LIVM - ECOLI - GREMLIN Contacts

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LIVM - High-affinity branched-chain amino acid transport system permease protein LivM

UniProt:	P22729	Sequences: MKPMHIAMALLSAAMFFVLAGVFMGVQLELDGTKLVVDTASDVRWQWVFIGTAVVFFFQLLRPAFQKGLKSVSGPKFILPAIDGSTVKQKLFLVALLVLAVAWPFMVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYTFALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRILLLNNTEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLVALLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAGTLFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEYSMLMLGGLMVLMMIWRPQGLLPMTRPQLKLKNGAAKGEQA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10541
Length:	425 (324)
Sequences:	1560 (873)
Seq/√Len:	48.5

ECOLI - LIVM YTFT LSRC YPHD YJFF LIVH XYLH
BACSU - YUFQ
HALSA - Q9HR22
SULSO - Q97UZ8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
172_G	321_A	4.600	1.00
273_V	277_F	3.713	1.00
377_E	380_R	3.660	1.00
152_T	174_M	3.596	1.00
180_F	317_T	3.381	1.00
131_V	139_V	3.225	1.00
151_Y	339_P	3.066	1.00
173_L	177_A	3.045	1.00
171_A	328_T	2.882	1.00
124_L	350_V	2.763	1.00
298_E	312_K	2.758	1.00
162_L	166_T	2.736	1.00
139_V	142_Y	2.703	1.00
122_I	366_I	2.489	1.00
293_A	301_C	2.450	1.00
361_S	365_V	2.429	1.00
176_A	321_A	2.413	1.00
118_T	370_I	2.380	1.00
172_G	325_F	2.353	1.00
130_V	315_A	2.329	1.00
344_F	348_A	2.278	1.00
248_S	251_F	2.259	1.00
286_P	290_A	2.237	1.00
200_G	406_L	2.170	1.00
307_S	310_R	2.046	1.00
385_Y	388_L	2.027	1.00
141_G	347_S	2.010	1.00
282_L	318_I	1.989	0.99
294_L	311_I	1.954	0.99
139_V	319_S	1.933	0.99
131_V	319_S	1.927	0.99
131_V	140_L	1.924	0.99
99_L	102_A	1.921	0.99
175_A	320_A	1.893	0.99
178_A	200_G	1.872	0.99
141_G	196_I	1.856	0.99
357_G	368_A	1.852	0.99
279_I	322_F	1.833	0.99
98_V	106_M	1.794	0.99
190_R	298_E	1.783	0.99
77_F	81_A	1.758	0.99
177_A	181_L	1.740	0.99
249_N	255_Y	1.740	0.99
377_E	386_S	1.737	0.99
183_G	313_L	1.710	0.98
203_E	206_R	1.698	0.98
353_I	368_A	1.641	0.98
80_P	84_G	1.632	0.98
247_F	250_F	1.628	0.98
123_I	272_V	1.623	0.98
100_A	269_L	1.611	0.98
88_K	92_F	1.608	0.98
139_V	297_D	1.602	0.97
182_L	201_F	1.585	0.97
201_F	204_I	1.574	0.97
109_R	113_D	1.569	0.97
132_V	140_L	1.563	0.97
83_D	177_A	1.558	0.97
102_A	106_M	1.552	0.97
76_K	79_L	1.548	0.97
150_A	331_A	1.536	0.97
91_L	98_V	1.528	0.97
142_Y	319_S	1.528	0.97
352_A	394_M	1.525	0.97
140_L	300_A	1.522	0.97
299_I	302_R	1.517	0.96
176_A	317_T	1.488	0.96
108_S	379_M	1.483	0.96
152_T	170_I	1.472	0.96
411_P	414_K	1.471	0.96
