NTDR - BACSU - GREMLIN Contacts

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NTDR - NTD biosynthesis operon regulator NtdR

UniProt:	O07567	Sequences: MPTIDEIAKLCNVSKTTVSRVLNNHPYVSKEKRDMILKAINELDYTPNYLARNFRRNKTQTIALSVPSIDHPFFAQLIKGVSHEVLFKNYKVIVFQTFYDKQTELELLELLKHKEVDGIILGTLENEWDQISPFLKYGPILLCNEYHHSADITIIGYDEFEAAYMGVVHLIERGHKKIGFCFDTPYSEAQCQRKEGYLKALQDYNLHHRSEWIFGEMFNIEDGFRVFHKIKDLKDRPSAIFTGNDQVAAGIIKQAMKNGFKVPEDLAVIGFDNQLICQVVTPTITTIDIPVIELGQQAVLKIIESISGNASLNRRIIKLPTKLIIREST	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	329 (321)
Sequences:	36600 (26406)
Seq/√Len:	1473.8

ECOLI - GALS GALR RBSR PURR ASCG CYTR CRA MALI IDNR LACI GNTR YCJW EBGR TRER TORT ALSB YTFQ RBSB XYLF ARAF YPHF LSRB DGAL XYLR
BACSU - NTDR CCPA KDGR RBSR EXUR YVDE DEGA MSMR YKVZ GANR 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
160_F	199_K	3.345	1.00
175_H	238_S	3.104	1.00
10_L	42_E	3.089	1.00
261_K	264_E	3.066	1.00
166_G	269_I	2.622	1.00
194_K	198_L	2.610	1.00
118_G	302_I	2.587	1.00
175_H	267_A	2.513	1.00
273_N	288_D	2.411	1.00
153_T	305_S	2.381	1.00
164_Y	203_D	2.328	1.00
30_K	34_D	2.265	1.00
224_F	257_K	2.233	1.00
38_K	42_E	2.214	1.00
84_E	87_F	2.176	1.00
34_D	38_K	2.166	1.00
228_H	258_N	2.152	1.00
84_E	300_L	2.140	1.00
171_I	204_Y	2.091	1.00
168_V	200_A	2.084	1.00
164_Y	200_A	2.076	1.00
164_Y	199_K	2.059	1.00
161_E	165_M	2.042	1.00
228_H	254_Q	2.031	1.00
297_Q	300_L	2.030	1.00
85_V	299_V	1.963	1.00
21_V	36_I	1.961	1.00
160_F	195_E	1.904	1.00
33_R	37_L	1.881	1.00
84_E	296_Q	1.869	1.00
162_A	271_F	1.867	1.00
22_L	40_I	1.864	1.00
170_L	239_A	1.844	1.00
5_D	15_K	1.839	1.00
163_A	167_V	1.838	1.00
168_V	172_E	1.822	1.00
255_A	266_L	1.816	1.00
80_G	295_G	1.815	1.00
304_E	309_N	1.793	1.00
232_D	258_N	1.783	1.00
167_V	197_Y	1.773	1.00
288_D	322_K	1.772	1.00
163_A	241_F	1.768	1.00
168_V	204_Y	1.756	1.00
223_G	250_G	1.749	1.00
83_H	292_I	1.733	1.00
10_L	39_A	1.723	1.00
11_C	39_A	1.701	1.00
164_Y	168_V	1.696	1.00
224_F	254_Q	1.690	1.00
177_K	209_R	1.686	1.00
290_P	293_E	1.675	1.00
260_F	265_D	1.649	1.00
179_G	237_P	1.646	1.00
63_A	116_V	1.635	1.00
84_E	88_K	1.630	1.00
180_F	243_G	1.627	1.00
227_F	251_I	1.626	1.00
80_G	292_I	1.615	1.00
242_T	251_I	1.612	1.00
297_Q	317_I	1.607	1.00
165_M	321_T	1.603	1.00
254_Q	258_N	1.594	1.00
261_K	265_D	1.589	1.00
143_C	298_A	1.568	1.00
37_L	41_N	1.543	1.00
177_K	236_R	1.539	1.00
161_E	164_Y	1.527	1.00
169_H	173_R	1.524	1.00
88_K	303_I	1.518	1.00
256_M	281_T	1.508	1.00
