BACR - HALSA - GREMLIN Contacts

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BACR - Bacteriorhodopsin

UniProt:	P02945	Sequences: MLELLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSAGDGAAATSD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	262 (221)
Sequences:	707 (504)
Seq/√Len:	33.9

HALSA - BACR BACH BACS2 BACS1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_I	101_F	7.432	1.00
103_T	128_D	4.038	1.00
32_L	226_V	3.618	1.00
93_W	97_A	3.589	1.00
98_D	102_T	3.489	1.00
34_G	67_F	3.425	1.00
98_D	229_K	3.414	1.00
37_T	63_P	3.372	1.00
72_S	150_W	3.304	1.00
27_A	74_L	3.162	1.00
134_T	154_S	2.732	1.00
151_W	155_T	2.699	1.00
194_L	227_S	2.672	1.00
130_I	157_A	2.578	1.00
41_L	60_T	2.443	1.00
36_G	230_V	2.306	0.99
63_P	233_G	2.181	0.99
131_M	135_G	2.179	0.99
59_T	109_D	2.139	0.99
40_F	233_G	2.062	0.98
59_T	233_G	2.049	0.98
127_A	160_Y	1.986	0.98
103_T	229_K	1.972	0.98
58_I	105_L	1.951	0.98
80_T	140_L	1.919	0.97
128_D	131_M	1.897	0.97
103_T	131_M	1.856	0.97
102_T	229_K	1.817	0.96
29_G	222_M	1.806	0.96
197_A	201_V	1.750	0.96
66_A	73_M	1.748	0.95
134_T	228_A	1.740	0.95
71_L	141_T	1.708	0.95
26_L	218_T	1.697	0.95
219_L	223_V	1.689	0.95
108_L	125_V	1.641	0.94
201_V	220_L	1.611	0.93
115_D	148_F	1.579	0.92
36_G	40_F	1.568	0.92
135_G	229_K	1.567	0.92
37_T	64_A	1.559	0.92
138_G	202_W	1.549	0.92
195_W	229_K	1.548	0.92
39_Y	43_K	1.538	0.91
107_L	128_D	1.498	0.90
147_R	152_A	1.493	0.90
100_L	129_G	1.477	0.89
202_W	217_E	1.466	0.89
134_T	150_W	1.457	0.89
207_E	217_E	1.428	0.88
69_M	73_M	1.426	0.88
148_F	203_L	1.405	0.87
98_D	103_T	1.384	0.86
59_T	125_V	1.381	0.86
66_A	102_T	1.380	0.86
131_M	161_I	1.357	0.85
99_W	135_G	1.350	0.85
151_W	196_S	1.347	0.85
202_W	208_G	1.345	0.84
34_G	64_A	1.334	0.84
102_T	105_L	1.296	0.82
163_Y	167_F	1.291	0.82
66_A	199_P	1.278	0.81
96_Y	99_W	1.268	0.81
66_A	229_K	1.266	0.81
153_I	204_I	1.245	0.79
203_L	209_A	1.242	0.79
197_A	220_L	1.227	0.78
158_M	162_L	1.223	0.78
32_L	230_V	1.222	0.78
174_E	181_A	1.215	0.78
160_Y	164_V	1.213	0.78
33_M	66_A	1.210	0.77
66_A	98_D	1.194	0.77
102_T	128_D	1.192	0.76
30_T	67_F	1.173	0.75
94_A	137_V	1.146	0.73
103_T	135_G	1.128	0.72
153_I	170_T	1.126	0.72
69_M	139_A	1.116	0.71
86_G	182_S	1.109	0.71
35_L	226_V	1.108	0.71
97_A	166_F	1.105	0.71
40_F	63_P	1.104	0.71
107_L	135_G	1.094	0.70
66_A	106_L	1.088	0.70
152_A	215_N	1.082	0.69
64_A	227_S	1.076	0.69
27_A	136_L	1.074	0.68
79_L	92_Y	1.067	0.68
66_A	131_M	1.057	0.67
96_Y	104_P	1.048	0.67
190_V	194_L	1.042	0.66
66_A	109_D	1.035	0.66
106_L	109_D	1.035	0.66
209_A	216_I	1.029	0.65
130_I	153_I	1.021	0.65
25_W	29_G	1.015	0.64
136_L	140_L	1.002	0.63
67_F	71_L	0.989	0.62
201_V	224_L	0.989	0.62
62_V	105_L	0.977	0.61
152_A	156_A	0.972	0.61
101_F	160_Y	0.969	0.60
204_I	212_V	0.965	0.60
103_T	195_W	0.963	0.60
99_W	199_P	0.962	0.60
