LYSR - ECOLI - GREMLIN Contacts

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LYSR - Transcriptional activator protein LysR

UniProt:	P03030	Sequences: MAAVNLRHIEIFHAVMTAGSLTEAAHLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSWYGLDRIVSAAESLREFRQGELSIACLPVFSQSFLPQLLQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETLHTPAGTERTELLSLDEVCVLPPGHPLAVKKVLTPDDFQGENYISLSRTDSYRQLLDQLFTEHQVKRRMIVETHSAASVCAMVRAGVGISVVNPLTALDYAASGLVVRRFSIAVPFTVSLIRPLHRPSSALVQAFSGHLQAGLPKLVTSLDAILSSATTA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10551
Length:	311 (288)
Sequences:	79703 (57981)
Seq/√Len:	3416.5

ECOLI - LYSR YFER YBHD CYSB OXYR PGRR TDCA CYNR CBL YAFC XAPR AAER TTDR YNFL LEUO NHAR METR DMLR ICIA YDHB YCAN NAC ILVY YEEY YBDO HCAR DSDC YEIE YDCI YGFI YBEF YFIE YHJC YAHB ABGR GCVA YIDZ ALLS YHAJ YNEJ YIAU LRHA PERR YJIE HDFR
BACSU - YCGK YWBI GLTC YTLI CYSL ALSR YYBE BSDA YWQM GLTR YVBU CITR YUST YOFA YOAU YXJO CZCR YKUM YRAN

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
73_R	77_G	3.607	1.00
18_A	27_L	3.438	1.00
161_T	291_Q	2.751	1.00
99_A	144_H	2.579	1.00
70_E	84_A	2.448	1.00
234_V	241_S	2.371	1.00
176_H	192_E	2.265	1.00
115_P	293_G	2.220	1.00
14_A	27_L	2.217	1.00
167_D	245_P	2.214	1.00
165_S	268_T	2.204	1.00
162_E	165_S	2.190	1.00
95_E	126_N	2.169	1.00
23_E	26_H	2.157	1.00
17_T	72_Q	2.156	1.00
231_C	251_Y	2.132	1.00
95_E	124_S	2.098	1.00
162_E	268_T	2.058	1.00
185_T	188_D	2.039	1.00
11_I	38_E	2.032	1.00
13_H	68_F	2.024	1.00
48_L	63_Q	2.024	1.00
165_S	266_P	1.984	1.00
70_E	77_G	1.978	1.00
97_S	126_N	1.976	1.00
11_I	35_V	1.949	1.00
115_P	289_H	1.940	1.00
21_L	39_L	1.937	1.00
14_A	17_T	1.935	1.00
195_I	239_G	1.922	1.00
13_H	72_Q	1.919	1.00
16_M	60_P	1.915	1.00
135_L	147_G	1.902	1.00
74_S	78_L	1.897	1.00
13_H	17_T	1.879	1.00
14_A	18_A	1.876	1.00
169_V	245_P	1.829	1.00
68_F	72_Q	1.817	1.00
67_L	81_I	1.767	1.00
52_E	59_H	1.754	1.00
193_N	221_I	1.716	1.00
138_W	143_R	1.707	1.00
116_F	286_F	1.676	1.00
66_R	84_A	1.669	1.00
160_R	270_S	1.668	1.00
17_T	27_L	1.624	1.00
235_R	251_Y	1.618	1.00
12_F	68_F	1.611	1.00
172_L	259_R	1.592	1.00
16_M	68_F	1.591	1.00
11_I	30_T	1.590	1.00
13_H	71_V	1.573	1.00
18_A	23_E	1.560	1.00
22_T	32_Q	1.555	1.00
159_E	275_L	1.555	1.00
116_F	123_V	1.545	1.00
