TQSA - ECOLI - GREMLIN Contacts

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TQSA - AI-2 transport protein TqsA

UniProt:	P0AFS5	Sequences: MAKPIITLNGLKIVIMLGMLVIILCGIRFAAEIIVPFILALFIAVILNPLVQHMVRWRVPRVLAVSILMTIIVMAMVLLLAYLGSALNELTRTLPQYRNSIMTPLQALEPLLQRVGIDVSVDQLAHYIDPNAAMTLLTNLLTQLSNAMSSIFLLLLTVLFMLLEVPQLPGKFQQMMARPVEGMAAIQRAIDSVSHYLVLKTAISIITGLVAWAMLAALDVRFAFVWGLLAFALNYIPNIGSVLAAIPPIAQVLVFNGFYEALLVLAGYLLINLVFGNILEPRIMGRGLGLSTLVVFLSLIFWGWLLGPVGMLLSVPLTIIVKIALEQTAGGQSIAVLLSDLNKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13928
Length:	344 (317)
Sequences:	11032 (8655)
Seq/√Len:	486.1

ECOLI - TQSA YHHT PERM YDIK
BACSU - YUBA YUEF YTVI YDBI YRRI
HALSA - Q9HPX5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
212_W	227_G	4.881	1.00
214_M	267_G	4.862	1.00
53_H	57_W	3.847	1.00
86_A	90_L	3.288	1.00
85_S	90_L	3.108	1.00
298_S	318_T	3.018	1.00
45_V	190_I	2.863	1.00
53_H	56_R	2.815	1.00
90_L	95_P	2.697	1.00
208_G	231_F	2.591	1.00
55_V	61_R	2.545	1.00
60_P	63_L	2.392	1.00
262_L	266_A	2.387	1.00
212_W	216_A	2.358	1.00
259_Y	263_L	2.344	1.00
43_I	158_V	2.336	1.00
249_I	265_L	2.279	1.00
208_G	227_G	2.243	1.00
59_V	67_I	2.198	1.00
322_K	326_E	2.167	1.00
93_T	96_Q	2.036	1.00
75_A	79_L	1.952	1.00
215_L	220_V	1.931	1.00
40_A	158_V	1.894	1.00
266_A	270_L	1.869	1.00
120_S	123_Q	1.863	1.00
184_A	327_Q	1.854	1.00
159_L	163_L	1.823	1.00
249_I	261_A	1.810	1.00
201_T	235_Y	1.778	1.00
199_L	283_I	1.777	1.00
21_V	25_C	1.774	1.00
113_Q	116_G	1.770	1.00
263_L	266_A	1.717	1.00
62_V	66_S	1.709	1.00
188_R	327_Q	1.704	1.00
48_N	52_Q	1.692	1.00
213_A	216_A	1.677	1.00
211_A	230_A	1.676	1.00
95_P	99_N	1.636	1.00
189_A	320_I	1.633	1.00
28_R	31_A	1.632	1.00
154_L	158_V	1.629	1.00
173_Q	183_M	1.622	1.00
77_V	81_A	1.613	1.00
211_A	271_I	1.613	1.00
99_N	102_M	1.606	1.00
123_Q	126_H	1.603	1.00
164_E	291_S	1.593	1.00
119_V	122_D	1.589	1.00
157_T	293_L	1.586	1.00
122_D	125_A	1.573	1.00
257_G	260_E	1.566	1.00
121_V	124_L	1.559	1.00
212_W	223_A	1.538	1.00
282_R	286_R	1.523	1.00
119_V	123_Q	1.514	1.00
37_F	297_L	1.510	1.00
229_L	233_L	1.506	1.00
48_N	61_R	1.491	1.00
157_T	161_M	1.487	1.00
221_R	255_F	1.487	1.00
51_V	68_L	1.480	1.00
216_A	223_A	1.478	1.00
223_A	227_G	1.477	1.00
65_V	69_M	1.463	1.00
207_T	234_N	1.461	1.00
210_V	271_I	1.449	1.00
106_Q	109_E	1.448	1.00
303_G	311_M	1.429	1.00
50_L	68_L	1.429	1.00
118_D	122_D	1.414	1.00
117_I	120_S	1.412	1.00
233_L	244_A	1.410	1.00
