NTRB - ECOLI - GREMLIN Contacts

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NTRB - Nitrogen regulation protein NR(II)

UniProt:	P0AFB5	Sequences: MATGTQPDAGQILNSLINSILLIDDNLAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFSLNIELMQESLEAGQGFTDNEVTLVIDGRSHILSVTAQRMPDGMILLEMAPMDNQRRLSQEQLQHAQQVAARDLVRGLAHEIKNPLGGLRGAAQLLSKALPDPSLLEYTKVIIEQADRLRNLVDRLLGPQLPGTRVTESIHKVAERVVTLVSMELPDNVRLIRDYDPSLPELAHDPDQIEQVLLNIVRNALQALGPEGGEIILRTRTAFQLTLHGERYRLAARIDVEDNGPGIPPHLQDTLFYPMVSGREGGTGLGLSIARNLIDQHSGKIEFTSWPGHTEFSVYLPIRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10387
Length:	349 (326)
Sequences:	50095 (41680)
Seq/√Len:	2308.5

ECOLI - NTRB ARCB RCSD ATOS RCSC EVGS DPIB PHOR DCUS ZRAS NARX BARA TORS NARQ KDPD CREC CUSS GLRK CPXA BAES PHOQ RSTB YEDV ENVZ QSEC BASS YPDA UHPB
BACSU - KINE KINA YYCG PHOR RESE KINC MALK DCTS CITS KIND DEGS YHCY YVRG KINB YCLK CSSS GLNK YKOH COMP YCBM LYTS YVCQ BCES YXDK YRKQ NATK LIAS
HALSA - Q9HQ16 O51970 Q9HRE4 Q9HR10 Q9HQG5 Q9HRG1 Q9HNM2 Q9HQB9 BAT Q9HNA6 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
152_A	171_I	3.126	1.00
197_E	233_H	3.111	1.00
18_N	109_A	3.066	1.00
331_E	342_S	3.043	1.00
287_D	291_G	2.984	1.00
286_E	340_E	2.956	1.00
320_R	324_D	2.769	1.00
280_A	344_Y	2.702	1.00
335_W	338_H	2.687	1.00
253_L	288_N	2.683	1.00
293_P	296_L	2.450	1.00
156_S	172_I	2.439	1.00
282_R	344_Y	2.400	1.00
284_D	340_E	2.397	1.00
282_R	342_S	2.387	1.00
263_R	284_D	2.373	1.00
233_H	326_H	2.343	1.00
221_I	259_E	2.337	1.00
221_I	261_I	2.331	1.00
125_A	128_V	2.326	1.00
284_D	342_S	2.306	1.00
297_Q	332_F	2.291	1.00
196_T	232_A	2.255	1.00
21_L	106_L	2.235	1.00
223_D	263_R	2.230	1.00
319_A	330_I	2.226	1.00
156_S	169_K	2.189	1.00
149_R	175_A	2.129	1.00
261_I	286_E	2.113	1.00
265_R	282_R	2.099	1.00
195_V	235_P	2.044	1.00
13_L	31_Y	2.042	1.00
332_F	341_F	1.996	1.00
205_R	239_E	1.994	1.00
35_A	38_Q	1.994	1.00
263_R	286_E	1.970	1.00
121_Q	125_A	1.960	1.00
323_I	328_G	1.959	1.00
241_V	323_I	1.948	1.00
149_R	176_D	1.920	1.00
265_R	284_D	1.915	1.00
198_S	201_K	1.913	1.00
297_Q	334_S	1.896	1.00
19_S	39_L	1.892	1.00
161_D	164_L	1.877	1.00
24_D	28_A	1.876	1.00
219_R	259_E	1.876	1.00
301_F	330_I	1.861	1.00
259_E	288_N	1.826	1.00
333_T	340_E	1.804	1.00
19_S	108_M	1.799	1.00
223_D	261_I	1.795	1.00
292_I	296_L	1.790	1.00
334_S	339_T	1.748	1.00
323_I	343_V	1.739	1.00
121_Q	124_H	1.732	1.00
294_P	297_Q	1.729	1.00
241_V	319_A	1.728	1.00
115_R	118_S	1.696	1.00
333_T	342_S	1.688	1.00
329_K	344_Y	1.688	1.00
292_I	300_L	1.671	1.00
151_A	167_Y	1.665	1.00