8_H	38_E	1.543	1.00
181_K	188_D	1.532	1.00
91_F	122_D	1.513	1.00
31_S	34_T	1.506	1.00
62_V	65_L	1.502	1.00
8_H	45_V	1.471	1.00
5_N	8_H	1.462	1.00
8_H	41_R	1.453	1.00
137_E	141_A	1.450	1.00
49_K	52_E	1.450	1.00
161_T	273_R	1.447	1.00
13_H	75_W	1.436	1.00
70_E	73_R	1.431	1.00
20_S	23_E	1.431	1.00
287_S	291_Q	1.417	1.00
204_R	208_D	1.410	1.00
279_S	283_V	1.401	1.00
149_T	272_I	1.399	1.00
14_A	28_L	1.398	1.00
151_T	270_S	1.394	1.00
74_S	81_I	1.392	1.00
159_E	273_R	1.379	1.00
70_E	80_R	1.368	1.00
106_Q	228_A	1.351	1.00
257_V	260_R	1.348	1.00
6_L	78_L	1.347	1.00
93_Q	122_D	1.336	1.00
146_L	283_V	1.335	1.00
273_R	287_S	1.331	1.00
115_P	119_R	1.327	1.00
271_L	287_S	1.322	1.00
140_S	157_G	1.321	1.00
97_S	128_V	1.307	1.00
67_L	82_V	1.301	1.00
285_A	288_G	1.296	1.00
146_L	271_L	1.288	1.00
45_V	82_V	1.285	1.00
117_L	221_I	1.280	1.00
172_L	240_I	1.280	1.00
166_L	246_L	1.277	1.00
192_E	240_I	1.274	1.00
54_V	59_H	1.267	1.00
230_V	241_S	1.265	1.00
138_W	144_H	1.257	1.00
77_G	80_R	1.231	1.00
211_F	216_V	1.228	1.00
119_R	289_H	1.220	1.00
40_A	44_K	1.219	1.00
65_L	69_E	1.211	1.00
69_E	73_R	1.206	1.00
245_P	249_L	1.205	1.00
232_A	235_R	1.193	1.00
70_E	81_I	1.192	1.00
12_F	51_F	1.190	1.00
117_L	193_N	1.180	1.00
66_R	69_E	1.176	1.00
114_Q	118_A	1.171	1.00
177_P	192_E	1.164	1.00
115_P	118_A	1.163	1.00
195_I	230_V	1.163	1.00
162_E	270_S	1.159	1.00
12_F	50_L	1.157	1.00
37_R	40_A	1.142	1.00
96_L	286_F	1.141	1.00
30_T	34_T	1.139	1.00
12_F	16_M	1.132	1.00
259_R	262_S	1.130	1.00
160_R	272_I	1.130	1.00
37_R	41_R	1.126	1.00
126_N	223_E	1.116	1.00
15_V	24_A	1.109	1.00
36_S	40_A	1.106	1.00
10_E	79_D	1.102	1.00
116_F	289_H	1.099	1.00
288_G	291_Q	1.091	1.00
7_R	10_E	1.088	1.00
120_Y	285_A	1.085	1.00
224_T	230_V	1.084	1.00
274_P	277_R	1.081	1.00
114_Q	236_A	1.079	1.00
21_L	58_L	1.079	1.00
193_N	219_R	1.077	1.00
60_P	64_G	1.074	1.00
105_S	129_P	1.069	1.00
73_R	80_R	1.067	1.00
74_S	77_G	1.067	1.00
14_A	24_A	1.065	1.00
9_I	71_V	1.064	1.00
289_H	293_G	1.055	1.00
38_E	41_R	1.052	1.00
284_Q	288_G	1.048	1.00
174_P	257_V	1.047	1.00
231_C	235_R	1.043	1.00
183_V	262_S	1.042	1.00
173_P	237_G	1.039	1.00
184_L	188_D	1.033	1.00
139_L	147_G	1.033	1.00
112_L	290_L	1.028	1.00
249_L	253_A	1.021	1.00
66_R	70_E	1.021	1.00
161_T	287_S	1.016	1.00
130_Q	138_W	1.009	1.00