397_M	410_R	1.459	0.96
100_A	104_P	1.437	0.95
92_F	95_A	1.432	0.95
188_R	324_G	1.431	0.95
122_I	272_V	1.426	0.95
411_P	415_L	1.424	0.95
82_I	85_S	1.400	0.94
123_I	275_S	1.398	0.94
78_I	81_A	1.388	0.94
194_L	289_R	1.388	0.94
88_K	95_A	1.374	0.94
186_V	316_F	1.370	0.94
114_I	200_G	1.367	0.94
91_L	95_A	1.366	0.94
151_Y	221_G	1.362	0.94
137_L	203_E	1.349	0.93
129_N	365_V	1.341	0.93
355_V	360_G	1.321	0.93
77_F	94_V	1.320	0.93
163_G	166_T	1.311	0.92
137_L	141_G	1.308	0.92
164_F	395_V	1.305	0.92
132_V	351_L	1.305	0.92
145_F	175_A	1.304	0.92
139_V	143_G	1.299	0.92
247_F	251_F	1.284	0.91
249_N	254_K	1.283	0.91
76_K	80_P	1.282	0.91
252_G	256_D	1.269	0.91
162_L	167_C	1.261	0.91
403_Q	407_P	1.253	0.90
138_L	192_D	1.252	0.90
135_S	315_A	1.249	0.90
144_G	205_V	1.239	0.90
129_N	203_E	1.217	0.89
287_L	291_W	1.214	0.89
301_C	308_P	1.213	0.89
291_W	315_A	1.212	0.89
150_A	337_V	1.208	0.89
249_N	252_G	1.205	0.89
165_W	169_P	1.183	0.88
76_K	81_A	1.178	0.87
183_G	354_V	1.174	0.87
83_D	87_V	1.170	0.87
208_L	212_N	1.166	0.87
152_T	156_L	1.165	0.87
196_I	204_I	1.164	0.87
97_L	104_P	1.163	0.87
321_A	325_F	1.163	0.87
192_D	196_I	1.161	0.87
275_S	279_I	1.154	0.86
78_I	181_L	1.154	0.86
138_L	388_L	1.154	0.86
147_A	189_L	1.149	0.86
401_R	405_L	1.147	0.86
194_L	357_G	1.136	0.85
83_D	88_K	1.130	0.85
96_L	235_F	1.126	0.85
128_L	194_L	1.125	0.85
145_F	193_Y	1.124	0.85
87_V	92_F	1.120	0.85
193_Y	316_F	1.119	0.85
290_A	311_I	1.118	0.85
123_I	196_I	1.118	0.85
141_G	145_F	1.118	0.85
290_A	306_L	1.107	0.84
188_R	191_G	1.107	0.84
186_V	201_F	1.103	0.84
171_A	175_A	1.099	0.83
92_F	99_L	1.091	0.83
96_L	100_A	1.089	0.83
102_A	105_F	1.087	0.83
139_V	401_R	1.085	0.83
87_V	91_L	1.085	0.83
140_L	347_S	1.082	0.83
351_L	373_V	1.073	0.82
127_G	216_T	1.068	0.82
179_G	320_A	1.068	0.82
276_L	280_N	1.068	0.82
96_L	101_V	1.062	0.81
79_L	82_I	1.061	0.81
139_V	409_T	1.056	0.81
77_F	92_F	1.050	0.81
132_V	355_V	1.046	0.80
191_G	347_S	1.043	0.80
99_L	159_Y	1.041	0.80
407_P	414_K	1.036	0.80
340_E	356_L	1.030	0.79
156_L	326_A	1.019	0.79
397_M	407_P	1.018	0.78
266_L	273_V	1.013	0.78
125_G	353_I	1.009	0.78
131_V	179_G	1.009	0.78
277_F	281_R	1.007	0.78
147_A	205_V	1.006	0.78
172_G	328_T	1.004	0.78
145_F	347_S	1.004	0.78
399_I	402_P	1.002	0.77
141_G	193_Y	1.001	0.77
408_M	415_L	0.999	0.77
98_V	389_M	0.997	0.77
346_E	355_V	0.994	0.77
148_I	174_M	0.991	0.77
83_D	86_T	0.990	0.77
113_D	333_R	0.986	0.76
104_P	265_Y	0.980	0.76
167_C	170_I	0.979	0.76
78_I	99_L	0.968	0.75
247_F	253_L	0.968	0.75
195_A	293_A	0.963	0.74