42_Q	85_I	1.638	1.00
258_G	288_N	1.626	1.00
21_L	36_A	1.610	1.00
210_V	243_L	1.610	1.00
148_L	175_A	1.598	1.00
200_H	264_T	1.596	1.00
299_T	305_V	1.595	1.00
253_L	260_I	1.579	1.00
241_V	322_L	1.558	1.00
21_L	29_I	1.554	1.00
156_S	165_L	1.528	1.00
179_R	183_D	1.521	1.00
234_D	237_Q	1.519	1.00
34_P	38_Q	1.496	1.00
296_L	299_T	1.488	1.00
14_N	34_P	1.478	1.00
324_D	329_K	1.470	1.00
283_I	343_V	1.469	1.00
10_G	14_N	1.460	1.00
242_L	283_I	1.455	1.00
50_T	54_E	1.439	1.00
153_Q	172_I	1.436	1.00
252_A	306_S	1.430	1.00
37_Q	44_S	1.425	1.00
331_E	344_Y	1.410	1.00
194_R	232_A	1.404	1.00
322_L	326_H	1.399	1.00
114_Q	118_S	1.397	1.00
253_L	258_G	1.389	1.00
233_H	238_I	1.388	1.00
198_S	230_E	1.378	1.00
16_L	20_I	1.372	1.00
93_S	109_A	1.357	1.00
152_A	172_I	1.348	1.00
229_P	266_T	1.346	1.00
129_A	132_D	1.344	1.00
155_L	168_T	1.344	1.00
124_H	128_V	1.337	1.00
94_V	108_M	1.331	1.00
32_A	36_A	1.329	1.00
296_L	305_V	1.319	1.00
293_P	336_P	1.316	1.00
237_Q	240_Q	1.314	1.00
302_Y	305_V	1.306	1.00
299_T	302_Y	1.305	1.00
151_A	170_V	1.303	1.00
116_R	120_E	1.302	1.00
214_L	250_L	1.296	1.00
93_S	114_Q	1.295	1.00
124_H	127_Q	1.293	1.00
334_S	338_H	1.272	1.00
224_Y	264_T	1.268	1.00
211_S	215_P	1.263	1.00
159_L	164_L	1.256	1.00
172_I	176_D	1.249	1.00
68_E	72_A	1.248	1.00
155_L	164_L	1.246	1.00
57_S	60_S	1.230	1.00
32_A	37_Q	1.198	1.00
247_R	251_Q	1.196	1.00
147_G	174_Q	1.184	1.00
280_A	329_K	1.172	1.00
43_S	46_K	1.165	1.00
158_A	164_L	1.164	1.00
148_L	171_I	1.158	1.00
9_A	13_L	1.155	1.00
241_V	343_V	1.150	1.00
121_Q	128_V	1.150	1.00
205_R	235_P	1.149	1.00
123_Q	126_Q	1.148	1.00
277_Y	282_R	1.145	1.00
300_L	332_F	1.128	1.00
237_Q	325_Q	1.122	1.00
36_A	40_L	1.121	1.00
91_I	115_R	1.120	1.00
123_Q	127_Q	1.108	1.00
196_T	230_E	1.095	1.00
22_L	105_L	1.095	1.00
200_H	204_E	1.092	1.00
28_A	51_P	1.091	1.00
152_A	175_A	1.088	1.00
34_P	37_Q	1.083	1.00
23_I	106_L	1.080	1.00
113_N	116_R	1.079	1.00
67_Q	71_E	1.077	1.00
292_I	332_F	1.075	1.00
296_L	307_G	1.073	1.00
204_E	222_R	1.065	1.00
169_K	173_E	1.059	1.00
149_R	172_I	1.051	1.00
51_P	54_E	1.038	1.00
292_I	297_Q	1.033	1.00
32_A	47_L	1.031	1.00
79_N	115_R	1.029	1.00
197_E	202_V	1.025	1.00
37_Q	43_S	1.023	1.00
200_H	224_Y	1.019	1.00
22_L	31_Y	1.018	1.00
334_S	337_G	1.016	1.00
210_V	246_V	1.007	1.00
292_I	339_T	1.006	1.00
147_G	151_A	1.005	1.00
180_N	236_D	1.003	1.00
261_I	288_N	0.999	1.00
170_V	174_Q	0.996	1.00
84_V	88_R	0.995	1.00
194_R	326_H	0.991	1.00
152_A	168_T	0.987	1.00
152_A	156_S	0.986	1.00
149_R	179_R	0.983	1.00
235_P	239_E	0.976	1.00
24_D	30_H	0.973	1.00
