ADRA - ECOLI - GREMLIN Contacts

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ADRA - Probable diguanylate cyclase AdrA

UniProt:	P0AAP1	Sequences: MFPKIMNDENFFKKAAAHGEEPPLTPQNEHQRSGLRFARRVRLPRAVGLAGMFLPIASTLVSHPPPGWWWLVLVGWAFVWPHLAWQIASRAVDPLSREIYNLKTDAVLAGMWVGVMGVNVLPSTAMLMIMCLNLMGAGGPRLFVAGLVLMVVSCLVTLELTGITVSFNSAPLEWWLSLPIIVIYPLLFGWVSYQTATKLAEHKRRLQVMSTRDGMTGVYNRRHWETMLRNEFDNCRRHNRDATLLIIDIDHFKSINDTWGHDVGDEAIVALTRQLQITLRGSDVIGRFGGDEFAVIMSGTPAESAITAMLRVHEGLNTLRLPNTPQVTLRISVGVAPLNPQMSHYREWLKSADLALYKAKKAGRNRTEVAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11257
Length:	371 (323)
Sequences:	13149 (12189)
Seq/√Len:	678.2

ECOLI - ADRA YEAI YCDT YEGE YEDQ YNEF YDAM DOSC YFEA YEAJ DOSP YFIN YEAP YFGF GMR YLIF YLIE YHJK CSRD
BACSU - YHCK YTRP YKOW YDAK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
280_R	283_D	4.315	1.00
251_H	364_R	4.084	1.00
208_V	212_R	3.835	1.00
245_L	309_M	3.486	1.00
245_L	333_V	3.425	1.00
228_L	345_Y	3.391	1.00
359_A	368_E	3.294	1.00
243_T	337_P	3.291	1.00
219_Y	223_H	3.145	1.00
224_W	294_A	2.974	1.00
218_V	272_T	2.687	1.00
317_N	365_N	2.686	1.00
310_L	313_H	2.616	1.00
249_I	271_L	2.537	1.00
332_S	359_A	2.454	1.00
224_W	286_G	2.453	1.00
199_L	203_K	2.449	1.00
218_V	285_I	2.442	1.00
288_F	294_A	2.403	1.00
243_T	305_A	2.375	1.00
362_A	368_E	2.363	1.00
266_E	269_V	2.350	1.00
274_Q	319_L	2.345	1.00
339_N	342_M	2.282	1.00
262_D	350_K	2.236	1.00
313_H	367_T	2.222	1.00
231_E	234_N	2.167	1.00
301_P	304_S	2.156	1.00
275_L	285_I	2.129	1.00
203_K	206_L	2.125	1.00
223_H	227_M	2.036	1.00
362_A	366_R	2.007	1.00
267_A	329_L	1.997	1.00
247_I	333_V	1.996	1.00
358_K	362_A	1.988	1.00
344_H	347_E	1.983	1.00
316_L	331_I	1.960	1.00
247_I	331_I	1.947	1.00
255_I	267_A	1.945	1.00
227_M	230_N	1.927	1.00
216_T	268_I	1.922	1.00
350_K	354_L	1.912	1.00
313_H	317_N	1.858	1.00
297_M	308_A	1.821	1.00
359_A	366_R	1.820	1.00
279_L	285_I	1.802	1.00
250_D	332_S	1.794	1.00
207_Q	211_T	1.766	1.00
330_R	365_N	1.752	1.00
246_I	356_L	1.718	1.00
219_Y	284_V	1.700	1.00
245_L	297_M	1.695	1.00
271_L	316_L	1.688	1.00
358_K	368_E	1.680	1.00
242_A	348_W	1.666	1.00
270_A	273_R	1.664	1.00
192_S	195_T	1.650	1.00
211_T	226_T	1.631	1.00
249_I	331_I	1.627	1.00
278_T	311_R	1.626	1.00
273_R	276_Q	1.623	1.00
255_I	327_V	1.602	1.00
263_V	266_E	1.599	1.00
196_A	199_L	1.596	1.00
358_K	361_K	1.592	1.00
246_I	288_F	1.570	1.00
343_S	351_S	1.551	1.00
221_R	265_D	1.551	1.00
288_F	349_L	1.543	1.00
195_T	199_L	1.543	1.00
308_A	311_R	1.527	1.00
310_L	314_E	1.522	1.00
