LIVH - ECOLI - GREMLIN Contacts

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LIVH - High-affinity branched-chain amino acid transport system permease protein LivH

UniProt:	P0AEX7	Sequences: MSEQFLYFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGIDTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEGSRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEVEKV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10538
Length:	308 (266)
Sequences:	30720 (19424)
Seq/√Len:	1191.0

ECOLI - LIVH LIVM YTFT LSRC YJFF YPHD XYLH LSRD RBSC ARAH MGLC ALSC
BACSU - YUFQ YUFP RBSC
HALSA - Q9HR22 Q9HR23
SULSO - Q97UZ9 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
81_I	214_A	4.030	1.00
85_S	210_V	3.676	1.00
85_S	214_A	3.120	1.00
53_V	83_I	2.961	1.00
89_W	210_V	2.866	1.00
191_L	205_I	2.826	1.00
57_I	79_G	2.614	1.00
23_A	164_T	2.593	1.00
184_C	208_T	2.546	1.00
30_T	257_A	2.518	1.00
97_R	202_D	2.495	1.00
200_N	203_R	2.457	1.00
84_A	217_A	2.405	1.00
174_F	180_M	2.349	1.00
88_G	213_A	2.345	1.00
203_R	207_L	2.288	1.00
172_T	176_R	2.254	1.00
91_I	114_M	2.252	1.00
173_I	177_Y	2.228	1.00
89_W	206_A	2.187	1.00
183_A	204_V	2.159	1.00
241_K	268_E	2.149	1.00
93_R	97_R	2.141	1.00
180_M	207_L	2.110	1.00
170_A	174_F	1.979	1.00
48_M	122_V	1.951	1.00
25_I	242_A	1.945	1.00
81_I	218_V	1.930	1.00
84_A	213_A	1.915	1.00
54_S	80_A	1.903	1.00
74_A	78_V	1.871	1.00
19_G	265_G	1.850	1.00
54_S	221_V	1.816	1.00
187_C	204_V	1.763	1.00
77_F	221_V	1.759	1.00
169_L	173_I	1.717	1.00
116_I	119_Q	1.703	1.00
26_A	257_A	1.700	1.00
32_V	212_G	1.699	1.00
186_A	194_A	1.680	1.00
92_E	206_A	1.677	1.00
67_D	75_A	1.675	1.00
31_M	171_L	1.638	1.00
19_G	262_L	1.593	1.00
23_A	261_G	1.573	1.00
179_R	183_A	1.557	1.00
241_K	284_S	1.556	1.00
38_M	107_A	1.554	1.00
35_I	185_R	1.548	1.00
67_D	74_A	1.509	1.00
114_M	118_L	1.507	1.00
56_M	60_A	1.502	1.00
58_I	76_G	1.491	1.00
81_I	221_V	1.489	1.00
180_M	184_C	1.480	1.00
87_Y	118_L	1.476	1.00
45_E	119_Q	1.443	1.00
253_S	256_G	1.435	1.00
192_K	195_S	1.433	1.00
191_L	195_S	1.428	1.00
168_M	258_M	1.416	1.00
49_I	87_Y	1.402	1.00
56_M	125_T	1.394	1.00
249_G	256_G	1.385	1.00
25_I	47_Y	1.379	1.00
207_L	210_V	1.374	1.00
97_R	206_A	1.354	1.00
47_Y	223_L	1.348	1.00
183_A	199_I	1.343	1.00
67_D	73_V	1.341	1.00
28_G	215_M	1.337	1.00
183_A	194_A	1.334	1.00
75_A	78_V	1.327	1.00
57_I	64_M	1.316	1.00
36_I	208_T	1.314	1.00
24_L	222_L	1.309	1.00
24_L	219_A	1.299	1.00
249_G	260_G	1.295	1.00
199_I	204_V	1.276	1.00
194_A	199_I	1.275	1.00
31_M	208_T	1.271	1.00
23_A	258_M	1.253	1.00
15_G	265_G	1.251	1.00
