YHCY - BACSU - GREMLIN Contacts

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YHCY - Sensor histidine kinase YhcY

UniProt:	O07527	Sequences: MSKTRMEKLKTLKTIAETLNQGHDIKATLDEVLKELLSLTNLQSGWIFLIEEDGSYTLAADAYLPPALSRKEKVLMCEGECYCLTKFNNGGLRKAANIMNCKRIESAENLHCFDTEGITHHATVPLEDGDRRFGLLNVAAAGKTMFDEEELHLLESVAFQIGTAIQRMRLSEYQQKNALLMERNRLAQELHDSVNQMLFSVSLTAKAAKTLTKDENLQQMIDFIQNLSQDALAEMKALIWQLRPGGLEKGLAEAIKSYGALIGLKIIFTQKGCPVLTDEQEHMLWRVVQEALNNCKKHAGTDTAYVSLTASLCHAELDIIDHGAGFRYEAHAGLPSLGIKGMKERAEKAGAKFWIESALGTGTKLSIRLPLKSRKGGAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	379 (332)
Sequences:	48169 (42303)
Seq/√Len:	2321.7

ECOLI - ARCB NARX RCSD EVGS RCSC KDPD ATOS TORS BARA NARQ DCUS DPIB PHOR ZRAS NTRB CREC GLRK YPDA BAES ENVZ CPXA PHOQ CUSS QSEC RSTB UHPB YEDV BASS
BACSU - YHCY KINE KINA YYCG COMP PHOR RESE KINC CITS DCTS LYTS DEGS KIND MALK YCLK YVRG YKOH CSSS KINB YRKQ YDFH YFIJ GLNK LIAS YVCQ YCBM YXJM BCES DESK YVFT YESM YXDK
HALSA - Q9HQG5 Q9HRG1 Q9HQ16 Q9HNM2 O51970 Q9HRE4 Q9HR10 BAT Q9HNA6 Q9HQB9 Q9HQE9 Q9HQ15

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
354_W	366_S	3.599	1.00
205_A	224_I	3.472	1.00
320_I	364_K	3.438	1.00
321_D	325_G	3.128	1.00
343_K	347_E	2.982	1.00
358_A	361_T	2.968	1.00
299_A	322_H	2.911	1.00
316_E	368_R	2.793	1.00
314_H	368_R	2.788	1.00
307_S	318_D	2.776	1.00
327_R	330_A	2.751	1.00
316_E	366_S	2.746	1.00
318_D	366_S	2.686	1.00
318_D	364_K	2.684	1.00
209_K	225_Q	2.662	1.00
267_I	303_T	2.639	1.00
279_E	349_A	2.609	1.00
269_T	307_S	2.494	1.00
342_M	353_F	2.475	1.00
209_K	222_D	2.433	1.00
355_I	365_L	2.403	1.00
309_T	316_E	2.380	1.00
305_Y	320_I	2.367	1.00
202_S	228_S	2.364	1.00
287_V	346_A	2.279	1.00
267_I	305_Y	2.270	1.00
269_T	305_Y	2.214	1.00
45_G	140_A	2.189	1.00
307_S	320_I	2.179	1.00
309_T	318_D	2.172	1.00
303_T	322_H	2.129	1.00
356_E	364_K	2.099	1.00
326_F	330_A	2.084	1.00
356_E	366_S	2.083	1.00
202_S	229_Q	1.995	1.00
346_A	351_A	1.957	1.00
299_A	304_A	1.939	1.00
352_K	368_R	1.938	1.00
253_E	285_W	1.935	1.00
173_Y	176_K	1.926	1.00
310_A	371_L	1.916	1.00
246_G	249_K	1.903	1.00
357_S	363_T	1.893	1.00
346_A	367_I	1.863	1.00
62_A	65_P	1.862	1.00
265_K	303_T	1.855	1.00
302_D	322_H	1.834	1.00
287_V	342_M	1.822	1.00
40_T	58_L	1.812	1.00
357_S	361_T	1.772	1.00
46_W	66_P	1.771	1.00
204_T	220_M	1.750	1.00
206_K	225_Q	1.731	1.00
48_F	137_N	1.715	1.00
280_Q	283_M	1.711	1.00
311_S	316_E	1.697	1.00
347_E	352_K	1.683	1.00
209_K	218_Q	1.677	1.00
248_E	308_L	1.667	1.00
51_E	55_S	1.650	1.00
317_L	367_I	1.645	1.00
201_V	228_S	1.642	1.00
33_L	37_L	1.629	1.00
354_W	368_R	1.629	1.00
232_L	236_K	1.623	1.00