293_E	297_Q	1.498	1.00
195_E	199_K	1.493	1.00
169_H	172_E	1.487	1.00
171_I	200_A	1.482	1.00
214_F	229_K	1.475	1.00
254_Q	257_K	1.465	1.00
273_N	326_R	1.444	1.00
21_V	40_I	1.439	1.00
7_I	39_A	1.438	1.00
158_D	161_E	1.429	1.00
293_E	296_Q	1.423	1.00
269_I	285_T	1.423	1.00
37_L	40_I	1.414	1.00
198_L	202_Q	1.410	1.00
60_Q	117_D	1.404	1.00
192_Q	195_E	1.402	1.00
169_H	325_I	1.396	1.00
200_A	203_D	1.387	1.00
303_I	307_S	1.375	1.00
224_F	228_H	1.338	1.00
177_K	238_S	1.338	1.00
255_A	260_F	1.338	1.00
84_E	299_V	1.337	1.00
224_F	253_K	1.328	1.00
10_L	43_L	1.327	1.00
209_R	212_W	1.322	1.00
167_V	171_I	1.320	1.00
179_G	230_I	1.314	1.00
217_M	222_D	1.309	1.00
228_H	257_K	1.305	1.00
5_D	9_K	1.303	1.00
30_K	33_R	1.290	1.00
162_A	321_T	1.285	1.00
227_F	240_I	1.276	1.00
60_Q	90_Y	1.276	1.00
167_V	200_A	1.273	1.00
35_M	39_A	1.273	1.00
62_I	85_V	1.262	1.00
167_V	196_G	1.255	1.00
6_E	9_K	1.254	1.00
163_A	196_G	1.254	1.00
300_L	304_E	1.248	1.00
227_F	255_A	1.243	1.00
228_H	232_D	1.243	1.00
132_S	136_K	1.242	1.00
160_F	164_Y	1.239	1.00
165_M	168_V	1.230	1.00
95_F	107_L	1.230	1.00
29_S	32_K	1.224	1.00
39_A	42_E	1.224	1.00
20_R	25_H	1.222	1.00
252_I	268_V	1.219	1.00
120_I	298_A	1.217	1.00
85_V	92_V	1.206	1.00
63_A	111_L	1.204	1.00
196_G	200_A	1.203	1.00
175_H	239_A	1.203	1.00
168_V	203_D	1.203	1.00
229_K	233_L	1.193	1.00
39_A	43_L	1.191	1.00
32_K	35_M	1.186	1.00
81_V	299_V	1.179	1.00
95_F	111_L	1.177	1.00
7_I	11_C	1.175	1.00
4_I	15_K	1.171	1.00
64_L	81_V	1.160	1.00
81_V	120_I	1.155	1.00
160_F	192_Q	1.153	1.00
292_I	296_Q	1.151	1.00
7_I	43_L	1.141	1.00
200_A	204_Y	1.141	1.00
176_K	238_S	1.125	1.00
197_Y	201_L	1.115	1.00
234_K	237_P	1.107	1.00
221_E	225_R	1.107	1.00
61_T	91_K	1.105	1.00
181_C	251_I	1.104	1.00
160_F	196_G	1.101	1.00
109_E	133_P	1.096	1.00
226_V	229_K	1.094	1.00
34_D	37_L	1.089	1.00
166_G	241_F	1.088	1.00
199_K	203_D	1.088	1.00
38_K	41_N	1.085	1.00
61_T	93_I	1.083	1.00
88_K	300_L	1.082	1.00
297_Q	301_K	1.081	1.00
180_F	194_K	1.077	1.00
64_L	92_V	1.071	1.00
82_S	86_L	1.070	1.00
245_D	286_T	1.069	1.00
219_N	222_D	1.069	1.00
250_G	254_Q	1.069	1.00
173_R	325_I	1.066	1.00
178_I	201_L	1.065	1.00
21_V	28_V	1.062	1.00
240_I	251_I	1.061	1.00
295_G	299_V	1.058	1.00
4_I	18_V	1.055	1.00
24_N	33_R	1.045	1.00
201_L	206_L	1.038	1.00
195_E	198_L	1.035	1.00
105_L	109_E	1.030	1.00
245_D	270_G	1.018	1.00
177_K	235_D	1.013	1.00
86_L	103_T	1.012	1.00
169_H	285_T	1.008	1.00
172_E	204_Y	1.007	1.00
296_Q	300_L	1.006	1.00