57_I	66_I	1.239	1.00
11_Q	269_A	1.239	1.00
29_Y	242_A	1.238	1.00
93_R	206_A	1.236	1.00
76_G	80_A	1.235	1.00
206_A	210_V	1.231	1.00
29_Y	246_A	1.225	1.00
135_S	138_N	1.219	1.00
80_A	84_A	1.211	1.00
187_C	201_T	1.202	1.00
147_E	150_S	1.201	1.00
27_I	171_L	1.197	1.00
38_M	205_I	1.195	1.00
43_H	216_A	1.193	1.00
187_C	194_A	1.190	1.00
53_V	57_I	1.182	1.00
38_M	209_F	1.179	1.00
269_A	272_S	1.176	1.00
66_I	75_A	1.174	1.00
78_V	82_V	1.170	1.00
15_G	266_I	1.168	1.00
172_T	177_Y	1.134	1.00
82_V	85_S	1.133	1.00
96_Y	202_D	1.124	1.00
45_E	118_L	1.123	1.00
195_S	202_D	1.115	1.00
210_V	214_A	1.108	1.00
96_Y	111_A	1.100	1.00
213_A	217_A	1.100	1.00
26_A	245_A	1.093	1.00
176_R	185_R	1.088	1.00
167_A	215_M	1.077	1.00
54_S	225_Q	1.073	1.00
26_A	246_A	1.072	1.00
28_G	43_H	1.069	1.00
207_L	211_I	1.062	1.00
19_G	261_G	1.061	1.00
245_A	260_G	1.059	1.00
46_V	87_Y	1.052	1.00
66_I	79_G	1.044	1.00
35_I	252_G	1.043	1.00
56_M	126_E	1.043	1.00
123_S	126_E	1.042	1.00
168_M	215_M	1.038	1.00
94_V	110_S	1.034	1.00
268_E	284_S	1.028	1.00
251_I	257_A	1.020	1.00
279_Y	282_V	1.017	1.00
149_F	152_S	1.016	1.00
220_G	224_G	1.015	1.00
204_V	207_L	1.015	1.00
166_L	170_A	1.014	1.00
25_I	219_A	1.012	1.00
52_Y	122_V	1.003	1.00
91_I	110_S	0.995	1.00
80_A	221_V	0.995	1.00
85_S	217_A	0.995	1.00
171_L	211_I	0.994	1.00
245_A	261_G	0.989	1.00
20_S	161_W	0.988	1.00
238_A	241_K	0.987	1.00
13_F	17_T	0.986	1.00
162_I	166_L	0.980	1.00
40_N	43_H	0.979	1.00
180_M	204_V	0.978	1.00
44_G	239_G	0.976	1.00
55_F	59_A	0.972	1.00
184_C	204_V	0.972	1.00
195_S	201_T	0.970	1.00
211_I	215_M	0.968	1.00
86_A	89_W	0.966	1.00
57_I	76_G	0.965	1.00
57_I	60_A	0.964	1.00
30_T	246_A	0.961	1.00
169_L	172_T	0.957	1.00
52_Y	232_P	0.956	1.00
148_N	151_A	0.955	1.00
212_G	216_A	0.953	1.00
264_L	284_S	0.938	1.00
30_T	252_G	0.936	1.00
255_P	259_I	0.935	1.00
21_T	219_A	0.932	1.00
160_I	222_L	0.929	1.00
126_E	129_R	0.928	1.00
97_R	103_K	0.925	1.00
78_V	81_I	0.923	1.00
115_S	119_Q	0.916	1.00
159_V	162_I	0.910	1.00
33_Y	246_A	0.905	1.00
193_M	197_L	0.904	1.00
152_S	155_T	0.901	1.00
49_I	53_V	0.898	1.00
271_S	283_V	0.898	1.00
95_A	110_S	0.897	1.00
290_L	294_V	0.897	1.00
203_R	206_A	0.897	1.00
81_I	217_A	0.890	1.00
45_E	115_S	0.889	1.00
44_G	237_M	0.884	1.00
182_R	185_R	0.881	1.00
155_T	162_I	0.878	1.00
165_F	169_L	0.877	1.00
29_Y	43_H	0.875	1.00
270_L	274_Y	0.872	1.00
51_S	224_G	0.872	1.00
164_T	168_M	0.868	1.00
26_A	261_G	0.866	1.00
133_L	136_L	0.865	1.00
23_A	168_M	0.859	1.00
126_E	131_V	0.858	1.00
36_I	184_C	0.856	1.00
30_T	251_I	0.853	1.00
32_V	40_N	0.852	1.00
