YCJW - ECOLI - GREMLIN Contacts

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YCJW - Uncharacterized HTH-type transcriptional regulator YcjW

UniProt:	P77615	Sequences: MSPTIYDIARVAGVSKSTVSRVLNKQTNISPEAREKVLRAIEELQYQPNKLARALTSSGFDAIMVISTRSTKTTAGNPFFSEVLHAITAKAEEEGFDVILQTSHNPAEDLQKCESKIKQKMIKGIIMLSSPADESFFAQLDKYDIPVVVIGKVEGQYAHVYSVDTDNFGDSIALTDALIESGHQNIACLHAPLDVHVSVDRVNGYKQSLAAHNIAVRDEWIVDGGYTHETALKAARQLLSQSPLPEAVFATDSLKLMSIYRAAAEKNIAIPQQLAVVGYSNETLSFILTPAPGGIDVPTQELGQQSCELLFRLISGKPSPQNITVATHMTLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13920
Length:	332 (315)
Sequences:	36073 (26309)
Seq/√Len:	1482.3

ECOLI - YCJW LACI GALR GALS CYTR IDNR MALI PURR CRA GNTR ASCG RBSR TRER EBGR TORT RBSB ALSB XYLF YTFQ LSRB YPHF ARAF DGAL XYLR
BACSU - DEGA CCPA KDGR NTDR RBSR YKVZ MSMR EXUR GANR YVDE 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
168_F	207_Q	3.373	1.00
183_H	246_E	3.185	1.00
11_V	43_E	3.144	1.00
269_A	272_Q	3.096	1.00
174_L	277_V	2.664	1.00
124_G	310_L	2.624	1.00
202_V	206_K	2.591	1.00
183_H	275_A	2.545	1.00
281_N	296_D	2.504	1.00
161_Y	313_L	2.421	1.00
172_I	211_A	2.341	1.00
31_P	35_E	2.269	1.00
232_L	265_E	2.244	1.00
39_R	43_E	2.233	1.00
90_K	93_E	2.212	1.00
35_E	39_R	2.186	1.00
90_K	308_E	2.147	1.00
236_R	266_K	2.147	1.00
176_D	208_S	2.102	1.00
305_Q	308_E	2.081	1.00
169_G	173_A	2.079	1.00
179_I	212_H	2.073	1.00
172_I	207_Q	2.064	1.00
172_I	208_S	2.037	1.00
236_R	262_A	2.008	1.00
91_A	307_C	1.987	1.00
22_V	37_V	1.987	1.00
170_D	279_Y	1.939	1.00
34_R	38_L	1.912	1.00
168_F	203_N	1.911	1.00
86_A	303_G	1.879	1.00
178_L	247_A	1.875	1.00
171_S	175_T	1.872	1.00
90_K	304_Q	1.872	1.00
176_D	180_E	1.869	1.00
23_L	41_I	1.865	1.00
6_Y	16_K	1.864	1.00
263_A	274_L	1.862	1.00
231_A	258_S	1.824	1.00
240_S	266_K	1.814	1.00
312_R	317_K	1.812	1.00
171_S	249_F	1.783	1.00
175_T	205_Y	1.774	1.00
89_A	300_Q	1.753	1.00
176_D	212_H	1.745	1.00
177_A	181_S	1.744	1.00
11_V	40_A	1.710	1.00
172_I	176_D	1.709	1.00
12_A	40_A	1.702	1.00
232_L	262_A	1.680	1.00
235_A	259_I	1.673	1.00
268_I	273_Q	1.652	1.00
188_C	251_T	1.651	1.00
187_A	245_P	1.645	1.00
64_M	122_I	1.635	1.00
86_A	300_Q	1.628	1.00
298_P	301_E	1.627	1.00
250_A	259_I	1.606	1.00
269_A	273_Q	1.603	1.00
90_K	94_E	1.583	1.00
262_A	266_K	1.580	1.00
150_I	306_S	1.566	1.00
185_N	217_R	1.558	1.00
38_L	42_E	1.531	1.00
169_G	172_I	1.528	1.00
264_A	289_T	1.517	1.00
185_N	244_L	1.504	1.00
222_V	237_Q	1.504	1.00
