YHDY - BACSU - GREMLIN Contacts

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YHDY - Uncharacterized MscS family protein YhdY

UniProt:	O07594	Sequences: MPDYLQQYFTLDNIIQIGISLAILLVFLILRKLFTRYFFNLLFNLTNRPKTEIFKQVVLAFDKPARWFFVALGLFLAIRYSPFLDEQMPVISKIYRSLIVALLCWGLCNLTATSSFIFHKVNQRFELDMDDILAPFLSKLLRFVIIALSVSVIAQEFNYDVNGFVAGLGLGGLAFALAAKDTISNFFGGIIIITEKPFTIGDWVETSTVTGSVEDITFRSTRFRTAQGALVTVPNSTLSMEAITNWTRMTKRQITFSIHVSYATPIENLERSIHSLRTMLLEHEGVDNEIIMVNFDTFADSYYNLFFNFYTKTTVWAENLNIREDINYKIIEILGAEGVQFAYPGQMVVVKQKHESDQFQVNLNKEEKERA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	371 (323)
Sequences:	6291 (4858)
Seq/√Len:	270.3

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
104_C	149_S	5.552	1.00
265_P	268_N	4.247	1.00
277_R	281_L	4.171	1.00
214_E	224_R	3.572	1.00
267_E	332_E	3.528	1.00
297_T	304_N	3.242	1.00
299_A	304_N	3.061	1.00
259_H	302_Y	3.031	1.00
331_I	335_G	2.973	1.00
268_N	271_R	2.917	1.00
205_E	210_T	2.845	1.00
283_H	325_D	2.834	1.00
333_I	336_A	2.721	1.00
278_T	282_E	2.703	1.00
329_K	332_E	2.647	1.00
332_E	336_A	2.603	1.00
268_N	337_E	2.556	1.00
180_K	184_S	2.538	1.00
49_P	54_F	2.491	1.00
295_F	303_Y	2.478	1.00
313_T	318_E	2.471	1.00
333_I	337_E	2.447	1.00
296_D	306_F	2.410	1.00
279_M	329_K	2.386	1.00
195_E	219_R	2.369	1.00
309_F	326_I	2.300	1.00
204_V	213_V	2.284	1.00
267_E	270_E	2.134	1.00
300_D	304_N	2.108	1.00
262_Y	298_F	2.048	1.00
268_N	272_S	2.024	1.00
270_E	328_Y	2.012	1.00
205_E	244_T	1.995	1.00
269_L	305_L	1.986	1.00
259_H	304_N	1.970	1.00
273_I	330_I	1.963	1.00
260_V	269_L	1.951	1.00
267_E	271_R	1.936	1.00
255_T	306_F	1.921	1.00
215_D	222_R	1.898	1.00
272_S	333_I	1.896	1.00
257_S	304_N	1.882	1.00
271_R	278_T	1.881	1.00
221_T	235_N	1.867	1.00
258_I	330_I	1.866	1.00
257_S	306_F	1.849	1.00
225_T	231_V	1.838	1.00
261_S	340_Q	1.837	1.00
334_L	339_V	1.829	1.00
205_E	208_T	1.816	1.00
203_W	210_T	1.767	1.00
237_T	241_E	1.764	1.00
270_E	273_I	1.731	1.00
319_N	323_R	1.730	1.00
265_P	269_L	1.730	1.00
116_F	120_K	1.686	1.00
259_H	301_S	1.677	1.00
203_W	212_S	1.676	1.00
214_E	230_L	1.665	1.00
203_W	226_A	1.660	1.00
323_R	327_N	1.659	1.00
280_L	307_F	1.646	1.00
205_E	246_W	1.607	1.00
278_T	281_L	1.599	1.00
300_D	346_Q	1.597	1.00
97_S	153_I	1.597	1.00
173_L	176_A	1.565	1.00
272_S	278_T	1.550	1.00
325_D	329_K	1.544	1.00
199_T	248_R	1.540	1.00
118_F	121_V	1.533	1.00
163_G	166_A	1.530	1.00
49_P	55_K	1.528	1.00
260_V	334_L	1.527	1.00
278_T	333_I	1.521	1.00