260_E	263_L	1.406	1.00
104_P	108_L	1.395	1.00
20_L	24_L	1.392	1.00
51_V	65_V	1.382	1.00
120_S	124_L	1.382	1.00
269_L	273_L	1.375	1.00
51_V	61_R	1.366	1.00
125_A	128_I	1.360	1.00
90_L	94_L	1.344	1.00
100_S	104_P	1.340	1.00
54_M	71_I	1.331	1.00
279_L	283_I	1.320	1.00
88_N	92_R	1.309	1.00
65_V	159_L	1.309	1.00
96_Q	99_N	1.305	1.00
245_A	249_I	1.296	1.00
111_L	114_R	1.296	1.00
274_V	279_L	1.283	1.00
97_Y	101_I	1.279	1.00
170_G	174_Q	1.274	1.00
122_D	126_H	1.267	1.00
100_S	103_T	1.257	1.00
258_F	261_A	1.248	1.00
87_L	90_L	1.248	1.00
265_L	269_L	1.244	1.00
226_W	248_P	1.244	1.00
111_L	115_V	1.242	1.00
252_V	264_V	1.242	1.00
214_M	218_L	1.241	1.00
85_S	95_P	1.240	1.00
259_Y	262_L	1.236	1.00
192_S	319_I	1.235	1.00
248_P	264_V	1.226	1.00
47_L	162_L	1.224	1.00
73_V	77_V	1.213	1.00
112_L	115_V	1.211	1.00
125_A	129_D	1.209	1.00
99_N	103_T	1.207	1.00
120_S	125_A	1.207	1.00
17_L	21_V	1.201	1.00
203_I	275_F	1.200	1.00
96_Q	100_S	1.200	1.00
59_V	64_A	1.199	1.00
51_V	162_L	1.186	1.00
60_P	64_A	1.183	1.00
299_L	311_M	1.179	1.00
294_V	318_T	1.169	1.00
44_A	161_M	1.169	1.00
126_H	129_D	1.168	1.00
40_A	154_L	1.162	1.00
207_T	271_I	1.156	1.00
214_M	263_L	1.156	1.00
227_G	231_F	1.144	1.00
89_E	93_T	1.143	1.00
55_V	64_A	1.142	1.00
24_L	28_R	1.139	1.00
272_N	276_G	1.138	1.00
104_P	107_A	1.132	1.00
218_L	267_G	1.122	1.00
62_V	163_L	1.118	1.00
65_V	79_L	1.116	1.00
164_E	167_Q	1.112	1.00
51_V	55_V	1.103	1.00
13_I	17_L	1.102	1.00
48_N	165_V	1.100	1.00
302_W	306_L	1.099	1.00
121_V	125_A	1.097	1.00
43_I	154_L	1.096	1.00
107_A	110_P	1.092	1.00
59_V	63_L	1.091	1.00
258_F	262_L	1.089	1.00
36_P	40_A	1.088	1.00
198_V	202_A	1.087	1.00
93_T	97_Y	1.087	1.00
185_A	324_A	1.086	1.00
126_H	130_P	1.082	1.00
220_V	252_V	1.076	1.00
213_A	217_A	1.073	1.00
188_R	326_E	1.071	1.00
64_A	68_L	1.067	1.00
212_W	224_F	1.065	1.00
204_S	234_N	1.059	1.00
127_Y	130_P	1.057	1.00
276_G	280_E	1.056	1.00
309_V	313_L	1.056	1.00
61_R	65_V	1.053	1.00
302_W	318_T	1.045	1.00
47_L	72_I	1.040	1.00
167_Q	170_G	1.037	1.00
103_T	107_A	1.036	1.00
253_L	261_A	1.036	1.00
298_S	302_W	1.031	1.00
153_L	157_T	1.030	1.00
123_Q	127_Y	1.028	1.00
51_V	64_A	1.020	1.00
214_M	271_I	1.020	1.00
107_A	111_L	1.019	1.00
294_V	322_K	1.016	1.00
137_L	141_L	1.016	1.00
203_I	207_T	1.016	1.00
201_T	205_I	1.013	1.00
102_M	106_Q	1.011	1.00
203_I	279_L	1.010	1.00
195_H	199_L	1.009	1.00
50_L	53_H	1.008	1.00
14_V	18_G	1.004	1.00
41_L	161_M	1.002	1.00
