Q9HRJ9 - HALSA - GREMLIN Contacts

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Q9HRJ9 - Cytochrome c oxidase subunit II

UniProt:	Q9HRJ9	Sequences: MRGKRLVPVLVAGIAVLVAFVDPAAASSGYQSATEELIRNLNSQLVAAAITITLLVEGILVYTVWKFRNADEAKPTKENRRLEITWTVATAVVLLFVGVSAYSAMGTPYLLSSGDDVQAAMANEDSATVTVEGVQWYWNYDYAGSNVSMSSGAGNDTVVGNQPLVLPADTEVTIQTESNDVIHAFHAPELGLKMDALPGQQNHLVTNDLDEGTYQLYCAEFCGAGHSKMLSKIHVVDRDTYDAYINDPENVSVGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	255 (210)
Sequences:	5850 (3092)
Seq/√Len:	213.4

ECOLI - CYOA
BACSU - COX2 QOX2
HALSA - Q9HRJ9 Q9HN94
SULSO - Q97UN4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
237_D	240_T	4.074	1.00
238_R	242_D	3.861	1.00
165_V	236_V	3.774	1.00
176_T	196_A	3.591	1.00
170_T	238_R	3.491	1.00
129_V	164_L	3.384	1.00
134_V	139_N	3.101	1.00
168_A	235_V	3.091	1.00
208_D	235_V	2.936	1.00
166_L	208_D	2.845	1.00
211_E	237_D	2.699	1.00
168_A	211_E	2.612	1.00
132_E	177_E	2.463	1.00
163_P	234_H	2.326	1.00
174_I	206_T	2.299	1.00
130_T	141_D	2.211	1.00
45_L	97_V	2.137	1.00
128_T	173_T	2.055	1.00
193_K	220_E	2.043	1.00
126_S	170_T	1.995	1.00
236_V	240_T	1.974	1.00
211_E	235_V	1.950	1.00
218_C	222_C	1.942	1.00
130_T	175_Q	1.900	1.00
134_V	179_N	1.896	1.00
176_T	194_M	1.875	1.00
145_S	241_Y	1.864	1.00
168_A	238_R	1.839	1.00
171_E	207_N	1.822	1.00
186_H	219_A	1.796	1.00
184_A	219_A	1.794	1.00
184_A	193_K	1.787	1.00
213_T	234_H	1.783	1.00
166_L	233_I	1.759	1.00
213_T	232_K	1.709	1.00
133_G	196_A	1.709	1.00
132_E	141_D	1.693	1.00
240_T	243_A	1.684	1.00
128_T	175_Q	1.656	1.00
127_A	241_Y	1.654	1.00
43_S	47_A	1.647	1.00
195_D	220_E	1.644	1.00
36_E	209_L	1.586	1.00
173_T	203_H	1.559	1.00
216_L	231_S	1.558	1.00
165_V	234_H	1.517	1.00
147_V	245_I	1.504	1.00
131_V	174_I	1.490	1.00
33_A	207_N	1.490	1.00
160_G	232_K	1.475	1.00
172_V	208_D	1.465	1.00
175_Q	201_Q	1.454	1.00
190_L	233_I	1.447	1.00
134_V	137_Y	1.439	1.00
37_L	40_N	1.417	1.00
163_P	232_K	1.397	1.00
184_A	220_E	1.391	1.00
109_Y	112_S	1.387	1.00
191_G	206_T	1.384	1.00
126_S	171_E	1.381	1.00
194_M	204_L	1.366	1.00
190_L	208_D	1.359	1.00
183_H	218_C	1.358	1.00
81_R	85_T	1.323	1.00
187_A	233_I	1.319	1.00
222_C	226_H	1.313	1.00
140_Y	164_L	1.301	1.00
140_Y	231_S	1.266	1.00
211_E	240_T	1.260	1.00
163_P	213_T	1.256	1.00
183_H	222_C	1.244	1.00
88_V	92_V	1.236	1.00
130_T	177_E	1.214	1.00
129_V	166_L	1.207	1.00
215_Q	232_K	1.206	1.00
30_Y	35_E	1.198	1.00
31_Q	210_D	1.183	1.00
218_C	226_H	1.181	1.00
166_L	206_T	1.156	1.00
193_K	219_A	1.148	1.00
58_G	62_Y	1.133	1.00
61_V	65_W	1.121	1.00
99_V	103_S	1.119	1.00
217_Y	230_L	1.115	1.00
129_V	174_I	1.110	1.00
168_A	237_D	1.109	1.00
174_I	204_L	1.096	1.00
123_N	126_S	1.078	1.00
53_T	57_E	1.071	1.00
31_Q	189_E	1.069	1.00
33_A	209_L	1.067	1.00
23_P	26_A	1.064	1.00