94_E	311_F	1.501	1.00
177_A	180_E	1.501	1.00
203_N	207_Q	1.498	1.00
22_V	41_I	1.493	1.00
179_I	208_S	1.485	1.00
301_E	305_Q	1.481	1.00
166_D	169_G	1.461	1.00
262_A	265_E	1.460	1.00
8_I	40_A	1.459	1.00
61_D	123_K	1.430	1.00
38_L	41_I	1.426	1.00
277_V	293_G	1.417	1.00
301_E	304_Q	1.412	1.00
206_K	210_A	1.406	1.00
200_D	203_N	1.404	1.00
305_Q	323_I	1.396	1.00
90_K	307_C	1.379	1.00
217_R	220_W	1.374	1.00
263_A	268_I	1.343	1.00
208_S	211_A	1.342	1.00
185_N	246_E	1.338	1.00
175_T	179_I	1.331	1.00
236_R	265_E	1.331	1.00
235_A	248_V	1.329	1.00
311_F	315_S	1.326	1.00
232_L	261_R	1.326	1.00
232_L	236_R	1.318	1.00
11_V	44_L	1.314	1.00
187_A	238_L	1.303	1.00
63_I	91_A	1.302	1.00
175_T	208_S	1.300	1.00
6_Y	10_R	1.294	1.00
171_S	204_G	1.276	1.00
308_E	312_R	1.275	1.00
7_D	10_R	1.274	1.00
31_P	34_R	1.272	1.00
175_T	204_G	1.269	1.00
138_A	142_K	1.264	1.00
61_D	96_F	1.263	1.00
36_K	40_A	1.258	1.00
30_S	33_A	1.249	1.00
236_R	240_S	1.242	1.00
204_G	208_S	1.241	1.00
183_H	247_A	1.236	1.00
235_A	263_A	1.231	1.00
40_A	43_E	1.224	1.00
173_A	176_D	1.222	1.00
126_I	306_S	1.222	1.00
168_F	172_I	1.220	1.00
176_D	211_A	1.216	1.00
260_Y	276_V	1.215	1.00
225_G	230_T	1.210	1.00
21_R	26_Q	1.209	1.00
8_I	12_A	1.204	1.00
40_A	44_L	1.203	1.00
101_Q	113_C	1.201	1.00
101_Q	117_I	1.200	1.00
64_M	117_I	1.198	1.00
5_I	16_K	1.192	1.00
87_I	307_C	1.187	1.00
91_A	98_V	1.184	1.00
237_Q	241_Q	1.175	1.00
184_Q	246_E	1.170	1.00
8_I	44_L	1.167	1.00
65_V	87_I	1.160	1.00
177_A	293_G	1.157	1.00
33_A	36_K	1.157	1.00
300_Q	304_Q	1.154	1.00
87_I	126_I	1.153	1.00
168_F	200_D	1.149	1.00
205_Y	209_L	1.146	1.00
189_L	259_I	1.125	1.00
94_E	308_E	1.125	1.00
115_S	139_Q	1.118	1.00
208_S	212_H	1.109	1.00
258_S	262_A	1.108	1.00
174_L	249_F	1.103	1.00
229_E	233_K	1.102	1.00
168_F	204_G	1.101	1.00
253_S	294_G	1.098	1.00
186_I	209_L	1.089	1.00
65_V	98_V	1.087	1.00
62_A	97_D	1.086	1.00
62_A	99_I	1.083	1.00
234_A	237_Q	1.082	1.00
39_R	42_E	1.082	1.00
35_E	38_L	1.080	1.00
188_C	202_V	1.079	1.00
207_Q	211_A	1.077	1.00
5_I	19_V	1.070	1.00
22_V	29_I	1.069	1.00
248_V	259_I	1.064	1.00
303_G	307_C	1.058	1.00
25_K	34_R	1.058	1.00
88_T	92_E	1.047	1.00
305_Q	309_L	1.045	1.00
227_T	230_T	1.042	1.00
179_I	214_I	1.041	1.00
203_N	206_K	1.035	1.00
185_N	243_P	1.030	1.00
111_Q	115_S	1.028	1.00
51_L	54_A	1.017	1.00
49_N	55_L	1.016	1.00
205_Y	249_F	1.013	1.00
180_E	212_H	1.013	1.00
253_S	278_G	1.012	1.00
92_E	109_D	1.007	1.00