213_P	216_I	0.961	0.60
41_L	162_L	0.960	0.60
202_W	224_L	0.955	0.59
83_P	88_Q	0.953	0.59
29_G	33_M	0.952	0.59
94_A	101_F	0.952	0.59
176_M	180_V	0.949	0.59
102_T	135_G	0.943	0.58
204_I	220_L	0.941	0.58
135_G	232_F	0.940	0.58
132_I	229_K	0.933	0.57
136_L	221_F	0.925	0.57
212_V	219_L	0.925	0.57
91_I	139_A	0.922	0.57
119_G	123_A	0.916	0.56
162_L	166_F	0.916	0.56
105_L	138_G	0.914	0.56
141_T	146_Y	0.914	0.56
33_M	230_V	0.906	0.55
232_F	237_L	0.905	0.55
203_L	220_L	0.903	0.55
239_S	243_F	0.901	0.55
239_S	242_I	0.900	0.55
38_L	64_A	0.896	0.54
91_I	212_V	0.885	0.53
150_W	213_P	0.878	0.53
166_F	192_V	0.877	0.53
124_L	164_V	0.870	0.52
22_E	214_L	0.865	0.52
34_G	184_F	0.862	0.52
71_L	209_A	0.853	0.51
33_M	135_G	0.850	0.51
36_G	234_L	0.847	0.50
92_Y	218_T	0.845	0.50
35_L	159_L	0.845	0.50
59_T	63_P	0.844	0.50
75_L	208_G	0.842	0.50
31_A	67_F	0.839	0.50
29_G	66_A	0.833	0.49
140_L	207_E	0.832	0.49
37_T	155_T	0.828	0.49
177_R	181_A	0.828	0.49
130_I	175_S	0.821	0.48
158_M	192_V	0.818	0.48
78_G	217_E	0.817	0.48
229_K	233_G	0.817	0.48
34_G	226_V	0.814	0.47
190_V	235_I	0.806	0.47
37_T	47_V	0.803	0.47
212_V	216_I	0.800	0.46
90_P	214_L	0.797	0.46
109_D	236_L	0.794	0.46
62_V	106_L	0.790	0.45
134_T	153_I	0.783	0.45
132_I	230_V	0.779	0.45
194_L	228_A	0.777	0.44
38_L	42_V	0.776	0.44
184_F	188_R	0.769	0.44
76_G	92_Y	0.767	0.44
33_M	163_Y	0.763	0.43
113_L	240_R	0.762	0.43
99_W	104_P	0.759	0.43
96_Y	232_F	0.757	0.43
162_L	187_L	0.753	0.42
91_I	158_M	0.753	0.42
111_A	121_I	0.748	0.42
115_D	152_A	0.746	0.42
150_W	223_V	0.743	0.42
173_A	176_M	0.739	0.41
69_M	72_S	0.735	0.41
182_S	185_K	0.734	0.41
103_T	132_I	0.725	0.40
196_S	199_P	0.724	0.40
44_G	64_A	0.718	0.40
140_L	146_Y	0.716	0.39
71_L	149_V	0.714	0.39
156_A	231_G	0.712	0.39
126_G	161_I	0.712	0.39
87_E	213_P	0.711	0.39
64_A	68_T	0.710	0.39
79_L	82_V	0.706	0.39
66_A	195_W	0.704	0.38
125_V	129_G	0.703	0.38
68_T	130_I	0.703	0.38
107_L	116_A	0.702	0.38
22_E	90_P	0.699	0.38
141_T	145_S	0.697	0.38
235_I	238_R	0.695	0.38
161_I	164_V	0.693	0.38
131_M	155_T	0.692	0.37
30_T	71_L	0.692	0.37
216_I	220_L	0.690	0.37
25_W	209_A	0.690	0.37
191_T	228_A	0.690	0.37
151_W	156_A	0.685	0.37
158_M	196_S	0.682	0.37
34_G	234_L	0.682	0.37
42_V	46_G	0.681	0.37
24_I	28_L	0.677	0.36
122_L	163_Y	0.675	0.36
62_V	232_F	0.675	0.36
22_E	140_L	0.673	0.36
206_S	217_E	0.672	0.36
191_T	236_L	0.663	0.35
55_F	121_I	0.663	0.35
36_G	171_S	0.661	0.35
131_M	195_W	0.660	0.35
185_K	193_V	0.657	0.35
131_M	199_P	0.653	0.34
119_G	167_F	0.653	0.34
44_G	48_S	0.652	0.34
56_Y	237_L	0.650	0.34
57_A	117_D	0.650	0.34
99_W	198_Y	0.647	0.34
130_I	151_W	0.646	0.34
138_G	151_W	0.646	0.34
107_L	228_A	0.641	0.34
140_L	152_A	0.641	0.34
122_L	172_K	0.639	0.33
98_D	109_D	0.638	0.33
24_I	27_A	0.634	0.33
62_V	109_D	0.633	0.33
53_K	79_L	0.632	0.33
32_L	46_G	0.628	0.33