287_V	345_R	1.610	1.00
181_M	185_R	1.575	1.00
169_R	173_Y	1.552	1.00
208_A	221_I	1.551	1.00
173_Y	177_N	1.547	1.00
345_R	349_A	1.543	1.00
279_E	284_L	1.542	1.00
183_R	187_A	1.535	1.00
111_H	115_T	1.525	1.00
299_A	302_D	1.521	1.00
225_Q	229_Q	1.490	1.00
258_Y	289_Q	1.474	1.00
61_D	65_P	1.436	1.00
128_D	131_R	1.436	1.00
288_V	317_L	1.422	1.00
127_E	132_R	1.422	1.00
168_M	171_S	1.407	1.00
204_T	223_F	1.402	1.00
69_S	112_C	1.395	1.00
43_Q	47_I	1.392	1.00
205_A	225_Q	1.390	1.00
270_Q	308_L	1.386	1.00
327_R	359_L	1.380	1.00
180_L	183_R	1.375	1.00
48_F	56_Y	1.367	1.00
211_L	217_L	1.364	1.00
200_S	227_L	1.354	1.00
172_E	176_K	1.344	1.00
212_T	217_L	1.344	1.00
287_V	367_I	1.334	1.00
293_N	297_K	1.334	1.00
208_A	217_L	1.329	1.00
171_S	175_Q	1.327	1.00
146_F	150_E	1.326	1.00
46_W	139_A	1.323	1.00
275_V	310_A	1.321	1.00
121_H	139_A	1.293	1.00
201_V	224_I	1.286	1.00
64_L	71_K	1.276	1.00
205_A	228_S	1.262	1.00
32_V	35_E	1.250	1.00
326_F	363_T	1.246	1.00
324_A	332_A	1.232	1.00
283_M	286_R	1.224	1.00
315_A	371_L	1.224	1.00
41_N	61_D	1.222	1.00
180_L	184_N	1.220	1.00
120_H	140_A	1.189	1.00
59_A	63_Y	1.186	1.00
283_M	348_K	1.184	1.00
248_E	252_A	1.183	1.00
30_D	34_K	1.178	1.00
63_Y	67_A	1.176	1.00
222_D	226_N	1.171	1.00
48_F	63_Y	1.170	1.00
175_Q	178_A	1.163	1.00
111_H	117_G	1.162	1.00
26_K	30_D	1.161	1.00
36_L	40_T	1.160	1.00
202_S	225_Q	1.151	1.00
200_S	204_T	1.139	1.00
357_S	360_G	1.136	1.00
346_A	353_F	1.134	1.00
37_L	41_N	1.130	1.00
233_A	282_H	1.125	1.00
171_S	174_Q	1.124	1.00
249_K	253_E	1.120	1.00
252_A	268_F	1.110	1.00
250_G	254_A	1.097	1.00
170_L	174_Q	1.093	1.00
246_G	276_L	1.088	1.00
142_G	146_F	1.084	1.00
218_Q	222_D	1.079	1.00
314_H	352_K	1.072	1.00
194_V	231_A	1.071	1.00
223_F	227_L	1.064	1.00
145_M	148_E	1.052	1.00
214_D	217_L	1.049	1.00
253_E	281_E	1.045	1.00
70_R	73_K	1.045	1.00
125_P	132_R	1.042	1.00
295_C	304_A	1.039	1.00
264_L	268_F	1.027	1.00
288_V	292_L	1.026	1.00
172_E	175_Q	1.020	1.00
219_Q	223_F	1.018	1.00
248_E	270_Q	1.017	1.00
202_S	232_L	1.014	1.00
110_L	116_E	1.013	1.00
311_S	368_R	1.005	1.00
60_A	63_Y	0.999	1.00
286_R	345_R	0.997	1.00
193_S	197_M	0.996	1.00
85_T	89_N	0.995	1.00
326_F	355_I	0.994	1.00
281_E	285_W	0.993	1.00
205_A	209_K	0.986	1.00
31_E	35_E	0.984	1.00
219_Q	222_D	0.984	1.00
185_R	189_E	0.981	1.00
143_K	146_F	0.980	1.00
193_S	290_E	0.979	1.00
61_D	64_L	0.979	1.00
178_A	181_M	0.974	1.00
258_Y	292_L	0.972	1.00
30_D	33_L	0.971	1.00
313_C	371_L	0.971	1.00
203_L	207_A	0.968	1.00
195_N	232_L	0.964	1.00
305_Y	322_H	0.961	1.00
285_W	289_Q	0.959	1.00
50_I	56_Y	0.957	1.00
190_L	238_L	0.956	1.00
