YNAI - ECOLI - GREMLIN Contacts

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YNAI - Low conductance mechanosensitive channel YnaI

UniProt:	P0AEB5	Sequences: MIAELFTNNALNLVIIFGSCAALILMSFWFRRGNRKRKGFLFHAVQFLIYTIIISAVGSIINYVIENYKLKFITPGVIDFICTSLIAVILTIKLFLLINQFEKQQIKKGRDITSARIMSRIIKITIIVVLVLLYGEHFGMSLSGLLTFGGIGGLAVGMAGKDILSNFFSGIMLYFDRPFSIGDWIRSPDRNIEGTVAEIGWRITKITTFDNRPLYVPNSLFSSISVENPGRMTNRRITTTIGLRYEDAAKVGVIVEAVREMLKNHPAIDQRQTLLVYFNQFADSSLNIMVYCFTKTTVWAEWLAAQQDVYLKIIDIVQSHGADFAFPSQTLYMDNITPPEQGR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13924
Length:	343 (307)
Sequences:	8138 (6186)
Seq/√Len:	353.0

ECOLI - YNAI YBIO MSCM MSCK MSCS YBDG
BACSU - YHDY YFKC YKUT
HALSA - Q9HQH2 Q9HNG6 Q9HQ04
SULSO - Q97V66 Q7LXV0 Q97V08 Q97V46

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
91_T	130_L	4.655	1.00
252_G	315_D	4.463	1.00
314_I	318_Q	3.706	1.00
259_R	263_K	3.671	1.00
197_A	207_T	3.645	1.00
186_R	193_E	3.474	1.00
253_V	320_H	3.394	1.00
280_Q	287_N	3.363	1.00
256_E	260_E	3.018	1.00
188_P	191_N	2.950	1.00
316_I	319_S	2.926	1.00
255_V	311_L	2.830	1.00
265_H	308_D	2.806	1.00
316_I	320_H	2.771	1.00
282_A	287_N	2.753	1.00
242_G	285_S	2.679	1.00
258_V	313_I	2.645	1.00
184_W	193_E	2.553	1.00
260_E	264_N	2.388	1.00
279_N	289_M	2.342	1.00
312_K	315_D	2.339	1.00
161_K	165_S	2.327	1.00
257_A	316_I	2.305	1.00
260_E	316_I	2.288	1.00
315_D	319_S	2.281	1.00
253_V	256_E	2.261	1.00
220_L	224_I	2.212	1.00
278_F	286_L	2.164	1.00
240_T	289_M	2.162	1.00
176_D	202_R	2.066	1.00
257_A	320_H	2.021	1.00
198_E	205_K	1.960	1.00
184_W	195_T	1.955	1.00
292_C	309_V	1.944	1.00
185_I	196_V	1.934	1.00
262_L	290_V	1.906	1.00
306_Q	310_Y	1.899	1.00
243_L	254_I	1.891	1.00
244_R	323_D	1.882	1.00
186_R	227_E	1.868	1.00
186_R	229_P	1.847	1.00
184_W	209_F	1.835	1.00
255_V	259_R	1.827	1.00
261_M	316_I	1.820	1.00
47_F	51_T	1.808	1.00
261_M	312_K	1.787	1.00
264_N	312_K	1.784	1.00
241_I	313_I	1.762	1.00
296_T	301_E	1.734	1.00
240_T	287_N	1.731	1.00
254_I	288_I	1.726	1.00
197_A	213_P	1.712	1.00
186_R	191_N	1.702	1.00
208_T	214_L	1.666	1.00
238_T	289_M	1.660	1.00
283_D	287_N	1.649	1.00
242_G	287_N	1.649	1.00
269_D	272_Q	1.642	1.00
154_L	157_G	1.626	1.00
99_N	123_K	1.587	1.00
248_A	253_V	1.582	1.00
317_V	322_A	1.580	1.00
245_Y	281_F	1.570	1.00
188_P	225_S	1.532	1.00
283_D	329_Q	1.509	1.00
204_T	218_N	1.501	1.00
