Cyt_bd_oxida_II - PFAM28P - GREMLIN Contacts

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Cyt_bd_oxida_II - Cytochrome bd terminal oxidase subunit II

PFAM:	PF02322	Sequences: LPTIWFVLIGVLLAGYVVLDGFDLGVGILLPFARTDERERRVMINSIGPVWDGNEVWLVLAGGALFAAFPLAYATLFSGLYLPLMLMLLGLILRGVAFEFRSKADSPRWRRFWDWAFFIGSLLAALLQGVALGNLVQGVPVAGGFFDLLNPFALLTGLLLVALYALHGATWLALKTEGELQERARRLARRLALAALVLLAAFSLATPLAPPLIAGLLWLVPLLLAVLALLLWALLLLRRGREGWAPFLASALAIALVLAGLGISLYPYLLPSDPAYSLTIWNAASSPYTLKVMLVVALIGLPLVLAYTAWVYRVF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	315 (310)
Sequences:	20673 (13131)
Seq/√Len:	745.8
META:	0.789

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
150_N	153_A	4.354	1.00
287_P	291_K	3.602	1.00
28_I	165_A	2.936	1.00
18_V	251_A	2.730	1.00
186_R	190_R	2.630	1.00
133_G	156_T	2.619	1.00
126_L	161_V	2.579	1.00
39_E	183_R	2.572	1.00
165_A	191_L	2.558	1.00
126_L	157_G	2.535	1.00
26_V	43_M	2.504	1.00
309_A	313_R	2.430	1.00
101_R	114_D	2.387	1.00
43_M	172_L	2.311	1.00
122_L	161_V	2.290	1.00
170_T	188_A	2.252	1.00
80_L	139_V	2.177	1.00
11_V	15_G	2.128	1.00
152_F	206_T	2.101	1.00
225_A	229_L	2.092	1.00
112_F	115_W	2.053	1.00
115_W	119_I	2.048	1.00
68_A	293_M	1.984	1.00
187_L	190_R	1.982	1.00
306_A	309_A	1.953	1.00
130_V	157_G	1.949	1.00
93_L	116_A	1.909	1.00
144_G	147_D	1.888	1.00
185_R	189_R	1.879	1.00
28_I	161_V	1.876	1.00
162_A	198_L	1.872	1.00
163_L	254_I	1.854	1.00
14_A	255_A	1.769	1.00
126_L	130_V	1.766	1.00
118_F	122_L	1.752	1.00
272_S	277_S	1.743	1.00
234_L	238_R	1.727	1.00
224_L	228_A	1.717	1.00
169_A	188_A	1.714	1.00
112_F	116_A	1.707	1.00
41_R	45_N	1.704	1.00
90_G	123_L	1.697	1.00
193_L	197_V	1.692	1.00
46_S	175_K	1.684	1.00
137_Q	150_N	1.663	1.00
179_E	182_E	1.661	1.00
106_S	109_W	1.660	1.00
278_L	283_A	1.658	1.00
181_Q	185_R	1.653	1.00
288_Y	291_K	1.649	1.00
111_R	115_W	1.647	1.00
125_A	160_L	1.645	1.00
87_M	128_Q	1.626	1.00
242_E	245_A	1.625	1.00
227_L	231_L	1.624	1.00
28_I	122_L	1.623	1.00
291_K	295_V	1.617	1.00
199_L	257_V	1.612	1.00
205_A	209_A	1.611	1.00
268_Y	277_S	1.605	1.00
31_P	118_F	1.598	1.00
297_A	301_L	1.595	1.00
295_V	299_I	1.565	1.00
29_L	169_A	1.561	1.00
86_L	127_L	1.550	1.00
2_P	284_A	1.547	1.00
195_A	199_L	1.534	1.00
224_L	227_L	1.504	1.00
167_H	251_A	1.499	1.00
231_L	249_A	1.483	1.00
142_A	147_D	1.472	1.00
125_A	164_Y	1.470	1.00
173_A	181_Q	1.462	1.00