209_L	243_L	0.969	1.00
165_L	169_K	0.968	1.00
141_I	178_L	0.967	1.00
301_F	332_F	0.963	1.00
207_V	211_S	0.962	1.00
115_R	119_Q	0.961	1.00
237_Q	322_L	0.947	1.00
323_I	330_I	0.946	1.00
77_T	93_S	0.946	1.00
63_I	67_Q	0.938	1.00
46_K	85_I	0.936	1.00
79_N	82_T	0.928	1.00
251_Q	308_R	0.927	1.00
166_E	170_V	0.925	1.00
203_A	264_T	0.922	1.00
240_Q	322_L	0.920	1.00
96_A	104_I	0.919	1.00
225_D	265_R	0.916	1.00
206_V	239_E	0.915	1.00
207_V	222_R	0.906	1.00
303_P	321_N	0.895	1.00
202_V	206_V	0.890	1.00
174_Q	177_R	0.890	1.00
22_L	30_H	0.888	1.00
246_V	260_I	0.887	1.00
112_D	116_R	0.884	1.00
23_I	29_I	0.883	1.00
201_K	205_R	0.883	1.00
242_L	246_V	0.877	1.00
199_I	283_I	0.877	1.00
323_I	345_L	0.874	1.00
116_R	119_Q	0.873	1.00
282_R	331_E	0.871	1.00
194_R	233_H	0.870	1.00
206_V	210_V	0.863	1.00
244_N	319_A	0.863	1.00
19_S	36_A	0.862	1.00
301_F	341_F	0.862	1.00
117_L	120_E	0.862	1.00
245_I	319_A	0.859	1.00
69_S	72_A	0.858	1.00
160_P	164_L	0.855	1.00
260_I	264_T	0.850	1.00
64_E	68_E	0.848	1.00
242_L	285_V	0.839	1.00
249_A	260_I	0.837	1.00
57_S	89_S	0.837	1.00
162_P	165_L	0.837	1.00
137_L	185_L	0.827	1.00
16_L	107_E	0.827	1.00
142_K	183_D	0.827	1.00
218_V	250_L	0.824	1.00
58_Y	61_L	0.823	1.00
90_H	110_P	0.822	1.00
287_D	339_T	0.822	1.00
225_D	228_L	0.821	1.00
142_K	179_R	0.817	1.00
139_H	143_N	0.817	1.00
21_L	108_M	0.816	1.00
328_G	345_L	0.812	1.00
136_G	303_P	0.812	1.00
239_E	243_L	0.809	1.00
19_S	35_A	0.809	1.00
291_G	339_T	0.809	1.00
292_I	298_D	0.801	1.00
300_L	341_F	0.798	1.00
209_L	239_E	0.797	1.00
31_Y	44_S	0.796	1.00
23_I	96_A	0.795	1.00
91_I	112_D	0.788	1.00
78_D	81_V	0.782	1.00
321_N	324_D	0.780	1.00
207_V	220_L	0.779	1.00
204_E	208_T	0.779	1.00
245_I	341_F	0.775	1.00
319_A	323_I	0.774	1.00
166_E	169_K	0.773	1.00
80_E	115_R	0.772	1.00
251_Q	306_S	0.771	1.00
277_Y	280_A	0.770	1.00
143_N	150_G	0.770	1.00
9_A	12_I	0.769	1.00
34_P	44_S	0.763	1.00
42_Q	46_K	0.762	1.00
184_R	237_Q	0.759	1.00
246_V	262_L	0.757	1.00
237_Q	326_H	0.755	1.00
294_P	335_W	0.753	1.00
140_E	240_Q	0.752	1.00
37_Q	47_L	0.752	1.00
203_A	262_L	0.752	1.00
208_T	211_S	0.749	1.00
97_Q	105_L	0.748	1.00
96_A	106_L	0.745	1.00
80_E	94_V	0.745	1.00
161_D	165_L	0.744	1.00
81_V	91_I	0.744	1.00
225_D	264_T	0.742	1.00
23_I	104_I	0.741	1.00
132_D	136_G	0.740	1.00
245_I	330_I	0.740	1.00
201_K	235_P	0.740	1.00
202_V	233_H	0.739	1.00
23_I	52_L	0.734	1.00
84_V	90_H	0.733	1.00
150_G	154_L	0.733	1.00
28_A	49_G	0.733	1.00
149_R	153_Q	0.732	1.00
11_Q	15_S	0.732	1.00
265_R	277_Y	0.728	1.00
238_I	326_H	0.728	1.00
180_N	184_R	0.726	1.00
