RBSR - BACSU - GREMLIN Contacts

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RBSR - Ribose operon repressor

UniProt:	P36944	Sequences: MATIKDVAGAAGVSVATVSRNLNDNGYVHEETRTRVIAAMAKLNYYPNEVARSLYKRESRLIGLLLPDITNPFFPQLARGAEDELNREGYRLIFGNSDEELKKELEYLQTFKQNHVAGIIAATNYPDLEEYSGMNYPVVFLDRTLEGAPSVSSDGYTGVKLAAQAIIHGKSQRITLLRGPAHLPTAQDRFNGALEILKQAEVDFQVIETASFSIKDAQSMAKELFASYPATDGVIASNDIQAAAVLHEALRRGKNVPEDIQIIGYDDIPQSGLLFPPLSTIKQPAYDMGKEAAKLLLGIIKKQPLAETAIQMPVTYIGRKTTRKED	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	326 (318)
Sequences:	37161 (26838)
Seq/√Len:	1505.0

ECOLI - GALS GALR PURR ASCG CRA RBSR LACI CYTR MALI IDNR GNTR EBGR YCJW TRER TORT ALSB RBSB YTFQ XYLF YPHF ARAF LSRB DGAL XYLR
BACSU - RBSR YKVZ KDGR CCPA NTDR MSMR DEGA YVDE EXUR 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
156_Y	195_E	3.354	1.00
171_S	232_D	3.179	1.00
10_A	42_K	3.111	1.00
255_N	258_E	3.037	1.00
162_A	263_I	2.583	1.00
190_F	194_L	2.559	1.00
118_G	296_L	2.550	1.00
171_S	261_Q	2.456	1.00
267_D	282_K	2.448	1.00
149_P	299_I	2.333	1.00
160_K	199_Q	2.271	1.00
30_E	34_T	2.229	1.00
218_Q	251_R	2.223	1.00
84_E	87_R	2.200	1.00
38_A	42_K	2.186	1.00
34_T	38_A	2.157	1.00
84_E	294_K	2.139	1.00
169_G	322_T	2.138	1.00
222_K	252_R	2.113	1.00
160_K	195_E	2.071	1.00
291_E	294_K	2.056	1.00
160_K	196_I	2.020	1.00
164_Q	196_I	2.018	1.00
157_T	161_L	2.015	1.00
167_I	200_A	2.014	1.00
222_K	248_E	1.952	1.00
85_L	293_A	1.940	1.00
21_N	36_V	1.931	1.00
158_G	265_Y	1.895	1.00
156_Y	191_N	1.883	1.00
33_R	37_I	1.873	1.00
80_G	289_G	1.866	1.00
159_V	163_A	1.865	1.00
22_L	40_M	1.855	1.00
164_Q	168_H	1.830	1.00
226_A	252_R	1.821	1.00
84_E	290_K	1.818	1.00
5_K	15_V	1.816	1.00
298_G	303_Q	1.815	1.00
249_A	260_I	1.797	1.00
166_I	233_G	1.792	1.00
217_A	244_A	1.785	1.00
282_K	315_T	1.768	1.00
83_D	286_Y	1.752	1.00
159_V	235_I	1.742	1.00
163_A	193_A	1.728	1.00
164_Q	200_A	1.680	1.00
160_K	164_Q	1.672	1.00
11_A	39_A	1.659	1.00
218_Q	248_E	1.654	1.00
10_A	39_A	1.645	1.00
254_K	259_D	1.644	1.00
221_A	245_V	1.629	1.00
175_T	231_T	1.625	1.00
63_G	116_V	1.623	1.00
284_P	287_D	1.617	1.00
291_E	310_I	1.616	1.00
176_L	237_S	1.607	1.00
80_G	286_Y	1.603	1.00
236_A	245_V	1.598	1.00
161_L	314_V	1.586	1.00
84_E	88_E	1.551	1.00
255_N	259_D	1.548	1.00
277_P	320_K	1.547	1.00
248_E	252_R	1.536	1.00
37_I	41_A	1.516	1.00
157_T	160_K	1.513	1.00
141_L	292_A	1.505	1.00
173_R	230_A	1.500	1.00
191_N	195_E	1.491	1.00
165_A	168_H	1.472	1.00