62_Y	66_K	1.050	1.00
92_V	96_F	1.048	1.00
218_C	229_M	1.045	1.00
31_Q	214_Y	1.040	1.00
36_E	40_N	1.040	1.00
44_Q	48_A	1.018	1.00
215_Q	230_L	1.017	1.00
242_D	246_N	1.014	1.00
175_Q	203_H	1.011	1.00
169_D	209_L	1.005	1.00
82_L	86_W	0.999	1.00
37_L	104_A	0.985	1.00
214_Y	235_V	0.981	1.00
50_I	54_L	0.977	1.00
131_V	140_Y	0.970	1.00
86_W	90_T	0.967	1.00
44_Q	96_F	0.961	1.00
35_E	39_R	0.955	1.00
166_L	235_V	0.952	1.00
243_A	246_N	0.952	1.00
139_N	148_S	0.951	1.00
44_Q	51_T	0.948	1.00
194_M	202_N	0.945	1.00
83_E	86_W	0.941	0.99
135_Q	181_V	0.939	0.99
166_L	172_V	0.934	0.99
39_R	43_S	0.933	0.99
187_A	190_L	0.912	0.99
135_Q	180_D	0.906	0.99
32_S	190_L	0.899	0.99
40_N	44_Q	0.896	0.99
79_N	83_E	0.893	0.99
243_A	247_D	0.892	0.99
208_D	211_E	0.888	0.99
160_G	163_P	0.883	0.99
52_I	56_V	0.879	0.99
84_I	88_V	0.878	0.99
225_G	228_K	0.877	0.99
226_H	229_M	0.872	0.99
169_D	238_R	0.860	0.99
83_E	87_T	0.850	0.99
164_L	174_I	0.848	0.99
222_C	229_M	0.846	0.99
197_L	200_Q	0.840	0.99
128_T	144_G	0.836	0.99
25_A	28_S	0.833	0.99
185_F	233_I	0.830	0.99
137_Y	161_N	0.829	0.99
140_Y	185_F	0.827	0.99
26_A	30_Y	0.824	0.99
103_S	110_L	0.824	0.99
192_L	204_L	0.823	0.99
211_E	236_V	0.822	0.99
142_Y	241_Y	0.820	0.99
21_V	24_A	0.814	0.99
211_E	214_Y	0.813	0.99
182_I	197_L	0.802	0.98
167_P	172_V	0.787	0.98
123_N	205_V	0.784	0.98
178_S	182_I	0.782	0.98
57_E	61_V	0.781	0.98
27_S	30_Y	0.774	0.98
136_W	181_V	0.770	0.98
145_S	245_I	0.768	0.98
43_S	46_V	0.758	0.98
129_V	142_Y	0.757	0.98
180_D	183_H	0.753	0.98
28_S	31_Q	0.752	0.98
190_L	235_V	0.751	0.98
35_E	38_I	0.751	0.98
122_A	205_V	0.749	0.97
131_V	176_T	0.749	0.97
162_Q	248_P	0.746	0.97
47_A	51_T	0.744	0.97
195_D	219_A	0.740	0.97
41_L	45_L	0.733	0.97
95_L	99_V	0.731	0.97
33_A	37_L	0.729	0.97
28_S	32_S	0.728	0.97
177_E	201_Q	0.727	0.97
183_H	226_H	0.727	0.97
93_V	96_F	0.721	0.97
239_D	243_A	0.718	0.97
57_E	60_L	0.717	0.97
142_Y	164_L	0.705	0.96
145_S	149_M	0.705	0.96
83_E	90_T	0.702	0.96
80_R	84_I	0.698	0.96
140_Y	216_L	0.693	0.96
22_D	25_A	0.689	0.96
164_L	233_I	0.684	0.96
28_S	189_E	0.680	0.96
36_E	39_R	0.679	0.96
123_N	171_E	0.677	0.95
55_L	59_I	0.674	0.95
31_Q	35_E	0.670	0.95
42_N	46_V	0.670	0.95
135_Q	221_F	0.669	0.95
159_V	163_P	0.668	0.95
171_E	205_V	0.668	0.95
34_T	38_I	0.661	0.95
44_Q	103_S	0.660	0.95
241_Y	245_I	0.659	0.95
127_A	170_T	0.658	0.95
181_V	222_C	0.658	0.95
208_D	233_I	0.656	0.95
40_N	43_S	0.655	0.95
174_I	185_F	0.649	0.94
172_V	206_T	0.648	0.94
186_H	193_K	0.645	0.94
187_A	214_Y	0.642	0.94
216_L	233_I	0.641	0.94
125_D	128_T	0.640	0.94
186_H	192_L	0.638	0.94
47_A	50_I	0.636	0.94
73_A	76_T	0.635	0.94
176_T	204_L	0.633	0.94
131_V	185_F	0.632	0.93
24_A	29_G	0.630	0.93
91_A	94_L	0.628	0.93
21_V	25_A	0.627	0.93
122_A	171_E	0.626	0.93
29_G	39_R	0.620	0.93