175_A	179_R	0.726	1.00
213_E	247_R	0.724	1.00
44_S	48_F	0.722	1.00
218_V	253_L	0.722	1.00
188_P	317_S	0.721	1.00
183_D	187_G	0.718	1.00
18_N	35_A	0.718	1.00
328_G	346_P	0.716	1.00
154_L	167_Y	0.712	1.00
206_V	243_L	0.711	1.00
197_E	235_P	0.710	1.00
151_A	171_I	0.709	1.00
117_L	121_Q	0.708	1.00
170_V	173_E	0.706	1.00
140_E	244_N	0.705	1.00
171_I	175_A	0.703	1.00
65_L	69_S	0.703	1.00
53_P	61_L	0.699	1.00
245_I	343_V	0.694	1.00
214_L	218_V	0.692	1.00
173_E	205_R	0.691	1.00
80_E	83_L	0.686	1.00
306_S	311_G	0.686	1.00
126_Q	129_A	0.683	1.00
23_I	66_M	0.682	1.00
142_K	186_L	0.682	1.00
187_G	237_Q	0.680	1.00
210_V	250_L	0.679	1.00
114_Q	117_L	0.677	1.00
216_D	250_L	0.672	1.00
199_I	281_A	0.670	1.00
249_A	285_V	0.668	1.00
111_M	115_R	0.664	1.00
60_S	81_V	0.663	1.00
12_I	105_L	0.661	1.00
252_A	290_P	0.661	1.00
92_L	108_M	0.659	1.00
83_L	89_S	0.659	1.00
151_A	174_Q	0.659	1.00
85_I	88_R	0.658	1.00
23_I	27_L	0.656	1.00
40_L	108_M	0.654	1.00
306_S	310_G	0.654	1.00
255_P	258_G	0.653	1.00
81_V	89_S	0.651	1.00
210_V	247_R	0.651	1.00
244_N	247_R	0.650	1.00
66_M	70_L	0.650	1.00
42_Q	47_L	0.649	1.00
18_N	107_E	0.647	1.00
63_I	66_M	0.647	1.00
227_S	266_T	0.645	1.00
253_L	257_G	0.645	1.00
177_R	239_E	0.644	1.00
13_L	20_I	0.643	1.00
158_A	161_D	0.641	1.00
259_E	286_E	0.641	1.00
169_K	172_I	0.639	1.00
204_E	207_V	0.638	1.00
140_E	143_N	0.637	1.00
50_T	55_L	0.636	1.00
328_G	343_V	0.635	1.00
65_L	68_E	0.633	1.00
223_D	265_R	0.632	1.00
155_L	167_Y	0.632	1.00
252_A	308_R	0.630	1.00
95_T	109_A	0.629	1.00
194_R	327_S	0.629	1.00
206_V	246_V	0.629	1.00
217_N	257_G	0.623	1.00
203_A	242_L	0.622	1.00
141_I	144_P	0.622	1.00
147_G	150_G	0.622	1.00
56_L	61_L	0.622	1.00
140_E	181_L	0.622	1.00
33_N	36_A	0.620	1.00
145_L	182_V	0.617	1.00
10_G	31_Y	0.615	1.00
277_Y	344_Y	0.614	1.00
241_V	326_H	0.614	1.00
155_L	171_I	0.613	1.00
153_Q	156_S	0.612	1.00
331_E	343_V	0.612	1.00
143_N	147_G	0.611	1.00
321_N	325_Q	0.609	1.00
164_L	167_Y	0.609	1.00
297_Q	301_F	0.607	1.00
20_I	107_E	0.606	1.00
251_Q	310_G	0.605	1.00
240_Q	243_L	0.604	1.00
19_S	92_L	0.604	1.00
147_G	170_V	0.602	1.00
214_L	220_L	0.601	1.00
262_L	285_V	0.600	1.00
248_N	315_G	0.598	1.00
314_L	318_I	0.597	1.00
32_A	44_S	0.596	1.00
201_K	204_E	0.595	1.00
113_N	117_L	0.594	1.00
280_A	346_P	0.593	1.00
98_R	104_I	0.593	1.00
228_L	264_T	0.591	1.00
176_D	179_R	0.591	1.00
139_H	244_N	0.590	1.00
56_L	60_S	0.589	1.00
303_P	317_S	0.588	1.00
12_I	15_S	0.587	1.00
198_S	228_L	0.584	1.00
216_D	253_L	0.584	1.00
133_L	137_L	0.583	1.00
186_L	190_L	0.583	1.00
35_A	39_L	0.582	1.00
