BACH - HALSA - GREMLIN Contacts

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BACH - Halorhodopsin

UniProt:	P0DMH7	Sequences: MSITSVPGVVDAGVLGAQSAAAVRENALLSSSLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVSISSYLGLLSGLTVGMIEMPAGHALAGEMVRSQWGRYLTWALSTPMILLALGLLADVDLGSLFTVIAADIGMCVTGLAAAMTTSALLFRWAFYAISCAFFVVVLSALVTDWAASASSAGTAEIFDTLRVLTVVLWLGYPIVWAVGVEGLALVQSVGVTSWAYSVLDVFAKYVFAFILLRWVANNERTVAVAGQTLGTMSSDD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	274 (225)
Sequences:	691 (493)
Seq/√Len:	32.8

HALSA - BACH BACR 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
72_V	114_L	6.752	1.00
116_T	141_D	3.790	1.00
39_L	239_V	3.703	1.00
44_I	70_P	3.567	1.00
41_G	74_I	3.565	1.00
106_W	110_L	3.562	1.00
79_G	164_F	3.346	1.00
111_T	115_S	3.320	1.00
111_T	242_K	3.242	1.00
34_W	81_L	3.171	1.00
165_Y	169_C	2.864	1.00
147_T	168_S	2.766	1.00
206_L	240_F	2.647	1.00
143_G	171_F	2.532	1.00
48_V	67_L	2.441	0.99
97_L	100_E	2.416	0.99
47_F	246_A	2.315	0.99
43_A	243_Y	2.249	0.99
144_M	148_G	2.140	0.99
25_E	227_V	2.054	0.98
70_P	246_A	2.000	0.98
66_T	246_A	1.970	0.98
140_A	174_V	1.898	0.97
209_G	213_V	1.881	0.97
116_T	242_K	1.880	0.97
213_V	233_A	1.855	0.96
151_A	214_W	1.825	0.96
66_T	122_A	1.818	0.96
41_G	71_L	1.782	0.96
115_S	242_K	1.739	0.95
73_S	80_L	1.731	0.95
76_S	80_L	1.717	0.95
128_D	162_W	1.713	0.94
43_A	47_F	1.707	0.94
116_T	144_M	1.705	0.94
87_G	153_M	1.674	0.94
33_L	231_S	1.659	0.93
111_T	116_T	1.633	0.93
147_T	241_A	1.629	0.93
207_W	242_K	1.629	0.93
65_A	118_M	1.601	0.92
141_D	144_M	1.601	0.92
26_N	228_G	1.561	0.91
165_Y	208_L	1.557	0.91
40_A	73_S	1.553	0.91
148_G	242_K	1.494	0.89
24_R	103_R	1.459	0.88
78_L	154_T	1.458	0.88
120_L	141_D	1.439	0.87
44_I	71_L	1.427	0.87
109_Y	112_W	1.421	0.87
232_W	236_V	1.372	0.85
215_A	221_L	1.367	0.84
214_W	220_G	1.360	0.84
113_A	142_I	1.350	0.84
121_L	138_I	1.334	0.83
162_W	215_A	1.331	0.83
214_W	230_T	1.326	0.83
147_T	164_F	1.325	0.83
216_V	233_A	1.319	0.82
219_E	230_T	1.314	0.82
161_R	166_A	1.313	0.82
73_S	115_S	1.292	0.81
112_W	148_G	1.278	0.80
115_S	118_M	1.258	0.79
144_M	175_V	1.246	0.78
107_G	150_A	1.244	0.78
47_F	70_P	1.238	0.78
46_V	50_M	1.234	0.78
164_F	226_S	1.207	0.76
167_I	216_V	1.206	0.76
73_S	242_K	1.201	0.76
66_T	138_I	1.191	0.75
73_S	211_P	1.182	0.75
86_V	105_Q	1.177	0.74
172_F	176_L	1.170	0.74
40_A	148_G	1.165	0.74
41_G	239_V	1.149	0.72
120_L	148_G	1.139	0.72
37_V	74_I	1.129	0.71
73_S	111_T	1.128	0.71
202_L	206_L	1.126	0.71
166_A	228_G	1.125	0.71
116_T	207_W	1.123	0.71
33_L	173_V	1.116	0.70
39_L	243_Y	1.115	0.70
42_I	239_V	1.077	0.67
32_S	36_N	1.074	0.67
215_A	233_A	1.060	0.66
44_I	74_I	1.059	0.66
115_S	141_D	1.057	0.66
110_L	180_V	1.052	0.66
115_S	148_G	1.045	0.65
177_S	181_T	1.040	0.65
153_M	219_E	1.033	0.64
73_S	144_M	1.026	0.64
36_N	235_S	1.018	0.63
118_M	151_A	1.008	0.62
164_F	236_V	0.997	0.61
73_S	122_A	0.991	0.61
209_G	233_A	0.983	0.60
41_G	196_F	0.980	0.60
71_L	240_F	0.976	0.60
