CYTR - ECOLI - GREMLIN Contacts

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CYTR - HTH-type transcriptional repressor CytR

UniProt:	P0ACN7	Sequences: MKAKKQETAATMKDVALKAKVSTATVSRALMNPDKVSQATRNRVEKAAREVGYLPQPMGRNVKRNESRTILVIVPDICDPFFSEIIRGIEVTAANHGYLVLIGDCAHQNQQEKTFIDLIITKQIDGMLLLGSRLPFDASIEEQRNLPPMVMANEFAPELELPTVHIDNLTAAFDAVNYLYEQGHKRIGCIAGPEEMPLCHYRLQGYVQALRRCGIMVDPQYIARGDFTFEAGSKAMQQLLDLPQPPTAVFCHSDVMALGALSQAKRQGLKVPEDLSIIGFDNIDLTQFCDPPLTTIAQPRYEIGREAMLLLLDQMQGQHVGSGSRLMDCELIIRGSTRALP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10200
Length:	341 (326)
Sequences:	35863 (26031)
Seq/√Len:	1441.7

ECOLI - CYTR GALS GALR PURR IDNR LACI ASCG GNTR MALI RBSR CRA YCJW EBGR TRER TORT ALSB YTFQ RBSB XYLF YPHF LSRB ARAF DGAL XYLR
BACSU - KDGR CCPA DEGA NTDR MSMR RBSR EXUR YKVZ GANR ARAR YVDE 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
169_L	208_Q	3.372	1.00
184_H	247_T	3.317	1.00
18_K	50_E	3.126	1.00
270_K	273_E	3.061	1.00
175_A	278_I	2.647	1.00
126_G	311_L	2.592	1.00
203_L	207_V	2.565	1.00
282_N	297_A	2.538	1.00
184_H	276_S	2.520	1.00
162_P	314_Q	2.337	1.00
173_F	212_R	2.322	1.00
233_S	266_R	2.251	1.00
38_Q	42_N	2.207	1.00
46_K	50_E	2.204	1.00
92_T	95_N	2.185	1.00
42_N	46_K	2.161	1.00
92_T	309_L	2.148	1.00
237_Q	267_Q	2.106	1.00
180_Y	213_C	2.071	1.00
306_E	309_L	2.071	1.00
177_N	209_A	2.042	1.00
173_F	208_Q	2.041	1.00
182_Q	337_T	2.029	1.00
173_F	209_A	2.024	1.00
170_T	174_D	1.996	1.00
29_A	44_V	1.980	1.00
237_Q	263_Q	1.977	1.00
93_A	308_M	1.970	1.00
172_A	176_V	1.917	1.00
169_L	204_Q	1.907	1.00
171_A	280_F	1.898	1.00
88_G	304_G	1.892	1.00
41_R	45_E	1.891	1.00
30_L	48_A	1.888	1.00
232_G	259_G	1.880	1.00
177_N	181_E	1.871	1.00
179_L	248_A	1.859	1.00
13_K	23_T	1.829	1.00
92_T	305_R	1.810	1.00
172_A	250_F	1.803	1.00
313_D	318_Q	1.792	1.00
264_A	275_L	1.790	1.00
241_D	267_Q	1.773	1.00
297_A	330_E	1.772	1.00
176_V	206_Y	1.760	1.00
91_V	301_Y	1.738	1.00
177_N	213_C	1.710	1.00
19_A	47_A	1.709	1.00
18_K	47_A	1.680	1.00
233_S	263_Q	1.680	1.00
173_F	177_N	1.673	1.00
306_E	325_R	1.667	1.00
299_P	302_E	1.653	1.00
71_L	124_I	1.651	1.00
88_G	301_Y	1.635	1.00
236_M	260_A	1.633	1.00
188_G	246_P	1.629	1.00
189_C	252_H	1.627	1.00
292_P	335_G	1.620	1.00
174_D	329_C	1.609	1.00
251_C	260_A	1.599	1.00
269_L	274_D	1.599	1.00
186_R	218_D	1.589	1.00
270_K	274_D	1.563	1.00
263_Q	267_Q	1.545	1.00
265_K	290_D	1.542	1.00
92_T	96_H	1.531	1.00
152_A	307_A	1.522	1.00
282_N	334_R	1.520	1.00
45_E	49_R	1.512	1.00
186_R	245_P	1.508	1.00