225_I	297_D	0.962	0.74
152_T	160_Y	0.958	0.74
91_L	94_V	0.958	0.74
176_A	181_L	0.958	0.74
98_V	274_L	0.958	0.74
84_G	88_K	0.956	0.74
95_A	101_V	0.951	0.74
194_L	316_F	0.951	0.74
93_L	103_W	0.951	0.74
251_F	256_D	0.948	0.73
157_N	332_A	0.942	0.73
126_L	366_I	0.941	0.73
77_F	99_L	0.940	0.73
165_W	168_L	0.928	0.72
197_V	320_A	0.924	0.71
93_L	277_F	0.916	0.71
137_L	197_V	0.915	0.71
90_K	105_F	0.915	0.71
227_K	256_D	0.912	0.70
166_T	170_I	0.905	0.70
284_R	294_L	0.903	0.70
403_Q	414_K	0.901	0.69
126_L	275_S	0.899	0.69
332_A	337_V	0.898	0.69
85_S	98_V	0.898	0.69
80_P	83_D	0.895	0.69
202_G	388_L	0.892	0.69
278_V	318_I	0.891	0.69
140_L	199_L	0.890	0.68
280_N	283_L	0.890	0.68
366_I	409_T	0.888	0.68
268_A	329_L	0.887	0.68
103_W	107_V	0.887	0.68
77_F	83_D	0.885	0.68
320_A	355_V	0.883	0.68
310_R	314_T	0.878	0.67
300_A	386_S	0.877	0.67
200_G	308_P	0.875	0.67
84_G	87_V	0.873	0.67
194_L	290_A	0.873	0.67
192_D	300_A	0.870	0.67
352_A	390_L	0.870	0.67
98_V	273_V	0.867	0.66
192_D	203_E	0.865	0.66
180_F	283_L	0.864	0.66
294_L	308_P	0.864	0.66
83_D	100_A	0.862	0.66
177_A	370_I	0.859	0.66
173_L	273_V	0.859	0.66
78_I	91_L	0.859	0.66
250_F	270_L	0.858	0.66
97_L	371_L	0.858	0.66
212_N	215_I	0.855	0.65
182_L	316_F	0.850	0.65
84_G	367_L	0.849	0.65
358_G	368_A	0.849	0.65
154_A	222_I	0.846	0.65
128_L	138_L	0.844	0.64
285_M	294_L	0.841	0.64
196_I	203_E	0.837	0.64
86_T	90_K	0.836	0.64
380_R	386_S	0.834	0.63
412_Q	415_L	0.830	0.63
272_V	310_R	0.827	0.63
198_T	316_F	0.827	0.63
234_E	249_N	0.824	0.62
171_A	371_L	0.821	0.62
306_L	394_M	0.819	0.62
178_A	204_I	0.817	0.62
300_A	306_L	0.816	0.62
116_T	267_V	0.814	0.62
78_I	83_D	0.811	0.61
217_G	221_G	0.810	0.61
141_G	183_G	0.810	0.61
407_P	412_Q	0.808	0.61
226_P	234_E	0.807	0.61
76_K	84_G	0.806	0.61
344_F	351_L	0.805	0.61
85_S	90_K	0.801	0.60
179_G	353_I	0.801	0.60
306_L	311_I	0.800	0.60
209_L	339_P	0.799	0.60
194_L	398_M	0.797	0.60
95_A	107_V	0.791	0.59
279_I	385_Y	0.789	0.59
187_L	313_L	0.789	0.59
195_A	203_E	0.787	0.59
84_G	94_V	0.782	0.58
138_L	196_I	0.777	0.58
135_S	294_L	0.776	0.58
170_I	208_L	0.775	0.58
163_G	313_L	0.771	0.57
147_A	182_L	0.770	0.57
85_S	162_L	0.769	0.57
77_F	80_P	0.768	0.57
207_I	348_A	0.764	0.57
168_L	390_L	0.764	0.57
94_V	98_V	0.756	0.56
80_P	87_V	0.754	0.56
408_M	414_K	0.752	0.55
139_V	192_D	0.749	0.55
142_Y	348_A	0.748	0.55
275_S	322_F	0.747	0.55
276_L	285_M	0.747	0.55
296_E	394_M	0.747	0.55
78_I	82_I	0.747	0.55
183_G	291_W	0.746	0.55
159_Y	162_L	0.744	0.55
131_V	194_L	0.744	0.55
86_T	92_F	0.743	0.55