245_F	250_L	0.976	0.60
108_R	242_K	0.970	0.59
83_G	105_Q	0.967	0.59
47_F	66_T	0.955	0.58
154_T	160_F	0.953	0.58
42_I	173_V	0.953	0.58
116_T	148_G	0.952	0.58
149_L	156_S	0.950	0.58
66_T	70_P	0.950	0.58
148_G	245_F	0.945	0.57
145_C	242_K	0.938	0.57
112_W	211_P	0.938	0.57
69_I	118_M	0.933	0.56
120_L	129_V	0.925	0.56
120_L	241_A	0.921	0.55
221_L	229_V	0.920	0.55
76_S	152_A	0.919	0.55
166_A	170_A	0.918	0.55
109_Y	117_P	0.917	0.55
149_L	234_Y	0.914	0.55
188_S	193_A	0.909	0.54
100_E	205_V	0.908	0.54
43_A	247_F	0.903	0.54
149_L	153_M	0.895	0.53
137_V	178_A	0.891	0.53
173_V	180_V	0.883	0.52
213_V	237_L	0.882	0.52
143_G	167_I	0.881	0.52
128_D	166_A	0.879	0.52
73_S	119_I	0.877	0.52
36_N	40_A	0.875	0.51
74_I	78_L	0.873	0.51
194_E	197_D	0.870	0.51
82_S	219_E	0.864	0.50
37_V	41_G	0.861	0.50
174_V	178_A	0.861	0.50
180_V	204_V	0.861	0.50
75_S	143_G	0.860	0.50
172_F	204_V	0.859	0.50
40_A	177_S	0.858	0.50
129_V	133_S	0.857	0.50
38_A	75_S	0.856	0.50
176_L	180_V	0.852	0.49
119_I	122_A	0.836	0.48
166_A	221_L	0.831	0.48
104_S	152_A	0.831	0.48
167_I	184_A	0.831	0.48
175_V	178_A	0.830	0.48
89_I	205_V	0.828	0.48
128_D	204_V	0.828	0.48
48_V	176_L	0.827	0.47
40_A	243_Y	0.825	0.47
64_G	130_D	0.818	0.47
84_L	154_T	0.816	0.47
112_W	117_P	0.814	0.46
34_W	149_L	0.811	0.46
160_F	163_A	0.811	0.46
144_M	169_C	0.808	0.46
116_T	145_C	0.798	0.45
78_L	82_S	0.798	0.45
45_L	71_L	0.796	0.45
47_F	249_L	0.796	0.45
226_S	229_V	0.795	0.45
170_A	244_V	0.794	0.45
151_A	165_Y	0.782	0.44
76_S	127_A	0.779	0.43
69_I	122_A	0.775	0.43
84_L	160_F	0.772	0.43
242_K	246_A	0.772	0.43
28_L	229_V	0.772	0.43
62_I	134_L	0.769	0.43
109_Y	245_F	0.768	0.43
162_W	165_Y	0.766	0.42
46_V	137_V	0.763	0.42
156_S	222_A	0.763	0.42
89_I	96_A	0.762	0.42
214_W	237_L	0.760	0.42
130_D	151_A	0.755	0.42
147_T	167_I	0.755	0.42
53_T	56_P	0.753	0.41
174_V	179_L	0.752	0.41
144_M	207_W	0.750	0.41
137_V	183_W	0.749	0.41
78_L	162_W	0.747	0.41
127_A	151_A	0.745	0.41
107_G	114_L	0.744	0.41
145_C	243_Y	0.742	0.40
78_L	163_A	0.741	0.40
138_I	236_V	0.740	0.40
156_S	220_G	0.737	0.40
153_M	161_R	0.728	0.39
112_W	210_Y	0.727	0.39
73_S	108_R	0.722	0.39
229_V	233_A	0.720	0.39
202_L	248_I	0.719	0.39
84_L	102_V	0.718	0.39
172_F	208_L	0.717	0.38
49_Y	135_F	0.715	0.38
27_A	95_H	0.707	0.38
252_W	255_N	0.704	0.37
79_G	256_N	0.704	0.37
76_S	79_G	0.703	0.37
206_L	241_A	0.703	0.37
127_A	184_A	0.702	0.37
36_N	75_S	0.702	0.37
78_L	221_L	0.701	0.37
224_V	229_V	0.698	0.37
156_S	164_F	0.696	0.37
185_A	244_V	0.694	0.37
185_A	191_G	0.693	0.37
126_L	253_V	0.691	0.36
175_V	245_F	0.689	0.36
60_R	86_V	0.687	0.36
61_L	75_S	0.686	0.36
69_I	119_I	0.685	0.36
203_T	241_A	0.682	0.36
50_M	135_F	0.682	0.36
138_I	142_I	0.679	0.36
40_A	111_T	0.679	0.36
36_N	142_I	0.677	0.35
161_R	219_E	0.674	0.35
201_V	205_V	0.674	0.35
51_G	71_L	0.672	0.35
165_Y	168_S	0.671	0.35
153_M	157_A	0.670	0.35
148_G	211_P	0.670	0.35
124_G	134_L	0.669	0.35
125_L	128_D	0.666	0.35
115_S	151_A	0.656	0.34