66_S	70_T	0.998	1.00
157_T	297_L	0.990	1.00
39_L	154_L	0.985	1.00
215_L	230_A	0.985	1.00
25_C	29_F	0.984	1.00
263_L	267_G	0.979	1.00
110_P	113_Q	0.977	1.00
37_F	157_T	0.975	1.00
208_G	212_W	0.973	1.00
207_T	211_A	0.971	1.00
60_P	65_V	0.970	1.00
252_V	261_A	0.968	1.00
147_A	151_I	0.968	1.00
200_K	280_E	0.960	1.00
278_I	282_R	0.957	1.00
40_A	44_A	0.957	1.00
63_L	66_S	0.956	1.00
106_Q	110_P	0.951	1.00
261_A	265_L	0.950	1.00
89_E	92_R	0.944	1.00
218_L	260_E	0.944	1.00
215_L	264_V	0.943	1.00
120_S	127_Y	0.942	1.00
207_T	241_S	0.937	1.00
124_L	127_Y	0.936	1.00
215_L	226_W	0.935	1.00
85_S	89_E	0.933	1.00
222_F	225_V	0.932	1.00
61_R	166_P	0.931	1.00
270_L	274_V	0.928	1.00
84_G	87_L	0.927	1.00
109_E	113_Q	0.924	1.00
218_L	264_V	0.923	1.00
251_Q	255_F	0.920	1.00
321_V	325_L	0.919	1.00
124_L	128_I	0.917	1.00
103_T	106_Q	0.916	1.00
229_L	244_A	0.916	1.00
118_D	125_A	0.911	1.00
18_G	22_I	0.907	1.00
165_V	169_P	0.904	1.00
267_G	271_I	0.902	1.00
298_S	314_S	0.901	1.00
209_L	212_W	0.898	1.00
205_I	231_F	0.898	1.00
171_K	174_Q	0.889	1.00
61_R	64_A	0.889	1.00
105_L	109_E	0.887	1.00
206_I	210_V	0.883	1.00
92_R	95_P	0.877	1.00
202_A	206_I	0.873	1.00
274_V	278_I	0.871	1.00
184_A	188_R	0.870	1.00
52_Q	55_V	0.869	1.00
290_L	318_T	0.863	1.00
231_F	235_Y	0.863	1.00
140_L	144_L	0.862	1.00
62_V	65_V	0.860	1.00
243_L	247_P	0.860	1.00
209_L	213_A	0.859	1.00
250_A	254_V	0.857	1.00
203_I	280_E	0.854	1.00
203_I	234_N	0.854	1.00
275_F	280_E	0.849	1.00
21_V	24_L	0.848	1.00
84_G	88_N	0.846	1.00
227_G	230_A	0.843	1.00
167_Q	171_K	0.841	1.00
88_N	91_T	0.840	1.00
121_V	127_Y	0.840	1.00
211_A	215_L	0.829	1.00
234_N	241_S	0.825	1.00
324_A	328_T	0.823	1.00
195_H	287_G	0.823	1.00
17_L	20_L	0.822	1.00
171_K	175_M	0.822	1.00
273_L	277_N	0.820	1.00
69_M	158_V	0.818	1.00
40_A	157_T	0.813	1.00
86_A	89_E	0.807	1.00
14_V	17_L	0.804	1.00
26_G	30_A	0.802	1.00
75_A	78_L	0.800	1.00
297_L	301_F	0.800	1.00
185_A	327_Q	0.800	1.00
169_P	173_Q	0.797	1.00
245_A	268_Y	0.794	1.00
141_L	145_S	0.793	1.00
226_W	251_Q	0.791	1.00
314_S	318_T	0.789	1.00
191_D	195_H	0.788	1.00
205_I	209_L	0.787	1.00
33_I	301_F	0.786	1.00
203_I	284_M	0.781	1.00
253_L	258_F	0.777	1.00
15_I	19_M	0.774	1.00
62_V	159_L	0.773	1.00
110_P	114_R	0.771	1.00
218_L	263_L	0.768	1.00
16_M	20_L	0.767	1.00
91_T	95_P	0.767	1.00
216_A	219_D	0.763	1.00
83_L	86_A	0.760	1.00
44_A	158_V	0.759	1.00
71_I	74_M	0.758	1.00
284_M	295_V	0.752	1.00