175_A	324_G	0.743	0.55
202_G	369_A	0.742	0.54
76_K	87_V	0.741	0.54
202_G	347_S	0.740	0.54
170_I	321_A	0.739	0.54
366_I	412_Q	0.736	0.54
283_L	306_L	0.735	0.54
141_G	144_G	0.730	0.53
170_I	174_M	0.726	0.53
144_G	194_L	0.723	0.53
353_I	373_V	0.720	0.52
122_I	251_F	0.720	0.52
84_G	96_L	0.719	0.52
102_A	160_Y	0.714	0.52
130_V	296_E	0.714	0.52
84_G	278_V	0.712	0.51
169_P	273_V	0.711	0.51
90_K	95_A	0.710	0.51
276_L	362_Q	0.709	0.51
83_D	97_L	0.709	0.51
195_A	320_A	0.707	0.51
151_Y	336_F	0.704	0.51
186_V	355_V	0.704	0.51
138_L	141_G	0.700	0.50
170_I	173_L	0.698	0.50
137_L	390_L	0.697	0.50
187_L	355_V	0.696	0.50
137_L	201_F	0.695	0.50
339_P	354_V	0.692	0.49
119_M	207_I	0.689	0.49
116_T	120_I	0.687	0.49
357_G	360_G	0.686	0.49
250_F	254_K	0.686	0.49
197_V	292_E	0.685	0.49
250_F	396_L	0.682	0.48
79_L	102_A	0.679	0.48
80_P	366_I	0.679	0.48
114_I	374_V	0.678	0.48
120_I	326_A	0.676	0.48
284_R	412_Q	0.674	0.48
130_V	134_L	0.673	0.47
322_F	378_L	0.673	0.47
282_L	367_L	0.673	0.47
179_G	185_P	0.671	0.47
124_L	127_G	0.670	0.47
138_L	315_A	0.669	0.47
382_F	396_L	0.668	0.47
278_V	335_G	0.668	0.47
300_A	352_A	0.662	0.46
87_V	93_L	0.660	0.46
274_L	310_R	0.658	0.46
361_S	406_L	0.655	0.46
99_L	103_W	0.655	0.46
118_T	272_V	0.654	0.46
92_F	393_L	0.652	0.45
182_L	197_V	0.651	0.45
83_D	99_L	0.651	0.45
294_L	297_D	0.648	0.45
97_L	100_A	0.647	0.45
177_A	235_F	0.647	0.45
85_S	88_K	0.645	0.45
127_G	323_A	0.643	0.44
137_L	193_Y	0.642	0.44
315_A	347_S	0.640	0.44
379_M	389_M	0.640	0.44
352_A	365_V	0.640	0.44
287_L	314_T	0.640	0.44
124_L	146_Y	0.635	0.44
366_I	369_A	0.633	0.43
184_F	356_L	0.633	0.43
99_L	274_L	0.632	0.43
283_L	393_L	0.632	0.43
86_T	89_Q	0.629	0.43
141_G	149_G	0.626	0.43
89_Q	95_A	0.625	0.43
103_W	115_A	0.625	0.43
93_L	96_L	0.622	0.42
398_M	401_R	0.622	0.42
194_L	347_S	0.621	0.42
250_F	253_L	0.620	0.42
173_L	370_I	0.620	0.42
182_L	202_G	0.619	0.42
91_L	102_A	0.618	0.42
82_I	173_L	0.617	0.42
178_A	273_V	0.617	0.42
179_G	187_L	0.617	0.42
192_D	296_E	0.615	0.42
83_D	98_V	0.612	0.41
161_G	318_I	0.612	0.41
121_Y	346_E	0.609	0.41
200_G	360_G	0.608	0.41
122_I	271_L	0.606	0.41
85_S	102_A	0.605	0.41
92_F	101_V	0.605	0.41
89_Q	389_M	0.605	0.41
96_L	217_G	0.604	0.41
115_A	411_P	0.603	0.41
195_A	202_G	0.600	0.40
131_V	142_Y	0.599	0.40
187_L	386_S	0.597	0.40
143_G	347_S	0.595	0.40
166_T	181_L	0.595	0.40
159_Y	163_G	0.595	0.40
110_G	114_I	0.593	0.40
129_N	196_I	0.592	0.39
175_A	355_V	0.590	0.39
131_V	291_W	0.589	0.39
80_P	166_T	0.588	0.39
349_F	386_S	0.588	0.39