338_L	348_W	1.493	1.00
242_A	338_L	1.486	1.00
214_G	222_R	1.482	1.00
278_T	315_G	1.479	1.00
257_D	357_Y	1.476	1.00
270_A	274_Q	1.462	1.00
246_I	349_L	1.458	1.00
227_M	231_E	1.443	1.00
342_M	351_S	1.437	1.00
227_M	284_V	1.435	1.00
271_L	275_L	1.424	1.00
270_A	320_R	1.423	1.00
266_E	270_A	1.410	1.00
253_K	257_D	1.399	1.00
227_M	286_G	1.382	1.00
211_T	223_H	1.375	1.00
254_S	258_T	1.340	1.00
306_I	310_L	1.338	1.00
223_H	284_V	1.332	1.00
202_H	205_R	1.327	1.00
200_A	203_K	1.321	1.00
353_D	357_Y	1.320	1.00
305_A	335_V	1.310	1.00
335_V	367_T	1.300	1.00
192_S	196_A	1.300	1.00
279_L	295_V	1.298	1.00
240_R	299_G	1.296	1.00
209_M	222_R	1.288	1.00
199_L	202_H	1.285	1.00
251_H	254_S	1.280	1.00
261_H	353_D	1.266	1.00
272_T	285_I	1.262	1.00
313_H	333_V	1.261	1.00
253_K	357_Y	1.255	1.00
225_E	346_R	1.250	1.00
314_E	318_T	1.241	1.00
336_A	348_W	1.238	1.00
225_E	229_R	1.235	1.00
252_F	268_I	1.231	1.00
279_L	283_D	1.231	1.00
274_Q	320_R	1.225	1.00
261_H	357_Y	1.220	1.00
251_H	291_D	1.220	1.00
351_S	355_A	1.215	1.00
256_N	264_G	1.203	1.00
223_H	226_T	1.201	1.00
231_E	298_S	1.199	1.00
270_A	319_L	1.193	1.00
291_D	330_R	1.183	1.00
267_A	320_R	1.179	1.00
212_R	219_Y	1.178	1.00
294_A	349_L	1.172	1.00
247_I	275_L	1.167	1.00
221_R	225_E	1.154	1.00
359_A	363_G	1.152	1.00
211_T	219_Y	1.144	1.00
224_W	296_I	1.136	1.00
219_Y	286_G	1.126	1.00
309_M	333_V	1.124	1.00
279_L	312_V	1.121	1.00
195_T	200_A	1.120	1.00
345_Y	349_L	1.114	1.00
267_A	291_D	1.111	1.00
205_R	209_M	1.099	1.00
290_G	357_Y	1.092	1.00
319_L	322_P	1.091	1.00
269_V	272_T	1.086	1.00
229_R	233_D	1.086	1.00
228_L	296_I	1.083	1.00
271_L	329_L	1.079	1.00
286_G	294_A	1.077	1.00
203_K	207_Q	1.074	1.00
245_L	295_V	1.074	1.00
309_M	367_T	1.064	1.00
71_L	75_G	1.062	1.00
347_E	350_K	1.054	1.00
269_V	273_R	1.051	1.00
271_L	331_I	1.045	1.00
305_A	309_M	1.031	1.00
223_H	286_G	1.025	1.00
313_H	365_N	1.023	1.00
205_R	208_V	1.021	1.00
309_M	335_V	1.018	1.00
277_I	315_G	1.018	1.00
229_R	345_Y	1.015	1.00
110_G	114_G	1.010	1.00
306_I	367_T	1.004	1.00
302_A	337_P	0.997	1.00
300_T	304_S	0.994	1.00
224_W	228_L	0.991	1.00
204_R	207_Q	0.990	1.00
315_G	318_T	0.990	1.00
247_I	295_V	0.990	1.00
249_I	330_R	0.985	1.00
283_D	311_R	0.973	1.00
336_A	351_S	0.973	1.00
292_E	353_D	0.971	1.00
248_D	360_K	0.964	1.00
270_A	321_L	0.961	1.00
231_E	242_A	0.960	1.00
275_L	295_V	0.955	1.00
244_L	349_L	0.953	1.00
243_T	335_V	0.952	1.00
226_T	230_N	0.948	1.00
235_C	338_L	0.935	1.00
273_R	277_I	0.934	1.00
336_A	352_A	0.931	1.00
196_A	200_A	0.930	1.00