170_T	173_F	1.506	1.00
29_A	48_A	1.500	1.00
167_D	170_T	1.493	1.00
178_Y	182_Q	1.487	1.00
223_A	238_Q	1.487	1.00
204_Q	208_Q	1.482	1.00
180_Y	209_A	1.466	1.00
302_E	306_E	1.465	1.00
263_Q	266_R	1.455	1.00
178_Y	181_E	1.443	1.00
278_I	294_T	1.436	1.00
96_H	312_L	1.424	1.00
45_E	48_A	1.416	1.00
15_V	47_A	1.406	1.00
201_Y	204_Q	1.403	1.00
207_V	211_R	1.400	1.00
68_R	125_D	1.399	1.00
171_A	329_C	1.395	1.00
302_E	305_R	1.394	1.00
178_Y	333_I	1.390	1.00
92_T	308_M	1.363	1.00
176_V	205_G	1.354	1.00
176_V	180_Y	1.351	1.00
264_A	269_L	1.323	1.00
237_Q	266_R	1.314	1.00
186_R	247_T	1.312	1.00
209_A	212_R	1.306	1.00
233_S	262_S	1.302	1.00
172_A	205_G	1.299	1.00
13_K	17_L	1.291	1.00
178_Y	337_T	1.288	1.00
188_G	239_L	1.285	1.00
18_K	51_V	1.285	1.00
184_H	248_A	1.283	1.00
312_L	316_Q	1.281	1.00
236_M	249_V	1.280	1.00
176_V	209_A	1.279	1.00
233_S	237_Q	1.269	1.00
218_D	221_Y	1.268	1.00
15_V	19_A	1.264	1.00
14_D	17_L	1.261	1.00
37_S	40_T	1.252	1.00
309_L	313_D	1.251	1.00
68_R	98_Y	1.251	1.00
237_Q	241_D	1.247	1.00
28_R	33_P	1.243	1.00
70_I	93_A	1.243	1.00
38_Q	41_R	1.242	1.00
205_G	209_A	1.241	1.00
236_M	264_A	1.228	1.00
140_I	144_R	1.221	1.00
103_G	115_F	1.220	1.00
12_M	23_T	1.217	1.00
47_A	50_E	1.216	1.00
243_P	246_P	1.211	1.00
226_D	231_A	1.210	1.00
43_R	47_A	1.206	1.00
169_L	173_F	1.205	1.00
103_G	119_I	1.202	1.00
128_L	307_A	1.198	1.00
174_D	177_N	1.192	1.00
276_S	337_T	1.185	1.00
238_Q	242_L	1.183	1.00
71_L	119_I	1.182	1.00
93_A	100_V	1.179	1.00
261_L	277_I	1.176	1.00
47_A	51_V	1.170	1.00
89_I	308_M	1.162	1.00
89_I	128_L	1.161	1.00
169_L	201_Y	1.160	1.00
185_K	247_T	1.156	1.00
72_V	89_I	1.155	1.00
177_N	212_R	1.151	1.00
15_V	51_V	1.145	1.00
40_T	43_R	1.132	1.00
206_Y	210_L	1.126	1.00
230_E	234_K	1.124	1.00
301_Y	305_R	1.116	1.00
46_K	49_R	1.108	1.00
96_H	309_L	1.102	1.00
259_G	263_Q	1.094	1.00
72_V	100_V	1.093	1.00
69_T	99_L	1.087	1.00
187_I	210_L	1.081	1.00
190_I	260_A	1.077	1.00
254_D	295_T	1.073	1.00
304_G	308_M	1.071	1.00
249_V	260_A	1.069	1.00
169_L	205_G	1.066	1.00
306_E	310_L	1.065	1.00
90_E	94_A	1.065	1.00
12_M	26_V	1.064	1.00
310_L	325_R	1.063	1.00
209_A	213_C	1.060	1.00
189_C	203_L	1.060	1.00
42_N	45_E	1.059	1.00
208_Q	212_R	1.058	1.00
175_A	250_F	1.058	1.00
29_A	36_V	1.057	1.00
235_A	238_Q	1.050	1.00
254_D	279_G	1.048	1.00
117_D	141_E	1.045	1.00
56_Q	62_V	1.042	1.00
228_T	231_A	1.035	1.00
180_Y	215_I	1.034	1.00
94_A	111_Q	1.025	1.00
69_T	101_L	1.024	1.00
181_E	213_C	1.021	1.00
113_K	117_D	1.021	1.00
182_Q	333_I	1.019	1.00
32_N	41_R	1.014	1.00
