MSMR - BACSU - GREMLIN Contacts

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MSMR - Uncharacterized HTH-type transcriptional regulator MsmR

UniProt:	O34829	Sequences: MVRIKDIALKAKVSSATVSRILNEDESLSVAGETRQRVINIAEELGYQTVAKRRKSRGQKQRAQPLIGVLSCLSPDQERQDPYFSSIRKGIEKECFEQEIFITNSIHLGSFQEHIFRELDGVIVIGRVHDEAVKHISGRLEHAVFINHSPDPQAYDSIGIDFESASRQAIDHLFDLGYKRLGYIGGQEKEHTLKDGQSIRRTIEDKRLTAFLESAAPQPEHVLIGEYSMREGYRLMKKAIDQGHLPEAFFIASDSMAIGALKALQEAGLQVPRDTAIVSFNGIEEAEFASTPLTTVKVYTEEMGRTGVKLLLDRLNGRTLPQHVTLPTTLIVRQSCGCTAKEVT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	344 (317)
Sequences:	32396 (24426)
Seq/√Len:	1371.9

ECOLI - GALS GALR PURR ASCG CYTR RBSR EBGR LACI CRA MALI GNTR IDNR YCJW TRER TORT ALSB RBSB YTFQ XYLF ARAF LSRB YPHF XYLR DGAL
BACSU - MSMR GANR EXUR RBSR KDGR YVDE CCPA NTDR DEGA YKVZ 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
178_Y	247_E	3.431	1.00
163_E	208_L	3.346	1.00
10_K	44_E	3.180	1.00
270_Q	273_R	3.097	1.00
169_A	278_V	2.715	1.00
282_G	297_K	2.599	1.00
178_Y	276_A	2.579	1.00
156_D	314_R	2.540	1.00
203_I	207_R	2.443	1.00
121_G	311_L	2.410	1.00
167_R	212_L	2.357	1.00
32_G	36_Q	2.212	1.00
233_Y	266_E	2.208	1.00
40_N	44_E	2.202	1.00
36_Q	40_N	2.179	1.00
94_E	309_K	2.107	1.00
94_E	97_E	2.059	1.00
174_F	213_E	2.045	1.00
237_K	267_A	2.043	1.00
306_T	309_K	2.010	1.00
232_G	259_G	1.983	1.00
90_G	304_G	1.981	1.00
166_S	170_I	1.978	1.00
264_L	275_T	1.957	1.00
176_L	336_C	1.949	1.00
95_C	308_V	1.948	1.00
21_I	38_V	1.934	1.00
167_R	208_L	1.933	1.00
171_D	175_D	1.932	1.00
22_L	42_A	1.920	1.00
35_R	39_I	1.920	1.00
165_A	280_F	1.905	1.00
167_R	209_T	1.894	1.00
171_D	209_T	1.879	1.00
164_S	168_Q	1.870	1.00
5_K	15_S	1.843	1.00
237_K	263_A	1.829	1.00
166_S	250_F	1.827	1.00
25_D	29_S	1.823	1.00
241_D	267_A	1.820	1.00
297_K	329_T	1.818	1.00
163_E	204_E	1.773	1.00
313_D	318_R	1.741	1.00
93_K	301_E	1.737	1.00
170_I	206_K	1.732	1.00
171_D	213_E	1.716	1.00
11_A	41_I	1.692	1.00
233_Y	263_A	1.675	1.00
167_R	171_D	1.641	1.00
292_P	334_Q	1.639	1.00
94_E	305_R	1.635	1.00
173_L	248_A	1.633	1.00
236_M	260_A	1.631	1.00
183_Y	252_A	1.630	1.00
68_G	119_L	1.630	1.00
269_L	274_D	1.629	1.00
90_G	301_E	1.623	1.00
10_K	41_I	1.622	1.00
168_Q	328_T	1.619	1.00
299_Y	302_E	1.615	1.00
306_T	324_V	1.603	1.00
270_Q	274_D	1.597	1.00
251_I	260_A	1.551	1.00
265_Q	290_S	1.541	1.00
21_I	42_A	1.535	1.00
282_G	333_R	1.522	1.00
161_D	164_S	1.506	1.00
146_I	307_G	1.505	1.00
39_I	43_E	1.496	1.00