88_K	307_S	1.005	1.00
171_I	206_L	1.000	1.00
242_T	247_V	0.999	1.00
90_Y	303_I	0.998	1.00
225_R	229_K	0.998	1.00
40_I	43_L	0.996	1.00
161_E	320_P	0.995	1.00
50_L	53_N	0.994	1.00
242_T	248_A	0.990	1.00
48_N	54_F	0.988	1.00
222_D	225_R	0.987	1.00
301_K	317_I	0.987	1.00
197_Y	241_F	0.985	1.00
103_T	106_E	0.983	1.00
223_G	227_F	0.981	1.00
191_C	195_E	0.980	1.00
220_I	253_K	0.978	1.00
214_F	226_V	0.971	1.00
153_T	301_K	0.971	1.00
297_Q	319_L	0.968	1.00
302_I	306_I	0.966	1.00
173_R	267_A	0.959	1.00
227_F	231_K	0.953	1.00
178_I	239_A	0.948	1.00
11_C	18_V	0.947	1.00
322_K	325_I	0.934	1.00
252_I	262_V	0.932	1.00
87_F	296_Q	0.932	1.00
185_P	215_G	0.928	1.00
166_G	287_I	0.923	1.00
112_K	137_Y	0.923	1.00
252_I	280_V	0.917	1.00
188_E	192_Q	0.915	1.00
79_K	83_H	0.914	1.00
167_V	201_L	0.906	1.00
120_I	302_I	0.901	1.00
24_N	37_L	0.899	1.00
171_I	176_K	0.892	1.00
48_N	51_A	0.891	1.00
288_D	324_I	0.886	1.00
78_I	82_S	0.883	1.00
157_Y	290_P	0.880	1.00
155_I	301_K	0.877	1.00
277_C	280_V	0.875	1.00
83_H	296_Q	0.875	1.00
301_K	304_E	0.872	1.00
62_I	120_I	0.870	1.00
198_L	208_H	0.870	1.00
240_I	266_L	0.868	1.00
208_H	211_E	0.867	1.00
161_E	321_T	0.862	1.00
290_P	319_L	0.859	1.00
260_F	266_L	0.859	1.00
47_P	52_R	0.854	1.00
256_M	283_T	0.852	1.00
255_A	268_V	0.848	1.00
81_V	295_G	0.848	1.00
51_A	54_F	0.847	1.00
77_L	143_C	0.842	1.00
177_K	212_W	0.841	1.00
231_K	254_Q	0.837	1.00
21_V	37_L	0.835	1.00
179_G	240_I	0.833	1.00
225_R	228_H	0.832	1.00
157_Y	321_T	0.829	1.00
118_G	306_I	0.826	1.00
158_D	318_K	0.826	1.00
64_L	78_I	0.824	1.00
245_D	273_N	0.822	1.00
156_G	318_K	0.818	1.00
158_D	320_P	0.816	1.00
176_K	206_L	0.814	1.00
73_F	291_V	0.813	1.00
109_E	113_H	0.812	1.00
273_N	324_I	0.808	1.00
199_K	202_Q	0.808	1.00
128_W	132_S	0.806	1.00
290_P	322_K	0.806	1.00
216_E	247_V	0.804	1.00
13_V	36_I	0.801	1.00
182_F	194_K	0.799	1.00
186_Y	191_C	0.798	1.00
49_Y	52_R	0.795	1.00
31_E	34_D	0.795	1.00
83_H	87_F	0.794	1.00
236_R	260_F	0.793	1.00
183_D	218_F	0.790	1.00
299_V	303_I	0.789	1.00
194_K	213_I	0.789	1.00
222_D	226_V	0.788	1.00
76_Q	292_I	0.784	1.00
80_G	84_E	0.783	1.00
157_Y	289_I	0.782	1.00
31_E	35_M	0.782	1.00
170_L	269_I	0.782	1.00
276_I	280_V	0.779	1.00
159_E	193_R	0.778	1.00
227_F	254_Q	0.778	1.00
181_C	242_T	0.773	1.00
81_V	92_V	0.768	1.00
227_F	230_I	0.765	1.00
192_Q	196_G	0.762	1.00
212_W	233_L	0.761	1.00
78_I	94_V	0.759	1.00
270_G	286_T	0.759	1.00
61_T	114_K	0.757	1.00
80_G	296_Q	0.757	1.00
16_T	20_R	0.752	1.00