21_V	26_A	0.620	0.93
168_A	209_L	0.615	0.93
155_N	159_V	0.613	0.92
133_G	137_Y	0.612	0.92
98_G	102_Y	0.612	0.92
173_T	205_V	0.611	0.92
27_S	39_R	0.611	0.92
48_A	97_V	0.610	0.92
39_R	191_G	0.610	0.92
127_A	172_V	0.609	0.92
126_S	238_R	0.609	0.92
94_L	100_S	0.609	0.92
180_D	218_C	0.604	0.92
44_Q	100_S	0.603	0.92
133_G	178_S	0.602	0.92
128_T	131_V	0.601	0.92
41_L	104_A	0.601	0.92
168_A	208_D	0.599	0.92
186_H	217_Y	0.598	0.91
90_T	248_P	0.597	0.91
98_G	101_A	0.596	0.91
125_D	170_T	0.596	0.91
32_S	36_E	0.596	0.91
77_K	82_L	0.595	0.91
33_A	36_E	0.594	0.91
178_S	196_A	0.591	0.91
132_E	179_N	0.590	0.91
168_A	210_D	0.590	0.91
217_Y	221_F	0.587	0.91
76_T	90_T	0.586	0.91
180_D	198_P	0.581	0.90
30_Y	34_T	0.578	0.90
130_T	143_A	0.578	0.90
85_T	89_A	0.577	0.90
49_A	53_T	0.577	0.90
76_T	79_N	0.577	0.90
50_I	57_E	0.576	0.90
191_G	216_L	0.573	0.90
181_V	220_E	0.573	0.90
59_I	84_I	0.572	0.90
182_I	198_P	0.572	0.90
82_L	90_T	0.571	0.89
137_Y	225_G	0.570	0.89
35_E	191_G	0.567	0.89
232_K	235_V	0.566	0.89
133_G	185_F	0.565	0.89
80_R	85_T	0.561	0.89
132_E	139_N	0.558	0.88
26_A	29_G	0.557	0.88
72_E	75_P	0.557	0.88
30_Y	39_R	0.557	0.88
156_D	160_G	0.555	0.88
84_I	87_T	0.553	0.88
244_Y	248_P	0.553	0.88
32_S	35_E	0.552	0.88
169_D	235_V	0.551	0.88
44_Q	91_A	0.551	0.88
186_H	204_L	0.549	0.88
42_N	45_L	0.548	0.88
61_V	64_V	0.547	0.87
81_R	84_I	0.545	0.87
32_S	206_T	0.544	0.87
62_Y	127_A	0.543	0.87
66_K	71_D	0.542	0.87
49_A	59_I	0.541	0.87
138_W	196_A	0.541	0.87
129_V	145_S	0.539	0.87
34_T	37_L	0.539	0.87
141_D	148_S	0.537	0.86
50_I	53_T	0.536	0.86
94_L	98_G	0.533	0.86
70_A	73_A	0.533	0.86
136_W	221_F	0.532	0.86
146_N	149_M	0.532	0.86
170_T	242_D	0.530	0.86
220_E	226_H	0.530	0.86
183_H	220_E	0.529	0.86
90_T	101_A	0.524	0.85
125_D	171_E	0.523	0.85
83_E	98_G	0.523	0.85
192_L	206_T	0.520	0.85
24_A	27_S	0.520	0.85
101_A	104_A	0.520	0.85
63_T	66_K	0.519	0.85
112_S	194_M	0.518	0.84
219_A	226_H	0.518	0.84
239_D	242_D	0.517	0.84
158_V	245_I	0.517	0.84
185_F	192_L	0.517	0.84
169_D	207_N	0.514	0.84
158_V	217_Y	0.512	0.84
32_S	192_L	0.509	0.83
89_A	92_V	0.509	0.83
124_E	169_D	0.508	0.83
137_Y	140_Y	0.508	0.83
49_A	97_V	0.504	0.83
139_N	179_N	0.502	0.83
204_L	207_N	0.500	0.82
52_I	101_A	0.500	0.82
140_Y	161_N	0.500	0.82

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
3hb3B	1	0.902	100	0.141	Contact Map
2gsmB	1	0.8902	100	0.167	Contact Map
1fftB	1	0.8392	100	0.171	Contact Map
1v54B	1	0.851	100	0.199	Contact Map
2yevB	1	0.8314	100	0.203	Contact Map
4txvB	1	0.5412	100	0.378	Contact Map
1cyxA	1	0.4706	100	0.421	Contact Map
3s8fB	1	0.6118	100	0.494	Contact Map
2cuaA	1	0.502	100	0.651	Contact Map
3sbqA	2	0.7608	99.9	0.679	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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