182_G	246_P	1.481	1.00
7_I	41_I	1.475	1.00
107_H	114_H	1.470	1.00
263_A	267_A	1.464	1.00
39_I	42_A	1.445	1.00
204_E	208_L	1.440	1.00
165_A	328_T	1.424	1.00
223_L	238_K	1.422	1.00
302_E	306_T	1.417	1.00
174_F	209_T	1.412	1.00
236_M	249_F	1.412	1.00
94_E	98_Q	1.409	1.00
180_R	218_Q	1.404	1.00
94_E	308_V	1.402	1.00
278_V	294_T	1.402	1.00
263_A	266_E	1.394	1.00
180_R	245_L	1.385	1.00
172_H	336_C	1.362	1.00
166_S	205_D	1.357	1.00
170_I	205_D	1.352	1.00
172_H	176_L	1.351	1.00
172_H	332_V	1.348	1.00
264_L	269_L	1.345	1.00
302_E	305_R	1.343	1.00
98_Q	312_L	1.340	1.00
218_Q	221_H	1.330	1.00
26_E	29_S	1.329	1.00
67_I	95_C	1.326	1.00
7_I	11_A	1.322	1.00
170_I	174_F	1.320	1.00
178_Y	248_A	1.311	1.00
164_S	167_R	1.309	1.00
65_P	120_D	1.306	1.00
201_R	204_E	1.305	1.00
237_K	266_E	1.296	1.00
170_I	209_T	1.286	1.00
172_H	175_D	1.285	1.00
226_E	231_E	1.277	1.00
171_D	212_L	1.270	1.00
31_A	34_T	1.269	1.00
205_D	209_T	1.265	1.00
32_G	35_R	1.258	1.00
10_K	45_L	1.257	1.00
182_G	239_A	1.252	1.00
6_D	9_L	1.252	1.00
20_R	25_D	1.249	1.00
236_M	264_L	1.248	1.00
207_R	211_F	1.245	1.00
5_K	9_L	1.231	1.00
41_I	45_L	1.231	1.00
309_K	313_D	1.226	1.00
261_L	277_I	1.222	1.00
65_P	100_I	1.214	1.00
237_K	241_D	1.212	1.00
209_T	212_L	1.211	1.00
91_I	123_I	1.202	1.00
276_A	336_C	1.201	1.00
69_V	91_I	1.201	1.00
180_R	247_E	1.193	1.00
7_I	45_L	1.192	1.00
37_R	41_I	1.191	1.00
233_Y	237_K	1.185	1.00
41_I	44_E	1.167	1.00
233_Y	262_K	1.162	1.00
111_F	114_H	1.158	1.00
4_I	15_S	1.154	1.00
163_E	201_R	1.153	1.00
184_I	260_A	1.150	1.00
181_L	210_A	1.141	1.00
91_I	308_V	1.139	1.00
134_K	138_G	1.134	1.00
95_C	102_I	1.133	1.00
243_G	246_P	1.131	1.00
34_T	37_R	1.120	1.00
168_Q	171_D	1.118	1.00
21_I	30_V	1.116	1.00
259_G	263_A	1.112	1.00
238_K	242_Q	1.108	1.00
210_A	215_A	1.104	1.00
254_D	295_T	1.101	1.00
175_D	213_E	1.099	1.00
123_I	307_G	1.097	1.00
249_F	260_A	1.091	1.00
4_I	18_V	1.088	1.00
50_V	53_R	1.087	1.00
254_D	279_S	1.083	1.00
179_K	247_E	1.082	1.00
163_E	167_R	1.079	1.00
69_V	102_I	1.076	1.00
312_L	316_N	1.076	1.00
301_E	305_R	1.072	1.00
230_R	234_R	1.069	1.00
304_G	308_V	1.067	1.00
40_N	43_E	1.065	1.00
310_L	324_V	1.061	1.00
36_Q	39_I	1.059	1.00
206_K	210_A	1.057	1.00
208_L	212_L	1.055	1.00
169_A	250_F	1.053	1.00
306_T	310_L	1.049	1.00
232_G	236_M	1.049	1.00
176_L	332_V	1.048	1.00
180_R	244_H	1.039	1.00
98_Q	309_K	1.033	1.00
183_Y	203_I	1.024	1.00
163_E	205_D	1.023	1.00
98_Q	316_N	1.011	1.00
42_A	45_L	1.006	1.00