100_D	103_T	0.750	1.00
98_F	103_T	0.749	1.00
106_E	109_E	0.749	1.00
59_T	117_D	0.747	1.00
180_F	241_F	0.745	1.00
67_P	74_F	0.744	1.00
46_T	113_H	0.739	1.00
201_L	208_H	0.739	1.00
17_T	20_R	0.737	1.00
93_I	116_V	0.737	1.00
231_K	258_N	0.737	1.00
58_K	117_D	0.731	1.00
62_I	299_V	0.727	1.00
133_P	136_K	0.727	1.00
165_M	287_I	0.727	1.00
132_S	135_L	0.725	1.00
248_A	270_G	0.721	1.00
63_A	119_I	0.719	1.00
253_K	256_M	0.718	1.00
273_N	277_C	0.716	1.00
255_A	262_V	0.716	1.00
20_R	27_Y	0.715	1.00
249_A	280_V	0.709	1.00
238_S	267_A	0.707	1.00
103_T	107_L	0.707	1.00
214_F	230_I	0.707	1.00
79_K	82_S	0.704	1.00
241_F	269_I	0.703	1.00
20_R	26_P	0.701	1.00
82_S	92_V	0.698	1.00
169_H	323_L	0.697	1.00
272_D	289_I	0.696	1.00
245_D	248_A	0.691	1.00
253_K	283_T	0.687	1.00
118_G	141_L	0.684	1.00
58_K	307_S	0.681	1.00
304_E	308_G	0.679	1.00
142_L	147_H	0.678	1.00
120_I	143_C	0.677	1.00
102_Q	106_E	0.676	1.00
135_L	140_I	0.676	1.00
164_Y	196_G	0.676	1.00
34_D	41_N	0.676	1.00
65_S	107_L	0.675	1.00
223_G	226_V	0.674	1.00
229_K	232_D	0.672	1.00
142_L	152_I	0.671	1.00
21_V	33_R	0.669	1.00
134_F	140_I	0.666	1.00
165_M	169_H	0.662	1.00
140_I	152_I	0.662	1.00
308_G	311_S	0.660	1.00
233_L	237_P	0.657	1.00
178_I	238_S	0.655	1.00
135_L	152_I	0.655	1.00
135_L	151_D	0.653	1.00
283_T	326_R	0.652	1.00
253_K	257_K	0.650	1.00
82_S	96_Q	0.649	1.00
214_F	233_L	0.648	1.00
233_L	236_R	0.647	1.00
171_I	201_L	0.646	1.00
216_E	222_D	0.646	1.00
108_L	119_I	0.646	1.00
190_Q	218_F	0.642	1.00
105_L	130_Q	0.642	1.00
46_T	109_E	0.636	1.00
93_I	114_K	0.635	1.00
135_L	138_G	0.634	1.00
256_M	282_P	0.634	1.00
35_M	38_K	0.634	1.00
130_Q	133_P	0.633	1.00
27_Y	32_K	0.632	1.00
141_L	155_I	0.630	1.00
180_F	197_Y	0.629	1.00
198_L	213_I	0.628	1.00
170_L	241_F	0.627	1.00
41_N	44_D	0.627	1.00
13_V	32_K	0.626	1.00
5_D	55_R	0.624	1.00
227_F	250_G	0.620	1.00
141_L	302_I	0.619	1.00
244_N	272_D	0.618	1.00
252_I	256_M	0.617	1.00
118_G	298_A	0.617	1.00
76_Q	291_V	0.614	1.00
79_K	292_I	0.613	1.00
164_Y	167_V	0.608	1.00
71_H	246_Q	0.603	1.00
77_L	291_V	0.603	1.00
159_E	192_Q	0.601	1.00
141_L	305_S	0.601	1.00
80_G	291_V	0.599	1.00
218_F	243_G	0.598	1.00
90_Y	117_D	0.596	1.00
20_R	28_V	0.594	1.00
59_T	91_K	0.594	1.00
253_K	281_T	0.593	1.00
197_Y	208_H	0.593	1.00
18_V	21_V	0.593	1.00
179_G	212_W	0.592	1.00
7_I	18_V	0.592	1.00
144_N	159_E	0.591	1.00
129_D	132_S	0.590	1.00
183_D	190_Q	0.589	1.00
18_V	40_I	0.587	1.00
220_I	250_G	0.586	1.00
249_A	274_Q	0.585	1.00
