IDNR - ECOLI - GREMLIN Contacts

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IDNR - HTH-type transcriptional regulator IdnR

UniProt:	P39343	Sequences: MRNHRISLQDIATLAGVTKMTVSRYIRSPKKVAKETGERIAKIMEEINYIPNRAPGMLLNAQSYTLGILIPSFQNQLFADILAGIESVTSEHNYQTLIANYNYDRDSEEESVINLLSYNIDGIILSEKYHTIRTVKFLRSATIPVVELMDVQGERLDMEVGFDNRQAAFDMVCTMLEKRVRHKILYLGSKDDTRDEQRYQGYCDAMMLHNLSPLRMNPRAISSIHLGMQLMRDALSANPDLDGVFCTNDDIAMGALLLCRERNLAVPEQISIAGFHGLEIGRQMIPSLASVITPRFDIGRMAAQMLLSKIKNNDHNHNTVDLGYQIYHGNTL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12538
Length:	332 (321)
Sequences:	36465 (26301)
Seq/√Len:	1468.0

ECOLI - IDNR GNTR CYTR GALR GALS LACI MALI CRA PURR RBSR ASCG YCJW EBGR TRER TORT ALSB YTFQ RBSB XYLF YPHF LSRB ARAF DGAL XYLR
BACSU - CCPA KDGR DEGA RBSR NTDR YVDE YKVZ GANR MSMR EXUR ARAR CCPB RBSB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
165_R	204_D	3.376	1.00
180_V	242_D	3.199	1.00
14_L	46_E	3.108	1.00
265_A	268_E	3.082	1.00
171_M	273_A	2.642	1.00
122_G	306_L	2.609	1.00
199_Y	203_C	2.579	1.00
180_V	271_S	2.556	1.00
277_G	292_I	2.487	1.00
158_M	309_K	2.469	1.00
169_F	208_L	2.346	1.00
228_M	261_E	2.263	1.00
34_K	38_E	2.247	1.00
42_K	46_E	2.218	1.00
88_V	91_E	2.214	1.00
38_E	42_K	2.177	1.00
88_V	304_Q	2.149	1.00
232_R	262_R	2.121	1.00
169_F	204_D	2.072	1.00
301_M	304_Q	2.065	1.00
173_C	205_A	2.041	1.00
176_L	209_H	2.033	1.00
169_F	205_A	2.028	1.00
232_R	258_L	2.028	1.00
166_Q	170_D	2.016	1.00
25_Y	40_I	1.971	1.00
89_T	303_A	1.965	1.00
167_A	275_F	1.913	1.00
165_R	200_Q	1.908	1.00
37_G	41_A	1.902	1.00
168_A	172_V	1.888	1.00
84_G	299_G	1.884	1.00
26_I	44_M	1.880	1.00
227_G	254_G	1.862	1.00
259_C	270_I	1.860	1.00
175_M	243_G	1.851	1.00
173_C	177_E	1.849	1.00
88_V	300_R	1.846	1.00
9_Q	19_K	1.844	1.00
236_S	262_R	1.822	1.00
168_A	245_F	1.803	1.00
308_S	313_N	1.803	1.00
172_V	202_Y	1.774	1.00
292_I	325_Q	1.765	1.00
87_S	296_F	1.757	1.00
173_C	209_H	1.719	1.00
15_A	43_I	1.695	1.00
169_F	173_C	1.687	1.00
14_L	43_I	1.673	1.00
228_M	258_L	1.668	1.00
294_P	297_D	1.663	1.00
264_L	269_Q	1.645	1.00
301_M	320_V	1.638	1.00
170_D	324_Y	1.627	1.00
185_L	247_T	1.626	1.00
67_G	120_I	1.626	1.00
184_I	241_L	1.625	1.00
174_T	178_K	1.623	1.00
231_M	255_A	1.619	1.00
84_G	296_F	1.617	1.00
88_V	92_H	1.594	1.00
246_C	255_A	1.589	1.00
265_A	269_Q	1.582	1.00
258_L	262_R	1.571	1.00
148_L	302_A	1.553	1.00
41_A	45_E	1.531	1.00
166_Q	169_F	1.526	1.00
200_Q	204_D	1.515	1.00
25_Y	44_M	1.508	1.00
92_H	307_L	1.496	1.00