253_K	261_H	0.923	1.00
197_T	200_A	0.922	1.00
355_A	359_A	0.910	1.00
249_I	268_I	0.909	1.00
215_M	221_R	0.909	1.00
302_A	306_I	0.905	1.00
252_F	267_A	0.902	1.00
195_T	198_K	0.899	1.00
275_L	279_L	0.898	1.00
262_D	266_E	0.892	1.00
193_Y	197_T	0.890	1.00
289_G	357_Y	0.888	1.00
274_Q	315_G	0.886	1.00
245_L	335_V	0.886	1.00
343_S	347_E	0.884	1.00
248_D	357_Y	0.884	1.00
246_I	294_A	0.882	1.00
241_D	340_P	0.880	1.00
253_K	353_D	0.875	1.00
250_D	364_R	0.874	1.00
285_I	295_V	0.873	1.00
193_Y	199_L	0.872	1.00
263_V	327_V	0.871	1.00
210_S	220_N	0.867	1.00
253_K	256_N	0.864	1.00
280_R	311_R	0.864	1.00
232_F	338_L	0.861	1.00
72_V	75_G	0.860	1.00
227_M	296_I	0.857	1.00
215_M	268_I	0.853	1.00
192_S	197_T	0.852	1.00
248_D	261_H	0.846	1.00
244_L	348_W	0.845	1.00
289_G	353_D	0.844	1.00
228_L	232_F	0.844	1.00
339_N	351_S	0.842	1.00
323_N	326_Q	0.842	1.00
289_G	292_E	0.842	1.00
280_R	300_T	0.841	1.00
276_Q	285_I	0.834	1.00
308_A	312_V	0.834	1.00
322_P	327_V	0.833	1.00
330_R	363_G	0.833	1.00
120_V	124_T	0.831	1.00
336_A	355_A	0.830	1.00
280_R	308_A	0.828	1.00
279_L	308_A	0.827	1.00
314_E	317_N	0.825	1.00
261_H	292_E	0.824	1.00
303_E	306_I	0.823	1.00
256_N	290_G	0.822	1.00
297_M	305_A	0.818	1.00
234_N	298_S	0.818	1.00
255_I	263_V	0.814	1.00
78_F	81_P	0.800	1.00
253_K	290_G	0.795	1.00
333_V	367_T	0.795	1.00
309_M	313_H	0.793	1.00
221_R	288_F	0.793	1.00
257_D	353_D	0.792	1.00
262_D	288_F	0.790	1.00
341_Q	351_S	0.790	1.00
224_W	288_F	0.785	1.00
283_D	308_A	0.783	1.00
198_K	201_E	0.782	1.00
193_Y	196_A	0.780	1.00
143_F	146_G	0.775	1.00
316_L	320_R	0.771	1.00
304_S	307_T	0.760	1.00
232_F	345_Y	0.759	1.00
134_L	138_G	0.759	1.00
309_M	331_I	0.749	1.00
275_L	312_V	0.749	1.00
51_G	54_L	0.747	1.00
291_D	359_A	0.746	1.00
235_C	242_A	0.745	1.00
211_T	222_R	0.745	1.00
84_A	88_A	0.745	1.00
295_V	312_V	0.744	1.00
310_L	367_T	0.744	1.00
71_L	74_V	0.743	1.00
246_I	352_A	0.741	1.00
214_G	225_E	0.739	1.00
254_S	291_D	0.736	1.00
249_I	252_F	0.733	1.00
82_H	86_Q	0.727	1.00
86_Q	90_R	0.726	1.00
290_G	353_D	0.724	1.00
55_P	59_T	0.722	1.00
212_R	218_V	0.722	1.00
321_L	326_Q	0.721	1.00
75_G	79_V	0.720	1.00
248_D	291_D	0.720	1.00
257_D	261_H	0.719	1.00
196_A	203_K	0.718	1.00
292_E	357_Y	0.716	1.00
351_S	354_L	0.716	1.00
54_L	58_S	0.715	1.00
302_A	305_A	0.714	1.00
142_L	146_G	0.714	1.00
81_P	84_A	0.713	1.00
217_G	269_V	0.713	1.00
316_L	329_L	0.713	1.00
262_D	346_R	0.711	1.00
347_E	351_S	0.708	1.00
202_H	209_M	0.706	1.00
225_E	228_L	0.704	1.00
266_E	323_N	0.696	1.00