221_E	224_F	0.584	1.00
255_A	258_N	0.582	1.00
177_K	207_H	0.581	1.00
244_N	247_V	0.581	1.00
169_H	269_I	0.580	1.00
178_I	197_Y	0.579	1.00
241_F	271_F	0.574	1.00
62_I	306_I	0.571	1.00
62_I	118_G	0.569	1.00
256_M	261_K	0.569	1.00
305_S	308_G	0.569	1.00
285_T	323_L	0.567	1.00
146_Y	154_I	0.565	1.00
144_N	189_A	0.565	1.00
90_Y	306_I	0.561	1.00
73_F	77_L	0.561	1.00
141_L	301_K	0.560	1.00
95_F	110_L	0.559	1.00
301_K	305_S	0.559	1.00
224_F	250_G	0.558	1.00
166_G	239_A	0.557	1.00
276_I	279_V	0.555	1.00
242_T	270_G	0.555	1.00
62_I	90_Y	0.555	1.00
278_Q	283_T	0.554	1.00
218_F	247_V	0.551	1.00
25_H	28_V	0.550	1.00
198_L	210_S	0.550	1.00
52_R	56_R	0.549	1.00
141_L	298_A	0.549	1.00
85_V	90_Y	0.548	1.00
181_C	226_V	0.544	1.00
46_T	50_L	0.543	1.00
187_S	190_Q	0.543	1.00
292_I	295_G	0.542	1.00
61_T	117_D	0.542	1.00
101_K	105_L	0.541	1.00
72_P	246_Q	0.540	1.00
260_F	263_P	0.539	1.00
177_K	237_P	0.537	1.00
190_Q	243_G	0.537	1.00
142_L	154_I	0.534	1.00
133_P	137_Y	0.534	1.00
226_V	230_I	0.532	1.00
224_F	227_F	0.530	1.00
155_I	297_Q	0.530	1.00
194_K	208_H	0.529	1.00
262_V	265_D	0.529	1.00
271_F	289_I	0.529	1.00
81_V	85_V	0.529	1.00
112_K	115_E	0.526	1.00
277_C	284_I	0.526	1.00
245_D	274_Q	0.525	1.00
111_L	116_V	0.525	1.00
231_K	255_A	0.524	1.00
28_V	33_R	0.523	1.00
157_Y	271_F	0.522	1.00
13_V	18_V	0.521	1.00
287_I	321_T	0.519	1.00
251_I	255_A	0.518	1.00
118_G	139_P	0.517	1.00
318_K	321_T	0.517	1.00
249_A	276_I	0.515	1.00
85_V	303_I	0.515	1.00
109_E	112_K	0.512	1.00
116_V	119_I	0.511	1.00
297_Q	304_E	0.510	1.00
18_V	36_I	0.510	1.00
182_F	215_G	0.508	1.00
16_T	25_H	0.508	1.00
97_T	104_E	0.508	1.00
236_R	265_D	0.507	1.00
74_F	122_G	0.507	1.00
208_H	213_I	0.507	1.00
157_Y	162_A	0.507	1.00
11_C	21_V	0.507	1.00
216_E	223_G	0.505	1.00
99_Y	145_E	0.505	1.00
80_G	83_H	0.504	1.00
177_K	234_K	0.504	1.00
237_P	240_I	0.504	1.00
173_R	238_S	0.503	1.00
239_A	267_A	0.501	1.00
159_E	189_A	0.501	1.00
106_E	110_L	0.501	1.00
280_V	283_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
3dbiA	2	0.8237	100	0.051	Contact Map
2hsgA	1	0.9878	100	0.056	Contact Map
2o20A	2	0.8298	100	0.062	Contact Map
1qpzA	2	0.9939	100	0.065	Contact Map
3bilA	2	0.769	100	0.073	Contact Map
3kjxA	2	0.997	100	0.074	Contact Map
4o5aA	2	0.8024	100	0.076	Contact Map
3e3mA	2	0.8024	100	0.077	Contact Map
3ctpA	2	0.7994	100	0.081	Contact Map
3h5oA	2	0.8116	100	0.083	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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