260_R	285_I	1.486	1.00
176_L	205_A	1.484	1.00
297_D	301_M	1.483	1.00
174_T	177_E	1.479	1.00
277_G	329_G	1.474	1.00
163_D	166_Q	1.462	1.00
11_I	43_I	1.453	1.00
258_L	261_E	1.448	1.00
41_A	44_M	1.445	1.00
64_Y	121_D	1.415	1.00
273_A	289_A	1.407	1.00
197_Q	200_Q	1.400	1.00
182_H	240_D	1.398	1.00
297_D	300_R	1.395	1.00
88_V	303_A	1.382	1.00
203_C	207_M	1.361	1.00
228_M	257_L	1.361	1.00
174_T	328_H	1.358	1.00
259_C	264_L	1.345	1.00
307_L	311_K	1.330	1.00
172_V	176_L	1.327	1.00
167_A	324_Y	1.327	1.00
221_I	226_L	1.320	1.00
172_V	201_G	1.316	1.00
232_R	261_E	1.312	1.00
184_I	234_A	1.303	1.00
205_A	208_L	1.301	1.00
231_M	244_V	1.301	1.00
228_M	232_R	1.298	1.00
9_Q	13_T	1.293	1.00
218_P	233_D	1.292	1.00
136_K	140_S	1.291	1.00
172_V	205_A	1.289	1.00
14_L	47_I	1.284	1.00
66_L	89_T	1.280	1.00
304_Q	308_S	1.270	1.00
168_A	201_G	1.269	1.00
34_K	37_G	1.268	1.00
10_D	13_T	1.267	1.00
201_G	205_A	1.257	1.00
64_Y	94_Y	1.256	1.00
231_M	259_C	1.253	1.00
180_V	243_G	1.248	1.00
39_R	43_I	1.245	1.00
67_G	115_L	1.244	1.00
33_A	36_T	1.243	1.00
11_I	15_A	1.238	1.00
232_R	236_S	1.235	1.00
99_A	111_S	1.233	1.00
124_I	302_A	1.229	1.00
165_R	169_F	1.227	1.00
24_R	29_P	1.226	1.00
256_L	272_I	1.222	1.00
182_H	214_L	1.222	1.00
99_A	115_L	1.219	1.00
43_I	46_E	1.209	1.00
43_I	47_I	1.202	1.00
170_D	173_C	1.198	1.00
8_L	19_K	1.192	1.00
85_I	124_I	1.191	1.00
89_T	96_T	1.191	1.00
173_C	208_L	1.191	1.00
85_I	303_A	1.190	1.00
182_H	242_D	1.175	1.00
68_I	85_I	1.171	1.00
165_R	197_Q	1.170	1.00
233_D	237_A	1.167	1.00
11_I	47_I	1.162	1.00
36_T	39_R	1.143	1.00
113_I	137_F	1.141	1.00
186_Y	255_A	1.131	1.00
296_F	300_R	1.123	1.00
225_H	229_Q	1.122	1.00
254_G	258_L	1.122	1.00
202_Y	206_M	1.117	1.00
65_T	95_Q	1.117	1.00
92_H	304_Q	1.105	1.00
249_D	290_S	1.102	1.00
165_R	201_G	1.101	1.00
204_D	208_L	1.095	1.00
171_M	245_F	1.093	1.00
299_G	303_A	1.092	1.00
68_I	96_T	1.090	1.00
42_K	45_E	1.081	1.00
178_K	328_H	1.081	1.00
38_E	41_A	1.079	1.00
8_L	22_V	1.078	1.00
86_E	90_S	1.077	1.00
244_V	255_A	1.075	1.00
185_L	199_Y	1.069	1.00
183_K	206_M	1.068	1.00
301_M	305_M	1.062	1.00
181_R	242_D	1.059	1.00
205_A	209_H	1.059	1.00
230_L	233_D	1.055	1.00
206_M	211_L	1.054	1.00
223_S	226_L	1.053	1.00
238_N	241_L	1.052	1.00
65_T	97_L	1.052	1.00
210_N	213_P	1.049	1.00
249_D	274_G	1.045	1.00
25_Y	32_V	1.041	1.00
90_S	107_S	1.041	1.00
28_S	37_G	1.038	1.00
176_L	211_L	1.027	1.00
52_N	58_L	1.025	1.00
174_T	289_A	1.021	1.00
227_G	231_M	1.019	1.00
109_E	113_I	1.016	1.00