51_E	57_T	0.953	1.00
49_L	134_G	0.951	1.00
69_S	73_K	0.949	1.00
227_L	230_D	0.948	1.00
205_A	221_I	0.948	1.00
291_A	342_M	0.945	1.00
49_L	58_L	0.945	1.00
34_K	38_S	0.936	1.00
59_A	64_L	0.933	1.00
321_D	362_G	0.933	1.00
290_E	342_M	0.932	1.00
120_H	144_T	0.930	1.00
278_D	372_K	0.930	1.00
311_S	314_H	0.929	1.00
292_L	304_A	0.928	1.00
344_E	347_E	0.927	1.00
271_K	308_L	0.925	1.00
254_A	285_W	0.922	1.00
271_K	309_T	0.922	1.00
64_L	70_R	0.919	1.00
179_L	183_R	0.918	1.00
346_A	369_L	0.914	1.00
59_A	74_V	0.913	1.00
213_K	217_L	0.911	1.00
170_L	176_K	0.909	1.00
257_S	289_Q	0.909	1.00
283_M	345_R	0.905	1.00
255_I	258_Y	0.904	1.00
255_I	268_F	0.902	1.00
259_G	296_K	0.901	1.00
291_A	365_L	0.895	1.00
195_N	236_K	0.892	1.00
233_A	237_A	0.890	1.00
169_R	172_E	0.888	1.00
254_A	258_Y	0.887	1.00
316_E	354_W	0.885	1.00
170_L	173_Y	0.884	1.00
215_E	218_Q	0.882	1.00
56_Y	60_A	0.878	1.00
271_K	274_P	0.876	1.00
264_L	296_K	0.871	1.00
119_T	122_A	0.870	1.00
178_A	182_E	0.868	1.00
27_A	31_E	0.866	1.00
169_R	176_K	0.865	1.00
252_A	256_K	0.865	1.00
254_A	257_S	0.863	1.00
351_A	369_L	0.857	1.00
97_N	100_N	0.849	1.00
29_L	32_V	0.849	1.00
250_G	253_E	0.842	1.00
193_S	286_R	0.838	1.00
192_D	290_E	0.836	1.00
147_D	150_E	0.835	1.00
257_S	285_W	0.834	1.00
109_N	117_G	0.826	1.00
298_H	332_A	0.818	1.00
202_S	206_K	0.815	1.00
123_T	135_L	0.815	1.00
241_Q	340_K	0.813	1.00
239_I	243_R	0.811	1.00
288_V	319_I	0.806	1.00
50_I	123_T	0.806	1.00
251_L	308_L	0.804	1.00
193_S	234_E	0.802	1.00
73_K	112_C	0.797	1.00
49_L	57_T	0.794	1.00
86_K	90_G	0.791	1.00
204_T	224_I	0.789	1.00
237_A	283_M	0.789	1.00
224_I	228_S	0.788	1.00
58_L	71_K	0.788	1.00
61_D	71_K	0.784	1.00
55_S	78_E	0.784	1.00
174_Q	177_N	0.782	1.00
277_T	280_Q	0.781	1.00
328_Y	358_A	0.780	1.00
79_G	82_Y	0.777	1.00
29_L	33_L	0.777	1.00
196_Q	203_L	0.774	1.00
204_T	227_L	0.772	1.00
25_I	28_T	0.770	1.00
240_W	283_M	0.769	1.00
60_A	66_P	0.768	1.00
95_A	98_I	0.767	1.00
118_I	145_M	0.766	1.00
64_L	74_V	0.766	1.00
342_M	346_A	0.764	1.00
223_F	226_N	0.761	1.00
85_T	88_N	0.760	1.00
196_Q	200_S	0.760	1.00
200_S	203_L	0.758	1.00
36_L	39_L	0.757	1.00
250_G	255_I	0.753	1.00
300_G	324_A	0.751	1.00
199_F	202_S	0.751	1.00
200_S	223_F	0.747	1.00
191_H	197_M	0.745	1.00
292_L	306_V	0.745	1.00
294_N	338_G	0.744	1.00
291_A	367_I	0.744	1.00
226_N	253_E	0.743	1.00
82_Y	87_F	0.741	1.00
247_L	317_L	0.740	1.00
123_T	137_N	0.739	1.00
265_K	268_F	0.738	1.00
195_N	239_I	0.737	1.00
321_D	363_T	0.736	1.00
79_G	84_L	0.735	1.00
120_H	123_T	0.735	1.00
35_E	39_L	0.734	1.00
254_A	289_Q	0.733	1.00
88_N	91_G	0.732	1.00
287_V	349_A	0.730	1.00