332_S	357_Y	0.695	1.00
259_W	327_V	0.695	1.00
65_P	68_W	0.691	1.00
218_V	286_G	0.690	1.00
244_L	294_A	0.689	1.00
313_H	330_R	0.688	1.00
206_L	209_M	0.687	1.00
320_R	328_T	0.686	1.00
242_A	296_I	0.685	1.00
212_R	276_Q	0.684	1.00
225_E	286_G	0.682	1.00
338_L	342_M	0.681	1.00
250_D	363_G	0.677	1.00
151_V	154_C	0.675	1.00
232_F	242_A	0.672	1.00
200_A	204_R	0.668	1.00
238_H	299_G	0.667	1.00
155_L	159_E	0.665	1.00
274_Q	322_P	0.664	1.00
261_H	291_D	0.664	1.00
101_N	105_D	0.663	1.00
283_D	297_M	0.663	1.00
256_N	360_K	0.662	1.00
206_L	211_T	0.658	1.00
356_L	364_R	0.658	1.00
307_T	311_R	0.657	1.00
324_T	327_V	0.657	1.00
152_V	156_V	0.656	1.00
173_E	177_S	0.655	1.00
272_T	275_L	0.654	1.00
257_D	292_E	0.654	1.00
252_F	291_D	0.652	1.00
306_I	335_V	0.651	1.00
228_L	242_A	0.650	1.00
300_T	305_A	0.648	1.00
188_F	191_V	0.644	1.00
256_N	291_D	0.643	1.00
237_R	282_S	0.641	1.00
259_W	263_V	0.641	1.00
211_T	214_G	0.640	1.00
291_D	360_K	0.640	1.00
267_A	321_L	0.640	1.00
332_S	363_G	0.639	1.00
248_D	256_N	0.639	1.00
58_S	62_S	0.637	1.00
291_D	363_G	0.634	1.00
253_K	292_E	0.631	1.00
284_V	296_I	0.630	1.00
192_S	199_L	0.629	1.00
237_R	280_R	0.627	1.00
222_R	225_E	0.627	1.00
218_V	275_L	0.624	1.00
225_E	345_Y	0.623	1.00
85_W	89_S	0.622	1.00
224_W	345_Y	0.621	1.00
305_A	337_P	0.619	1.00
53_F	57_A	0.618	1.00
251_H	356_L	0.618	1.00
288_F	291_D	0.618	1.00
69_W	72_V	0.617	1.00
274_Q	278_T	0.617	1.00
271_L	320_R	0.616	1.00
90_R	94_P	0.615	1.00
69_W	80_W	0.613	1.00
197_T	201_E	0.613	1.00
209_M	214_G	0.613	1.00
135_M	139_G	0.611	1.00
261_H	360_K	0.611	1.00
118_V	121_L	0.609	1.00
195_T	203_K	0.608	1.00
275_L	293_F	0.607	1.00
261_H	290_G	0.606	1.00
117_G	124_T	0.606	1.00
55_P	58_S	0.606	1.00
339_N	343_S	0.606	1.00
121_L	124_T	0.605	1.00
113_V	116_M	0.604	1.00
356_L	359_A	0.602	1.00
115_V	118_V	0.602	1.00
248_D	264_G	0.602	1.00
231_E	296_I	0.601	1.00
135_M	138_G	0.600	1.00
99_I	102_L	0.598	1.00
264_G	291_D	0.597	1.00
100_Y	103_K	0.597	1.00
224_W	349_L	0.597	1.00
250_D	356_L	0.596	1.00
59_T	62_S	0.593	1.00
357_Y	360_K	0.593	1.00
125_A	129_I	0.592	1.00
109_A	112_W	0.590	1.00
235_C	238_H	0.590	1.00
70_W	73_L	0.590	1.00
74_V	78_F	0.590	1.00
253_K	360_K	0.589	1.00
110_G	113_V	0.589	1.00
247_I	285_I	0.588	1.00
114_G	117_G	0.587	1.00
243_T	309_M	0.584	1.00
157_T	161_T	0.581	1.00
111_M	114_G	0.581	1.00
202_H	206_L	0.581	1.00
112_W	116_M	0.580	1.00
88_A	91_A	0.579	1.00
60_L	64_P	0.577	1.00
116_M	120_V	0.577	1.00
291_D	331_I	0.576	1.00
250_D	330_R	0.576	1.00
177_S	181_I	0.576	1.00