154_D	157_T	1.468	1.00
167_I	196_I	1.468	1.00
88_E	297_L	1.459	1.00
250_L	275_F	1.458	1.00
287_D	291_E	1.451	1.00
21_N	40_M	1.446	1.00
248_E	251_R	1.440	1.00
7_V	39_A	1.423	1.00
263_I	279_S	1.404	1.00
37_I	40_M	1.404	1.00
173_R	205_Q	1.400	1.00
267_D	319_R	1.398	1.00
188_D	191_N	1.391	1.00
194_L	198_K	1.388	1.00
165_A	318_G	1.372	1.00
287_D	290_K	1.366	1.00
218_Q	247_H	1.358	1.00
84_E	293_A	1.354	1.00
60_R	117_A	1.348	1.00
158_G	314_V	1.340	1.00
211_S	216_D	1.337	1.00
297_L	301_K	1.334	1.00
222_K	251_R	1.334	1.00
163_A	167_I	1.327	1.00
175_T	224_L	1.319	1.00
249_A	254_K	1.316	1.00
221_A	234_V	1.304	1.00
173_R	232_D	1.298	1.00
159_V	192_G	1.294	1.00
218_Q	222_K	1.290	1.00
163_A	192_G	1.276	1.00
196_I	199_Q	1.276	1.00
10_A	43_L	1.275	1.00
163_A	196_I	1.269	1.00
208_E	223_E	1.262	1.00
5_K	9_G	1.260	1.00
294_K	298_G	1.251	1.00
221_A	249_A	1.243	1.00
63_G	111_F	1.241	1.00
156_Y	160_K	1.240	1.00
60_R	90_Y	1.239	1.00
62_I	85_L	1.235	1.00
6_D	9_G	1.234	1.00
30_E	33_R	1.233	1.00
165_A	322_T	1.229	1.00
171_S	233_G	1.228	1.00
222_K	226_A	1.226	1.00
29_H	32_T	1.225	1.00
20_R	25_N	1.212	1.00
7_V	11_A	1.210	1.00
192_G	196_I	1.209	1.00
129_E	133_G	1.208	1.00
120_I	292_A	1.203	1.00
35_R	39_A	1.202	1.00
95_G	107_Y	1.200	1.00
161_L	164_Q	1.197	1.00
246_L	262_I	1.195	1.00
95_G	111_F	1.191	1.00
39_A	42_K	1.186	1.00
39_A	43_L	1.185	1.00
85_L	92_L	1.176	1.00
165_A	169_G	1.171	1.00
172_Q	232_D	1.162	1.00
164_Q	199_Q	1.159	1.00
7_V	43_L	1.145	1.00
81_A	293_A	1.144	1.00
223_E	227_S	1.142	1.00
156_Y	188_D	1.139	1.00
228_Y	231_T	1.137	1.00
286_Y	290_K	1.136	1.00
64_L	81_A	1.132	1.00
32_T	35_R	1.131	1.00
193_A	197_L	1.125	1.00
109_Q	130_E	1.125	1.00
4_I	15_V	1.122	1.00
81_A	120_I	1.114	1.00
215_K	219_S	1.104	1.00
244_A	248_E	1.104	1.00
61_L	91_R	1.100	1.00
64_L	92_L	1.096	1.00
156_Y	192_G	1.092	1.00
261_Q	322_T	1.090	1.00
177_L	245_V	1.089	1.00
88_E	294_K	1.089	1.00
176_L	190_F	1.081	1.00
196_I	200_A	1.081	1.00
167_I	202_V	1.076	1.00
174_I	197_L	1.075	1.00
162_A	235_I	1.075	1.00
82_E	86_N	1.069	1.00
289_G	293_A	1.067	1.00
4_I	18_V	1.065	1.00
38_A	41_A	1.063	1.00
234_V	245_V	1.059	1.00
61_L	93_I	1.058	1.00
195_E	199_Q	1.057	1.00
295_L	310_I	1.056	1.00
213_S	216_D	1.054	1.00
239_D	280_T	1.054	1.00
34_T	37_I	1.052	1.00
21_N	28_V	1.047	1.00
220_M	223_E	1.043	1.00
168_H	200_A	1.036	1.00
291_E	295_L	1.031	1.00
173_R	229_P	1.021	1.00
191_N	194_L	1.020	1.00
239_D	264_G	1.015	1.00
105_L	109_Q	1.015	1.00
