CYOC - ECOLI - GREMLIN Contacts

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CYOC - Cytochrome bo(3) ubiquinol oxidase subunit 3

UniProt:	P0ABJ3	Sequences: MATDTLTHATAHAHEHGHHDAGGTKIFGFWIYLMSDCILFSILFATYAVLVNGTAGGPTGKDIFELPFVLVETFLLLFSSITYGMAAIAMYKNNKSQVISWLALTWLFGAGFIGMEIYEFHHLIVNGMGPDRSGFLSAFFALVGTHGLHVTSGLIWMAVLMVQIARRGLTSTNRTRIMCLSLFWHFLDVVWICVFTVVYLMGAM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10180
Length:	204 (183)
Sequences:	5377 (2680)
Seq/√Len:	198.1

ECOLI - CYOC
BACSU - COX3 QOX3
HALSA - Q9HRK1
SULSO - Q97UN0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
75_L	111_G	4.006	1.00
82_T	105_T	3.360	1.00
103_A	161_M	3.250	1.00
94_N	97_Q	3.172	1.00
98_V	164_I	3.043	1.00
175_T	179_C	2.938	1.00
85_M	101_W	2.880	1.00
38_I	41_S	2.784	1.00
95_K	99_I	2.598	1.00
50_L	134_G	2.482	1.00
106_W	154_L	2.424	1.00
68_F	115_M	2.251	1.00
89_A	97_Q	2.197	1.00
114_G	118_Y	2.117	1.00
120_F	143_V	2.099	1.00
156_W	180_L	2.027	1.00
158_A	162_V	2.019	1.00
68_F	118_Y	1.997	1.00
142_L	198_V	1.985	1.00
70_L	74_F	1.968	1.00
113_I	151_T	1.961	1.00
82_T	104_L	1.940	1.00
117_I	121_H	1.913	1.00
96_S	100_S	1.910	1.00
99_I	165_A	1.794	1.00
118_Y	122_H	1.775	1.00
86_A	98_V	1.770	1.00
157_M	180_L	1.717	1.00
75_L	115_M	1.695	1.00
142_L	194_V	1.691	1.00
83_Y	157_M	1.676	1.00
39_L	145_T	1.660	1.00
83_Y	181_S	1.641	1.00
160_L	180_L	1.639	1.00
46_T	138_A	1.617	1.00
95_K	167_R	1.614	1.00
86_A	102_L	1.577	1.00
33_L	182_L	1.544	1.00
185_H	188_D	1.535	1.00
103_A	107_L	1.524	1.00
99_I	161_M	1.518	1.00
74_F	78_F	1.493	1.00
99_I	164_I	1.485	1.00
106_W	158_A	1.483	1.00
72_E	115_M	1.449	1.00
177_I	181_S	1.436	1.00
80_S	185_H	1.428	1.00
113_I	147_G	1.423	1.00
113_I	154_L	1.415	1.00
109_G	154_L	1.386	1.00
67_P	71_V	1.379	1.00
48_A	197_V	1.358	1.00
100_S	104_L	1.332	1.00
81_I	85_M	1.322	1.00
114_G	117_I	1.314	1.00
85_M	89_A	1.290	1.00
65_E	122_H	1.284	1.00
82_T	108_F	1.278	1.00
91_Y	178_M	1.260	1.00
93_N	171_S	1.249	1.00
95_K	164_I	1.238	1.00
97_Q	101_W	1.186	1.00
110_A	154_L	1.161	1.00
90_M	98_V	1.154	1.00
86_A	177_I	1.150	1.00
68_F	72_E	1.144	1.00
148_L	152_S	1.143	1.00
22_G	26_I	1.139	1.00
100_S	103_A	1.130	1.00
138_A	142_L	1.113	1.00
196_T	200_L	1.112	1.00
151_T	155_I	1.105	1.00
88_I	92_K	1.092	1.00
36_D	119_E	1.090	1.00
154_L	158_A	1.089	1.00
21_A	24_T	1.080	1.00
89_A	101_W	1.068	1.00
90_M	177_I	1.067	1.00
94_N	100_S	1.063	1.00
84_G	88_I	1.057	1.00
51_V	54_T	1.057	1.00