261_L	271_V	1.001	1.00
174_F	215_A	1.000	1.00
50_V	56_S	1.000	1.00
24_E	35_R	0.999	1.00
209_T	213_E	0.992	1.00
299_Y	326_L	0.991	1.00
251_I	257_A	0.991	1.00
188_E	224_I	0.988	1.00
176_L	276_A	0.988	1.00
235_L	238_K	0.980	1.00
306_T	326_L	0.963	1.00
52_K	55_K	0.956	1.00
311_L	315_L	0.954	1.00
261_L	289_A	0.949	1.00
69_V	88_R	0.947	1.00
169_A	296_V	0.939	1.00
53_R	56_S	0.939	1.00
66_L	103_T	0.938	1.00
234_R	238_K	0.938	1.00
181_L	248_A	0.938	1.00
297_K	331_I	0.938	1.00
11_A	18_V	0.933	1.00
228_S	231_E	0.932	1.00
204_E	207_R	0.924	1.00
236_M	240_I	0.923	1.00
160_I	299_Y	0.923	1.00
92_E	96_F	0.923	1.00
305_R	309_K	0.922	1.00
93_K	305_R	0.920	1.00
164_S	327_P	0.915	1.00
207_R	217_P	0.902	1.00
279_S	295_T	0.901	1.00
180_R	221_H	0.900	1.00
170_I	210_A	0.898	1.00
161_D	325_T	0.897	1.00
49_T	54_R	0.891	1.00
186_G	227_Y	0.891	1.00
251_I	256_M	0.888	1.00
174_F	179_K	0.885	1.00
100_I	312_L	0.880	1.00
206_K	250_F	0.879	1.00
157_S	323_H	0.879	1.00
329_T	332_V	0.876	1.00
111_F	115_I	0.874	1.00
158_I	310_L	0.872	1.00
67_I	123_I	0.872	1.00
156_D	322_Q	0.871	1.00
64_Q	120_D	0.869	1.00
332_V	336_C	0.864	1.00
91_I	304_G	0.861	1.00
231_E	234_R	0.860	1.00
254_D	257_A	0.860	1.00
123_I	311_L	0.858	1.00
225_G	256_M	0.858	1.00
179_K	215_A	0.857	1.00
223_L	235_L	0.853	1.00
24_E	39_I	0.851	1.00
172_H	294_T	0.849	1.00
164_S	328_T	0.846	1.00
160_I	328_T	0.845	1.00
97_E	305_R	0.844	1.00
254_D	282_G	0.844	1.00
66_L	101_F	0.841	1.00
21_I	39_I	0.837	1.00
156_D	310_L	0.836	1.00
159_G	325_T	0.835	1.00
229_M	262_K	0.832	1.00
221_H	242_Q	0.828	1.00
107_H	111_F	0.826	1.00
210_A	217_P	0.825	1.00
269_L	275_T	0.820	1.00
249_F	275_T	0.817	1.00
282_G	331_I	0.813	1.00
182_G	249_F	0.811	1.00
240_I	263_A	0.809	1.00
217_P	220_E	0.807	1.00
310_L	313_D	0.806	1.00
245_L	269_L	0.805	1.00
162_F	202_T	0.805	1.00
308_V	312_L	0.804	1.00
17_T	20_R	0.802	1.00
282_G	286_A	0.799	1.00
299_Y	329_T	0.799	1.00
107_H	110_S	0.799	1.00
172_H	330_L	0.799	1.00
281_N	298_V	0.795	1.00
160_I	298_V	0.793	1.00
110_S	114_H	0.793	1.00
161_D	327_P	0.792	1.00
112_Q	116_F	0.791	1.00
89_K	93_K	0.788	1.00
294_T	336_C	0.784	1.00
33_E	36_Q	0.784	1.00
173_L	278_V	0.783	1.00
264_L	277_I	0.783	1.00
86_S	301_E	0.781	1.00
51_A	54_R	0.778	1.00
33_E	37_R	0.776	1.00
247_E	276_A	0.775	1.00
63_A	120_D	0.774	1.00
83_Y	300_T	0.771	1.00
13_V	38_V	0.770	1.00
121_G	315_L	0.770	1.00
111_F	116_F	0.769	1.00
250_F	278_V	0.767	1.00
20_R	26_E	0.763	1.00
258_I	289_A	0.763	1.00