96_F	311_F	1.006	1.00
242_S	245_P	1.002	1.00
216_V	219_E	1.000	1.00
250_A	255_K	0.999	1.00
304_Q	308_E	0.994	1.00
94_E	315_S	0.991	1.00
233_K	237_Q	0.986	1.00
250_A	256_L	0.982	1.00
228_H	261_R	0.978	1.00
41_I	44_L	0.973	1.00
231_A	235_A	0.970	1.00
193_L	223_D	0.970	1.00
230_T	233_K	0.970	1.00
209_L	214_I	0.966	1.00
222_V	234_A	0.965	1.00
310_L	314_I	0.962	1.00
186_I	247_A	0.961	1.00
196_H	200_D	0.957	1.00
199_V	203_N	0.956	1.00
206_K	216_V	0.952	1.00
260_Y	270_I	0.946	1.00
12_A	19_V	0.944	1.00
115_S	119_Q	0.933	1.00
235_A	239_L	0.929	1.00
169_G	326_A	0.929	1.00
260_Y	288_L	0.928	1.00
181_S	275_A	0.926	1.00
109_D	112_K	0.924	1.00
161_Y	309_L	0.922	1.00
174_L	295_I	0.920	1.00
93_E	304_Q	0.919	1.00
165_T	298_P	0.916	1.00
49_N	52_A	0.907	1.00
126_I	310_L	0.906	1.00
309_L	323_I	0.905	1.00
184_Q	214_I	0.901	1.00
25_K	38_L	0.897	1.00
89_A	304_Q	0.896	1.00
85_H	89_A	0.891	1.00
84_L	88_T	0.887	1.00
175_T	209_L	0.885	1.00
179_I	184_Q	0.883	1.00
48_P	53_R	0.883	1.00
52_A	55_L	0.880	1.00
87_I	303_G	0.874	1.00
134_E	138_A	0.871	1.00
163_V	309_L	0.870	1.00
233_K	236_R	0.864	1.00
65_V	84_L	0.859	1.00
63_I	126_I	0.855	1.00
194_D	199_V	0.855	1.00
22_V	38_L	0.848	1.00
248_V	274_L	0.847	1.00
268_I	274_L	0.845	1.00
309_L	312_R	0.840	1.00
83_V	150_I	0.836	1.00
263_A	276_V	0.830	1.00
187_A	248_V	0.828	1.00
278_G	294_G	0.827	1.00
264_A	291_A	0.827	1.00
239_L	262_A	0.827	1.00
60_F	123_K	0.824	1.00
191_A	226_Y	0.821	1.00
162_S	322_N	0.821	1.00
220_W	241_Q	0.821	1.00
298_P	325_V	0.820	1.00
253_S	281_N	0.817	1.00
190_H	202_V	0.817	1.00
281_N	285_S	0.811	1.00
124_G	314_I	0.810	1.00
166_D	324_T	0.808	1.00
106_P	109_D	0.807	1.00
202_V	221_I	0.803	1.00
209_L	216_V	0.803	1.00
167_N	201_R	0.801	1.00
185_N	220_W	0.800	1.00
32_E	35_E	0.800	1.00
214_I	217_R	0.798	1.00
207_Q	210_A	0.798	1.00
165_T	297_V	0.793	1.00
14_V	37_V	0.792	1.00
230_T	234_A	0.789	1.00
50_K	53_R	0.788	1.00
244_L	268_I	0.787	1.00
139_Q	142_K	0.786	1.00
89_A	93_E	0.786	1.00
79_F	299_T	0.784	1.00
178_L	277_V	0.783	1.00
166_D	326_A	0.781	1.00
86_A	90_K	0.780	1.00
305_Q	325_V	0.777	1.00
82_E	300_Q	0.777	1.00
235_A	262_A	0.776	1.00
307_C	311_F	0.773	1.00
87_I	98_V	0.772	1.00
62_A	120_K	0.765	1.00
189_L	250_A	0.760	1.00
224_G	255_K	0.759	1.00
118_K	143_Y	0.759	1.00
188_C	249_F	0.759	1.00
246_E	275_A	0.757	1.00
59_G	123_K	0.756	1.00
86_A	304_Q	0.756	1.00
84_L	100_L	0.753	1.00
18_T	21_R	0.752	1.00
17_S	21_R	0.749	1.00