308_D	312_K	1.494	1.00
84_S	134_Y	1.470	1.00
162_D	165_S	1.466	1.00
24_I	28_F	1.456	1.00
257_A	260_E	1.426	1.00
242_G	284_S	1.422	1.00
252_G	256_E	1.413	1.00
267_A	308_D	1.399	1.00
188_P	224_I	1.396	1.00
267_A	301_E	1.393	1.00
253_V	257_A	1.386	1.00
312_K	316_I	1.382	1.00
252_G	311_L	1.373	1.00
265_H	312_K	1.368	1.00
33_G	36_K	1.367	1.00
302_W	306_Q	1.358	1.00
19_S	23_L	1.350	1.00
246_E	326_F	1.345	1.00
84_S	138_F	1.340	1.00
243_L	251_V	1.336	1.00
126_I	130_L	1.307	1.00
243_L	247_D	1.301	1.00
301_E	304_A	1.299	1.00
88_V	92_I	1.284	1.00
242_G	282_A	1.276	1.00
18_G	22_A	1.263	1.00
23_L	27_S	1.213	1.00
27_S	31_R	1.206	1.00
144_G	147_T	1.205	1.00
294_T	305_A	1.200	1.00
263_K	270_Q	1.193	1.00
256_E	259_R	1.190	1.00
180_S	231_R	1.188	1.00
307_Q	311_L	1.186	1.00
255_V	307_Q	1.186	1.00
194_G	206_I	1.184	1.00
179_F	204_T	1.177	1.00
265_H	309_V	1.174	1.00
265_H	268_I	1.162	1.00
304_A	308_D	1.158	1.00
260_E	263_K	1.154	1.00
220_L	225_S	1.143	1.00
183_D	231_R	1.142	1.00
220_L	223_S	1.141	1.00
151_I	160_G	1.137	1.00
237_I	292_C	1.128	1.00
45_V	51_T	1.112	1.00
196_V	206_I	1.111	1.00
148_F	151_I	1.107	1.00
214_L	227_E	1.101	1.00
103_K	119_S	1.098	1.00
244_R	247_D	1.095	1.00
15_I	19_S	1.087	1.00
235_R	302_W	1.084	1.00
326_F	330_T	1.081	1.00
283_D	327_P	1.081	1.00
163_I	169_S	1.076	1.00
276_V	290_V	1.073	1.00
95_F	123_K	1.072	1.00
242_G	326_F	1.071	1.00
187_S	221_F	1.065	1.00
87_A	137_H	1.062	1.00
15_I	22_A	1.062	1.00
264_N	316_I	1.057	1.00
77_V	81_I	1.056	1.00
254_I	317_V	1.049	1.00
87_A	130_L	1.042	1.00
205_K	213_P	1.040	1.00
254_I	258_V	1.034	1.00
91_T	95_F	1.033	1.00
172_M	222_S	1.033	1.00
80_F	83_T	1.031	1.00
245_Y	326_F	1.027	1.00
28_F	32_R	1.027	1.00
192_I	225_S	1.023	1.00
36_K	41_L	1.022	1.00
303_L	307_Q	1.019	1.00
242_G	245_Y	1.019	1.00
243_L	317_V	1.016	1.00
247_D	323_D	1.007	1.00
159_A	164_L	1.006	1.00
247_D	251_V	1.005	1.00
317_V	324_F	1.005	1.00
284_S	326_F	1.005	1.00
280_Q	310_Y	1.002	1.00
240_T	280_Q	0.991	1.00
211_N	293_F	0.988	1.00
279_N	287_N	0.987	1.00
258_V	290_V	0.985	1.00
278_F	310_Y	0.983	1.00
252_G	255_V	0.983	1.00
151_I	155_A	0.977	1.00
79_D	83_T	0.970	1.00
177_R	180_S	0.967	1.00
257_A	319_S	0.953	1.00
258_V	262_L	0.950	1.00
247_D	254_I	0.949	1.00
45_V	53_I	0.946	1.00
93_K	97_L	0.943	1.00
27_S	30_F	0.941	1.00
281_F	286_L	0.940	1.00
257_A	322_A	0.935	1.00
246_E	314_I	0.933	1.00