217_G	220_N	0.584	0.39
131_V	332_A	0.583	0.39
79_L	84_G	0.583	0.39
136_G	295_R	0.582	0.39
126_L	276_L	0.582	0.39
104_P	107_V	0.581	0.38
251_F	254_K	0.581	0.38
92_F	97_L	0.581	0.38
79_L	177_A	0.580	0.38
403_Q	408_M	0.578	0.38
193_Y	347_S	0.576	0.38
137_L	319_S	0.575	0.38
114_I	375_S	0.575	0.38
273_V	363_F	0.572	0.38
95_A	99_L	0.570	0.37
94_V	101_V	0.567	0.37
205_V	350_V	0.566	0.37
195_A	301_C	0.566	0.37
365_V	383_N	0.563	0.37
166_T	274_L	0.560	0.36
85_S	99_L	0.560	0.36
129_N	134_L	0.558	0.36
76_K	98_V	0.555	0.36
233_L	250_F	0.554	0.36
408_M	412_Q	0.554	0.36
123_I	326_A	0.553	0.36
142_Y	192_D	0.551	0.36
179_G	195_A	0.551	0.36
82_I	86_T	0.550	0.36
83_D	96_L	0.550	0.36
139_V	196_I	0.549	0.35
204_I	211_N	0.548	0.35
121_Y	146_Y	0.547	0.35
77_F	102_A	0.547	0.35
197_V	312_K	0.547	0.35
129_N	135_S	0.546	0.35
152_T	173_L	0.544	0.35
138_L	347_S	0.543	0.35
248_S	252_G	0.543	0.35
303_S	306_L	0.543	0.35
139_V	199_L	0.541	0.35
127_G	322_F	0.540	0.35
142_Y	206_R	0.537	0.34
381_D	405_L	0.536	0.34
139_V	182_L	0.536	0.34
156_L	166_T	0.536	0.34
80_P	100_A	0.535	0.34
141_G	182_L	0.535	0.34
218_G	221_G	0.534	0.34
189_L	289_R	0.534	0.34
204_I	355_V	0.534	0.34
118_T	389_M	0.533	0.34
77_F	84_G	0.532	0.34
87_V	99_L	0.531	0.34
150_A	355_V	0.530	0.34
81_A	84_G	0.529	0.34
98_V	102_A	0.529	0.34
194_L	197_V	0.529	0.34
317_T	340_E	0.528	0.33
289_R	312_K	0.528	0.33
279_I	366_I	0.524	0.33
76_K	95_A	0.524	0.33
254_K	325_F	0.524	0.33
99_L	107_V	0.524	0.33
203_E	398_M	0.524	0.33
290_A	394_M	0.523	0.33
131_V	296_E	0.523	0.33
368_A	394_M	0.522	0.33
148_I	342_F	0.522	0.33
128_L	394_M	0.520	0.33
86_T	250_F	0.518	0.33
87_V	95_A	0.515	0.32
356_L	368_A	0.514	0.32
408_M	411_P	0.513	0.32
145_F	179_G	0.513	0.32
129_N	145_F	0.513	0.32
391_G	395_V	0.513	0.32
388_L	392_G	0.510	0.32
88_K	94_V	0.510	0.32
124_L	326_A	0.508	0.32
76_K	107_V	0.506	0.32
151_Y	216_T	0.505	0.31
229_T	251_F	0.502	0.31
226_P	307_S	0.502	0.31
171_A	228_P	0.501	0.31
232_G	336_F	0.500	0.31
81_A	85_S	0.500	0.31

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
4g1uA	2	0.6235	94.9	0.936	Contact Map
2nq2A	2	0.6212	91.9	0.943	Contact Map
2qi9A	2	0.6612	90.6	0.945	Contact Map
2onkC	2	0.5506	45.8	0.962	Contact Map
2i68A	2	0.1812	13.9	0.971	Contact Map
3d31C	2	0.5459	11.4	0.972	Contact Map
2gfpA	2	0.4259	8.2	0.974	Contact Map
4tphA	2	0.4659	7.2	0.974	Contact Map
4xnjA	1	0.4847	4.6	0.977	Contact Map
2kncA	1	0.1106	3.9	0.977	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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