222_V	238_L	0.748	1.00
32_E	36_K	0.747	1.00
112_K	115_S	0.740	1.00
21_R	27_T	0.740	1.00
164_D	324_T	0.740	1.00
239_L	266_K	0.735	1.00
47_Q	119_Q	0.731	1.00
68_T	80_F	0.731	1.00
64_M	125_I	0.730	1.00
173_A	295_I	0.729	1.00
222_V	241_Q	0.728	1.00
235_A	238_L	0.725	1.00
253_S	256_L	0.724	1.00
261_R	291_A	0.724	1.00
138_A	141_D	0.722	1.00
85_H	88_T	0.721	1.00
173_A	177_A	0.721	1.00
200_D	204_G	0.719	1.00
261_R	264_A	0.719	1.00
99_I	122_I	0.715	1.00
141_D	160_V	0.715	1.00
88_T	98_V	0.715	1.00
63_I	307_C	0.712	1.00
257_M	288_L	0.710	1.00
312_R	316_G	0.708	1.00
21_R	28_N	0.707	1.00
161_Y	321_Q	0.707	1.00
249_F	277_V	0.706	1.00
153_V	322_N	0.706	1.00
280_S	297_V	0.705	1.00
164_D	322_N	0.705	1.00
256_L	278_G	0.704	1.00
109_D	113_C	0.702	1.00
263_A	270_I	0.700	1.00
124_G	148_V	0.698	1.00
104_H	109_D	0.695	1.00
149_V	154_E	0.695	1.00
185_N	215_A	0.689	1.00
172_I	204_G	0.685	1.00
241_Q	244_L	0.685	1.00
108_E	112_K	0.680	1.00
22_V	34_R	0.679	1.00
198_S	226_Y	0.675	1.00
59_G	315_S	0.674	1.00
126_I	150_I	0.673	1.00
237_Q	240_S	0.672	1.00
35_E	42_E	0.672	1.00
141_D	159_H	0.669	1.00
88_T	102_T	0.668	1.00
231_A	234_A	0.667	1.00
66_I	113_C	0.666	1.00
141_D	147_V	0.665	1.00
264_A	290_P	0.665	1.00
235_A	258_S	0.663	1.00
316_G	319_S	0.662	1.00
186_I	246_E	0.660	1.00
205_Y	216_V	0.652	1.00
6_Y	56_T	0.651	1.00
47_Q	115_S	0.650	1.00
179_I	209_L	0.650	1.00
140_L	147_V	0.647	1.00
147_V	160_V	0.646	1.00
118_K	145_I	0.646	1.00
151_G	197_V	0.637	1.00
226_Y	251_T	0.637	1.00
148_V	310_L	0.636	1.00
261_R	265_E	0.635	1.00
188_C	205_Y	0.635	1.00
99_I	120_K	0.635	1.00
111_Q	136_F	0.634	1.00
148_V	313_L	0.627	1.00
42_E	45_Q	0.624	1.00
114_E	125_I	0.624	1.00
14_V	33_A	0.623	1.00
124_G	306_S	0.622	1.00
252_D	280_S	0.622	1.00
28_N	33_A	0.620	1.00
86_A	299_T	0.618	1.00
85_H	300_Q	0.618	1.00
312_R	321_Q	0.616	1.00
214_I	219_E	0.615	1.00
82_E	299_T	0.614	1.00
136_F	139_Q	0.613	1.00
178_L	249_F	0.613	1.00
151_G	167_N	0.612	1.00
202_V	223_D	0.612	1.00
224_G	230_T	0.608	1.00
172_I	175_T	0.607	1.00
241_Q	245_P	0.606	1.00
19_V	22_V	0.605	1.00
77_N	254_L	0.604	1.00
186_I	205_Y	0.604	1.00
260_Y	264_A	0.603	1.00
19_V	41_I	0.601	1.00
149_V	160_V	0.599	1.00
36_K	39_R	0.597	1.00
191_A	198_S	0.596	1.00
83_V	299_T	0.596	1.00
148_V	163_V	0.594	1.00
125_I	145_I	0.593	1.00
8_I	19_V	0.591	1.00
263_A	266_K	0.589	1.00
206_K	221_I	0.588	1.00
63_I	314_I	0.586	1.00
174_L	247_A	0.585	1.00
63_I	124_G	0.585	1.00
252_D	255_K	0.584	1.00