186_R	244_Q	1.004	1.00
204_Q	207_V	1.002	1.00
210_L	215_I	0.997	1.00
251_C	256_M	0.996	1.00
58_M	61_N	0.996	1.00
232_G	236_M	0.993	1.00
48_A	51_V	0.990	1.00
251_C	257_A	0.990	1.00
182_Q	276_S	0.988	1.00
194_E	224_R	0.987	1.00
223_A	235_A	0.981	1.00
311_L	315_M	0.981	1.00
305_R	309_L	0.975	1.00
306_E	327_M	0.973	1.00
111_Q	114_T	0.972	1.00
96_H	316_Q	0.970	1.00
98_Y	312_L	0.966	1.00
19_A	26_V	0.964	1.00
170_T	328_D	0.964	1.00
234_K	238_Q	0.959	1.00
297_A	332_I	0.956	1.00
206_Y	250_F	0.954	1.00
200_H	204_Q	0.950	1.00
231_A	234_K	0.940	1.00
261_L	289_C	0.936	1.00
175_A	296_I	0.933	1.00
197_P	201_Y	0.927	1.00
229_F	262_S	0.922	1.00
187_I	248_A	0.920	1.00
95_N	305_R	0.919	1.00
117_D	121_T	0.914	1.00
236_M	240_L	0.912	1.00
178_Y	294_T	0.911	1.00
87_R	91_V	0.906	1.00
91_V	305_R	0.898	1.00
59_G	62_V	0.897	1.00
176_V	210_L	0.896	1.00
128_L	311_L	0.895	1.00
56_Q	59_G	0.895	1.00
163_T	324_S	0.892	1.00
166_I	299_P	0.888	1.00
167_D	326_L	0.886	1.00
180_Y	185_K	0.884	1.00
330_E	333_I	0.880	1.00
299_P	327_M	0.880	1.00
70_I	128_L	0.880	1.00
186_R	221_Y	0.877	1.00
261_L	271_V	0.875	1.00
89_I	304_G	0.866	1.00
299_P	330_E	0.866	1.00
32_N	45_E	0.866	1.00
192_G	227_F	0.864	1.00
55_P	60_R	0.863	1.00
72_V	86_I	0.859	1.00
234_K	237_Q	0.850	1.00
207_V	217_V	0.849	1.00
254_D	282_N	0.846	1.00
195_E	200_H	0.842	1.00
249_V	275_L	0.842	1.00
188_G	249_V	0.841	1.00
164_V	310_L	0.839	1.00
221_Y	242_L	0.838	1.00
29_A	45_E	0.835	1.00
170_T	329_C	0.831	1.00
264_A	277_I	0.829	1.00
279_G	295_T	0.829	1.00
240_L	263_Q	0.829	1.00
86_I	90_E	0.828	1.00
333_I	337_T	0.827	1.00
265_K	292_P	0.824	1.00
166_I	329_C	0.824	1.00
165_H	326_L	0.822	1.00
185_K	215_I	0.821	1.00
162_P	310_L	0.819	1.00
310_L	313_D	0.818	1.00
269_L	275_L	0.816	1.00
126_G	315_M	0.816	1.00
11_T	14_D	0.811	1.00
282_N	332_I	0.808	1.00
85_I	152_A	0.808	1.00
168_N	202_R	0.806	1.00
225_G	256_M	0.803	1.00
81_F	300_R	0.802	1.00
167_D	328_D	0.796	1.00
166_I	298_Q	0.794	1.00
203_L	222_I	0.793	1.00
191_A	203_L	0.790	1.00
39_A	42_N	0.790	1.00
162_P	323_G	0.789	1.00
179_L	278_I	0.788	1.00
190_I	251_C	0.785	1.00
178_Y	331_L	0.784	1.00
136_F	140_I	0.783	1.00
258_L	289_C	0.781	1.00
245_P	269_L	0.781	1.00
208_Q	211_R	0.780	1.00
25_T	28_R	0.775	1.00
21_V	44_V	0.774	1.00
91_V	95_N	0.772	1.00
84_E	301_Y	0.771	1.00
57_P	60_R	0.771	1.00
308_M	312_L	0.771	1.00
67_S	125_D	0.771	1.00
88_G	305_R	0.769	1.00
75_P	82_F	0.764	1.00
294_T	337_T	0.759	1.00
120_I	145_N	0.759	1.00
108_Q	111_Q	0.759	1.00
189_C	250_F	0.759	1.00
89_I	100_V	0.758	1.00