232_A	236_A	1.003	1.00
11_I	28_L	1.003	1.00
256_L	260_R	0.998	1.00
174_P	255_G	0.996	1.00
111_Q	236_A	0.995	1.00
171_V	248_A	0.994	1.00
170_C	240_I	0.993	1.00
235_R	256_L	0.991	1.00
140_S	155_P	0.991	1.00
82_V	86_E	0.990	1.00
79_D	83_S	0.977	1.00
251_Y	256_L	0.976	1.00
205_Q	208_D	0.972	1.00
30_T	35_V	0.971	1.00
12_F	60_P	0.969	1.00
167_D	266_P	0.967	1.00
16_M	51_F	0.965	1.00
250_D	254_S	0.962	1.00
79_D	82_V	0.960	1.00
116_F	120_Y	0.959	1.00
67_L	71_V	0.951	1.00
15_V	21_L	0.950	1.00
224_T	233_M	0.948	1.00
172_L	176_H	0.941	1.00
76_Y	80_R	0.935	1.00
119_R	292_A	0.935	1.00
176_H	193_N	0.935	1.00
196_S	220_M	0.934	1.00
138_W	141_A	0.931	1.00
289_H	292_A	0.930	1.00
16_M	64_G	0.929	1.00
24_A	35_V	0.923	1.00
51_F	58_L	0.921	1.00
112_L	289_H	0.918	1.00
12_F	42_F	0.913	1.00
280_S	283_V	0.902	1.00
207_L	211_F	0.902	1.00
169_V	258_V	0.901	1.00
41_R	44_K	0.898	1.00
48_L	85_A	0.898	1.00
157_G	275_L	0.898	1.00
124_S	219_R	0.897	1.00
176_H	179_A	0.892	1.00
144_H	147_G	0.890	1.00
180_V	193_N	0.885	1.00
99_A	135_L	0.883	1.00
128_V	138_W	0.879	1.00
99_A	149_T	0.877	1.00
23_E	27_L	0.874	1.00
69_E	72_Q	0.873	1.00
248_A	251_Y	0.864	1.00
172_L	177_P	0.863	1.00
102_P	226_S	0.861	1.00
171_V	258_V	0.856	1.00
188_D	191_G	0.855	1.00
171_V	241_S	0.853	1.00
123_V	282_L	0.852	1.00
194_Y	218_R	0.846	1.00
193_N	220_M	0.846	1.00
151_T	268_T	0.845	1.00
158_T	272_I	0.844	1.00
19_G	59_H	0.841	1.00
7_R	38_E	0.840	1.00
235_R	255_G	0.839	1.00
22_T	26_H	0.838	1.00
98_I	146_L	0.838	1.00
288_G	292_A	0.836	1.00
28_L	35_V	0.830	1.00
136_E	140_S	0.829	1.00
99_A	147_G	0.828	1.00
73_R	76_Y	0.822	1.00
6_L	75_W	0.812	1.00
128_V	144_H	0.810	1.00
177_P	182_K	0.808	1.00
54_V	57_R	0.806	1.00
167_D	260_R	0.798	1.00
159_E	162_E	0.795	1.00
63_Q	85_A	0.791	1.00
40_A	49_K	0.790	1.00
19_G	65_L	0.789	1.00
15_V	39_L	0.785	1.00
12_F	67_L	0.784	1.00
16_M	19_G	0.783	1.00
94_G	282_L	0.782	1.00
92_R	120_Y	0.778	1.00
173_P	238_V	0.777	1.00
77_G	81_I	0.776	1.00
15_V	51_F	0.775	1.00
114_Q	238_V	0.771	1.00
167_D	264_A	0.770	1.00
94_G	123_V	0.769	1.00
279_S	284_Q	0.767	1.00
17_T	68_F	0.763	1.00
32_Q	36_S	0.761	1.00
205_Q	209_Q	0.761	1.00
187_D	190_Q	0.760	1.00
179_A	257_V	0.759	1.00
86_E	89_R	0.757	1.00
251_Y	254_S	0.756	1.00
210_L	214_H	0.755	1.00