48_N	54_L	1.015	1.00
50_V	53_S	1.012	1.00
193_A	235_I	1.011	1.00
24_D	33_R	1.006	1.00
88_E	301_K	0.998	1.00
194_L	204_F	0.997	1.00
236_A	242_A	0.994	1.00
217_A	221_A	0.991	1.00
86_N	103_K	0.987	1.00
290_K	294_K	0.983	1.00
236_A	241_Q	0.979	1.00
219_S	223_E	0.974	1.00
216_D	219_S	0.972	1.00
90_Y	297_L	0.970	1.00
40_M	43_L	0.969	1.00
291_E	312_M	0.965	1.00
187_Q	191_N	0.962	1.00
169_G	318_G	0.958	1.00
173_R	203_D	0.951	1.00
296_L	300_I	0.949	1.00
157_T	313_P	0.938	1.00
174_I	233_G	0.933	1.00
165_A	279_S	0.933	1.00
184_P	188_D	0.929	1.00
103_K	106_E	0.929	1.00
51_A	54_L	0.925	1.00
214_I	247_H	0.925	1.00
11_A	18_V	0.924	1.00
87_R	290_K	0.922	1.00
250_L	277_P	0.920	1.00
48_N	51_A	0.919	1.00
246_L	256_V	0.918	1.00
162_A	281_I	0.916	1.00
221_A	225_F	0.916	1.00
109_Q	113_Q	0.914	1.00
120_I	296_L	0.911	1.00
79_R	83_D	0.904	1.00
282_K	317_I	0.903	1.00
208_E	220_M	0.898	1.00
169_G	261_Q	0.894	1.00
163_A	197_L	0.893	1.00
83_D	290_K	0.890	1.00
197_L	202_V	0.882	1.00
149_P	295_L	0.882	1.00
246_L	274_L	0.876	1.00
167_I	172_Q	0.875	1.00
315_T	318_G	0.873	1.00
172_Q	202_V	0.869	1.00
47_P	52_R	0.868	1.00
24_D	37_I	0.864	1.00
182_H	187_Q	0.863	1.00
154_D	311_Q	0.860	1.00
62_I	120_I	0.859	1.00
284_P	312_M	0.858	1.00
181_A	209_T	0.858	1.00
284_P	315_T	0.857	1.00
150_S	309_A	0.857	1.00
78_A	82_E	0.856	1.00
81_A	289_G	0.854	1.00
179_G	212_F	0.850	1.00
234_V	260_I	0.846	1.00
151_V	295_L	0.846	1.00
73_F	285_A	0.845	1.00
153_S	284_P	0.842	1.00
254_K	260_I	0.841	1.00
219_S	222_K	0.840	1.00
197_L	204_F	0.835	1.00
175_T	234_V	0.834	1.00
239_D	267_D	0.833	1.00
249_A	262_I	0.832	1.00
225_F	248_E	0.831	1.00
21_N	37_I	0.824	1.00
64_L	78_A	0.823	1.00
264_G	280_T	0.821	1.00
157_T	314_V	0.821	1.00
210_A	241_Q	0.819	1.00
202_V	205_Q	0.815	1.00
195_E	198_K	0.814	1.00
178_R	190_F	0.809	1.00
100_E	103_K	0.805	1.00
31_E	34_T	0.804	1.00
295_L	298_G	0.799	1.00
152_S	311_Q	0.798	1.00
153_S	283_Q	0.792	1.00
76_Q	286_Y	0.789	1.00
318_G	322_T	0.789	1.00
267_D	317_I	0.787	1.00
81_A	92_L	0.784	1.00
216_D	220_M	0.783	1.00
59_S	117_A	0.780	1.00
155_G	189_R	0.780	1.00
83_D	87_R	0.779	1.00
166_I	263_I	0.778	1.00
118_G	300_I	0.778	1.00
153_S	314_V	0.776	1.00
49_E	52_R	0.774	1.00
80_G	290_K	0.773	1.00
77_L	141_L	0.772	1.00
152_S	309_A	0.771	1.00
230_A	254_K	0.768	1.00
154_D	313_P	0.767	1.00
61_L	114_N	0.767	1.00
177_L	236_A	0.766	1.00
106_E	109_Q	0.764	1.00
165_A	316_Y	0.763	1.00
13_V	36_V	0.763	1.00