193_S	196_Q	0.730	1.00
32_V	36_L	0.722	1.00
86_K	91_G	0.722	1.00
284_L	349_A	0.722	1.00
149_E	152_H	0.717	1.00
283_M	349_A	0.716	1.00
208_A	220_M	0.716	1.00
80_E	84_L	0.716	1.00
303_T	320_I	0.716	1.00
222_D	225_Q	0.714	1.00
192_D	196_Q	0.713	1.00
271_K	275_V	0.713	1.00
67_A	109_N	0.712	1.00
251_L	288_V	0.711	1.00
177_N	181_M	0.709	1.00
148_E	152_H	0.707	1.00
87_F	90_G	0.707	1.00
291_A	353_F	0.707	1.00
27_A	30_D	0.706	1.00
113_F	117_G	0.701	1.00
325_G	363_T	0.701	1.00
264_L	299_A	0.698	1.00
28_T	32_V	0.698	1.00
35_E	38_S	0.694	1.00
259_G	264_L	0.693	1.00
35_E	49_L	0.692	1.00
128_D	133_F	0.691	1.00
182_E	185_R	0.691	1.00
207_A	211_L	0.691	1.00
71_K	75_L	0.690	1.00
33_L	36_L	0.690	1.00
255_I	266_I	0.685	1.00
91_G	95_A	0.685	1.00
236_K	240_W	0.685	1.00
46_W	63_Y	0.683	1.00
216_N	220_M	0.683	1.00
355_I	363_T	0.682	1.00
87_F	91_G	0.680	1.00
101_C	104_I	0.677	1.00
232_L	235_M	0.677	1.00
326_F	365_L	0.676	1.00
211_L	220_M	0.674	1.00
25_I	29_L	0.672	1.00
81_C	84_L	0.669	1.00
250_G	258_Y	0.668	1.00
186_L	190_L	0.668	1.00
228_S	232_L	0.667	1.00
230_D	285_W	0.666	1.00
249_K	281_E	0.666	1.00
208_A	224_I	0.666	1.00
324_A	363_T	0.665	1.00
259_G	262_I	0.664	1.00
247_L	315_A	0.658	1.00
273_C	310_A	0.658	1.00
252_A	270_Q	0.657	1.00
45_G	138_V	0.657	1.00
206_K	209_K	0.657	1.00
96_A	100_N	0.655	1.00
252_A	255_I	0.655	1.00
198_L	235_M	0.654	1.00
102_K	105_E	0.653	1.00
251_L	306_V	0.652	1.00
209_K	221_I	0.652	1.00
82_Y	86_K	0.651	1.00
38_S	42_L	0.649	1.00
217_L	220_M	0.648	1.00
262_I	296_K	0.647	1.00
298_H	324_A	0.646	1.00
250_G	257_S	0.643	1.00
308_L	317_L	0.637	1.00
50_I	54_G	0.634	1.00
297_K	332_A	0.634	1.00
206_K	210_T	0.633	1.00
240_W	243_R	0.632	1.00
211_L	214_D	0.630	1.00
147_D	151_L	0.630	1.00
274_P	308_L	0.629	1.00
250_G	279_E	0.628	1.00
28_T	31_E	0.624	1.00
82_Y	85_T	0.622	1.00
344_E	348_K	0.621	1.00
207_A	220_M	0.619	1.00
111_H	114_D	0.619	1.00
84_L	88_N	0.618	1.00
58_L	61_D	0.617	1.00
44_S	139_A	0.617	1.00
201_V	205_A	0.615	1.00
199_F	203_L	0.614	1.00
326_F	357_S	0.614	1.00
51_E	54_G	0.611	1.00
295_C	319_I	0.610	1.00
112_C	117_G	0.608	1.00
69_S	74_V	0.606	1.00
43_Q	46_W	0.606	1.00
59_A	67_A	0.605	1.00
337_L	341_G	0.605	1.00
253_E	257_S	0.604	1.00
229_Q	233_A	0.603	1.00
269_T	309_T	0.601	1.00
194_V	197_M	0.601	1.00
220_M	224_I	0.600	1.00
146_F	149_E	0.598	1.00
291_A	319_I	0.598	1.00
290_E	293_N	0.598	1.00
297_K	331_H	0.597	1.00
56_Y	59_A	0.597	1.00
77_C	81_C	0.597	1.00
282_H	285_W	0.596	1.00
49_L	136_L	0.596	1.00
204_T	207_A	0.592	1.00
80_E	83_C	0.592	1.00
142_G	145_M	0.591	1.00
249_K	252_A	0.590	1.00
286_R	289_Q	0.590	1.00