86_A	164_I	1.055	1.00
97_Q	100_S	1.055	1.00
45_A	49_V	1.053	1.00
78_F	81_I	1.053	1.00
43_L	145_T	1.051	1.00
119_E	199_Y	1.046	1.00
84_G	87_A	1.041	1.00
162_V	166_R	1.033	1.00
107_L	111_G	1.033	1.00
183_F	187_L	1.020	1.00
57_G	136_L	1.015	1.00
71_V	115_M	1.014	1.00
90_M	174_R	0.999	1.00
47_Y	51_V	0.988	1.00
72_E	194_V	0.984	1.00
38_I	42_I	0.983	1.00
89_A	94_N	0.977	0.99
139_F	147_G	0.974	0.99
75_L	108_F	0.973	0.99
16_H	20_D	0.970	0.99
29_F	33_L	0.966	0.99
101_W	104_L	0.965	0.99
155_I	159_V	0.959	0.99
106_W	157_M	0.952	0.99
32_Y	183_F	0.946	0.99
128_M	136_L	0.941	0.99
163_Q	168_G	0.939	0.99
163_Q	176_R	0.937	0.99
87_A	91_Y	0.927	0.99
50_L	138_A	0.924	0.99
23_G	27_F	0.924	0.99
20_D	23_G	0.921	0.99
86_A	101_W	0.914	0.99
43_L	142_L	0.909	0.99
129_G	136_L	0.900	0.99
82_T	101_W	0.898	0.99
43_L	141_A	0.891	0.99
38_I	48_A	0.890	0.99
116_E	196_T	0.889	0.99
19_H	23_G	0.885	0.99
152_S	156_W	0.878	0.99
141_A	145_T	0.873	0.99
100_S	165_A	0.871	0.99
69_V	116_E	0.869	0.99
139_F	143_V	0.856	0.99
123_L	139_F	0.855	0.99
85_M	97_Q	0.854	0.99
110_A	114_G	0.851	0.99
120_F	140_F	0.849	0.99
106_W	161_M	0.838	0.98
132_R	136_L	0.837	0.98
169_L	176_R	0.826	0.98
87_A	178_M	0.807	0.98
21_A	25_K	0.806	0.98
30_W	34_M	0.806	0.98
152_S	183_F	0.806	0.98
98_V	102_L	0.805	0.98
96_S	99_I	0.800	0.98
32_Y	36_D	0.794	0.98
128_M	132_R	0.793	0.98
103_A	165_A	0.782	0.98
159_V	162_V	0.781	0.98
63_I	123_L	0.777	0.97
16_H	19_H	0.775	0.97
47_Y	50_L	0.775	0.97
76_L	139_F	0.771	0.97
161_M	165_A	0.770	0.97
146_H	149_H	0.769	0.97
162_V	165_A	0.765	0.97
18_H	21_A	0.762	0.97
70_L	195_F	0.757	0.97
111_G	115_M	0.755	0.97
19_H	22_G	0.755	0.97
34_M	38_I	0.752	0.97
28_G	32_Y	0.748	0.97
116_E	139_F	0.747	0.97
87_A	181_S	0.743	0.97
184_W	191_W	0.741	0.97
193_C	197_V	0.740	0.97
63_I	128_M	0.723	0.96
66_L	195_F	0.719	0.96
102_L	161_M	0.719	0.96
89_A	92_K	0.707	0.96
47_Y	61_K	0.695	0.95
17_G	21_A	0.693	0.95
25_K	175_T	0.691	0.95
49_V	53_G	0.687	0.95
141_A	144_G	0.681	0.95
53_G	192_I	0.680	0.95
113_I	117_I	0.677	0.94
27_F	31_I	0.670	0.94
22_G	173_N	0.667	0.94
103_A	162_V	0.667	0.94
79_S	108_F	0.665	0.94
133_S	136_L	0.665	0.94
119_E	187_L	0.662	0.94
52_N	201_M	0.661	0.94
26_I	178_M	0.659	0.94
121_H	127_G	0.658	0.94
119_E	188_D	0.658	0.94
41_S	45_A	0.656	0.93
69_V	72_E	0.654	0.93
79_S	105_T	0.654	0.93
57_G	132_R	0.650	0.93
116_E	147_G	0.649	0.93
49_V	52_N	0.645	0.93
80_S	200_L	0.643	0.93
67_P	70_L	0.643	0.93