29_L	227_V	0.653	0.34
224_V	232_W	0.653	0.34
77_Y	80_L	0.650	0.33
170_A	229_V	0.650	0.33
87_G	151_A	0.649	0.33
112_W	145_C	0.649	0.33
85_T	102_V	0.648	0.33
38_A	74_I	0.644	0.33
123_L	184_A	0.643	0.33
136_T	178_A	0.643	0.33
221_L	224_V	0.642	0.33
29_L	153_M	0.642	0.33
81_L	166_A	0.635	0.32
63_W	250_L	0.632	0.32
60_R	135_F	0.631	0.32
176_L	199_L	0.628	0.32
219_E	229_V	0.628	0.32
141_D	241_A	0.628	0.32
144_M	211_P	0.627	0.32
41_G	203_T	0.627	0.32
45_L	48_V	0.624	0.31
39_L	145_C	0.624	0.31
134_L	196_F	0.621	0.31
248_I	251_R	0.620	0.31
114_L	174_V	0.618	0.31
163_A	215_A	0.611	0.31
42_I	58_R	0.610	0.30
219_E	222_A	0.610	0.30
195_I	202_L	0.607	0.30
104_S	224_V	0.603	0.30
152_A	214_W	0.602	0.30
189_S	192_T	0.595	0.29
86_V	89_I	0.587	0.29
189_S	193_A	0.584	0.29
108_R	148_G	0.583	0.29
114_L	236_V	0.582	0.29
122_A	249_L	0.582	0.29
85_T	230_T	0.580	0.28
138_I	255_N	0.577	0.28
173_V	208_L	0.577	0.28
69_I	245_F	0.577	0.28
44_I	169_C	0.575	0.28
103_R	217_G	0.575	0.28
37_V	78_L	0.573	0.28
216_V	221_L	0.571	0.28
45_L	133_S	0.571	0.28
102_V	105_Q	0.566	0.27
153_M	166_A	0.565	0.27
77_Y	210_Y	0.565	0.27
135_F	186_S	0.564	0.27
168_S	199_L	0.564	0.27
32_S	235_S	0.559	0.27
116_T	206_L	0.558	0.27
135_F	177_S	0.558	0.27
196_F	200_R	0.557	0.27
123_L	203_T	0.557	0.27
44_I	66_T	0.556	0.27
27_A	212_I	0.555	0.27
51_G	179_L	0.555	0.27
131_L	139_A	0.554	0.27
128_D	183_W	0.553	0.27
73_S	116_T	0.552	0.27
81_L	237_L	0.550	0.26
139_A	143_G	0.550	0.26
132_G	136_T	0.549	0.26
83_G	154_T	0.547	0.26
49_Y	53_T	0.543	0.26
50_M	181_T	0.543	0.26
48_V	69_I	0.541	0.26
147_T	171_F	0.540	0.26
65_A	115_S	0.539	0.26
165_Y	170_A	0.537	0.26
142_I	215_A	0.537	0.26
41_G	247_F	0.536	0.26
29_L	103_R	0.536	0.26
71_L	174_V	0.534	0.25
166_A	169_C	0.532	0.25
47_F	68_M	0.530	0.25
120_L	134_L	0.528	0.25
226_S	259_T	0.526	0.25
141_D	242_K	0.525	0.25
31_S	34_W	0.523	0.25
101_M	255_N	0.520	0.25
87_G	106_W	0.519	0.24
32_S	221_L	0.517	0.24
53_T	129_V	0.517	0.24
38_A	113_A	0.513	0.24
40_A	144_M	0.512	0.24
164_F	168_S	0.512	0.24
96_A	100_E	0.510	0.24
73_S	241_A	0.509	0.24
175_V	241_A	0.509	0.24
206_L	212_I	0.508	0.24
114_L	234_Y	0.507	0.24
151_A	174_V	0.507	0.24
208_L	212_I	0.506	0.24
116_T	241_A	0.506	0.24
73_S	207_W	0.505	0.24
195_I	213_V	0.505	0.24
96_A	204_V	0.505	0.24
148_G	241_A	0.505	0.24
45_L	63_W	0.502	0.23
146_V	150_A	0.501	0.23
222_A	230_T	0.500	0.23
144_M	242_K	0.500	0.23
252_W	256_N	0.500	0.23

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
3wqjA	3	0.8467	100	0.259	Contact Map
2jafA	3	0.8759	100	0.265	Contact Map
1m0kA	3	0.8029	100	0.271	Contact Map
3qbgA	3	0.9124	100	0.273	Contact Map
4l35A	3	0.8577	100	0.278	Contact Map
3wt9A	1	0.8467	100	0.278	Contact Map
4fbzA	3	0.854	100	0.281	Contact Map
4qi1A	3	0.8212	100	0.282	Contact Map
3am6A	3	0.8102	100	0.291	Contact Map
3qapA	1	0.792	100	0.298	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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