146_L	286_F	0.752	1.00
78_L	81_I	0.749	1.00
8_H	11_I	0.749	1.00
66_R	88_L	0.747	1.00
18_A	24_A	0.746	1.00
171_V	243_V	0.745	1.00
185_T	262_S	0.744	1.00
233_M	238_V	0.738	1.00
117_L	238_V	0.736	1.00
175_G	179_A	0.736	1.00
80_R	84_A	0.736	1.00
59_H	65_L	0.730	1.00
281_A	285_A	0.730	1.00
204_R	223_E	0.728	1.00
119_R	285_A	0.725	1.00
115_P	292_A	0.724	1.00
78_L	82_V	0.722	1.00
182_K	258_V	0.722	1.00
112_L	293_G	0.722	1.00
140_S	158_T	0.722	1.00
63_Q	88_L	0.721	1.00
190_Q	216_V	0.715	1.00
19_G	57_R	0.715	1.00
21_L	35_V	0.714	1.00
60_P	65_L	0.713	1.00
63_Q	66_R	0.711	1.00
34_T	38_E	0.710	1.00
130_Q	135_L	0.710	1.00
97_S	144_H	0.709	1.00
148_L	290_L	0.708	1.00
100_C	105_S	0.706	1.00
21_L	57_R	0.706	1.00
81_I	85_A	0.705	1.00
10_E	14_A	0.703	1.00
245_P	258_V	0.703	1.00
244_N	247_T	0.702	1.00
52_E	61_T	0.702	1.00
207_L	210_L	0.702	1.00
71_V	74_S	0.701	1.00
116_F	285_A	0.699	1.00
15_V	35_V	0.699	1.00
43_E	48_L	0.697	1.00
176_H	180_V	0.694	1.00
173_P	176_H	0.692	1.00
187_D	214_H	0.689	1.00
178_L	192_E	0.687	1.00
142_Q	274_P	0.686	1.00
210_L	213_E	0.685	1.00
63_Q	67_L	0.683	1.00
52_E	57_R	0.680	1.00
171_V	252_A	0.679	1.00
226_S	229_S	0.676	1.00
256_L	259_R	0.675	1.00
72_Q	76_Y	0.674	1.00
222_V	233_M	0.674	1.00
191_G	219_R	0.673	1.00
209_Q	212_T	0.671	1.00
97_S	145_D	0.670	1.00
208_D	212_T	0.666	1.00
206_L	210_L	0.665	1.00
172_L	178_L	0.664	1.00
169_V	259_R	0.661	1.00
197_L	230_V	0.660	1.00
71_V	75_W	0.659	1.00
100_C	109_L	0.658	1.00
198_S	223_E	0.658	1.00
43_E	53_R	0.657	1.00
209_Q	213_E	0.657	1.00
76_Y	79_D	0.654	1.00
277_R	280_S	0.654	1.00
96_L	282_L	0.651	1.00
145_D	283_V	0.648	1.00
24_A	28_L	0.648	1.00
248_A	252_A	0.645	1.00
67_L	85_A	0.644	1.00
175_G	178_L	0.640	1.00
62_V	66_R	0.640	1.00
39_L	43_E	0.639	1.00
80_R	83_S	0.637	1.00
194_Y	240_I	0.636	1.00
65_L	68_F	0.631	1.00
285_A	289_H	0.629	1.00
7_R	41_R	0.627	1.00
124_S	223_E	0.627	1.00
170_C	189_F	0.623	1.00
211_F	218_R	0.621	1.00
26_H	29_H	0.621	1.00
15_V	20_S	0.618	1.00
175_G	237_G	0.618	1.00
10_E	13_H	0.616	1.00
106_Q	232_A	0.612	1.00
250_D	253_A	0.612	1.00
129_P	225_H	0.607	1.00
170_C	194_Y	0.605	1.00
102_P	131_E	0.604	1.00
70_E	74_S	0.602	1.00
93_Q	124_S	0.597	1.00
198_S	225_H	0.596	1.00
235_R	253_A	0.595	1.00
170_C	242_V	0.594	1.00
129_P	226_S	0.593	1.00