3_R	6_D	0.763	1.00
87_I	146_I	0.758	1.00
203_I	222_V	0.756	1.00
234_R	237_K	0.752	1.00
183_Y	250_F	0.748	1.00
20_R	29_S	0.747	1.00
159_G	323_H	0.746	1.00
185_G	203_I	0.745	1.00
68_G	122_V	0.744	1.00
168_Q	296_V	0.742	1.00
231_E	235_L	0.738	1.00
92_E	102_I	0.737	1.00
66_L	117_R	0.735	1.00
201_R	205_D	0.734	1.00
236_M	239_A	0.734	1.00
16_A	20_R	0.734	1.00
208_L	211_F	0.733	1.00
67_I	308_V	0.732	1.00
236_M	263_A	0.727	1.00
242_Q	246_P	0.725	1.00
91_I	102_I	0.725	1.00
184_I	251_I	0.724	1.00
90_G	94_E	0.724	1.00
189_K	194_K	0.722	1.00
240_I	267_A	0.711	1.00
90_G	305_R	0.711	1.00
63_A	316_N	0.709	1.00
174_F	210_A	0.707	1.00
225_G	231_E	0.702	1.00
294_T	330_L	0.701	1.00
145_F	150_P	0.698	1.00
289_A	292_P	0.697	1.00
232_G	235_L	0.694	1.00
236_M	259_G	0.693	1.00
135_H	138_G	0.688	1.00
223_L	239_A	0.684	1.00
181_L	247_E	0.684	1.00
313_D	317_G	0.683	1.00
264_L	271_V	0.680	1.00
242_Q	245_L	0.680	1.00
181_L	206_K	0.677	1.00
113_E	116_F	0.676	1.00
136_I	143_A	0.675	1.00
137_S	143_A	0.674	1.00
36_Q	43_E	0.674	1.00
262_K	292_P	0.673	1.00
292_P	333_R	0.672	1.00
149_S	323_H	0.671	1.00
121_G	144_V	0.668	1.00
301_E	304_G	0.660	1.00
262_K	265_Q	0.660	1.00
109_G	114_H	0.655	1.00
167_R	205_D	0.653	1.00
81_D	255_S	0.652	1.00
264_L	267_A	0.652	1.00
223_L	242_Q	0.650	1.00
176_L	247_E	0.650	1.00
18_V	21_I	0.650	1.00
313_D	322_Q	0.649	1.00
21_I	35_R	0.647	1.00
5_K	57_R	0.646	1.00
134_K	137_S	0.643	1.00
145_F	155_Y	0.639	1.00
253_S	281_N	0.639	1.00
137_S	155_Y	0.638	1.00
123_I	146_I	0.636	1.00
93_K	97_E	0.635	1.00
137_S	154_A	0.633	1.00
87_I	300_T	0.628	1.00
278_V	336_C	0.628	1.00
89_K	301_E	0.627	1.00
258_I	283_I	0.627	1.00
83_Y	87_I	0.625	1.00
20_R	30_V	0.624	1.00
183_Y	206_K	0.622	1.00
238_K	241_D	0.621	1.00
173_L	250_F	0.620	1.00
191_H	201_R	0.620	1.00
262_K	266_E	0.619	1.00
7_I	18_V	0.618	1.00
18_V	42_A	0.617	1.00
147_N	162_F	0.614	1.00
143_A	155_Y	0.612	1.00
86_S	300_T	0.612	1.00
43_E	46_G	0.611	1.00
37_R	40_N	0.611	1.00
89_K	92_E	0.611	1.00
280_F	298_V	0.610	1.00
121_G	307_G	0.607	1.00
13_V	34_T	0.606	1.00
95_C	312_L	0.604	1.00
162_F	201_R	0.604	1.00
167_R	170_I	0.603	1.00
227_Y	252_A	0.603	1.00
144_V	158_I	0.603	1.00
262_K	290_S	0.598	1.00
182_G	221_H	0.597	1.00
29_S	34_T	0.596	1.00
206_K	217_P	0.595	1.00
314_R	317_G	0.595	1.00
110_S	113_E	0.593	1.00
217_P	222_V	0.593	1.00
194_K	204_E	0.591	1.00
168_Q	172_H	0.591	1.00
107_H	115_I	0.590	1.00
103_T	119_L	0.590	1.00
203_I	224_I	0.590	1.00
