AAER - ECOLI - GREMLIN Contacts

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AAER - HTH-type transcriptional activator AaeR

UniProt:	P67662	Sequences: MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAMPMVVCAAKSYLTQYGIPEKPADLSSHSWLEYSVRPDNEFELIAPEGISTRLIPQGRFVTNDPMTLVRWLTAGAGIAYVPLMWVINEINRGELEILLPRYQSDPRPVYALYTEKDKLPLKVQVVINSLTDYFVEVGKLFQEMHGRGKEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12825
Length:	309 (288)
Sequences:	79680 (57889)
Seq/√Len:	3411.1

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
71_R	75_E	3.513	1.00
16_F	25_Q	3.366	1.00
156_R	289_T	2.694	1.00
97_G	139_L	2.630	1.00
68_G	82_Q	2.395	1.00
230_L	237_A	2.324	1.00
162_P	241_L	2.217	1.00
171_Y	187_H	2.205	1.00
113_K	291_Y	2.202	1.00
160_A	266_P	2.168	1.00
12_K	25_Q	2.150	1.00
157_R	160_A	2.145	1.00
21_A	24_R	2.137	1.00
15_E	70_R	2.136	1.00
93_T	124_N	2.100	1.00
93_T	122_S	2.066	1.00
157_R	266_P	2.031	1.00
180_K	183_D	2.020	1.00
227_V	247_E	1.996	1.00
11_A	66_Y	1.992	1.00
9_V	36_T	1.983	1.00
46_V	61_A	1.975	1.00
231_T	252_E	1.946	1.00
95_R	124_N	1.939	1.00
68_G	75_E	1.935	1.00
160_A	264_P	1.926	1.00
167_A	256_L	1.904	1.00
113_K	287_S	1.902	1.00
9_V	33_I	1.899	1.00
19_F	37_V	1.895	1.00
72_M	76_V	1.892	1.00
12_K	15_E	1.885	1.00
11_A	70_R	1.878	1.00
190_L	235_G	1.877	1.00
14_V	58_L	1.870	1.00
12_K	16_F	1.840	1.00
11_A	15_E	1.828	1.00
66_Y	70_R	1.799	1.00
164_V	241_L	1.787	1.00
231_T	247_E	1.764	1.00
65_Y	79_V	1.727	1.00
50_N	57_G	1.724	1.00
114_M	284_V	1.676	1.00
188_S	217_R	1.672	1.00
176_G	183_D	1.657	1.00
64_I	82_Q	1.641	1.00
155_S	268_Y	1.635	1.00
164_V	255_I	1.618	1.00
15_E	25_Q	1.615	1.00
10_F	66_Y	1.589	1.00
133_D	138_G	1.569	1.00
9_V	28_M	1.561	1.00
14_V	66_Y	1.561	1.00
11_A	69_C	1.558	1.00
16_F	21_A	1.545	1.00
154_F	273_E	1.533	1.00
89_T	120_G	1.523	1.00
60_E	63_R	1.520	1.00
20_T	30_V	1.516	1.00
114_M	121_L	1.511	1.00
6_R	36_T	1.489	1.00
132_P	136_A	1.481	1.00
6_R	43_E	1.466	1.00
29_S	32_S	1.447	1.00
11_A	73_L	1.442	1.00
200_F	204_A	1.432	1.00
47_K	50_N	1.431	1.00
156_R	271_Y	1.427	1.00
18_S	21_A	1.412	1.00
277_L	281_V	1.402	1.00
285_I	289_T	1.392	1.00
6_R	39_K	1.392	1.00
12_K	26_L	1.392	1.00
68_G	71_R	1.378	1.00
72_M	79_V	1.376	1.00
144_R	270_L	1.371	1.00
154_F	271_Y	1.365	1.00
146_G	268_Y	1.363	1.00
68_G	78_D	1.357	1.00
169_K	252_E	1.347	1.00
4_L	76_V	1.333	1.00
135_I	152_S	1.326	1.00
113_K	117_E	1.324	1.00
269_A	285_I	1.323	1.00
91_I	120_G	1.319	1.00
104_Q	224_M	1.317	1.00
141_V	281_V	1.316	1.00
3_R	6_R	1.314	1.00
271_Y	285_I	1.311	1.00
283_V	286_N	1.297	1.00
134_L	142_V	1.292	1.00
43_E	80_H	1.282	1.00
133_D	139_L	1.276	1.00
141_V	269_A	1.275	1.00
187_H	236_I	1.268	1.00
95_R	126_V	1.266	1.00