92_E	97_R	0.852	1.00
82_V	86_A	0.851	1.00
31_M	211_I	0.848	1.00
12_M	270_L	0.847	1.00
51_S	234_I	0.847	1.00
172_T	255_P	0.846	1.00
18_L	22_Y	0.844	1.00
50_G	84_A	0.844	1.00
237_M	241_K	0.842	1.00
47_Y	238_A	0.842	1.00
133_L	137_F	0.840	1.00
202_D	205_I	0.832	1.00
24_L	164_T	0.830	1.00
35_I	176_R	0.827	1.00
187_C	208_T	0.826	1.00
50_G	80_A	0.824	1.00
60_A	64_M	0.824	1.00
244_T	288_L	0.823	1.00
216_A	220_G	0.822	1.00
253_S	257_A	0.820	1.00
154_T	162_I	0.812	1.00
53_V	56_M	0.804	1.00
201_T	205_I	0.797	1.00
31_M	175_I	0.796	1.00
46_V	216_A	0.795	1.00
52_Y	126_E	0.793	1.00
55_F	230_I	0.793	1.00
174_F	177_Y	0.793	1.00
107_A	209_F	0.789	1.00
190_D	193_M	0.784	1.00
27_I	167_A	0.783	1.00
25_I	28_G	0.779	1.00
93_R	103_K	0.779	1.00
46_V	84_A	0.776	1.00
269_A	273_A	0.776	1.00
90_S	94_V	0.772	1.00
223_L	227_Y	0.768	1.00
175_I	184_C	0.760	1.00
150_S	153_I	0.759	1.00
54_S	58_I	0.758	1.00
25_I	43_H	0.750	1.00
158_A	162_I	0.748	1.00
257_A	261_G	0.747	1.00
51_S	230_I	0.747	1.00
11_Q	273_A	0.747	1.00
50_G	220_G	0.746	1.00
75_A	79_G	0.745	1.00
27_I	257_A	0.743	1.00
22_Y	241_K	0.743	1.00
214_A	217_A	0.737	1.00
24_L	167_A	0.736	1.00
159_V	163_V	0.732	1.00
202_D	206_A	0.732	1.00
281_D	284_S	0.727	1.00
183_A	200_N	0.727	1.00
286_A	290_L	0.725	1.00
153_I	156_M	0.724	1.00
278_E	281_D	0.724	1.00
47_Y	235_G	0.721	1.00
191_L	201_T	0.720	1.00
86_A	90_S	0.720	1.00
55_F	131_V	0.719	1.00
117_F	121_Y	0.718	1.00
54_S	76_G	0.717	1.00
28_G	216_A	0.717	1.00
187_C	205_I	0.713	1.00
84_A	88_G	0.712	1.00
81_I	85_S	0.708	1.00
161_W	165_F	0.704	1.00
170_A	173_I	0.703	1.00
262_L	266_I	0.701	1.00
50_G	83_I	0.697	1.00
89_W	93_R	0.692	1.00
134_P	138_N	0.690	1.00
214_A	218_V	0.690	1.00
41_F	243_F	0.687	1.00
19_G	23_A	0.685	1.00
47_Y	219_A	0.683	1.00
33_Y	243_F	0.681	1.00
246_A	251_I	0.676	1.00
268_E	280_K	0.670	1.00
49_I	84_A	0.670	1.00
129_R	132_A	0.664	1.00
22_Y	245_A	0.660	1.00
14_N	18_L	0.658	1.00
46_V	91_I	0.657	1.00
20_S	164_T	0.655	1.00
291_V	295_M	0.652	1.00
77_F	81_I	0.650	1.00
30_T	35_I	0.649	1.00
152_S	156_M	0.649	1.00
123_S	129_R	0.646	1.00
16_V	20_S	0.645	1.00
119_Q	239_G	0.645	1.00
64_M	67_D	0.645	1.00
10_Q	13_F	0.644	1.00
149_F	153_I	0.640	1.00
96_Y	206_A	0.639	1.00
73_V	136_L	0.638	1.00
261_G	265_G	0.636	1.00
53_V	79_G	0.628	1.00
180_M	211_I	0.628	1.00
123_S	128_S	0.626	1.00
38_M	191_L	0.625	1.00
92_E	96_Y	0.623	1.00
171_L	215_M	0.622	1.00
46_V	213_A	0.622	1.00
171_L	175_I	0.619	1.00
32_V	209_F	0.619	1.00
46_V	118_L	0.617	1.00
151_A	155_T	0.617	1.00
49_I	118_L	0.616	1.00
127_G	131_V	0.615	1.00