211_G	223_F	1.513	1.00
329_K	333_I	1.497	1.00
259_H	299_A	1.495	1.00
279_M	333_I	1.469	1.00
283_H	329_K	1.468	1.00
207_S	241_E	1.457	1.00
311_T	322_I	1.453	1.00
318_E	321_N	1.418	1.00
181_D	184_S	1.405	1.00
285_G	318_E	1.401	1.00
170_L	174_A	1.396	1.00
32_K	36_R	1.388	1.00
259_H	262_Y	1.363	1.00
285_G	325_D	1.359	1.00
28_L	32_K	1.351	1.00
343_Y	347_M	1.341	1.00
182_T	188_G	1.333	1.00
196_K	199_T	1.316	1.00
334_L	341_F	1.304	1.00
207_S	242_A	1.303	1.00
170_L	179_A	1.302	1.00
281_L	288_N	1.297	1.00
272_S	337_E	1.264	1.00
117_I	121_V	1.253	1.00
178_A	183_I	1.243	1.00
114_S	117_I	1.220	1.00
260_V	339_V	1.216	1.00
262_Y	341_F	1.214	1.00
118_F	122_N	1.212	1.00
66_R	70_V	1.212	1.00
263_A	340_Q	1.207	1.00
51_T	54_F	1.206	1.00
269_L	273_I	1.197	1.00
321_N	325_D	1.194	1.00
262_Y	343_Y	1.184	1.00
293_V	307_F	1.179	1.00
36_R	40_N	1.150	1.00
257_S	297_T	1.150	1.00
209_V	231_V	1.150	1.00
267_E	272_S	1.146	1.00
259_H	343_Y	1.138	1.00
272_S	339_V	1.133	1.00
97_S	157_F	1.130	1.00
296_D	304_N	1.128	1.00
324_E	328_Y	1.126	1.00
295_F	327_N	1.119	1.00
260_V	305_L	1.117	1.00
282_E	329_K	1.114	1.00
101_A	105_W	1.101	1.00
73_G	77_A	1.090	1.00
213_V	223_F	1.087	1.00
237_T	242_A	1.086	1.00
283_H	326_I	1.079	1.00
259_H	300_D	1.068	1.00
78_I	82_P	1.067	1.00
154_A	159_Y	1.066	1.00
263_A	343_Y	1.060	1.00
37_Y	41_L	1.056	1.00
343_Y	346_Q	1.054	1.00
93_K	96_R	1.045	1.00
27_F	31_R	1.044	1.00
210_T	226_A	1.041	1.00
265_P	270_E	1.033	1.00
260_V	264_T	1.029	1.00
230_L	248_R	1.025	1.00
41_L	45_L	1.025	1.00
271_R	337_E	1.019	1.00
279_M	326_I	1.010	1.00
294_N	324_E	1.008	1.00
22_A	25_L	1.007	1.00
269_L	272_S	1.002	1.00
302_Y	343_Y	1.001	1.00
266_I	270_E	1.001	1.00
204_V	223_F	0.999	1.00
299_A	302_Y	0.998	1.00
301_S	343_Y	0.995	1.00
33_L	37_Y	0.994	1.00
90_V	94_I	0.989	1.00
237_T	240_M	0.987	1.00
100_V	156_E	0.984	1.00
254_I	323_R	0.983	1.00
262_Y	300_D	0.981	1.00
280_L	286_V	0.981	1.00
265_P	272_S	0.980	1.00
263_A	331_I	0.979	1.00
175_F	183_I	0.971	1.00
253_Q	308_N	0.968	1.00
64_P	67_W	0.964	1.00
82_P	85_D	0.963	1.00
92_S	96_R	0.962	1.00
320_L	324_E	0.961	1.00
197_P	222_R	0.959	1.00
40_N	43_F	0.957	1.00
119_H	123_Q	0.954	1.00
225_T	229_A	0.953	1.00
100_V	149_S	0.952	1.00
254_I	309_F	0.949	1.00
224_R	228_G	0.947	1.00
74_L	77_A	0.944	1.00
67_W	71_A	0.943	1.00
40_N	44_N	0.943	1.00
226_A	308_N	0.940	1.00
60_A	64_P	0.935	1.00
198_F	221_T	0.927	1.00
266_I	305_L	0.922	1.00
108_C	146_I	0.921	1.00
259_H	298_F	0.921	1.00
231_V	244_T	0.915	1.00