231_A	235_A	0.758	1.00
165_H	324_S	0.758	1.00
39_A	43_R	0.756	1.00
88_G	92_T	0.756	1.00
24_A	28_R	0.754	1.00
281_D	298_Q	0.753	1.00
236_M	239_L	0.752	1.00
236_M	263_Q	0.749	1.00
201_Y	205_G	0.745	1.00
254_D	257_A	0.745	1.00
70_I	308_M	0.744	1.00
210_L	217_V	0.742	1.00
28_R	34_D	0.737	1.00
69_T	122_K	0.737	1.00
114_T	117_D	0.735	1.00
66_E	125_D	0.734	1.00
141_E	144_R	0.730	1.00
174_D	296_I	0.729	1.00
71_L	127_M	0.727	1.00
262_S	265_K	0.727	1.00
223_A	239_L	0.724	1.00
86_I	102_I	0.718	1.00
106_A	111_Q	0.717	1.00
54_L	121_T	0.715	1.00
142_E	149_M	0.714	1.00
240_L	267_Q	0.713	1.00
155_F	324_S	0.709	1.00
28_R	35_K	0.708	1.00
111_Q	115_F	0.704	1.00
87_R	90_E	0.703	1.00
257_A	279_G	0.702	1.00
101_L	124_I	0.701	1.00
217_V	220_Q	0.689	1.00
282_N	286_T	0.688	1.00
238_Q	241_D	0.688	1.00
90_E	100_V	0.688	1.00
250_F	278_I	0.687	1.00
173_F	205_G	0.684	1.00
151_M	156_A	0.683	1.00
294_T	331_L	0.682	1.00
223_A	242_L	0.678	1.00
66_E	316_Q	0.677	1.00
264_A	271_V	0.675	1.00
247_T	276_S	0.672	1.00
262_S	292_P	0.669	1.00
313_D	317_G	0.669	1.00
42_N	49_R	0.666	1.00
90_E	104_D	0.665	1.00
187_I	247_T	0.665	1.00
180_Y	210_L	0.660	1.00
151_M	161_L	0.659	1.00
143_Q	160_E	0.657	1.00
29_A	41_R	0.655	1.00
262_S	266_R	0.655	1.00
128_L	152_A	0.655	1.00
232_G	235_A	0.654	1.00
242_L	245_P	0.650	1.00
317_G	320_V	0.647	1.00
126_G	150_V	0.646	1.00
199_C	227_F	0.645	1.00
143_Q	149_M	0.643	1.00
225_G	231_A	0.642	1.00
179_L	250_F	0.640	1.00
153_N	168_N	0.638	1.00
149_M	161_L	0.635	1.00
236_M	259_G	0.634	1.00
253_S	281_D	0.631	1.00
242_L	246_P	0.630	1.00
73_I	115_F	0.626	1.00
153_N	198_L	0.626	1.00
110_Q	114_T	0.623	1.00
113_K	138_A	0.622	1.00
15_V	26_V	0.622	1.00
79_D	255_V	0.620	1.00
174_D	178_Y	0.618	1.00
35_K	40_T	0.617	1.00
88_G	300_R	0.617	1.00
126_G	307_A	0.617	1.00
227_F	252_H	0.616	1.00
26_V	29_A	0.616	1.00
87_R	301_Y	0.612	1.00
49_R	52_G	0.612	1.00
54_L	117_D	0.612	1.00
120_I	147_P	0.611	1.00
189_C	206_Y	0.610	1.00
116_I	127_M	0.609	1.00
13_K	63_K	0.609	1.00
101_L	122_K	0.607	1.00
187_I	206_Y	0.607	1.00
43_R	46_K	0.605	1.00
192_G	199_C	0.604	1.00
262_S	290_D	0.604	1.00
21_V	40_T	0.603	1.00
26_V	48_A	0.603	1.00
188_G	221_Y	0.600	1.00
261_L	265_K	0.596	1.00
140_I	143_Q	0.593	1.00
258_L	283_I	0.593	1.00
150_V	314_Q	0.593	1.00
191_A	224_R	0.591	1.00
168_N	201_Y	0.591	1.00
84_E	300_R	0.589	1.00
253_S	256_M	0.588	1.00
207_V	222_I	0.588	1.00
98_Y	125_D	0.588	1.00
85_I	300_R	0.588	1.00
173_F	176_V	0.587	1.00
203_L	224_R	0.586	1.00
206_Y	217_V	0.585	1.00
301_Y	304_G	0.584	1.00