257_A	317_V	0.932	1.00
36_K	40_F	0.924	1.00
135_G	140_M	0.923	1.00
134_Y	138_F	0.919	1.00
242_G	283_D	0.917	1.00
50_Y	54_I	0.912	1.00
49_I	53_I	0.912	1.00
62_N	66_E	0.911	1.00
22_A	26_M	0.899	1.00
43_H	46_Q	0.896	1.00
156_V	164_L	0.894	1.00
75_P	79_D	0.891	1.00
277_Y	307_Q	0.890	1.00
267_A	305_A	0.889	1.00
31_R	34_N	0.888	1.00
208_T	212_R	0.883	1.00
237_I	306_Q	0.883	1.00
31_R	35_R	0.875	1.00
262_L	268_I	0.871	1.00
267_A	304_A	0.869	1.00
20_C	24_I	0.866	1.00
236_R	293_F	0.865	1.00
28_F	31_R	0.864	1.00
19_S	22_A	0.860	1.00
246_E	323_D	0.856	1.00
241_I	258_V	0.854	1.00
245_Y	286_L	0.848	1.00
281_F	310_Y	0.847	1.00
55_S	59_S	0.846	1.00
282_A	285_S	0.844	1.00
203_I	215_Y	0.835	1.00
50_Y	53_I	0.831	1.00
213_P	231_R	0.825	1.00
192_I	214_L	0.823	1.00
212_R	227_E	0.821	1.00
102_E	105_Q	0.819	1.00
51_T	58_G	0.816	1.00
244_R	325_A	0.815	1.00
23_L	30_F	0.815	1.00
261_M	309_V	0.814	1.00
210_D	236_R	0.811	1.00
245_Y	324_F	0.811	1.00
259_R	274_L	0.810	1.00
146_L	155_A	0.809	1.00
251_V	288_I	0.808	1.00
32_R	35_R	0.806	1.00
76_G	80_F	0.804	1.00
284_S	329_Q	0.804	1.00
45_V	49_I	0.804	1.00
311_L	315_D	0.802	1.00
239_T	310_Y	0.801	1.00
254_I	322_A	0.800	1.00
309_V	313_I	0.798	1.00
61_I	65_I	0.792	1.00
152_G	156_V	0.792	1.00
29_W	33_G	0.790	1.00
259_R	276_V	0.788	1.00
285_S	326_F	0.788	1.00
245_Y	284_S	0.786	1.00
53_I	57_V	0.784	1.00
22_A	30_F	0.784	1.00
23_L	28_F	0.784	1.00
53_I	56_A	0.782	1.00
149_G	152_G	0.780	1.00
257_A	261_M	0.780	1.00
127_I	131_V	0.778	1.00
252_G	259_R	0.773	1.00
254_I	257_A	0.772	1.00
268_I	292_C	0.770	1.00
18_G	36_K	0.769	1.00
237_I	302_W	0.769	1.00
185_I	206_I	0.767	1.00
251_V	255_V	0.765	1.00
46_Q	50_Y	0.760	1.00
16_I	19_S	0.760	1.00
20_C	30_F	0.756	1.00
238_T	291_Y	0.756	1.00
261_M	265_H	0.756	1.00
176_D	203_I	0.754	1.00
43_H	47_F	0.751	1.00
262_L	276_V	0.751	1.00
259_R	262_L	0.750	1.00
28_F	34_N	0.745	1.00
195_T	207_T	0.744	1.00
240_T	279_N	0.744	1.00
22_A	34_N	0.743	1.00
64_V	68_Y	0.738	1.00
193_E	229_P	0.738	1.00
323_D	330_T	0.734	1.00
243_L	322_A	0.733	1.00
50_Y	58_G	0.732	1.00
185_I	221_F	0.731	1.00
262_L	309_V	0.730	1.00
165_S	223_S	0.729	0.99
62_N	65_I	0.725	0.99
188_P	220_L	0.724	0.99
113_T	174_Y	0.724	0.99
165_S	219_S	0.723	0.99
124_I	128_V	0.723	0.99
16_I	30_F	0.723	0.99
207_T	211_N	0.722	0.99
27_S	32_R	0.721	0.99
123_K	127_I	0.717	0.99
156_V	168_F	0.717	0.99