50_P	151_W	0.628	0.33
77_Y	146_Y	0.624	0.32
146_Y	149_V	0.622	0.32
33_M	98_D	0.620	0.32
93_W	217_E	0.617	0.32
29_G	68_T	0.615	0.32
26_L	159_L	0.611	0.31
31_A	68_T	0.611	0.31
114_V	138_G	0.610	0.31
112_L	115_D	0.609	0.31
40_F	236_L	0.609	0.31
54_K	68_T	0.607	0.31
189_N	193_V	0.607	0.31
121_I	184_F	0.606	0.31
38_L	234_L	0.604	0.31
117_D	138_G	0.603	0.31
173_A	194_L	0.602	0.31
77_Y	141_T	0.602	0.31
37_T	41_L	0.601	0.31
48_S	53_K	0.600	0.30
29_G	129_G	0.600	0.30
95_R	229_K	0.599	0.30
58_I	63_P	0.599	0.30
75_L	78_G	0.597	0.30
80_T	138_G	0.596	0.30
207_E	216_I	0.595	0.30
35_L	163_Y	0.589	0.30
44_G	169_F	0.588	0.30
40_F	186_V	0.585	0.29
166_F	189_N	0.583	0.29
126_G	130_I	0.582	0.29
183_T	239_S	0.580	0.29
139_A	202_W	0.580	0.29
82_V	142_K	0.580	0.29
31_A	100_L	0.578	0.29
70_Y	73_M	0.578	0.29
59_T	161_I	0.577	0.29
86_G	190_V	0.577	0.29
38_L	241_A	0.576	0.29
126_G	148_F	0.576	0.29
38_L	226_V	0.572	0.29
175_S	223_V	0.571	0.28
107_L	121_I	0.570	0.28
135_G	199_P	0.567	0.28
71_L	75_L	0.565	0.28
197_A	200_V	0.565	0.28
151_W	154_S	0.564	0.28
102_T	228_A	0.564	0.28
171_S	179_E	0.564	0.28
110_L	196_S	0.563	0.28
69_M	130_I	0.562	0.28
104_P	228_A	0.558	0.28
133_G	185_K	0.557	0.28
128_D	228_A	0.557	0.28
78_G	89_N	0.553	0.27
191_T	232_F	0.551	0.27
180_V	223_V	0.551	0.27
120_T	164_V	0.550	0.27
152_A	209_A	0.548	0.27
161_I	232_F	0.548	0.27
69_M	114_V	0.548	0.27
37_T	67_F	0.545	0.27
189_N	194_L	0.544	0.27
110_L	190_V	0.543	0.27
134_T	173_A	0.541	0.26
118_Q	126_G	0.541	0.26
152_A	155_T	0.540	0.26
159_L	196_S	0.540	0.26
68_T	75_L	0.536	0.26
207_E	210_G	0.535	0.26
25_W	31_A	0.535	0.26
124_L	169_F	0.535	0.26
100_L	219_L	0.532	0.26
76_G	141_T	0.532	0.26
75_L	207_E	0.531	0.26
160_Y	165_L	0.530	0.26
38_L	48_S	0.529	0.26
36_G	231_G	0.528	0.26
83_P	86_G	0.527	0.26
128_D	229_K	0.526	0.25
42_V	122_L	0.526	0.25
170_T	174_E	0.525	0.25
87_E	100_L	0.523	0.25
148_F	208_G	0.520	0.25
206_S	221_F	0.519	0.25
119_G	216_I	0.519	0.25
93_W	202_W	0.518	0.25
128_D	161_I	0.518	0.25
120_T	166_F	0.517	0.25
58_I	172_K	0.517	0.25
123_A	164_V	0.516	0.25
234_L	238_R	0.515	0.25
180_V	239_S	0.512	0.25
177_R	180_V	0.511	0.25
148_F	151_W	0.510	0.24
87_E	193_V	0.509	0.24
66_A	103_T	0.507	0.24
98_D	228_A	0.505	0.24
150_W	154_S	0.504	0.24
71_L	148_F	0.502	0.24
150_W	233_G	0.500	0.24

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
1m0kA	3	0.8473	100	0.19	Contact Map
4qi1A	3	0.8664	100	0.211	Contact Map
3wqjA	3	0.8893	100	0.214	Contact Map
4l35A	3	0.9084	100	0.218	Contact Map
4fbzA	3	0.9046	100	0.221	Contact Map
3wt9A	1	0.8855	100	0.223	Contact Map
3am6A	3	0.855	100	0.24	Contact Map
3qapA	1	0.8359	100	0.248	Contact Map
1xioA	2	0.813	100	0.25	Contact Map
3ddlA	2	0.9084	100	0.264	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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