212_M	215_P	0.582	1.00
91_I	111_M	0.580	1.00
176_D	180_N	0.579	1.00
119_Q	123_Q	0.579	1.00
193_T	234_D	0.577	1.00
218_V	222_R	0.577	1.00
146_G	150_G	0.576	1.00
202_V	239_E	0.575	1.00
156_S	168_T	0.575	1.00
158_A	167_Y	0.574	1.00
63_I	70_L	0.574	1.00
297_Q	341_F	0.574	1.00
128_V	131_R	0.573	1.00
266_T	279_L	0.572	1.00
25_D	103_M	0.572	1.00
82_T	91_I	0.570	1.00
40_L	82_T	0.570	1.00
297_Q	333_T	0.568	1.00
32_A	40_L	0.566	1.00
284_D	333_T	0.565	1.00
160_P	165_L	0.565	1.00
204_E	224_Y	0.563	1.00
22_L	99_M	0.560	1.00
202_V	238_I	0.558	1.00
187_G	191_P	0.558	1.00
153_Q	157_K	0.557	1.00
140_E	144_P	0.556	1.00
20_I	105_L	0.556	1.00
12_I	22_L	0.555	1.00
27_L	52_L	0.554	1.00
190_L	312_T	0.553	1.00
219_R	222_R	0.553	1.00
121_Q	127_Q	0.552	1.00
36_A	108_M	0.552	1.00
163_S	167_Y	0.552	1.00
32_A	48_F	0.550	1.00
203_A	222_R	0.549	1.00
82_T	89_S	0.549	1.00
52_L	56_L	0.549	1.00
203_A	207_V	0.548	1.00
197_E	232_A	0.548	1.00
264_T	283_I	0.548	1.00
236_D	239_E	0.548	1.00
132_D	303_P	0.548	1.00
294_P	298_D	0.546	1.00
266_T	281_A	0.542	1.00
69_S	74_Q	0.542	1.00
293_P	307_G	0.541	1.00
229_P	281_A	0.540	1.00
134_V	138_A	0.539	1.00
20_I	33_N	0.538	1.00
290_P	339_T	0.538	1.00
292_I	334_S	0.534	1.00
13_L	33_N	0.533	1.00
134_V	137_L	0.529	1.00
167_Y	170_V	0.529	1.00
179_R	182_V	0.529	1.00
200_H	226_P	0.529	1.00
21_L	94_V	0.528	1.00
217_N	256_E	0.526	1.00
19_S	33_N	0.526	1.00
9_A	31_Y	0.526	1.00
12_I	16_L	0.523	1.00
286_E	335_W	0.522	1.00
214_L	260_I	0.522	1.00
323_I	329_K	0.522	1.00
330_I	341_F	0.521	1.00
203_A	206_V	0.521	1.00
9_A	22_L	0.520	1.00
19_S	40_L	0.520	1.00
214_L	217_N	0.519	1.00
238_I	242_L	0.519	1.00
245_I	285_V	0.518	1.00
140_E	174_Q	0.517	1.00
94_V	106_L	0.516	1.00
67_Q	70_L	0.515	1.00
145_L	178_L	0.514	1.00
68_E	71_E	0.514	1.00
332_F	339_T	0.513	1.00
140_E	178_L	0.511	1.00
12_I	20_I	0.509	1.00
42_Q	55_L	0.509	1.00
91_I	94_V	0.507	1.00
255_P	288_N	0.507	1.00
225_D	266_T	0.507	1.00
69_S	73_G	0.506	1.00
166_E	208_T	0.504	1.00
245_I	323_I	0.503	1.00
279_L	346_P	0.501	1.00
293_P	297_Q	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
3a0rA	2	0.9169	100	0.203	Contact Map
4gczA	2	0.9771	100	0.204	Contact Map
4i5sA	2	0.9083	100	0.237	Contact Map
4r3aA	1	0.8653	100	0.337	Contact Map
4q20A	2	0.6246	100	0.455	Contact Map
2c2aA	2	0.6447	100	0.46	Contact Map
4mpcA	2	0.8252	100	0.464	Contact Map
3d36A	2	0.616	100	0.468	Contact Map
3jz3A	2	0.4384	100	0.468	Contact Map
4e01A	3	0.7994	100	0.468	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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