EXUR - ECOLI - GREMLIN Contacts

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EXUR - Exu regulon transcriptional regulator

UniProt:	P0ACL2	Sequences: MEITEPRRLYQQLAADLKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIHVVSNQPRHQQAADNNMEFANYGPFELLQARQLIESNIAEFAATQVTKQDIMKLMAIQEQARGEQCFRDSEWDLQFHIQVALATQNSALAAIVEKMWTQRSHNPYWKKLHEHIDSRTVDNWCDDHDQILKALIRKDPHAAKLAMWQHLENTKIMLFNETSDDFEFNADRYLFAENPVVHLDTATSGSK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12739
Length:	258 (202)
Sequences:	22471 (16475)
Seq/√Len:	1159.2

ECOLI - EXUR PDHR LLDR UXUR NANR GLCC DGOR YJJM YDFH YIEP MCBR FADR CSIR FRLR YEGW
BACSU - GNTR YCBG YDHC LUTR YVOA YMFC YURK
SULSO - Q97YR4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
125_M	203_I	3.582	1.00
110_E	211_K	3.235	1.00
206_D	209_A	2.851	1.00
27_L	30_D	2.750	1.00
132_R	196_D	2.701	1.00
20_R	25_V	2.647	1.00
20_R	41_E	2.346	1.00
103_L	107_N	2.246	1.00
35_E	46_R	2.191	1.00
96_E	157_S	2.157	1.00
123_K	149_Q	2.126	1.00
14_A	55_M	2.065	1.00
102_Q	219_E	2.034	1.00
18_K	59_E	1.961	1.00
63_E	73_V	1.919	1.00
13_L	44_V	1.901	1.00
114_T	207_P	1.897	1.00
99_Q	111_F	1.844	1.00
120_D	155_Q	1.810	1.00
121_I	203_I	1.797	1.00
201_A	209_A	1.764	1.00
64_V	70_I	1.759	1.00
117_T	120_D	1.719	1.00
135_Q	138_R	1.717	1.00
152_L	160_A	1.701	1.00
13_L	42_K	1.698	1.00
149_Q	152_L	1.664	1.00
16_D	20_R	1.630	1.00
106_S	215_W	1.598	1.00
194_D	220_N	1.581	1.00
128_Q	199_L	1.580	1.00
100_A	162_I	1.557	1.00
110_E	207_P	1.542	1.00
19_E	23_Q	1.536	1.00
211_K	215_W	1.521	1.00
106_S	211_K	1.507	1.00
209_A	213_A	1.507	1.00
7_R	15_A	1.506	1.00
107_N	110_E	1.490	1.00
147_H	195_H	1.445	1.00
200_K	204_R	1.428	1.00
148_I	164_E	1.425	1.00
14_A	59_E	1.418	1.00
197_Q	213_A	1.414	1.00
65_R	68_S	1.406	1.00
161_A	165_K	1.392	1.00
151_A	163_V	1.382	1.00
158_A	169_Q	1.379	1.00
109_A	210_A	1.374	1.00
127_I	142_W	1.365	1.00
120_D	153_A	1.361	1.00
102_Q	215_W	1.343	1.00
130_Q	142_W	1.327	1.00
125_M	199_L	1.326	1.00
132_R	192_C	1.320	1.00
204_R	209_A	1.318	1.00
125_M	129_E	1.314	1.00
102_Q	222_K	1.311	1.00
207_P	211_K	1.287	1.00
116_V	121_I	1.287	1.00
96_E	158_A	1.285	1.00
196_D	200_K	1.283	1.00
36_R	40_D	1.274	1.00
130_Q	145_Q	1.262	1.00
37_F	41_E	1.260	1.00
126_A	130_Q	1.231	1.00
175_Y	178_K	1.225	1.00
212_L	216_Q	1.192	1.00
65_R	71_H	1.185	1.00
38_I	49_V	1.184	1.00
127_I	149_Q	1.183	1.00
194_D	217_H	1.179	1.00
12_Q	16_D	1.170	1.00
31_K	71_H	1.169	1.00
16_D	19_E	1.164	1.00
128_Q	196_D	1.153	1.00
95_F	226_F	1.153	1.00
102_Q	106_S	1.145	1.00
116_V	205_K	1.137	1.00
148_I	152_L	1.134	1.00
57_E	64_V	1.125	1.00
110_E	208_H	1.124	1.00
16_D	42_K	1.116	1.00