200_Q	203_C	1.011	1.00
54_A	57_M	1.007	1.00
182_H	239_P	1.006	1.00
300_R	304_Q	1.001	1.00
246_C	252_A	1.000	1.00
177_E	209_H	1.000	1.00
305_M	320_V	0.993	1.00
44_M	47_I	0.993	1.00
306_L	310_I	0.991	1.00
92_H	311_K	0.991	1.00
229_Q	233_D	0.990	1.00
94_Y	307_L	0.988	1.00
202_Y	245_F	0.984	1.00
246_C	251_I	0.983	1.00
226_L	229_Q	0.983	1.00
301_M	322_L	0.981	1.00
107_S	110_E	0.969	1.00
166_Q	323_G	0.966	1.00
196_E	200_Q	0.959	1.00
183_K	243_G	0.956	1.00
178_K	271_S	0.955	1.00
15_A	22_V	0.952	1.00
203_C	213_P	0.947	1.00
158_M	305_M	0.947	1.00
256_L	266_V	0.946	1.00
91_E	300_R	0.934	1.00
224_I	257_L	0.931	1.00
231_M	235_L	0.925	1.00
256_L	284_M	0.923	1.00
325_Q	328_H	0.908	1.00
176_L	181_R	0.904	1.00
24_R	30_K	0.902	1.00
193_T	197_Q	0.902	1.00
172_V	206_M	0.901	1.00
83_A	87_S	0.900	1.00
162_F	294_P	0.899	1.00
87_S	300_R	0.898	1.00
218_P	230_L	0.896	1.00
171_M	291_V	0.894	1.00
51_P	56_G	0.893	1.00
206_M	213_P	0.889	1.00
55_P	58_L	0.885	1.00
124_I	306_L	0.884	1.00
159_E	319_T	0.882	1.00
181_R	211_L	0.879	1.00
28_S	41_A	0.877	1.00
85_I	299_G	0.875	1.00
160_V	305_M	0.870	1.00
52_N	55_P	0.870	1.00
260_R	287_S	0.867	1.00
82_L	86_E	0.864	1.00
68_I	82_L	0.864	1.00
294_P	322_L	0.863	1.00
190_K	219_R	0.862	1.00
188_G	222_S	0.861	1.00
66_L	124_I	0.860	1.00
191_D	196_E	0.857	1.00
132_I	136_K	0.854	1.00
249_D	277_G	0.853	1.00
184_I	244_V	0.850	1.00
229_Q	232_R	0.846	1.00
166_Q	324_Y	0.843	1.00
264_L	270_I	0.842	1.00
244_V	270_I	0.842	1.00
259_C	272_I	0.841	1.00
220_A	251_I	0.836	1.00
274_G	290_S	0.832	1.00
25_Y	41_A	0.831	1.00
235_L	258_L	0.829	1.00
163_D	321_D	0.829	1.00
104_D	107_S	0.828	1.00
305_M	308_S	0.827	1.00
163_D	323_G	0.825	1.00
240_D	264_L	0.821	1.00
81_I	148_L	0.818	1.00
292_I	327_Y	0.817	1.00
162_F	324_Y	0.816	1.00
122_G	310_I	0.814	1.00
161_G	321_D	0.812	1.00
77_L	295_R	0.810	1.00
158_M	318_N	0.809	1.00
113_I	117_S	0.806	1.00
187_L	199_Y	0.805	1.00
204_D	207_M	0.801	1.00
226_L	230_L	0.800	1.00
35_E	38_E	0.799	1.00
294_P	325_Q	0.799	1.00
164_N	198_R	0.797	1.00
53_R	56_G	0.796	1.00
63_S	121_D	0.792	1.00
65_T	118_Y	0.790	1.00
211_L	214_L	0.790	1.00
175_M	273_A	0.788	1.00
162_F	293_T	0.786	1.00
303_A	307_L	0.785	1.00
85_I	96_T	0.784	1.00
80_D	296_F	0.784	1.00
87_S	91_E	0.782	1.00
17_V	40_I	0.781	1.00
197_Q	201_G	0.780	1.00
137_F	140_S	0.780	1.00
84_G	300_R	0.779	1.00
21_T	24_R	0.773	1.00
277_G	327_Y	0.772	1.00
110_E	113_I	0.769	1.00
185_L	245_F	0.768	1.00
161_G	319_T	0.765	1.00
231_M	258_L	0.761	1.00
186_Y	246_C	0.761	1.00