189_R	238_R	1.451	1.00
288_Y	292_V	1.437	1.00
203_S	206_T	1.430	1.00
72_A	269_L	1.416	1.00
223_L	226_V	1.415	1.00
167_H	250_S	1.413	1.00
236_L	249_A	1.403	1.00
241_R	244_W	1.396	1.00
4_I	294_L	1.387	1.00
158_L	162_A	1.382	1.00
77_F	84_L	1.381	1.00
221_P	225_A	1.379	1.00
300_G	303_L	1.374	1.00
268_Y	272_S	1.373	1.00
210_P	214_A	1.366	1.00
9_I	64_A	1.365	1.00
226_V	229_L	1.355	1.00
4_I	8_L	1.349	1.00
185_R	240_G	1.340	1.00
42_V	176_T	1.329	1.00
13_L	65_L	1.324	1.00
279_T	282_N	1.319	1.00
35_T	39_E	1.313	1.00
173_A	185_R	1.308	1.00
120_G	124_A	1.298	1.00
33_A	43_M	1.298	1.00
14_A	259_A	1.288	1.00
199_L	203_S	1.282	1.00
225_A	228_A	1.278	1.00
216_L	219_L	1.271	1.00
226_V	230_L	1.267	1.00
202_F	206_T	1.260	1.00
76_L	270_L	1.252	1.00
220_V	223_L	1.251	1.00
305_L	309_A	1.251	1.00
84_L	131_A	1.243	1.00
235_L	239_R	1.230	1.00
217_L	263_I	1.218	1.00
265_L	283_A	1.218	1.00
182_E	186_R	1.215	1.00
223_L	227_L	1.211	1.00
154_L	158_L	1.198	1.00
212_L	215_G	1.191	1.00
20_D	24_L	1.186	1.00
44_I	98_F	1.182	1.00
12_L	15_G	1.178	1.00
162_A	194_A	1.176	1.00
116_A	120_G	1.175	1.00
181_Q	242_E	1.174	1.00
42_V	45_N	1.171	1.00
186_R	189_R	1.164	1.00
3_T	281_W	1.160	1.00
166_L	192_A	1.158	1.00
134_N	153_A	1.157	1.00
201_A	205_A	1.147	1.00
197_V	201_A	1.140	1.00
162_A	191_L	1.140	1.00
90_G	124_A	1.127	1.00
206_T	209_A	1.126	1.00
71_L	75_T	1.118	1.00
211_P	214_A	1.117	1.00
204_L	208_L	1.115	1.00
45_N	102_S	1.106	1.00
12_L	60_L	1.105	1.00
235_L	238_R	1.100	1.00
45_N	48_G	1.093	1.00
211_P	215_G	1.090	1.00
222_L	226_V	1.090	1.00
187_L	191_L	1.088	1.00
285_S	289_T	1.085	1.00
177_E	181_Q	1.083	1.00
195_A	198_L	1.078	1.00
252_L	256_L	1.073	1.00
180_L	184_A	1.066	1.00
14_A	258_L	1.060	1.00
22_F	247_F	1.058	1.00
205_A	210_P	1.058	1.00
287_P	290_L	1.055	1.00
209_A	212_L	1.053	1.00
268_Y	279_T	1.053	1.00
310_W	314_V	1.051	1.00
46_S	171_W	1.050	1.00
24_L	125_A	1.042	1.00
206_T	210_P	1.040	1.00
87_M	127_L	1.038	1.00
222_L	229_L	1.037	1.00
22_F	50_V	1.029	1.00
223_L	229_L	1.027	1.00
166_L	250_S	1.020	1.00
286_S	289_T	1.020	1.00
3_T	266_Y	1.014	1.00
255_A	259_A	1.014	1.00
108_R	111_R	1.013	1.00
7_V	11_V	1.009	1.00
166_L	233_A	1.001	1.00
136_V	265_L	0.998	1.00
166_L	191_L	0.992	1.00
198_L	202_F	0.991	1.00
115_W	118_F	0.985	1.00
155_L	201_A	0.984	1.00
222_L	225_A	0.983	1.00
26_V	172_L	0.982	1.00
75_T	141_V	0.979	1.00
80_L	134_N	0.979	1.00