216_A	227_G	0.750	1.00
158_V	162_L	0.750	1.00
234_N	280_E	0.745	1.00
117_I	121_V	0.744	1.00
87_L	91_T	0.741	1.00
112_L	116_G	0.741	1.00
178_R	181_E	0.738	1.00
255_F	260_E	0.732	1.00
230_A	234_N	0.728	1.00
125_A	130_P	0.725	1.00
204_S	208_G	0.725	1.00
285_G	295_V	0.724	1.00
94_L	97_Y	0.721	1.00
74_M	77_V	0.715	1.00
207_T	280_E	0.712	1.00
202_A	283_I	0.712	1.00
60_P	75_A	0.707	1.00
183_M	187_Q	0.705	1.00
194_S	198_V	0.704	1.00
97_Y	104_P	0.703	1.00
19_M	23_I	0.703	1.00
204_S	235_Y	0.702	1.00
117_I	122_D	0.700	1.00
173_Q	181_E	0.698	1.00
185_A	189_A	0.697	1.00
37_F	161_M	0.695	1.00
188_R	323_I	0.693	1.00
230_A	244_A	0.693	1.00
249_I	253_L	0.691	1.00
288_L	315_V	0.684	1.00
87_L	95_P	0.682	1.00
280_E	284_M	0.680	1.00
53_H	58_R	0.680	1.00
111_L	116_G	0.679	1.00
206_I	279_L	0.678	1.00
23_I	26_G	0.678	1.00
78_L	82_Y	0.677	1.00
101_I	104_P	0.676	1.00
47_L	50_L	0.669	1.00
280_E	283_I	0.667	1.00
146_N	150_S	0.667	1.00
117_I	124_L	0.666	1.00
208_G	224_F	0.663	1.00
98_R	102_M	0.663	1.00
85_S	99_N	0.662	1.00
52_Q	166_P	0.661	1.00
77_V	80_L	0.658	1.00
90_L	97_Y	0.658	1.00
188_R	192_S	0.656	1.00
292_T	296_F	0.656	1.00
60_P	79_L	0.655	1.00
36_P	285_G	0.655	1.00
211_A	227_G	0.653	1.00
175_M	325_L	0.652	1.00
203_I	283_I	0.651	1.00
189_A	323_I	0.650	1.00
47_L	68_L	0.649	1.00
64_A	75_A	0.648	1.00
272_N	275_F	0.644	1.00
133_A	137_L	0.642	1.00
44_A	48_N	0.641	1.00
48_N	162_L	0.641	1.00
173_Q	176_M	0.641	1.00
39_L	43_I	0.638	1.00
29_F	32_E	0.638	1.00
241_S	272_N	0.638	1.00
252_V	257_G	0.638	1.00
192_S	195_H	0.638	1.00
105_L	111_L	0.637	1.00
171_K	294_V	0.636	1.00
118_D	121_V	0.635	1.00
177_A	181_E	0.632	1.00
318_T	322_K	0.632	1.00
204_S	207_T	0.630	1.00
221_R	224_F	0.626	1.00
108_L	111_L	0.625	1.00
134_M	137_L	0.625	1.00
132_A	135_T	0.619	0.99
238_N	292_T	0.616	0.99
143_Q	146_N	0.614	0.99
302_W	317_L	0.614	0.99
170_G	183_M	0.611	0.99
138_T	142_T	0.610	0.99
61_R	75_A	0.609	0.99
200_K	234_N	0.606	0.99
133_A	136_L	0.606	0.99
230_A	268_Y	0.601	0.99
47_L	158_V	0.600	0.99
95_P	101_I	0.599	0.99
200_K	204_S	0.599	0.99
109_E	112_L	0.598	0.99
25_C	28_R	0.596	0.99
177_A	180_V	0.595	0.99
91_T	94_L	0.594	0.99
241_S	244_A	0.593	0.99
36_P	150_S	0.592	0.99
189_A	193_V	0.589	0.99
193_V	196_Y	0.589	0.99
20_L	23_I	0.589	0.99
208_G	228_L	0.588	0.99
52_Q	56_R	0.588	0.99
244_A	248_P	0.588	0.99
98_R	101_I	0.588	0.99
173_Q	177_A	0.588	0.99
84_G	90_L	0.586	0.99
13_I	16_M	0.582	0.99
308_P	311_M	0.580	0.99