96_F	314_I	0.583	1.00
257_M	282_E	0.583	1.00
249_F	279_Y	0.582	1.00
21_R	29_I	0.582	1.00
229_E	232_L	0.582	1.00
285_S	292_P	0.581	1.00
190_H	223_D	0.579	1.00
261_R	289_T	0.576	1.00
167_N	200_D	0.574	1.00
177_A	277_V	0.574	1.00
107_A	111_Q	0.572	1.00
60_F	97_D	0.568	1.00
187_A	220_W	0.567	1.00
47_Q	51_L	0.567	1.00
226_Y	255_K	0.567	1.00
264_A	269_A	0.566	1.00
286_F	291_A	0.561	1.00
153_V	162_S	0.560	1.00
285_S	294_G	0.558	1.00
79_F	83_V	0.558	1.00
228_H	258_S	0.557	1.00
279_Y	297_V	0.556	1.00
63_I	96_F	0.555	1.00
96_F	123_K	0.554	1.00
135_S	138_A	0.554	1.00
62_A	123_K	0.554	1.00
101_Q	116_K	0.553	1.00
250_A	278_G	0.553	1.00
309_L	313_L	0.553	1.00
148_V	306_S	0.546	1.00
165_T	170_D	0.546	1.00
163_V	305_Q	0.545	1.00
148_V	309_L	0.543	1.00
185_N	245_P	0.543	1.00
91_A	311_F	0.542	1.00
91_A	96_F	0.542	1.00
239_L	263_A	0.541	1.00
268_I	271_P	0.540	1.00
257_M	284_L	0.539	1.00
53_R	57_S	0.537	1.00
232_L	235_A	0.536	1.00
219_E	241_Q	0.535	1.00
300_Q	303_G	0.535	1.00
19_V	37_V	0.535	1.00
228_H	284_L	0.534	1.00
87_I	91_A	0.533	1.00
190_H	221_I	0.531	1.00
156_Q	159_H	0.530	1.00
270_I	273_Q	0.530	1.00
198_S	251_T	0.529	1.00
117_I	122_I	0.527	1.00
14_V	19_V	0.526	1.00
259_I	263_A	0.526	1.00
122_I	125_I	0.525	1.00
175_T	212_H	0.525	1.00
25_K	28_N	0.523	1.00
305_Q	312_R	0.522	1.00
12_A	22_V	0.522	1.00
115_S	118_K	0.521	1.00
245_P	268_I	0.521	1.00
139_Q	143_Y	0.520	1.00
78_P	254_L	0.519	1.00
149_V	162_S	0.517	1.00
26_Q	29_I	0.516	1.00
234_A	238_L	0.514	1.00
232_L	258_S	0.514	1.00
103_S	110_L	0.513	1.00
313_L	316_G	0.513	1.00
17_S	26_Q	0.512	1.00
85_H	104_H	0.511	1.00
245_P	248_V	0.511	1.00
281_N	294_G	0.509	1.00
29_I	34_R	0.509	1.00
216_V	221_I	0.507	1.00
90_K	311_F	0.507	1.00
80_F	128_L	0.507	1.00
235_A	250_A	0.506	1.00
12_A	37_V	0.506	1.00
202_V	216_V	0.505	1.00
190_H	193_L	0.502	1.00
7_D	11_V	0.502	1.00
228_H	254_L	0.501	1.00
189_L	234_A	0.501	1.00
253_S	282_E	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	0.9699	100	0.048	Contact Map
3dbiA	2	0.8102	100	0.058	Contact Map
1qpzA	2	0.9759	100	0.068	Contact Map
2o20A	2	0.8133	100	0.069	Contact Map
3kjxA	2	0.9819	100	0.073	Contact Map
4o5aA	2	0.7892	100	0.073	Contact Map
3bilA	2	0.756	100	0.078	Contact Map
3e3mA	2	0.7892	100	0.08	Contact Map
3h5oA	2	0.7952	100	0.088	Contact Map
1jyeA	2	0.7892	100	0.089	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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