71_L	283_A	0.979	1.00
268_Y	271_P	0.978	1.00
208_L	211_P	0.977	1.00
181_Q	243_G	0.976	1.00
170_T	250_S	0.970	1.00
36_D	110_R	0.969	1.00
188_A	237_L	0.968	1.00
234_L	237_L	0.967	1.00
127_L	130_V	0.966	1.00
272_S	276_Y	0.963	1.00
108_R	112_F	0.960	1.00
33_A	39_E	0.959	1.00
221_P	228_A	0.942	1.00
87_M	124_A	0.942	1.00
79_G	139_V	0.941	1.00
20_D	128_Q	0.940	1.00
176_T	181_Q	0.931	1.00
107_P	111_R	0.924	1.00
90_G	120_G	0.918	1.00
294_L	298_L	0.915	1.00
248_L	252_L	0.915	1.00
65_L	72_A	0.914	1.00
194_A	198_L	0.909	1.00
298_L	302_P	0.909	1.00
185_R	242_E	0.908	1.00
189_R	193_L	0.908	1.00
140_P	147_D	0.905	1.00
227_L	230_L	0.900	1.00
233_A	236_L	0.899	1.00
2_P	281_W	0.898	1.00
208_L	212_L	0.898	1.00
22_F	312_Y	0.890	1.00
6_F	280_I	0.887	1.00
182_E	240_G	0.885	1.00
190_R	193_L	0.882	1.00
221_P	224_L	0.881	1.00
236_L	244_W	0.881	1.00
130_V	154_L	0.880	1.00
233_A	249_A	0.879	1.00
198_L	201_A	0.878	1.00
106_S	112_F	0.876	1.00
13_L	61_A	0.874	1.00
192_A	234_L	0.871	1.00
166_L	195_A	0.867	1.00
205_A	208_L	0.860	1.00
42_V	180_L	0.860	1.00
225_A	231_L	0.858	1.00
67_A	293_M	0.857	1.00
225_A	256_L	0.855	1.00
156_T	202_F	0.855	1.00
15_G	305_L	0.852	1.00
182_E	185_R	0.852	1.00
159_L	198_L	0.849	1.00
134_N	150_N	0.848	1.00
166_L	170_T	0.848	1.00
159_L	162_A	0.844	1.00
30_L	44_I	0.841	1.00
135_L	270_L	0.837	1.00
200_A	204_L	0.835	1.00
8_L	297_A	0.832	1.00
31_P	115_W	0.831	1.00
206_T	213_I	0.830	1.00
203_S	210_P	0.827	1.00
83_P	130_V	0.827	1.00
195_A	202_F	0.827	1.00
202_F	205_A	0.827	1.00
155_L	205_A	0.825	1.00
184_A	188_A	0.824	1.00
188_A	191_L	0.822	1.00
141_V	276_Y	0.821	1.00
104_A	107_P	0.818	1.00
218_W	221_P	0.818	1.00
261_L	265_L	0.809	1.00
83_P	131_A	0.809	1.00
79_G	83_P	0.805	1.00
26_V	47_I	0.801	1.00
228_A	256_L	0.800	1.00
149_L	153_A	0.798	1.00
71_L	278_L	0.797	1.00
210_P	213_I	0.794	1.00
102_S	110_R	0.786	1.00
180_L	183_R	0.785	1.00
199_L	202_F	0.784	1.00
233_A	237_L	0.778	1.00
152_F	205_A	0.778	1.00
132_L	261_L	0.777	1.00
18_V	255_A	0.776	1.00
172_L	184_A	0.773	1.00
210_P	215_G	0.772	1.00
34_R	39_E	0.771	1.00
229_L	253_A	0.771	1.00
208_L	214_A	0.769	1.00
104_A	109_W	0.767	1.00
224_L	229_L	0.763	1.00
202_F	210_P	0.762	1.00
5_W	8_L	0.759	1.00
237_L	242_E	0.758	1.00
179_E	183_R	0.756	1.00
44_I	117_F	0.754	1.00
29_L	165_A	0.754	1.00
50_V	311_V	0.745	1.00
123_L	127_L	0.742	1.00
75_T	270_L	0.740	1.00