243_L	288_I	0.717	0.99
54_I	58_G	0.716	0.99
326_F	329_Q	0.712	0.99
77_V	80_F	0.712	0.99
36_K	42_F	0.712	0.99
61_I	64_V	0.707	0.99
95_F	99_N	0.706	0.99
23_L	26_M	0.706	0.99
21_A	24_I	0.705	0.99
152_G	155_A	0.701	0.99
178_P	205_K	0.699	0.99
286_L	314_I	0.697	0.99
303_L	306_Q	0.693	0.99
91_T	126_I	0.692	0.99
74_T	77_V	0.690	0.99
278_F	288_I	0.690	0.99
207_T	213_P	0.688	0.99
258_V	276_V	0.683	0.99
116_R	120_R	0.678	0.99
277_Y	303_L	0.678	0.99
26_M	31_R	0.676	0.99
187_S	216_V	0.675	0.99
176_D	205_K	0.671	0.99
22_A	32_R	0.670	0.99
64_V	67_N	0.668	0.99
275_L	291_Y	0.664	0.99
57_V	60_I	0.664	0.99
87_A	91_T	0.662	0.99
284_S	328_S	0.661	0.99
22_A	25_L	0.660	0.99
160_G	168_F	0.658	0.99
163_I	222_S	0.658	0.99
45_V	50_Y	0.657	0.99
143_S	147_T	0.655	0.99
27_S	35_R	0.653	0.99
53_I	62_N	0.653	0.99
33_G	40_F	0.651	0.99
251_V	286_L	0.650	0.99
23_L	36_K	0.650	0.99
148_F	153_G	0.649	0.99
56_A	60_I	0.647	0.99
86_I	89_I	0.646	0.99
101_F	105_Q	0.645	0.99
16_I	20_C	0.644	0.99
47_F	50_Y	0.643	0.99
19_S	32_R	0.642	0.99
324_F	328_S	0.641	0.99
72_F	76_G	0.641	0.99
18_G	23_L	0.640	0.99
116_R	198_E	0.640	0.99
57_V	61_I	0.638	0.99
30_F	33_G	0.636	0.99
25_L	28_F	0.635	0.99
251_V	314_I	0.633	0.99
279_N	306_Q	0.633	0.99
41_L	45_V	0.632	0.99
15_I	18_G	0.630	0.99
130_L	134_Y	0.630	0.99
255_V	288_I	0.626	0.98
281_F	313_I	0.626	0.98
24_I	27_S	0.625	0.98
26_M	30_F	0.625	0.98
99_N	119_S	0.625	0.98
251_V	278_F	0.621	0.98
133_L	136_E	0.619	0.98
187_S	192_I	0.618	0.98
19_S	26_M	0.617	0.98
45_V	58_G	0.615	0.98
158_M	163_I	0.613	0.98
86_I	90_L	0.612	0.98
317_V	320_H	0.610	0.98
256_E	263_K	0.610	0.98
169_S	222_S	0.609	0.98
16_I	23_L	0.608	0.98
245_Y	285_S	0.605	0.98
244_R	330_T	0.605	0.98
51_T	56_A	0.605	0.98
254_I	320_H	0.603	0.98
19_S	24_I	0.600	0.98
150_G	161_K	0.600	0.98
26_M	32_R	0.600	0.98
281_F	314_I	0.599	0.98
15_I	28_F	0.599	0.98
119_S	123_K	0.598	0.98
120_R	123_K	0.595	0.98
53_I	65_I	0.592	0.98
234_N	272_Q	0.591	0.98
323_D	328_S	0.590	0.98
254_I	261_M	0.587	0.98
47_F	53_I	0.585	0.98
45_V	60_I	0.582	0.98
164_L	168_F	0.582	0.98
284_S	327_P	0.581	0.98
290_V	313_I	0.579	0.97
244_R	328_S	0.579	0.97
278_F	281_F	0.579	0.97
59_S	62_N	0.578	0.97
245_Y	283_D	0.577	0.97
26_M	29_W	0.576	0.97
162_D	219_S	0.576	0.97
219_S	222_S	0.576	0.97
307_Q	310_Y	0.575	0.97
30_F	34_N	0.574	0.97
32_R	36_K	0.573	0.97
242_G	281_F	0.572	0.97
246_E	318_Q	0.571	0.97