211_L	215_R	0.757	1.00
84_G	88_V	0.753	1.00
71_P	78_F	0.752	1.00
35_E	39_R	0.751	1.00
276_H	293_T	0.749	1.00
20_M	24_R	0.748	1.00
242_D	271_S	0.744	1.00
235_L	262_R	0.739	1.00
82_L	98_I	0.738	1.00
170_D	291_V	0.732	1.00
116_L	141_A	0.728	1.00
231_M	234_A	0.727	1.00
253_M	284_M	0.724	1.00
277_G	281_G	0.724	1.00
67_G	123_I	0.722	1.00
136_K	139_R	0.720	1.00
83_A	86_E	0.718	1.00
97_L	120_I	0.718	1.00
249_D	252_A	0.712	1.00
62_Q	121_D	0.712	1.00
257_L	260_R	0.709	1.00
102_N	107_S	0.709	1.00
24_R	31_K	0.708	1.00
86_E	96_T	0.708	1.00
50_I	117_S	0.705	1.00
66_L	303_A	0.705	1.00
174_T	326_I	0.704	1.00
147_E	152_Q	0.697	1.00
107_S	111_S	0.697	1.00
237_A	240_D	0.694	1.00
252_A	274_G	0.694	1.00
245_F	273_A	0.692	1.00
169_F	201_G	0.691	1.00
259_C	266_V	0.689	1.00
257_L	287_S	0.688	1.00
183_K	242_D	0.687	1.00
227_G	230_L	0.687	1.00
122_G	146_V	0.687	1.00
151_V	319_T	0.686	1.00
237_A	241_L	0.684	1.00
220_A	226_L	0.682	1.00
233_D	236_S	0.681	1.00
25_Y	37_G	0.678	1.00
176_L	206_M	0.678	1.00
38_E	45_E	0.673	1.00
69_L	111_S	0.673	1.00
139_R	145_V	0.669	1.00
139_R	156_L	0.668	1.00
138_L	145_V	0.667	1.00
124_I	148_L	0.661	1.00
216_M	237_A	0.658	1.00
308_S	312_N	0.657	1.00
62_Q	311_K	0.654	1.00
106_D	110_E	0.652	1.00
195_D	222_S	0.648	1.00
86_E	100_N	0.645	1.00
116_L	143_I	0.642	1.00
312_N	315_H	0.641	1.00
257_L	261_E	0.640	1.00
112_V	123_I	0.640	1.00
170_D	174_T	0.639	1.00
248_N	276_H	0.637	1.00
50_I	113_I	0.636	1.00
185_L	202_Y	0.633	1.00
287_S	329_G	0.633	1.00
149_M	194_R	0.629	1.00
97_L	118_Y	0.629	1.00
231_M	254_G	0.628	1.00
256_L	260_R	0.627	1.00
182_H	213_P	0.626	1.00
183_K	202_Y	0.626	1.00
122_G	302_A	0.625	1.00
146_V	160_V	0.623	1.00
75_N	250_D	0.622	1.00
146_V	309_K	0.622	1.00
9_Q	59_L	0.622	1.00
146_V	306_L	0.621	1.00
308_S	318_N	0.618	1.00
109_E	134_T	0.616	1.00
80_D	295_R	0.615	1.00
175_M	245_F	0.614	1.00
17_V	36_T	0.613	1.00
31_K	36_T	0.612	1.00
45_E	48_N	0.611	1.00
22_V	25_Y	0.610	1.00
199_Y	217_N	0.609	1.00
149_M	164_N	0.607	1.00
11_I	22_V	0.606	1.00
84_G	295_R	0.604	1.00
218_P	234_A	0.604	1.00
222_S	247_T	0.603	1.00
169_F	172_V	0.603	1.00
39_R	42_K	0.600	1.00
134_T	137_F	0.599	1.00
66_L	122_G	0.595	1.00
224_I	280_I	0.595	1.00
248_N	251_I	0.595	1.00
202_Y	213_P	0.595	1.00
81_I	295_R	0.594	1.00
94_Y	310_I	0.594	1.00
224_I	254_G	0.590	1.00
253_M	278_L	0.590	1.00
225_H	228_M	0.588	1.00
83_A	296_F	0.587	1.00
147_E	157_D	0.587	1.00
218_P	237_A	0.586	1.00
164_N	197_Q	0.586	1.00
105_R	109_E	0.585	1.00