127_L	149_L	0.740	1.00
37_E	42_V	0.737	1.00
226_V	231_L	0.733	1.00
50_V	171_W	0.730	1.00
198_L	206_T	0.730	1.00
116_A	119_I	0.726	1.00
184_A	187_L	0.725	1.00
6_F	10_G	0.725	1.00
228_A	249_A	0.724	1.00
80_L	131_A	0.723	1.00
41_R	44_I	0.722	1.00
109_W	112_F	0.722	1.00
75_T	278_L	0.721	1.00
40_R	114_D	0.718	1.00
220_V	224_L	0.718	1.00
228_A	231_L	0.717	1.00
64_A	67_A	0.709	1.00
162_A	195_A	0.707	1.00
28_I	125_A	0.704	1.00
166_L	188_A	0.703	1.00
308_T	311_V	0.701	1.00
72_A	76_L	0.701	1.00
61_A	65_L	0.699	1.00
199_L	210_P	0.699	1.00
244_W	248_L	0.696	1.00
113_W	116_A	0.695	1.00
10_G	262_G	0.695	1.00
236_L	239_R	0.695	1.00
43_M	180_L	0.694	1.00
34_R	183_R	0.692	1.00
207_P	210_P	0.689	1.00
8_L	12_L	0.687	1.00
125_A	161_V	0.686	1.00
62_G	73_Y	0.686	1.00
83_P	148_L	0.686	1.00
148_L	151_P	0.685	1.00
89_L	93_L	0.683	1.00
143_G	147_D	0.682	1.00
3_T	7_V	0.678	1.00
178_G	182_E	0.677	1.00
14_A	18_V	0.676	1.00
96_V	100_F	0.674	1.00
211_P	268_Y	0.674	1.00
217_L	220_V	0.674	1.00
236_L	241_R	0.674	1.00
205_A	212_L	0.671	1.00
97_A	117_F	0.670	1.00
189_R	237_L	0.670	1.00
122_L	126_L	0.670	1.00
72_A	283_A	0.670	1.00
198_L	205_A	0.665	1.00
16_Y	20_D	0.664	1.00
9_I	65_L	0.660	1.00
295_V	298_L	0.659	1.00
306_A	310_W	0.659	1.00
249_A	252_L	0.655	1.00
223_L	230_L	0.654	1.00
39_E	42_V	0.653	1.00
265_L	268_Y	0.651	1.00
183_R	187_L	0.651	1.00
206_T	211_P	0.651	1.00
194_A	201_A	0.650	1.00
53_G	311_V	0.647	1.00
137_Q	209_A	0.645	1.00
5_W	293_M	0.645	1.00
225_A	230_L	0.644	1.00
74_A	78_S	0.643	1.00
220_V	263_I	0.643	1.00
224_L	231_L	0.642	1.00
133_G	153_A	0.642	1.00
27_G	121_S	0.640	1.00
203_S	207_P	0.639	1.00
195_A	205_A	0.638	1.00
136_V	261_L	0.638	1.00
52_D	99_E	0.638	1.00
173_A	188_A	0.637	1.00
84_L	87_M	0.637	1.00
138_G	141_V	0.637	1.00
223_L	228_A	0.636	1.00
133_G	202_F	0.630	1.00
44_I	102_S	0.629	1.00
85_M	89_L	0.627	1.00
52_D	55_E	0.623	1.00
166_L	169_A	0.623	1.00
221_P	227_L	0.620	1.00
41_R	102_S	0.620	1.00
173_A	242_E	0.619	1.00
16_Y	128_Q	0.618	1.00
142_A	145_F	0.618	1.00
204_L	207_P	0.615	1.00
236_L	240_G	0.614	1.00
247_F	251_A	0.614	1.00
206_T	212_L	0.613	1.00
122_L	125_A	0.612	1.00
124_A	128_Q	0.611	1.00
204_L	209_A	0.611	1.00
299_I	302_P	0.608	1.00
43_M	46_S	0.606	1.00
12_L	64_A	0.606	1.00
7_V	260_G	0.606	1.00
189_R	192_A	0.604	1.00
237_L	240_G	0.604	1.00
39_E	179_E	0.602	1.00
27_G	31_P	0.600	1.00