167_A	236_I	1.264	1.00
161_M	242_M	1.264	1.00
65_Y	80_H	1.260	1.00
115_L	217_R	1.252	1.00
241_L	245_I	1.243	1.00
52_S	57_G	1.240	1.00
226_L	237_A	1.240	1.00
247_E	252_E	1.238	1.00
63_R	67_Q	1.230	1.00
38_S	42_D	1.230	1.00
245_I	249_N	1.215	1.00
207_G	212_L	1.206	1.00
190_L	226_L	1.204	1.00
75_E	78_D	1.201	1.00
117_E	287_S	1.196	1.00
94_L	284_V	1.179	1.00
67_Q	71_R	1.179	1.00
228_R	231_T	1.178	1.00
115_L	188_S	1.173	1.00
172_L	187_H	1.173	1.00
10_F	49_L	1.173	1.00
241_L	255_I	1.172	1.00
113_K	116_K	1.171	1.00
177_I	254_E	1.169	1.00
64_I	67_Q	1.166	1.00
68_G	79_V	1.163	1.00
157_R	268_Y	1.158	1.00
112_A	116_K	1.158	1.00
169_K	254_E	1.148	1.00
155_S	270_L	1.145	1.00
10_F	48_L	1.132	1.00
28_M	32_S	1.123	1.00
10_F	14_V	1.115	1.00
8_S	77_Q	1.114	1.00
35_Q	38_S	1.113	1.00
13_V	22_A	1.112	1.00
34_S	38_S	1.111	1.00
114_M	287_S	1.104	1.00
19_F	56_I	1.092	1.00
188_S	215_Q	1.089	1.00
35_Q	39_K	1.087	1.00
272_T	275_D	1.083	1.00
5_K	8_S	1.082	1.00
220_T	226_L	1.080	1.00
124_N	219_V	1.077	1.00
71_R	78_D	1.070	1.00
118_Y	283_V	1.069	1.00
286_N	289_T	1.068	1.00
112_A	232_A	1.068	1.00
7_M	69_C	1.065	1.00
72_M	75_E	1.059	1.00
282_Q	286_N	1.057	1.00
58_L	62_G	1.056	1.00
12_K	22_A	1.055	1.00
166_C	255_I	1.054	1.00
110_L	288_L	1.046	1.00
36_T	39_K	1.040	1.00
287_S	291_Y	1.040	1.00
168_A	233_G	1.037	1.00
103_A	127_T	1.030	1.00
227_V	231_T	1.022	1.00
128_G	133_D	1.018	1.00
178_P	259_R	1.014	1.00
165_V	236_I	1.008	1.00
64_I	68_G	0.997	1.00
228_R	232_A	0.997	1.00
109_G	232_A	0.990	1.00
9_V	26_L	0.987	1.00
179_E	183_D	0.987	1.00
156_R	285_I	0.987	1.00
255_I	258_P	0.984	1.00
77_Q	81_E	0.983	1.00
117_E	290_D	0.982	1.00
14_V	49_L	0.982	1.00
80_H	84_Y	0.981	1.00
28_M	33_I	0.974	1.00
181_P	260_Y	0.973	1.00
166_C	244_V	0.973	1.00
77_Q	80_H	0.966	1.00
162_P	264_P	0.963	1.00
201_E	204_A	0.959	1.00
114_M	118_Y	0.957	1.00
13_V	19_F	0.950	1.00
10_F	58_L	0.944	1.00
171_Y	188_S	0.942	1.00
65_Y	69_C	0.941	1.00
246_N	250_R	0.934	1.00
191_E	216_G	0.933	1.00
167_A	171_Y	0.929	1.00
49_L	56_I	0.928	1.00
110_L	287_S	0.927	1.00
220_T	229_W	0.926	1.00
152_S	273_E	0.925	1.00
135_I	150_D	0.925	1.00
14_V	62_G	0.924	1.00
133_D	136_A	0.923	1.00
74_H	78_D	0.923	1.00
171_Y	174_Q	0.922	1.00
278_P	281_V	0.921	1.00
10_F	40_L	0.914	1.00
46_V	83_L	0.913	1.00
287_S	290_D	0.912	1.00
97_G	142_V	0.908	1.00
122_S	215_Q	0.896	1.00
139_L	142_V	0.894	1.00
244_V	247_E	0.888	1.00
22_A	33_I	0.887	1.00
153_L	270_L	0.883	1.00
39_K	42_D	0.875	1.00
97_G	144_R	0.870	1.00
67_Q	70_R	0.869	1.00
167_A	172_L	0.868	1.00
21_A	25_Q	0.856	1.00
171_Y	175_Y	0.855	1.00
100_S	222_D	0.854	1.00
96_I	141_V	0.854	1.00
20_T	24_R	0.852	1.00
126_V	133_D	0.851	1.00
183_D	186_S	0.850	1.00
286_N	290_D	0.847	1.00