205_Q	210_L	0.593	1.00
146_L	287_S	0.593	1.00
66_R	85_A	0.592	1.00
286_F	290_L	0.589	1.00
60_P	68_F	0.586	1.00
164_L	269_V	0.586	1.00
208_D	211_F	0.585	1.00
137_E	140_S	0.584	1.00
175_G	257_V	0.584	1.00
33_P	37_R	0.581	1.00
281_A	284_Q	0.580	1.00
178_L	181_K	0.580	1.00
230_V	234_V	0.579	1.00
96_L	146_L	0.576	1.00
109_L	112_L	0.575	1.00
83_S	87_S	0.575	1.00
166_L	267_F	0.574	1.00
159_E	276_H	0.573	1.00
178_L	184_L	0.573	1.00
183_V	188_D	0.572	1.00
111_Q	115_P	0.572	1.00
31_S	37_R	0.571	1.00
34_T	37_R	0.571	1.00
233_M	239_G	0.569	1.00
203_Y	207_L	0.567	1.00
113_L	125_L	0.567	1.00
46_I	85_A	0.565	1.00
7_R	11_I	0.561	1.00
39_L	51_F	0.558	1.00
51_F	60_P	0.558	1.00
273_R	284_Q	0.556	1.00
140_S	143_R	0.556	1.00
104_F	108_F	0.556	1.00
168_E	242_V	0.555	1.00
46_I	67_L	0.553	1.00
172_L	257_V	0.550	1.00
111_Q	114_Q	0.549	1.00
224_T	229_S	0.546	1.00
48_L	52_E	0.544	1.00
69_E	84_A	0.540	1.00
150_E	267_F	0.538	1.00
10_E	75_W	0.537	1.00
11_I	39_L	0.537	1.00
199_R	223_E	0.536	1.00
206_L	209_Q	0.534	1.00
94_G	122_D	0.532	1.00
139_L	158_T	0.531	1.00
137_E	143_R	0.530	1.00
5_N	45_V	0.529	1.00
11_I	24_A	0.528	1.00
227_A	244_N	0.526	1.00
176_H	240_I	0.524	1.00
243_V	248_A	0.524	1.00
252_A	255_G	0.523	1.00
71_V	78_L	0.523	1.00
94_G	120_Y	0.523	1.00
75_W	78_L	0.519	1.00
99_A	128_V	0.518	1.00
46_I	49_K	0.517	1.00
177_P	181_K	0.517	1.00
139_L	272_I	0.515	1.00
148_L	271_L	0.514	1.00
151_T	160_R	0.512	1.00
163_L	271_L	0.510	1.00
172_L	179_A	0.509	1.00
181_K	184_L	0.507	1.00
49_K	63_Q	0.507	1.00
75_W	79_D	0.507	1.00
190_Q	217_K	0.503	1.00
21_L	53_R	0.501	1.00
12_F	64_G	0.501	1.00
203_Y	206_L	0.501	1.00
106_Q	226_S	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
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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
3fzvA	4	0.9228	100	0.127	Contact Map
1uthA	2	0.7235	100	0.13	Contact Map
2esnA	3	0.9453	100	0.131	Contact Map
1ixcA	4	0.9357	100	0.14	Contact Map
1al3A	1	0.717	100	0.141	Contact Map
4x6gA	4	0.9711	100	0.147	Contact Map
3fxqA	3	0.9357	100	0.155	Contact Map
2h98A	2	0.6688	100	0.156	Contact Map
2h9bA	2	0.6785	100	0.162	Contact Map
3szpA	3	0.926	100	0.166	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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