256_F	327_N	0.908	1.00
111_T	145_I	0.906	1.00
252_R	319_N	0.906	1.00
31_R	35_T	0.906	1.00
266_I	331_I	0.904	1.00
168_L	171_G	0.904	1.00
297_T	327_N	0.900	1.00
32_K	35_T	0.899	1.00
279_M	283_H	0.899	1.00
45_L	48_R	0.893	1.00
21_L	25_L	0.887	1.00
272_S	334_L	0.882	1.00
171_G	174_A	0.880	1.00
108_C	142_R	0.878	1.00
340_Q	347_M	0.875	1.00
70_V	77_A	0.875	1.00
229_A	244_T	0.872	1.00
114_S	118_F	0.870	1.00
195_E	220_S	0.865	1.00
307_F	330_I	0.860	1.00
114_S	121_V	0.850	1.00
270_E	324_E	0.849	1.00
70_V	73_G	0.849	1.00
227_Q	253_Q	0.847	1.00
46_T	49_P	0.842	1.00
175_F	187_F	0.841	1.00
124_R	127_L	0.841	1.00
228_G	310_Y	0.834	0.99
261_S	341_F	0.833	0.99
257_S	296_D	0.833	0.99
44_N	48_R	0.831	0.99
262_Y	301_S	0.829	0.99
63_K	67_W	0.826	0.99
303_Y	331_I	0.826	0.99
187_F	239_S	0.826	0.99
66_R	78_I	0.824	0.99
180_K	236_S	0.824	0.99
115_S	118_F	0.823	0.99
19_I	23_I	0.821	0.99
171_G	175_F	0.817	0.99
165_V	174_A	0.817	0.99
61_F	64_P	0.815	0.99
301_S	341_F	0.811	0.99
171_G	178_A	0.810	0.99
181_D	185_N	0.810	0.99
19_I	22_A	0.809	0.99
78_I	81_S	0.807	0.99
120_K	124_R	0.802	0.99
298_F	331_I	0.801	0.99
300_D	344_P	0.800	0.99
285_G	322_I	0.799	0.99
226_A	246_W	0.795	0.99
262_Y	303_Y	0.795	0.99
68_F	72_L	0.794	0.99
300_D	341_F	0.794	0.99
77_A	81_S	0.794	0.99
298_F	327_N	0.789	0.99
191_I	239_S	0.784	0.99
104_C	108_C	0.779	0.99
298_F	303_Y	0.772	0.99
104_C	145_I	0.769	0.99
301_S	344_P	0.768	0.99
264_T	269_L	0.767	0.99
207_S	237_T	0.762	0.99
66_R	69_F	0.760	0.99
42_L	46_T	0.757	0.99
294_N	321_N	0.754	0.99
182_T	239_S	0.750	0.99
311_T	319_N	0.749	0.99
342_A	346_Q	0.749	0.99
264_T	303_Y	0.747	0.99
135_P	215_D	0.743	0.99
140_L	144_V	0.742	0.99
67_W	70_V	0.737	0.99
114_S	120_K	0.737	0.99
29_I	32_K	0.737	0.99
32_K	37_Y	0.733	0.99
341_F	345_G	0.730	0.99
263_A	335_G	0.730	0.99
143_F	147_A	0.729	0.99
56_Q	59_L	0.728	0.99
326_I	330_I	0.728	0.99
36_R	39_F	0.726	0.99
198_F	243_I	0.725	0.99
262_Y	302_Y	0.725	0.99
311_T	314_T	0.725	0.99
135_P	139_K	0.721	0.99
294_N	320_L	0.720	0.99
222_R	230_L	0.719	0.98
35_T	39_F	0.719	0.98
37_Y	40_N	0.718	0.98
273_I	307_F	0.715	0.98
262_Y	344_P	0.715	0.98
322_I	325_D	0.712	0.98
325_D	328_Y	0.711	0.98
74_L	78_I	0.710	0.98
22_A	26_V	0.710	0.98
292_M	308_N	0.707	0.98
46_T	55_K	0.707	0.98
210_T	246_W	0.698	0.98
146_I	150_V	0.698	0.98
173_L	181_D	0.696	0.98
197_P	243_I	0.696	0.98
263_A	347_M	0.696	0.98
206_T	233_V	0.695	0.98
88_M	92_S	0.694	0.98
261_S	342_A	0.694	0.98