8_L	301_L	0.594	1.00
173_A	237_L	0.593	1.00
224_L	256_L	0.593	1.00
174_L	247_F	0.591	1.00
191_L	194_A	0.590	1.00
253_A	257_V	0.590	1.00
107_P	110_R	0.587	1.00
37_E	41_R	0.587	1.00
183_R	186_R	0.586	1.00
42_V	177_E	0.584	1.00
207_P	211_P	0.582	1.00
292_V	296_V	0.580	1.00
174_L	244_W	0.579	1.00
119_I	123_L	0.577	1.00
142_A	146_F	0.576	1.00
231_L	236_L	0.575	1.00
178_G	181_Q	0.573	1.00
105_D	109_W	0.571	1.00
143_G	146_F	0.569	1.00
194_A	197_V	0.569	1.00
110_R	114_D	0.568	1.00
272_S	275_A	0.567	1.00
8_L	294_L	0.564	1.00
60_L	64_A	0.564	1.00
9_I	61_A	0.563	1.00
28_I	90_G	0.561	1.00
259_A	263_I	0.559	1.00
240_G	243_G	0.559	1.00
30_L	118_F	0.551	1.00
245_A	248_L	0.551	1.00
29_L	172_L	0.550	1.00
141_V	270_L	0.549	1.00
291_K	294_L	0.546	1.00
26_V	46_S	0.544	1.00
311_V	315_F	0.544	1.00
284_A	287_P	0.543	1.00
130_V	134_N	0.543	1.00
194_A	205_A	0.542	1.00
185_R	241_R	0.541	1.00
235_L	240_G	0.539	1.00
256_L	260_G	0.539	1.00
23_D	26_V	0.538	1.00
218_W	222_L	0.538	1.00
203_S	226_V	0.536	1.00
172_L	176_T	0.535	1.00
271_P	275_A	0.530	1.00
93_L	119_I	0.530	1.00
222_L	227_L	0.529	1.00
66_F	73_Y	0.527	1.00
80_L	83_P	0.526	1.00
167_H	170_T	0.526	1.00
174_L	243_G	0.526	1.00
22_F	54_N	0.525	1.00
56_V	59_V	0.523	1.00
202_F	212_L	0.523	1.00
95_G	100_F	0.521	1.00
135_L	139_V	0.520	1.00
199_L	253_A	0.520	1.00
127_L	131_A	0.519	1.00
126_L	158_L	0.518	1.00
24_L	91_L	0.517	1.00
311_V	314_V	0.515	1.00
239_R	242_E	0.514	1.00
2_P	290_L	0.513	1.00
170_T	233_A	0.511	1.00
32_F	187_L	0.511	1.00
194_A	210_P	0.511	1.00
93_L	120_G	0.509	1.00
168_G	172_L	0.508	1.00
32_F	118_F	0.508	1.00
271_P	277_S	0.508	1.00
97_A	116_A	0.507	1.00
289_T	292_V	0.505	1.00
33_A	36_D	0.505	1.00
245_A	249_A	0.504	1.00
62_G	77_F	0.503	1.00
171_W	314_V	0.503	1.00
201_A	210_P	0.503	1.00
303_L	306_A	0.502	1.00
137_Q	153_A	0.501	1.00
79_G	141_V	0.500	1.00

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
2mgyA	1	0.5143	6.9	0.963	Contact Map
1fftB	1	0.1333	2.6	0.97	Contact Map
3m73A	3	0.5746	2.5	0.97	Contact Map
2a65A	2	0.5333	2.4	0.97	Contact Map
4czbA	2	0.546	2.3	0.971	Contact Map
3pjzA	2	0.4063	2.1	0.971	Contact Map
4tq3A	1	0.4095	1.7	0.973	Contact Map
4p02A	1	0.3556	1.7	0.973	Contact Map
2gfpA	2	0.8508	1.6	0.973	Contact Map
4o6yA	2	0.619	1.5	0.974	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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