296_F	299_G	0.584	1.00
259_C	262_R	0.584	1.00
216_M	219_R	0.584	1.00
133_R	136_K	0.583	1.00
94_Y	121_D	0.583	1.00
245_F	275_F	0.582	1.00
260_R	265_A	0.579	1.00
77_L	81_I	0.579	1.00
260_R	286_P	0.578	1.00
182_H	216_M	0.578	1.00
22_V	44_M	0.577	1.00
257_L	285_I	0.573	1.00
289_A	326_I	0.570	1.00
99_A	114_N	0.569	1.00
32_V	37_G	0.568	1.00
188_G	195_D	0.567	1.00
174_T	273_A	0.565	1.00
63_S	95_Q	0.565	1.00
24_R	32_V	0.564	1.00
171_M	243_G	0.564	1.00
123_I	143_I	0.564	1.00
209_H	212_S	0.563	1.00
66_L	94_Y	0.563	1.00
253_M	280_I	0.563	1.00
66_L	310_I	0.557	1.00
145_V	157_D	0.557	1.00
281_G	288_L	0.556	1.00
139_R	157_D	0.555	1.00
222_S	251_I	0.551	1.00
195_D	247_T	0.551	1.00
309_K	312_N	0.550	1.00
230_L	234_A	0.550	1.00
146_V	302_A	0.548	1.00
151_V	159_E	0.547	1.00
50_I	54_A	0.546	1.00
305_M	309_K	0.545	1.00
281_G	290_S	0.545	1.00
65_T	121_D	0.543	1.00
89_T	307_L	0.543	1.00
246_C	274_G	0.539	1.00
210_N	214_L	0.538	1.00
275_F	293_T	0.538	1.00
282_R	287_S	0.534	1.00
76_Q	250_D	0.534	1.00
28_S	31_K	0.533	1.00
115_L	120_I	0.533	1.00
266_V	269_Q	0.532	1.00
178_K	242_D	0.531	1.00
301_M	308_S	0.529	1.00
146_V	305_M	0.529	1.00
228_M	231_M	0.528	1.00
89_T	94_Y	0.527	1.00
22_V	40_I	0.527	1.00
17_V	22_V	0.526	1.00
182_H	241_L	0.524	1.00
235_L	259_C	0.523	1.00
291_V	324_Y	0.523	1.00
113_I	116_L	0.523	1.00
85_I	89_T	0.523	1.00
321_D	324_Y	0.521	1.00
241_L	264_L	0.521	1.00
228_M	254_G	0.520	1.00
162_F	167_A	0.519	1.00
15_A	25_Y	0.517	1.00
249_D	278_L	0.516	1.00
241_L	244_V	0.515	1.00
137_F	141_A	0.514	1.00
15_A	40_I	0.511	1.00
294_P	298_I	0.511	1.00
160_V	301_M	0.511	1.00
120_I	123_I	0.511	1.00
101_Y	108_E	0.511	1.00
264_L	267_P	0.510	1.00
88_V	307_L	0.509	1.00
147_E	159_E	0.509	1.00
162_F	275_F	0.508	1.00
75_N	78_F	0.508	1.00
56_G	60_N	0.508	1.00
255_A	259_C	0.507	1.00
20_M	29_P	0.506	1.00
224_I	250_D	0.505	1.00
243_G	271_S	0.504	1.00
186_Y	230_L	0.504	1.00
298_I	322_L	0.503	1.00
289_A	328_H	0.502	1.00
10_D	14_L	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
2o20A	2	0.8223	100	0.053	Contact Map
2hsgA	1	0.9789	100	0.063	Contact Map
3dbiA	2	0.8163	100	0.069	Contact Map
3bilA	2	0.762	100	0.071	Contact Map
4o5aA	2	0.7982	100	0.072	Contact Map
3e3mA	2	0.7952	100	0.072	Contact Map
1qpzA	2	0.9849	100	0.073	Contact Map
3kjxA	2	0.994	100	0.074	Contact Map
3h5oA	2	0.8042	100	0.076	Contact Map
3jvdA	2	0.7801	100	0.081	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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