38_F	42_L	0.694	0.98
270_E	332_E	0.692	0.98
64_P	70_V	0.690	0.98
174_A	179_A	0.688	0.98
184_S	236_S	0.688	0.98
28_L	35_T	0.685	0.98
24_L	31_R	0.685	0.98
295_F	305_L	0.684	0.98
89_P	93_K	0.683	0.98
24_L	27_F	0.682	0.98
101_A	104_C	0.680	0.98
132_I	193_I	0.680	0.98
93_K	156_E	0.680	0.98
261_S	345_G	0.679	0.98
167_G	170_L	0.679	0.98
101_A	153_I	0.678	0.98
225_T	253_Q	0.678	0.98
41_L	44_N	0.678	0.98
176_A	180_K	0.677	0.98
79_R	83_F	0.677	0.98
51_T	55_K	0.675	0.98
153_I	157_F	0.675	0.98
267_E	328_Y	0.674	0.98
294_N	308_N	0.674	0.98
62_D	78_I	0.672	0.98
166_A	169_G	0.671	0.98
179_A	218_F	0.671	0.98
20_S	30_L	0.669	0.98
320_L	323_R	0.668	0.98
169_G	184_S	0.666	0.98
69_F	78_I	0.665	0.98
261_S	343_Y	0.665	0.98
60_A	69_F	0.664	0.97
184_S	240_M	0.664	0.97
81_S	85_D	0.659	0.97
203_W	246_W	0.655	0.97
286_V	309_F	0.654	0.97
72_L	76_L	0.652	0.97
39_F	46_T	0.651	0.97
123_Q	127_L	0.644	0.97
331_I	341_F	0.642	0.97
53_I	57_V	0.640	0.97
31_R	34_F	0.638	0.97
23_I	80_Y	0.637	0.97
116_F	119_H	0.637	0.97
301_S	345_G	0.637	0.97
18_G	21_L	0.636	0.97
36_R	43_F	0.636	0.97
170_L	173_L	0.635	0.97
194_T	218_F	0.635	0.97
147_A	151_S	0.634	0.97
115_S	119_H	0.634	0.97
269_L	303_Y	0.634	0.97
145_I	149_S	0.632	0.97
46_T	51_T	0.631	0.97
17_I	21_L	0.631	0.97
60_A	78_I	0.631	0.97
63_K	75_F	0.629	0.97
70_V	75_F	0.628	0.96
31_R	36_R	0.626	0.96
209_V	242_A	0.625	0.96
173_L	179_A	0.625	0.96
64_P	68_F	0.625	0.96
62_D	70_V	0.624	0.96
255_T	308_N	0.624	0.96
73_G	78_I	0.624	0.96
64_P	105_W	0.623	0.96
295_F	331_I	0.620	0.96
298_F	330_I	0.618	0.96
60_A	63_K	0.615	0.96
46_T	54_F	0.615	0.96
25_L	30_L	0.614	0.96
204_V	238_L	0.614	0.96
296_D	323_R	0.613	0.96
192_I	217_T	0.609	0.96
167_G	172_G	0.608	0.96
187_F	191_I	0.607	0.96
56_Q	60_A	0.607	0.96
197_P	220_S	0.605	0.96
342_A	345_G	0.602	0.96
32_K	41_L	0.600	0.95
149_S	153_I	0.600	0.95
287_D	312_K	0.599	0.95
36_R	41_L	0.597	0.95
136_F	139_K	0.596	0.95
280_L	291_I	0.592	0.95
262_Y	299_A	0.589	0.95
137_L	141_L	0.588	0.95
60_A	66_R	0.585	0.95
334_L	337_E	0.585	0.95
220_S	232_T	0.584	0.95
181_D	236_S	0.584	0.95
220_S	247_T	0.583	0.95
292_M	317_A	0.583	0.95
283_H	286_V	0.581	0.95
66_R	79_R	0.581	0.95
189_G	244_T	0.580	0.95
99_I	103_L	0.580	0.95
161_V	166_A	0.580	0.95
70_V	78_I	0.580	0.95
202_D	248_R	0.577	0.94
277_R	280_L	0.576	0.94
179_A	187_F	0.575	0.94
191_I	219_R	0.573	0.94
249_M	252_R	0.572	0.94
35_T	38_F	0.572	0.94
138_S	142_R	0.570	0.94
27_F	33_L	0.568	0.94
341_F	347_M	0.568	0.94