246_P	269_L	0.589	1.00
294_T	332_V	0.589	1.00
257_A	279_S	0.587	1.00
90_G	300_T	0.586	1.00
58_G	63_A	0.581	1.00
144_V	311_L	0.581	1.00
92_E	106_I	0.580	1.00
240_I	264_L	0.580	1.00
18_V	38_V	0.578	1.00
229_M	259_G	0.578	1.00
258_I	285_E	0.576	1.00
251_I	279_S	0.575	1.00
169_A	248_A	0.574	1.00
25_D	30_V	0.574	1.00
303_M	326_L	0.573	1.00
48_Q	52_K	0.573	1.00
81_D	84_F	0.571	1.00
108_L	114_H	0.571	1.00
67_I	315_L	0.570	1.00
253_S	256_M	0.569	1.00
88_R	92_E	0.565	1.00
296_V	328_T	0.563	1.00
55_K	58_G	0.562	1.00
78_E	89_K	0.560	1.00
233_Y	259_G	0.556	1.00
286_A	293_L	0.554	1.00
158_I	306_T	0.553	1.00
144_V	310_L	0.552	1.00
207_R	219_P	0.551	1.00
287_E	292_P	0.551	1.00
260_A	264_L	0.551	1.00
291_T	335_S	0.551	1.00
119_L	122_V	0.550	1.00
261_L	265_Q	0.549	1.00
185_G	224_I	0.549	1.00
250_F	280_F	0.548	1.00
13_V	18_V	0.547	1.00
310_L	314_R	0.546	1.00
229_M	285_E	0.544	1.00
11_A	21_I	0.543	1.00
231_E	256_M	0.540	1.00
16_A	25_D	0.539	1.00
67_I	121_G	0.539	1.00
144_V	307_G	0.536	1.00
180_R	246_P	0.534	1.00
100_I	120_D	0.533	1.00
122_V	141_E	0.533	1.00
160_I	165_A	0.532	1.00
266_E	290_S	0.528	1.00
109_G	113_E	0.527	1.00
160_I	280_F	0.527	1.00
54_R	58_G	0.527	1.00
100_I	315_L	0.526	1.00
82_P	255_S	0.524	1.00
262_K	287_E	0.524	1.00
144_V	314_R	0.523	1.00
180_R	216_A	0.522	1.00
131_E	134_K	0.521	1.00
66_L	120_D	0.519	1.00
11_A	38_V	0.516	1.00
265_Q	270_Q	0.516	1.00
172_H	278_V	0.515	1.00
245_L	274_D	0.515	1.00
163_E	166_S	0.513	1.00
306_T	313_D	0.513	1.00
299_Y	303_M	0.511	1.00
30_V	35_R	0.509	1.00
260_A	277_I	0.509	1.00
286_A	295_T	0.509	1.00
64_Q	100_I	0.507	1.00
283_I	295_T	0.507	1.00
149_S	157_S	0.506	1.00
190_E	193_L	0.506	1.00
220_E	242_Q	0.506	1.00
94_E	312_L	0.506	1.00
193_L	227_Y	0.505	1.00
15_S	57_R	0.505	1.00
124_V	145_F	0.504	1.00
227_Y	256_M	0.503	1.00
269_L	272_P	0.503	1.00
159_G	162_F	0.502	1.00
233_Y	236_M	0.501	1.00
246_P	249_F	0.501	1.00
286_A	289_A	0.501	1.00
91_I	95_C	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	0.7791	100	0.1	Contact Map
4o5aA	2	0.7558	100	0.113	Contact Map
2hsgA	1	0.9244	100	0.115	Contact Map
1qpzA	2	0.9506	100	0.119	Contact Map
2o20A	2	0.7733	100	0.122	Contact Map
3bilA	2	0.7209	100	0.126	Contact Map
3ctpA	2	0.7471	100	0.126	Contact Map
3kjxA	2	0.936	100	0.128	Contact Map
1jyeA	2	0.7587	100	0.128	Contact Map
3e3mA	2	0.7558	100	0.131	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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