88_A	92_V	0.575	1.00
263_V	325_P	0.574	1.00
116_M	119_N	0.573	1.00
52_M	59_T	0.570	1.00
119_N	122_P	0.570	1.00
120_V	123_S	0.569	1.00
109_A	113_V	0.569	1.00
346_R	350_K	0.567	1.00
291_D	357_Y	0.567	1.00
241_D	301_P	0.566	1.00
267_A	270_A	0.563	1.00
53_F	58_S	0.560	1.00
98_E	101_N	0.560	1.00
172_L	175_W	0.560	1.00
79_V	83_L	0.560	1.00
291_D	365_N	0.559	1.00
312_V	331_I	0.559	1.00
129_I	132_L	0.558	1.00
253_K	264_G	0.557	1.00
146_G	149_L	0.556	1.00
212_R	223_H	0.556	1.00
53_F	59_T	0.556	1.00
207_Q	226_T	0.555	1.00
63_H	66_P	0.555	1.00
133_N	138_G	0.555	1.00
262_D	349_L	0.554	1.00
214_G	288_F	0.554	1.00
278_T	283_D	0.550	1.00
236_R	338_L	0.548	1.00
227_M	298_S	0.548	1.00
255_I	322_P	0.547	1.00
236_R	343_S	0.546	1.00
57_A	61_V	0.545	1.00
228_L	244_L	0.544	1.00
156_V	159_E	0.544	1.00
241_D	337_P	0.542	1.00
153_S	157_T	0.538	1.00
119_N	123_S	0.538	1.00
252_F	359_A	0.537	1.00
244_L	352_A	0.536	1.00
148_V	152_V	0.535	1.00
136_G	139_G	0.534	1.00
240_R	298_S	0.533	1.00
252_F	256_N	0.533	1.00
98_E	102_L	0.532	1.00
204_R	208_V	0.529	1.00
207_Q	210_S	0.529	1.00
292_E	332_S	0.528	1.00
234_N	238_H	0.528	1.00
131_C	138_G	0.526	1.00
320_R	327_V	0.526	1.00
51_G	55_P	0.526	1.00
58_S	63_H	0.525	1.00
221_R	224_W	0.523	1.00
206_L	210_S	0.523	1.00
248_D	289_G	0.521	0.99
51_G	58_S	0.521	0.99
315_G	319_L	0.520	0.99
248_D	292_E	0.519	0.99
72_V	79_V	0.518	0.99
133_N	137_A	0.516	0.99
218_V	276_Q	0.515	0.99
243_T	297_M	0.515	0.99
271_L	319_L	0.514	0.99
145_A	148_V	0.513	0.99
117_G	121_L	0.513	0.99
101_N	104_T	0.513	0.99
174_W	177_S	0.512	0.99
142_L	145_A	0.512	0.99
317_N	328_T	0.510	0.99
83_L	86_Q	0.510	0.99
208_V	211_T	0.510	0.99
203_K	209_M	0.509	0.99
53_F	56_I	0.508	0.99
141_R	144_V	0.506	0.99
52_M	58_S	0.505	0.99
52_M	55_P	0.505	0.99
261_H	289_G	0.505	0.99
311_R	315_G	0.505	0.99
174_W	178_L	0.504	0.99
255_I	328_T	0.504	0.99
112_W	115_V	0.503	0.99
208_V	217_G	0.502	0.99
297_M	300_T	0.501	0.99
130_M	133_N	0.500	0.99
312_V	315_G	0.500	0.99
198_K	202_H	0.500	0.99

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
1w25A	2	0.6307	100	0.458	Contact Map
4j40A	2	0	100	0.464	Contact Map
3pjxA	1	0.4771	100	0.479	Contact Map
4rnhA	2	0.4232	100	0.481	Contact Map
3ignA	1	0.4447	100	0.487	Contact Map
3ezuA	2	0.8571	100	0.49	Contact Map
3mtkA	2	0.4259	100	0.497	Contact Map
3hvaA	1	0.434	100	0.508	Contact Map
3i5cA	2	0.5148	100	0.509	Contact Map
4urgA	1	0.4232	100	0.51	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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