150_V	202_L	1.116	1.00
138_R	141_E	1.114	1.00
95_F	222_K	1.113	1.00
101_R	105_E	1.106	1.00
209_A	212_L	1.100	1.00
116_V	120_D	1.098	1.00
200_K	203_I	1.095	1.00
20_R	42_K	1.093	1.00
116_V	153_A	1.089	1.00
215_W	219_E	1.088	1.00
106_S	110_E	1.084	1.00
143_D	147_H	1.083	1.00
26_Y	72_V	1.078	1.00
109_A	214_M	1.076	1.00
121_I	205_K	1.071	1.00
145_Q	149_Q	1.069	1.00
121_I	199_L	1.062	1.00
108_I	151_A	1.060	1.00
96_E	156_N	1.058	1.00
128_Q	132_R	1.053	1.00
109_A	113_A	1.050	1.00
57_E	62_V	1.049	1.00
128_Q	131_A	1.043	1.00
127_I	145_Q	1.035	1.00
99_Q	156_N	1.034	1.00
199_L	203_I	1.030	1.00
222_K	226_F	1.026	1.00
142_W	145_Q	1.025	1.00
147_H	217_H	1.021	1.00
149_Q	153_A	1.016	1.00
195_H	217_H	1.016	1.00
123_K	152_L	1.015	1.00
162_I	165_K	1.001	1.00
63_E	71_H	0.992	1.00
125_M	196_D	0.982	1.00
129_E	132_R	0.981	1.00
113_A	207_P	0.978	1.00
197_Q	216_Q	0.976	1.00
123_K	126_A	0.973	1.00
111_F	115_Q	0.971	1.00
35_E	50_R	0.970	1.00
34_A	37_F	0.969	1.00
146_F	199_L	0.966	1.00
154_T	160_A	0.965	1.00
201_A	206_D	0.961	1.00
107_N	211_K	0.961	1.00
51_E	54_I	0.960	1.00
122_M	126_A	0.948	1.00
197_Q	209_A	0.947	1.00
141_E	145_Q	0.935	1.00
198_I	214_M	0.934	1.00
7_R	12_Q	0.933	1.00
105_E	147_H	0.931	1.00
193_D	197_Q	0.930	1.00
123_K	127_I	0.927	1.00
53_I	70_I	0.918	1.00
65_R	69_G	0.917	1.00
20_R	26_Y	0.914	1.00
21_I	72_V	0.913	1.00
176_W	179_L	0.908	1.00
10_Y	55_M	0.900	1.00
55_M	58_V	0.894	1.00
113_A	202_L	0.891	1.00
62_V	70_I	0.887	1.00
68_S	71_H	0.887	1.00
208_H	212_L	0.886	1.00
31_K	69_G	0.872	1.00
107_N	111_F	0.872	1.00
208_H	211_K	0.871	1.00
101_R	218_L	0.866	1.00
129_E	133_G	0.866	1.00
121_I	125_M	0.866	1.00
14_A	18_K	0.865	1.00
130_Q	133_G	0.864	1.00
197_Q	200_K	0.858	1.00
39_A	49_V	0.858	1.00
127_I	130_Q	0.858	1.00
118_K	122_M	0.856	1.00
100_A	158_A	0.851	1.00
160_A	164_E	0.842	1.00
45_S	48_V	0.840	1.00
92_Y	155_Q	0.836	1.00
18_K	61_Y	0.836	1.00
53_I	62_V	0.832	1.00
92_Y	96_E	0.830	1.00
93_G	158_A	0.828	1.00
115_Q	155_Q	0.825	1.00
112_A	153_A	0.822	1.00
18_K	22_E	0.817	1.00
192_C	196_D	0.816	1.00
54_I	57_E	0.812	1.00
37_F	40_D	0.811	1.00
118_K	205_K	0.804	1.00
113_A	205_K	0.799	1.00
125_M	200_K	0.799	1.00
11_Q	55_M	0.798	1.00
116_V	202_L	0.797	1.00
198_I	213_A	0.793	1.00
113_A	210_A	0.791	1.00
131_A	139_D	0.791	1.00
120_D	123_K	0.790	1.00
174_P	177_K	0.789	1.00
129_E	196_D	0.786	1.00
9_L	12_Q	0.783	1.00
9_L	48_V	0.783	1.00
158_A	162_I	0.774	1.00
177_K	180_H	0.774	1.00
8_R	11_Q	0.772	1.00
99_Q	222_K	0.771	1.00
111_F	114_T	0.770	1.00
54_I	64_V	0.769	1.00
189_D	193_D	0.764	1.00
219_E	223_I	0.762	1.00
124_L	149_Q	0.761	1.00
38_I	53_I	0.759	1.00
197_Q	201_A	0.750	1.00