57_V	60_A	0.567	0.94
105_W	109_N	0.566	0.94
63_K	109_N	0.565	0.94
281_L	290_I	0.564	0.94
285_G	321_N	0.563	0.94
300_D	343_Y	0.563	0.94
120_K	123_Q	0.562	0.94
151_S	161_V	0.562	0.94
18_G	22_A	0.562	0.94
39_F	53_I	0.559	0.93
195_E	232_T	0.559	0.93
212_S	226_A	0.557	0.93
277_R	321_N	0.557	0.93
166_A	170_L	0.554	0.93
95_Y	144_V	0.554	0.93
39_F	44_N	0.554	0.93
266_I	303_Y	0.552	0.93
81_S	84_L	0.552	0.93
205_E	225_T	0.552	0.93
87_Q	90_V	0.547	0.93
29_I	33_L	0.546	0.93
200_I	216_I	0.545	0.93
258_I	295_F	0.544	0.92
177_L	182_T	0.544	0.92
266_I	328_Y	0.544	0.92
181_D	240_M	0.543	0.92
192_I	320_L	0.543	0.92
115_S	138_S	0.542	0.92
258_I	273_I	0.538	0.92
19_I	36_R	0.538	0.92
194_T	197_P	0.538	0.92
105_W	108_C	0.537	0.92
198_F	235_N	0.536	0.92
22_A	29_I	0.535	0.92
280_L	309_F	0.535	0.92
178_A	187_F	0.531	0.92
185_N	236_S	0.530	0.92
69_F	76_L	0.530	0.92
162_N	166_A	0.529	0.91
139_K	143_F	0.529	0.91
54_F	57_V	0.529	0.91
185_N	234_P	0.529	0.91
236_S	239_S	0.528	0.91
295_F	298_F	0.528	0.91
178_A	219_R	0.527	0.91
227_Q	255_T	0.527	0.91
212_S	224_R	0.527	0.91
168_L	218_F	0.527	0.91
270_E	277_R	0.526	0.91
155_Q	160_D	0.526	0.91
121_V	124_R	0.525	0.91
236_S	240_M	0.523	0.91
67_W	74_L	0.523	0.91
76_L	80_Y	0.521	0.91
308_N	320_L	0.521	0.91
198_F	238_L	0.521	0.91
52_E	85_D	0.521	0.91
203_W	244_T	0.520	0.91
270_E	293_V	0.519	0.91
63_K	66_R	0.519	0.91
23_I	40_N	0.517	0.90
258_I	305_L	0.517	0.90
55_K	58_V	0.516	0.90
203_W	252_R	0.516	0.90
206_T	238_L	0.515	0.90
61_F	81_S	0.515	0.90
167_G	230_L	0.513	0.90
277_R	291_I	0.513	0.90
265_P	271_R	0.513	0.90
264_T	268_N	0.513	0.90
93_K	97_S	0.512	0.90
64_P	69_F	0.510	0.90
313_T	317_A	0.509	0.90
299_A	303_Y	0.508	0.90
20_S	23_I	0.506	0.90
251_K	289_E	0.506	0.90
26_V	30_L	0.504	0.89
273_I	334_L	0.503	0.89
117_I	120_K	0.501	0.89
224_R	230_L	0.501	0.89
268_N	273_I	0.501	0.89
287_D	314_T	0.501	0.89
213_V	241_E	0.500	0.89
182_T	219_R	0.500	0.89
253_Q	310_Y	0.500	0.89

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
4hw9A	3	0.6792	100	0.302	Contact Map
5ajiA	3	0.7062	100	0.316	Contact Map
3udcA	3	0.6981	100	0.329	Contact Map
3j9pD	4	0.7332	33	0.954	Contact Map
4mt1A	3	0.8787	19.1	0.959	Contact Map
1nz9A	1	0.1294	18.9	0.959	Contact Map
2aalA	3	0.3019	18	0.959	Contact Map
3ne5A	3	0.8976	17.1	0.96	Contact Map
2lt1A	1	0.1698	15.4	0.961	Contact Map
2e6zA	1	0.1375	15.1	0.961	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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