92_I	96_L	0.570	0.97
51_T	55_S	0.569	0.97
179_F	221_F	0.568	0.97
18_G	28_F	0.567	0.97
236_R	291_Y	0.562	0.97
44_A	48_L	0.561	0.97
72_F	77_V	0.560	0.97
247_D	286_L	0.560	0.97
158_M	161_K	0.559	0.97
178_P	226_V	0.559	0.97
23_L	33_G	0.558	0.97
325_A	328_S	0.558	0.97
42_F	50_Y	0.556	0.97
25_L	29_W	0.555	0.97
168_F	222_S	0.553	0.97
22_A	33_G	0.551	0.97
30_F	36_K	0.551	0.97
40_F	45_V	0.549	0.97
176_D	215_Y	0.548	0.96
98_I	126_I	0.548	0.96
262_L	292_C	0.547	0.96
308_D	311_L	0.546	0.96
258_V	317_V	0.545	0.96
155_A	160_G	0.545	0.96
275_L	279_N	0.545	0.96
84_S	88_V	0.545	0.96
237_I	294_T	0.544	0.96
18_G	30_F	0.543	0.96
111_D	114_S	0.542	0.96
56_A	59_S	0.540	0.96
162_D	166_N	0.539	0.96
65_I	68_Y	0.539	0.96
60_I	67_N	0.536	0.96
129_V	132_L	0.535	0.96
175_F	178_P	0.534	0.96
17_F	20_C	0.534	0.96
24_I	31_R	0.534	0.96
95_F	127_I	0.533	0.96
51_T	64_V	0.529	0.96
89_I	92_I	0.528	0.96
192_I	227_E	0.528	0.96
111_D	177_R	0.528	0.96
179_F	185_I	0.527	0.96
60_I	64_V	0.527	0.96
147_T	150_G	0.526	0.96
51_T	54_I	0.526	0.96
205_K	215_Y	0.526	0.96
102_E	106_I	0.525	0.96
195_T	209_F	0.525	0.96
44_A	47_F	0.524	0.95
255_V	276_V	0.524	0.95
23_L	31_R	0.521	0.95
17_F	24_I	0.521	0.95
110_R	114_S	0.520	0.95
200_G	205_K	0.519	0.95
263_K	274_L	0.518	0.95
305_A	308_D	0.518	0.95
150_G	154_L	0.517	0.95
152_G	159_A	0.516	0.95
154_L	162_D	0.515	0.95
263_K	273_T	0.515	0.95
47_F	58_G	0.514	0.95
18_G	24_I	0.512	0.95
200_G	203_I	0.512	0.95
130_L	133_L	0.510	0.95
179_F	226_V	0.508	0.95
100_Q	105_Q	0.508	0.95
251_V	254_I	0.508	0.95
49_I	57_V	0.508	0.95
53_I	60_I	0.507	0.95
209_F	291_Y	0.505	0.95
43_H	49_I	0.505	0.95
282_A	326_F	0.504	0.94
141_S	144_G	0.503	0.94
29_W	35_R	0.503	0.94
179_F	218_N	0.503	0.94
88_V	134_Y	0.503	0.94
161_K	219_S	0.501	0.94
23_L	34_N	0.500	0.94
244_R	324_F	0.500	0.94
150_G	153_G	0.500	0.94

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
5ajiA	3	0.7638	100	0.261	Contact Map
4hw9A	3	0.7376	100	0.264	Contact Map
3udcA	3	0.7376	100	0.296	Contact Map
1nz9A	1	0.1458	26.5	0.951	Contact Map
2e6zA	1	0.1545	22.2	0.953	Contact Map
2qn6B	1	0.2624	19.2	0.954	Contact Map
3cnrA	1	0.2478	17.2	0.955	Contact Map
2aalA	3	0.2915	15.3	0.956	Contact Map
4hfiA	3	0.344	12.9	0.958	Contact Map
3j9pD	4	0.7114	12.6	0.958	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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