299_L	315_V	0.580	0.99
207_T	272_N	0.580	0.99
229_L	247_P	0.580	0.99
203_I	241_S	0.579	0.99
220_V	255_F	0.578	0.99
93_T	221_R	0.578	0.99
54_M	59_V	0.576	0.99
192_S	323_I	0.575	0.99
44_A	162_L	0.575	0.99
211_A	267_G	0.575	0.99
200_K	203_I	0.575	0.99
202_A	205_I	0.574	0.99
143_Q	147_A	0.573	0.99
306_L	310_G	0.573	0.99
170_G	173_Q	0.570	0.99
151_I	155_L	0.569	0.99
141_L	144_L	0.568	0.99
204_S	231_F	0.564	0.99
279_L	282_R	0.564	0.99
275_F	279_L	0.564	0.99
210_V	275_F	0.563	0.99
195_H	198_V	0.562	0.99
168_L	171_K	0.558	0.99
187_Q	191_D	0.557	0.99
157_T	300_I	0.557	0.99
231_F	234_N	0.556	0.99
220_V	223_A	0.556	0.99
153_L	300_I	0.554	0.99
211_A	231_F	0.554	0.99
290_L	295_V	0.553	0.99
207_T	275_F	0.553	0.99
295_V	315_V	0.552	0.99
94_L	98_R	0.551	0.99
54_M	67_I	0.550	0.99
104_P	109_E	0.550	0.99
90_L	99_N	0.545	0.99
72_I	79_L	0.542	0.99
149_S	153_L	0.541	0.99
198_V	287_G	0.541	0.99
118_D	129_D	0.540	0.99
188_R	191_D	0.539	0.99
244_A	315_V	0.537	0.99
136_L	140_L	0.537	0.99
210_V	214_M	0.536	0.99
97_Y	113_Q	0.533	0.99
234_N	275_F	0.532	0.98
161_M	293_L	0.531	0.98
90_L	101_I	0.530	0.98
199_L	319_I	0.529	0.98
160_F	164_E	0.527	0.98
160_F	291_S	0.526	0.98
230_A	241_S	0.526	0.98
132_A	136_L	0.525	0.98
169_P	187_Q	0.525	0.98
285_G	289_G	0.524	0.98
90_L	93_T	0.522	0.98
35_V	38_I	0.521	0.98
273_L	276_G	0.520	0.98
146_N	277_N	0.519	0.98
207_T	231_F	0.518	0.98
252_V	255_F	0.517	0.98
291_S	322_K	0.516	0.98
169_P	186_I	0.516	0.98
259_Y	266_A	0.515	0.98
254_V	258_F	0.514	0.98
200_K	235_Y	0.513	0.98
144_L	148_M	0.512	0.98
119_V	126_H	0.512	0.98
220_V	248_P	0.511	0.98
231_F	238_N	0.510	0.98
109_E	116_G	0.509	0.98
208_G	245_A	0.509	0.98
246_I	250_A	0.508	0.98
207_T	210_V	0.508	0.98
172_F	175_M	0.506	0.98
189_A	192_S	0.506	0.98
234_N	276_G	0.504	0.98
204_S	268_Y	0.503	0.98
323_I	327_Q	0.503	0.98
76_M	80_L	0.502	0.98
85_S	88_N	0.501	0.98
67_I	71_I	0.500	0.98

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
3mktA	1	0.9884	51.2	0.944	Contact Map
3w4tA	1	0.8837	49.5	0.944	Contact Map
4humA	1	0.9128	42.3	0.946	Contact Map
4lz6A	1	0.8924	20.4	0.954	Contact Map
2kv5A	1	0.0959	15.6	0.957	Contact Map
2ksdA	1	0.218	11.3	0.959	Contact Map
2kncA	1	0.1541	9.3	0.961	Contact Map
4b19A	1	0.0872	8.5	0.961	Contact Map
4r0cA	3	0.6308	8.3	0.962	Contact Map
4tkrA	2	0.3256	7.9	0.962	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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