91_I	95_A	0.611	1.00
30_T	254_I	0.610	1.00
54_S	220_G	0.610	1.00
95_A	107_A	0.607	1.00
104_R	202_D	0.607	1.00
46_V	50_G	0.606	1.00
17_T	226_F	0.604	1.00
58_I	225_Q	0.603	1.00
15_G	19_G	0.602	1.00
151_A	154_T	0.600	1.00
217_A	221_V	0.599	1.00
245_A	257_A	0.599	1.00
59_A	131_V	0.598	1.00
173_I	176_R	0.597	1.00
174_F	207_L	0.595	1.00
174_F	178_S	0.594	1.00
57_I	83_I	0.590	1.00
14_N	269_A	0.589	1.00
167_A	218_V	0.587	1.00
28_G	32_V	0.586	1.00
46_V	88_G	0.585	1.00
133_L	138_N	0.584	1.00
42_A	91_I	0.583	1.00
213_A	216_A	0.580	1.00
211_I	214_A	0.579	1.00
15_G	269_A	0.578	1.00
87_Y	91_I	0.577	1.00
128_S	131_V	0.576	1.00
147_E	152_S	0.574	1.00
22_Y	238_A	0.571	1.00
244_T	284_S	0.570	1.00
22_Y	261_G	0.569	1.00
275_L	279_Y	0.566	1.00
36_I	205_I	0.566	1.00
201_T	204_V	0.566	1.00
223_L	238_A	0.566	1.00
168_M	172_T	0.565	1.00
95_A	209_F	0.563	1.00
157_Q	226_F	0.562	1.00
116_I	120_N	0.562	1.00
135_S	139_G	0.561	1.00
194_A	201_T	0.560	1.00
12_M	16_V	0.560	1.00
241_K	281_D	0.560	1.00
50_G	216_A	0.560	1.00
124_L	127_G	0.558	1.00
36_I	187_C	0.553	1.00
31_M	174_F	0.551	1.00
134_P	137_F	0.551	1.00
81_I	84_A	0.550	1.00
271_S	275_L	0.545	1.00
248_L	291_V	0.545	1.00
17_T	161_W	0.544	1.00
88_G	210_V	0.544	1.00
115_S	239_G	0.542	1.00
73_V	225_Q	0.540	1.00
126_E	130_D	0.539	1.00
248_L	260_G	0.538	1.00
205_I	208_T	0.538	1.00
21_T	223_L	0.532	1.00
53_V	84_A	0.531	1.00
210_V	213_A	0.530	1.00
27_I	168_M	0.529	1.00
282_V	286_A	0.529	1.00
40_N	212_G	0.527	1.00
186_A	193_M	0.526	1.00
48_M	234_I	0.526	1.00
245_A	264_L	0.526	1.00
32_V	38_M	0.524	1.00
230_I	233_Y	0.523	1.00
66_I	74_A	0.521	1.00
27_I	169_L	0.519	1.00
111_A	115_S	0.518	1.00
256_G	260_G	0.517	1.00
124_L	129_R	0.515	1.00
185_R	252_G	0.515	1.00
53_V	80_A	0.515	1.00
192_K	196_L	0.514	1.00
136_L	139_G	0.514	1.00
163_V	166_L	0.510	1.00
27_I	172_T	0.509	1.00
16_V	19_G	0.508	1.00
124_L	279_Y	0.507	1.00
118_L	122_V	0.506	1.00
49_I	83_I	0.506	1.00
249_G	257_A	0.503	1.00
112_I	116_I	0.502	1.00
260_G	263_I	0.501	1.00
167_A	171_L	0.501	1.00
57_I	80_A	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
2nq2A	2	0.8149	95.7	0.884	Contact Map
2qi9A	2	0.8442	94.3	0.893	Contact Map
4g1uA	2	0.8149	92.7	0.899	Contact Map
2gfpA	2	0.6006	8.8	0.954	Contact Map
2cfqA	1	0.6234	3	0.963	Contact Map
2ksfA	1	0.3377	2.5	0.965	Contact Map
4m64A	1	0.6331	2.1	0.966	Contact Map
1u7gA	3	0.5162	1.9	0.967	Contact Map
3rlbA	1	0.3214	1.7	0.968	Contact Map
2m20A	2	0.1331	1.5	0.969	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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