y	0.554	0.53
53_R	246_L	0.554	0.53
74_A	177_R	0.553	0.53
183_V	239_G	0.553	0.53
122_A	139_A	0.553	0.53
44_I	174_N	0.553	0.53
42_F	72_T	0.551	0.53
34_I	41_G	0.551	0.53
213_G	217_E	0.548	0.52
34_I	43_Y	0.547	0.52
87_F	244_R	0.546	0.52
38_G	78_G	0.544	0.52
120_G	263_M	0.544	0.52
241_I	250_Y	0.544	0.52
202_E	221_F	0.542	0.52
222_G	233_M	0.540	0.51
21_W	47_A	0.539	0.51
176_S	246_L	0.539	0.51
47_A	71_S	0.536	0.51
126_F	134_S	0.533	0.50
53_R	68_F	0.532	0.50
40_A	64_G	0.528	0.50
223_L	278_V	0.527	0.50
83_V	165_F	0.525	0.49
19_E	22_P	0.525	0.49
141_P	145_L	0.525	0.49
69_I	187_V	0.524	0.49
126_F	129_A	0.524	0.49
129_A	136_A	0.523	0.49
147_S	202_E	0.523	0.49
108_G	122_A	0.522	0.49
233_M	237_L	0.522	0.49
35_T	81_G	0.521	0.49
157_V	160_S	0.521	0.49
87_F	92_W	0.519	0.49
64_G	77_A	0.519	0.49
189_G	214_G	0.519	0.49
264_Y	272_W	0.518	0.48
41_G	70_A	0.518	0.48
214_G	221_F	0.518	0.48
244_R	255_H	0.518	0.48
218_S	274_F	0.517	0.48
151_V	171_R	0.517	0.48
179_L	190_V	0.514	0.48
199_E	269_D	0.514	0.48
19_E	33_F	0.512	0.48
101_A	108_G	0.511	0.47
160_S	270_I	0.509	0.47
219_A	223_L	0.509	0.47
210_T	229_L	0.507	0.47
214_G	218_S	0.507	0.47
36_A	39_A	0.506	0.47
123_Y	169_A	0.504	0.47
170_L	174_N	0.504	0.47
210_T	217_E	0.504	0.47
130_G	134_S	0.502	0.46
25_F	30_W	0.502	0.46
28_A	99_S	0.501	0.46
24_G	98_G	0.501	0.46
168_V	259_S	0.500	0.46
19_E	142_D	0.500	0.46

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
1v54C	1	0.8877	100	0.192	Contact Map
1m56C	2	0.8947	100	0.192	Contact Map
1qleC	1	0.9228	100	0.194	Contact Map
2yevA	1	0.9228	100	0.254	Contact Map
1fftC	1	0.6456	100	0.429	Contact Map
1fftA	1	0	89.1	0.942	Contact Map
2mmuA	1	0.1719	6.2	0.973	Contact Map
2xq2A	2	0.2596	2.6	0.978	Contact Map
2wswA	3	0.2702	2.1	0.979	Contact Map
2a65A	2	0.5474	1.8	0.979	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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