34_M	37_C	0.639	0.93
60_G	133_S	0.639	0.93
77_L	81_I	0.639	0.93
36_D	199_Y	0.637	0.92
28_G	44_F	0.634	0.92
102_L	164_I	0.632	0.92
91_Y	174_R	0.631	0.92
37_C	186_F	0.630	0.92
160_L	177_I	0.629	0.92
189_V	196_T	0.622	0.91
29_F	179_C	0.620	0.91
79_S	188_D	0.618	0.91
72_E	119_E	0.612	0.91
197_V	201_M	0.608	0.91
56_G	133_S	0.607	0.90
35_S	42_I	0.607	0.90
116_E	136_L	0.598	0.90
186_F	190_V	0.598	0.90
130_P	136_L	0.597	0.90
83_Y	86_A	0.596	0.90
87_A	177_I	0.595	0.90
110_A	151_T	0.590	0.89
94_N	118_Y	0.590	0.89
63_I	67_P	0.589	0.89
29_F	32_Y	0.589	0.89
103_A	158_A	0.588	0.89
37_C	190_V	0.587	0.89
61_K	107_L	0.585	0.89
136_L	140_F	0.584	0.89
76_L	199_Y	0.582	0.89
150_V	187_L	0.582	0.89
59_T	63_I	0.581	0.89
164_I	169_L	0.580	0.88
133_S	137_S	0.578	0.88
96_S	114_G	0.572	0.88
164_I	167_R	0.571	0.88
59_T	62_D	0.569	0.87
66_L	70_L	0.567	0.87
23_G	34_M	0.566	0.87
43_L	182_L	0.566	0.87
16_H	22_G	0.563	0.87
128_M	133_S	0.561	0.87
102_L	177_I	0.559	0.87
153_G	184_W	0.558	0.86
16_H	27_F	0.554	0.86
80_S	188_D	0.548	0.85
47_Y	198_V	0.548	0.85
145_T	150_V	0.547	0.85
63_I	136_L	0.547	0.85
153_G	186_F	0.546	0.85
60_G	64_F	0.541	0.85
176_R	179_C	0.541	0.85
75_L	79_S	0.538	0.84
71_V	75_L	0.538	0.84
44_F	193_C	0.538	0.84
167_R	171_S	0.536	0.84
119_E	135_F	0.536	0.84
72_E	116_E	0.535	0.84
147_G	190_V	0.532	0.84
32_Y	76_L	0.529	0.83
36_D	187_L	0.529	0.83
37_C	41_S	0.527	0.83
44_F	135_F	0.527	0.83
79_S	187_L	0.524	0.83
160_L	176_R	0.524	0.83
110_A	158_A	0.523	0.83
64_F	67_P	0.519	0.82
153_G	185_H	0.519	0.82
78_F	108_F	0.518	0.82
29_F	156_W	0.518	0.82
76_L	119_E	0.518	0.82
106_W	109_G	0.516	0.82
108_F	111_G	0.513	0.82
96_S	107_L	0.513	0.82
28_G	36_D	0.510	0.81
61_K	65_E	0.510	0.81
118_Y	121_H	0.509	0.81
167_R	170_T	0.509	0.81
21_A	80_S	0.508	0.81
20_D	24_T	0.508	0.81
131_D	183_F	0.507	0.81
120_F	194_V	0.505	0.81
41_S	189_V	0.504	0.80
51_V	128_M	0.502	0.80
48_A	183_F	0.500	0.80

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
1fftC	1	0.9069	100	0.147	Contact Map
1qleC	1	0.9804	100	0.156	Contact Map
1m56C	2	0.9804	100	0.157	Contact Map
1v54C	1	0.9804	100	0.16	Contact Map
2yevA	1	0.9755	100	0.164	Contact Map
2jafA	3	0.8431	26.5	0.943	Contact Map
4phzK	1	0.5294	12.5	0.951	Contact Map
3qbgA	3	0.8873	9.9	0.953	Contact Map
1xioA	2	0.7941	6.3	0.957	Contact Map
3ddlA	2	0.7402	4.5	0.96	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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