275_V	371_L	0.588	1.00
84_L	87_F	0.584	1.00
240_W	244_P	0.583	1.00
306_V	319_I	0.582	1.00
191_H	290_E	0.582	1.00
39_L	43_Q	0.579	1.00
48_F	121_H	0.579	1.00
117_G	122_A	0.578	1.00
81_C	85_T	0.576	1.00
145_M	149_E	0.575	1.00
177_N	180_L	0.575	1.00
50_I	135_L	0.575	1.00
143_K	147_D	0.574	1.00
209_K	212_T	0.572	1.00
79_G	83_C	0.571	1.00
52_E	132_R	0.571	1.00
202_S	205_A	0.571	1.00
181_M	184_N	0.571	1.00
314_H	370_P	0.569	1.00
297_K	333_G	0.568	1.00
320_I	358_A	0.567	1.00
195_N	231_A	0.565	1.00
46_W	62_A	0.565	1.00
74_V	77_C	0.564	1.00
213_K	218_Q	0.564	1.00
254_A	292_L	0.563	1.00
109_N	112_C	0.563	1.00
306_V	317_L	0.562	1.00
26_K	29_L	0.561	1.00
118_I	121_H	0.561	1.00
93_R	97_N	0.561	1.00
270_Q	274_P	0.558	1.00
176_K	179_L	0.557	1.00
204_T	208_A	0.556	1.00
246_G	250_G	0.555	1.00
197_M	231_A	0.552	1.00
248_E	272_G	0.552	1.00
85_T	90_G	0.552	1.00
258_Y	293_N	0.550	1.00
250_G	285_W	0.550	1.00
187_A	190_L	0.548	1.00
193_S	341_G	0.546	1.00
318_D	356_E	0.546	1.00
183_R	191_H	0.546	1.00
179_L	182_E	0.543	1.00
86_K	89_N	0.542	1.00
126_L	134_G	0.541	1.00
184_N	189_E	0.540	1.00
144_T	148_E	0.539	1.00
354_W	367_I	0.538	1.00
90_G	93_R	0.538	1.00
340_K	344_E	0.536	1.00
91_G	98_I	0.536	1.00
46_W	60_A	0.532	1.00
304_A	319_I	0.532	1.00
214_D	218_Q	0.530	1.00
351_A	370_P	0.530	1.00
46_W	49_L	0.529	1.00
243_R	335_P	0.528	1.00
121_H	124_V	0.528	1.00
191_H	196_Q	0.528	1.00
240_W	286_R	0.526	1.00
351_A	367_I	0.526	1.00
35_E	58_L	0.525	1.00
184_N	245_G	0.525	1.00
191_H	195_N	0.524	1.00
45_G	62_A	0.523	1.00
284_L	288_V	0.523	1.00
82_Y	98_I	0.522	1.00
258_Y	296_K	0.521	1.00
220_M	223_F	0.521	1.00
48_F	139_A	0.520	1.00
168_M	172_E	0.519	1.00
63_Y	66_P	0.517	1.00
289_Q	293_N	0.517	1.00
109_N	114_D	0.516	1.00
114_D	117_G	0.515	1.00
113_F	116_E	0.513	1.00
353_F	365_L	0.513	1.00
263_G	301_T	0.512	1.00
49_L	59_A	0.511	1.00
39_L	42_L	0.511	1.00
124_V	136_L	0.509	1.00
174_Q	178_A	0.508	1.00
328_Y	357_S	0.508	1.00
189_E	196_Q	0.505	1.00
227_L	231_A	0.503	1.00
52_E	131_R	0.503	1.00
232_L	238_L	0.501	1.00
179_L	184_N	0.501	1.00
261_L	264_L	0.500	1.00
109_N	119_T	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
4i5sA	2	0.8681	100	0.362	Contact Map
3a0rA	2	0.8127	100	0.367	Contact Map
4gczA	2	0.8997	100	0.368	Contact Map
4r3aA	1	0.7995	100	0.422	Contact Map
4bixA	2	0.5435	100	0.469	Contact Map
4q20A	2	0.5409	100	0.47	Contact Map
4r39A	1	0.5251	100	0.474	Contact Map
4ctiA	2	0.5831	100	0.479	Contact Map
3d36A	2	0.5198	100	0.484	Contact Map
3jz3A	2	0.3852	100	0.484	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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