313_D	323_G	0.583	1.00
98_Y	315_M	0.583	1.00
292_P	334_R	0.582	1.00
278_I	337_T	0.581	1.00
250_F	280_F	0.581	1.00
251_C	279_G	0.581	1.00
264_A	267_Q	0.580	1.00
150_V	311_L	0.576	1.00
207_V	219_P	0.576	1.00
28_R	36_V	0.574	1.00
280_F	298_Q	0.573	1.00
138_A	141_E	0.573	1.00
81_F	85_I	0.571	1.00
286_T	293_L	0.571	1.00
70_I	98_Y	0.571	1.00
70_I	126_G	0.569	1.00
175_A	248_A	0.569	1.00
265_K	270_K	0.568	1.00
229_F	259_G	0.568	1.00
137_D	140_I	0.568	1.00
127_M	147_P	0.567	1.00
296_I	329_C	0.565	1.00
150_V	164_V	0.565	1.00
229_F	285_L	0.562	1.00
70_I	315_M	0.561	1.00
67_S	99_L	0.559	1.00
227_F	256_M	0.559	1.00
286_T	295_T	0.558	1.00
26_V	44_V	0.557	1.00
54_L	58_M	0.554	1.00
186_R	246_P	0.554	1.00
258_L	285_L	0.554	1.00
150_V	310_L	0.553	1.00
265_K	291_P	0.550	1.00
285_L	289_C	0.549	1.00
217_V	222_I	0.549	1.00
155_F	163_T	0.546	1.00
310_L	314_Q	0.545	1.00
287_Q	292_P	0.545	1.00
230_E	233_S	0.543	1.00
186_R	216_M	0.543	1.00
233_S	259_G	0.543	1.00
93_A	312_L	0.543	1.00
19_A	29_A	0.541	1.00
32_N	35_K	0.541	1.00
117_D	120_I	0.540	1.00
178_Y	278_I	0.538	1.00
36_V	41_R	0.534	1.00
150_V	307_A	0.534	1.00
303_I	327_M	0.531	1.00
151_M	163_T	0.527	1.00
199_C	252_H	0.526	1.00
286_T	289_C	0.525	1.00
164_V	306_E	0.523	1.00
21_V	26_V	0.523	1.00
119_I	124_I	0.522	1.00
143_Q	161_L	0.521	1.00
314_Q	317_G	0.521	1.00
82_F	130_L	0.520	1.00
186_R	243_P	0.519	1.00
306_E	313_D	0.516	1.00
240_L	264_A	0.516	1.00
289_C	292_P	0.516	1.00
118_L	121_T	0.515	1.00
60_R	64_R	0.513	1.00
203_L	217_V	0.513	1.00
246_P	249_V	0.513	1.00
103_G	118_L	0.512	1.00
19_A	44_V	0.512	1.00
87_R	106_A	0.510	1.00
105_C	112_E	0.510	1.00
246_P	269_L	0.509	1.00
33_P	36_V	0.509	1.00
233_S	236_M	0.509	1.00
269_L	272_P	0.508	1.00
80_P	255_V	0.507	1.00
294_T	333_I	0.506	1.00
109_N	113_K	0.506	1.00
235_A	239_L	0.505	1.00
191_A	222_I	0.505	1.00
24_A	33_P	0.504	1.00
254_D	283_I	0.504	1.00
314_Q	320_V	0.502	1.00
61_N	64_R	0.501	1.00
84_E	284_D	0.500	1.00
166_I	280_F	0.500	1.00
260_A	264_A	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
1qpzA	2	0.9736	100	0.081	Contact Map
3dbiA	2	0.8094	100	0.086	Contact Map
2hsgA	1	0.9589	100	0.088	Contact Map
4o5aA	2	0.7889	100	0.089	Contact Map
3bilA	2	0.7507	100	0.09	Contact Map
2o20A	2	0.8065	100	0.091	Contact Map
3e3mA	2	0.7859	100	0.098	Contact Map
3kjxA	2	0.9765	100	0.099	Contact Map
3ctpA	2	0.7801	100	0.106	Contact Map
3jvdA	2	0.7654	100	0.108	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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