293_A	297_L	0.760	1.00
130_E	133_G	0.756	1.00
17_T	20_R	0.756	1.00
188_D	192_G	0.755	1.00
221_A	224_L	0.752	1.00
176_L	235_I	0.749	1.00
31_E	35_R	0.746	1.00
112_K	134_M	0.744	1.00
78_A	94_F	0.742	1.00
16_A	20_R	0.738	1.00
131_Y	138_V	0.736	1.00
225_F	252_R	0.736	1.00
93_I	116_V	0.734	1.00
267_D	271_S	0.733	1.00
221_A	248_E	0.732	1.00
80_G	84_E	0.730	1.00
144_T	309_A	0.730	1.00
46_Y	113_Q	0.727	1.00
67_P	74_F	0.725	1.00
247_H	250_L	0.725	1.00
20_R	26_G	0.722	1.00
266_D	283_Q	0.720	1.00
242_A	264_G	0.718	1.00
161_L	281_I	0.714	1.00
279_S	316_Y	0.706	1.00
79_R	82_E	0.705	1.00
20_R	27_Y	0.705	1.00
103_K	107_Y	0.705	1.00
58_E	117_A	0.704	1.00
63_G	119_I	0.702	1.00
98_D	103_K	0.699	1.00
120_I	141_L	0.698	1.00
279_S	322_T	0.697	1.00
298_G	302_K	0.695	1.00
160_K	192_G	0.694	1.00
102_K	106_E	0.693	1.00
62_I	293_A	0.691	1.00
206_V	227_S	0.691	1.00
58_E	301_K	0.690	1.00
82_E	92_L	0.687	1.00
243_A	274_L	0.686	1.00
227_S	230_A	0.686	1.00
65_L	107_Y	0.685	1.00
235_I	263_I	0.684	1.00
193_A	204_F	0.684	1.00
210_A	216_D	0.676	1.00
249_A	256_V	0.675	1.00
223_E	226_A	0.674	1.00
190_F	207_I	0.673	1.00
239_D	242_A	0.673	1.00
140_F	145_L	0.667	1.00
132_S	138_V	0.666	1.00
227_S	231_T	0.664	1.00
167_I	197_L	0.662	1.00
82_E	96_N	0.662	1.00
118_G	139_V	0.661	1.00
247_H	251_R	0.657	1.00
34_T	41_A	0.657	1.00
232_D	261_Q	0.651	1.00
46_Y	109_Q	0.651	1.00
138_V	148_A	0.649	1.00
217_A	220_M	0.647	1.00
21_N	33_R	0.646	1.00
129_E	132_S	0.644	1.00
174_I	232_D	0.642	1.00
186_A	212_F	0.642	1.00
247_H	277_P	0.641	1.00
93_I	114_N	0.640	1.00
112_K	136_Y	0.639	1.00
5_K	55_Y	0.638	1.00
176_L	193_A	0.637	1.00
118_G	292_A	0.634	1.00
27_Y	32_T	0.633	1.00
302_K	305_L	0.629	1.00
221_A	244_A	0.627	1.00
166_I	235_I	0.627	1.00
71_N	240_I	0.626	1.00
179_G	186_A	0.624	1.00
108_L	119_I	0.624	1.00
243_A	270_Q	0.621	1.00
212_F	237_S	0.619	1.00
139_V	151_V	0.612	1.00
35_R	38_A	0.610	1.00
214_I	270_Q	0.609	1.00
142_D	185_T	0.607	1.00
238_N	266_D	0.607	1.00
41_A	44_N	0.606	1.00
206_V	209_T	0.604	1.00
162_A	233_G	0.604	1.00
161_L	165_A	0.604	1.00
18_V	40_M	0.601	1.00
80_G	285_A	0.600	1.00
79_R	286_Y	0.600	1.00
174_I	193_A	0.599	1.00
13_V	32_T	0.598	1.00
142_D	155_G	0.598	1.00
139_V	299_I	0.596	1.00
76_Q	285_A	0.596	1.00
215_K	218_Q	0.588	1.00
139_V	296_L	0.588	1.00
246_L	250_L	0.587	1.00
238_N	241_Q	0.587	1.00
250_L	276_P	0.587	1.00
77_L	285_A	0.586	1.00
249_A	252_R	0.585	1.00
18_V	21_N	0.585	1.00
155_G	188_D	0.583	1.00