203_I	207_G	0.847	1.00
121_L	280_K	0.847	1.00
188_S	216_G	0.847	1.00
5_K	36_T	0.847	1.00
13_V	37_V	0.844	1.00
189_W	214_P	0.843	1.00
175_Y	188_S	0.839	1.00
166_C	237_A	0.839	1.00
17_G	57_G	0.835	1.00
146_G	266_P	0.835	1.00
52_S	55_S	0.827	1.00
26_L	33_I	0.827	1.00
172_L	177_I	0.820	1.00
131_A	135_I	0.814	1.00
71_R	74_H	0.811	1.00
248_I	251_G	0.809	1.00
173_T	187_H	0.804	1.00
14_V	17_G	0.802	1.00
170_S	174_Q	0.799	1.00
10_F	65_Y	0.799	1.00
154_F	157_R	0.794	1.00
17_G	63_R	0.793	1.00
201_E	205_P	0.792	1.00
90_P	118_Y	0.791	1.00
61_A	83_L	0.791	1.00
13_V	49_L	0.790	1.00
38_S	47_K	0.784	1.00
4_L	73_L	0.784	1.00
141_V	284_V	0.779	1.00
126_V	139_L	0.779	1.00
92_G	280_K	0.776	1.00
112_A	234_A	0.776	1.00
247_E	250_R	0.774	1.00
206_E	210_T	0.773	1.00
182_A	185_S	0.772	1.00
30_V	34_S	0.771	1.00
168_A	234_A	0.769	1.00
277_L	282_Q	0.768	1.00
15_E	66_Y	0.768	1.00
244_V	248_I	0.763	1.00
75_E	79_V	0.763	1.00
76_V	79_V	0.757	1.00
58_L	63_R	0.751	1.00
143_I	288_L	0.750	1.00
229_W	234_A	0.747	1.00
117_E	283_V	0.747	1.00
16_F	22_A	0.746	1.00
84_Y	87_N	0.742	1.00
162_P	257_L	0.741	1.00
162_P	262_S	0.740	1.00
135_I	153_L	0.738	1.00
17_G	55_S	0.736	1.00
279_L	283_V	0.735	1.00
6_R	9_V	0.734	1.00
57_G	63_R	0.734	1.00
61_A	86_F	0.734	1.00
64_I	86_F	0.733	1.00
166_C	239_V	0.732	1.00
200_F	219_V	0.732	1.00
78_D	82_Q	0.728	1.00
113_K	290_D	0.727	1.00
95_R	139_L	0.721	1.00
248_I	255_I	0.719	1.00
185_S	212_L	0.717	1.00
166_C	248_I	0.715	1.00
174_Q	254_E	0.712	1.00
61_A	64_I	0.711	1.00
32_S	36_T	0.710	1.00
115_L	234_A	0.710	1.00
167_A	254_E	0.709	1.00
240_P	243_W	0.708	1.00
79_V	83_L	0.707	1.00
92_G	121_L	0.707	1.00
110_L	291_Y	0.707	1.00
13_V	33_I	0.706	1.00
69_C	72_M	0.706	1.00
180_K	259_R	0.705	1.00
76_V	80_H	0.704	1.00
202_L	206_E	0.704	1.00
8_S	12_K	0.702	1.00
19_F	55_S	0.702	1.00
205_P	208_I	0.694	1.00
19_F	33_I	0.694	1.00
114_M	283_V	0.694	1.00
95_R	140_D	0.692	1.00
222_D	225_T	0.687	1.00
186_S	215_Q	0.687	1.00
50_N	59_T	0.686	1.00
182_A	210_T	0.686	1.00
167_A	173_T	0.685	1.00
168_A	171_Y	0.684	1.00
199_E	203_I	0.682	1.00
207_G	214_P	0.681	1.00
98_C	107_L	0.681	1.00
50_N	55_S	0.680	1.00
98_C	103_A	0.678	1.00
41_E	46_V	0.675	1.00
61_A	65_Y	0.674	1.00
218_F	229_W	0.673	1.00
206_E	209_S	0.671	1.00
178_P	257_L	0.670	1.00
69_C	73_L	0.670	1.00
134_L	270_L	0.670	1.00
180_K	260_Y	0.668	1.00
94_L	280_K	0.667	1.00
70_R	74_H	0.665	1.00
199_E	202_L	0.665	1.00
275_D	278_P	0.665	1.00
74_H	77_Q	0.664	1.00
140_D	281_V	0.662	1.00
192_Y	226_L	0.662	1.00
78_D	81_E	0.656	1.00
205_P	209_S	0.655	1.00
41_E	51_R	0.652	1.00
122_S	219_V	0.649	1.00
170_S	173_T	0.647	1.00
193_S	219_V	0.644	1.00
65_Y	83_L	0.641	1.00
60_E	64_I	0.640	1.00
5_K	39_K	0.638	1.00
203_I	206_E	0.638	1.00
22_A	26_L	0.637	1.00
63_R	66_Y	0.634	1.00
246_N	249_N	0.632	1.00
37_V	41_E	0.632	1.00
24_R	27_Q	0.630	1.00
13_V	18_S	0.629	1.00
137_D	272_T	0.628	1.00
189_W	236_I	0.628	1.00
200_F	203_I	0.626	1.00
170_S	254_E	0.626	1.00
159_G	267_V	0.624	1.00
283_V	287_S	0.624	1.00
169_K	251_G	0.623	1.00
165_V	184_L	0.621	1.00
170_S	233_G	0.619	1.00
8_S	11_A	0.616	1.00
165_V	189_W	0.615	1.00
64_I	83_L	0.608	1.00
226_L	230_L	0.608	1.00
68_G	72_M	0.608	1.00
284_V	288_L	0.607	1.00
104_Q	228_R	0.605	1.00
141_V	285_I	0.604	1.00
204_A	208_I	0.603	1.00
173_T	179_E	0.602	1.00
193_S	221_N	0.602	1.00
100_S	129_I	0.601	1.00
154_F	274_K	0.599	1.00
229_W	235_G	0.599	1.00
58_L	66_Y	0.595	1.00
94_L	141_V	0.594	1.00
91_I	122_S	0.594	1.00
134_L	153_L	0.593	1.00
31_S	35_Q	0.587	1.00
107_L	110_L	0.586	1.00
279_L	282_Q	0.584	1.00
32_S	35_Q	0.583	1.00
5_K	9_V	0.583	1.00
165_V	238_Y	0.582	1.00
176_G	179_E	0.581	1.00
172_L	175_Y	0.578	1.00
161_M	265_R	0.577	1.00
81_E	85_A	0.577	1.00
44_L	83_L	0.574	1.00
163_M	238_Y	0.574	1.00
173_T	176_G	0.573	1.00
127_T	222_D	0.571	1.00
29_S	35_Q	0.569	1.00
44_L	65_Y	0.568	1.00
46_V	50_N	0.563	1.00
172_L	176_G	0.563	1.00
37_V	49_L	0.562	1.00
145_V	265_R	0.560	1.00
271_Y	282_Q	0.560	1.00
49_L	58_L	0.558	1.00
127_T	221_N	0.555	1.00
201_E	206_E	0.554	1.00
178_P	183_D	0.553	1.00
220_T	225_T	0.552	1.00
109_G	113_K	0.551	1.00
194_V	219_V	0.551	1.00
44_L	47_K	0.545	1.00
73_L	76_V	0.544	1.00
92_G	118_Y	0.542	1.00
69_C	76_V	0.542	1.00
109_G	112_A	0.541	1.00
67_Q	82_Q	0.541	1.00
223_P	240_P	0.540	1.00
9_V	37_V	0.538	1.00
111_T	123_V	0.538	1.00
102_M	106_V	0.536	1.00
167_A	174_Q	0.534	1.00
171_Y	236_I	0.533	1.00
97_G	128_G	0.533	1.00
8_S	73_L	0.533	1.00
143_I	269_A	0.531	1.00
239_V	244_V	0.527	1.00
73_L	77_Q	0.525	1.00
281_V	285_I	0.523	1.00
132_P	138_G	0.522	1.00
68_G	83_L	0.521	1.00
158_L	269_A	0.520	1.00
92_G	120_G	0.515	1.00
9_V	22_A	0.514	1.00
47_K	61_A	0.513	1.00
19_F	51_R	0.513	1.00
7_M	65_Y	0.512	1.00
104_Q	222_D	0.509	1.00
3_R	39_K	0.508	1.00
231_T	250_R	0.506	1.00
19_F	30_V	0.506	1.00
204_A	207_G	0.505	1.00
28_M	36_T	0.502	1.00
17_G	56_I	0.501	1.00
97_G	126_V	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
3fxqA	3	0.9385	100	0.116	Contact Map
2esnA	3	0.9417	100	0.12	Contact Map
3fzvA	4	0.9223	100	0.123	Contact Map
1uthA	2	0.7249	100	0.125	Contact Map
3hhgA	3	0.9482	100	0.128	Contact Map
3szpA	3	0.9385	100	0.129	Contact Map
1ixcA	4	0.9385	100	0.131	Contact Map
1al3A	1	0.7152	100	0.133	Contact Map
4x6gA	4	0.9709	100	0.146	Contact Map
2h98A	2	0.6796	100	0.147	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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