271_S	280_T	0.582	1.00
20_R	28_V	0.581	1.00
160_K	163_A	0.581	1.00
243_A	268_I	0.580	1.00
247_H	275_F	0.578	1.00
7_V	18_V	0.577	1.00
90_Y	300_I	0.576	1.00
59_S	91_R	0.576	1.00
214_I	244_A	0.576	1.00
271_S	278_L	0.575	1.00
277_P	319_R	0.573	1.00
208_E	227_S	0.573	1.00
140_F	148_A	0.571	1.00
250_L	255_N	0.568	1.00
169_G	232_D	0.566	1.00
235_I	265_Y	0.565	1.00
73_F	77_L	0.562	1.00
46_Y	50_V	0.562	1.00
62_I	300_I	0.561	1.00
208_E	224_L	0.560	1.00
286_Y	289_G	0.560	1.00
144_T	150_S	0.559	1.00
62_I	118_G	0.559	1.00
173_R	206_V	0.555	1.00
119_I	136_Y	0.554	1.00
173_R	231_T	0.552	1.00
52_R	56_K	0.552	1.00
265_Y	283_Q	0.550	1.00
25_N	28_V	0.547	1.00
132_S	148_A	0.547	1.00
95_G	110_T	0.546	1.00
263_I	322_T	0.545	1.00
165_A	263_I	0.544	1.00
295_L	299_I	0.543	1.00
220_M	224_L	0.540	1.00
90_Y	117_A	0.539	1.00
62_I	90_Y	0.538	1.00
97_S	104_E	0.538	1.00
85_L	90_Y	0.537	1.00
18_V	36_V	0.537	1.00
140_F	150_S	0.536	1.00
101_L	105_L	0.535	1.00
186_A	237_S	0.534	1.00
139_V	295_L	0.533	1.00
72_P	240_I	0.532	1.00
85_L	297_L	0.532	1.00
279_S	318_G	0.531	1.00
288_M	312_M	0.531	1.00
281_I	314_V	0.528	1.00
212_F	241_Q	0.528	1.00
236_A	264_G	0.526	1.00
111_F	116_V	0.526	1.00
299_I	305_L	0.526	1.00
206_V	210_A	0.525	1.00
116_V	119_I	0.525	1.00
61_L	117_A	0.525	1.00
13_V	18_V	0.525	1.00
139_V	292_A	0.524	1.00
210_A	217_A	0.522	1.00
16_A	25_N	0.520	1.00
124_N	127_D	0.519	1.00
274_L	277_P	0.519	1.00
79_R	98_D	0.518	1.00
272_G	277_P	0.517	1.00
218_Q	221_A	0.516	1.00
225_F	249_A	0.516	1.00
299_I	302_K	0.515	1.00
276_P	321_T	0.514	1.00
173_R	228_Y	0.514	1.00
109_Q	112_K	0.514	1.00
256_V	259_D	0.512	1.00
11_A	21_N	0.512	1.00
251_R	275_F	0.511	1.00
81_A	85_L	0.508	1.00
151_V	291_E	0.506	1.00
130_E	134_M	0.505	1.00
177_L	220_M	0.504	1.00
74_F	122_A	0.504	1.00
11_A	36_V	0.504	1.00
239_D	268_I	0.504	1.00
28_V	33_R	0.503	1.00
218_Q	244_A	0.502	1.00
153_S	158_G	0.502	1.00
231_T	234_V	0.501	1.00
231_T	254_K	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
2hsgA	1	0.9816	100	0.085	Contact Map
3ctpA	2	0.8067	100	0.087	Contact Map
3dbiA	2	0.8252	100	0.087	Contact Map
3bilA	2	0.7699	100	0.088	Contact Map
2o20A	2	0.8221	100	0.093	Contact Map
1qpzA	2	0.9969	100	0.093	Contact Map
4o5aA	2	0.8098	100	0.094	Contact Map
3jvdA	2	0.7945	100	0.099	Contact Map
3h5oA	2	0.8098	100	0.102	Contact Map
3e3mA	2	0.8006	100	0.104	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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