148_I	167_W	0.747	1.00
143_D	195_H	0.746	1.00
110_E	114_T	0.740	1.00
158_A	161_A	0.735	1.00
122_M	203_I	0.730	1.00
98_L	221_T	0.729	1.00
99_Q	115_Q	0.728	1.00
124_L	199_L	0.725	1.00
100_A	159_L	0.724	1.00
123_K	145_Q	0.723	1.00
10_Y	14_A	0.722	1.00
44_V	49_V	0.721	1.00
138_R	142_W	0.718	1.00
216_Q	220_N	0.708	1.00
213_A	216_Q	0.708	1.00
174_P	178_K	0.705	1.00
111_F	156_N	0.704	1.00
201_A	213_A	0.697	1.00
130_Q	138_R	0.694	1.00
198_I	210_A	0.691	1.00
100_A	108_I	0.684	1.00
122_M	125_M	0.678	1.00
55_M	59_E	0.678	1.00
128_Q	192_C	0.674	1.00
25_V	41_E	0.672	1.00
126_A	129_E	0.672	1.00
93_G	157_S	0.669	1.00
212_L	215_W	0.668	1.00
7_R	11_Q	0.668	1.00
112_A	116_V	0.665	1.00
121_I	202_L	0.661	1.00
145_Q	148_I	0.659	1.00
148_I	160_A	0.659	1.00
144_L	167_W	0.658	1.00
219_E	222_K	0.658	1.00
198_I	217_H	0.657	1.00
120_D	152_L	0.656	1.00
220_N	224_M	0.647	1.00
48_V	52_A	0.641	1.00
194_D	197_Q	0.639	1.00
76_Q	93_G	0.638	1.00
120_D	149_Q	0.635	1.00
108_I	154_T	0.628	1.00
176_W	180_H	0.624	1.00
103_L	159_L	0.620	1.00
112_A	154_T	0.617	1.00
105_E	195_H	0.611	1.00
26_Y	30_D	0.611	1.00
102_Q	218_L	0.609	1.00
139_D	191_W	0.606	1.00
99_Q	107_N	0.605	1.00
109_A	207_P	0.604	1.00
20_R	24_G	0.602	1.00
28_V	74_S	0.600	1.00
67_G	70_I	0.598	1.00
124_L	153_A	0.594	1.00
103_L	106_S	0.591	1.00
106_S	207_P	0.590	1.00
71_H	74_S	0.588	1.00
29_G	74_S	0.588	1.00
100_A	104_I	0.587	1.00
108_I	159_L	0.585	1.00
106_S	214_M	0.581	1.00
104_I	163_V	0.574	1.00
161_A	169_Q	0.570	1.00
118_K	203_I	0.570	1.00
36_R	39_A	0.569	1.00
151_A	167_W	0.567	1.00
107_N	159_L	0.566	1.00
223_I	227_N	0.562	1.00
17_L	38_I	0.559	1.00
223_I	226_F	0.556	1.00
131_A	192_C	0.555	1.00
105_E	218_L	0.554	1.00
32_L	62_V	0.554	1.00
42_K	49_V	0.550	1.00
198_I	201_A	0.548	1.00
54_I	58_V	0.548	1.00
113_A	214_M	0.546	1.00
10_Y	51_E	0.546	1.00
201_A	207_P	0.545	1.00
175_Y	179_L	0.545	1.00
112_A	150_V	0.544	1.00
110_E	215_W	0.543	1.00
92_Y	157_S	0.537	1.00
92_Y	95_F	0.535	1.00
22_E	61_Y	0.534	1.00
216_Q	219_E	0.534	1.00
93_G	96_E	0.532	1.00
119_Q	123_K	0.530	1.00
26_Y	32_L	0.530	1.00
40_D	43_N	0.529	1.00
109_A	150_V	0.524	1.00
124_L	127_I	0.516	1.00
106_S	109_A	0.516	1.00
187_T	190_N	0.514	1.00
193_D	196_D	0.514	1.00
20_R	23_Q	0.514	1.00
210_A	214_M	0.512	1.00
95_F	99_Q	0.509	1.00
108_I	150_V	0.507	1.00
194_D	216_Q	0.504	1.00
26_Y	41_E	0.501	1.00
132_R	193_D	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
3sxyA	2	0.7674	100	0.249	Contact Map
3c7jA	4	0.845	100	0.264	Contact Map
4p96A	2	0.9109	100	0.267	Contact Map
2hs5A	1	0.7868	100	0.267	Contact Map
3ihuA	1	0.7752	100	0.272	Contact Map
4p9fA	1	0.8023	100	0.275	Contact Map
2di3A	2	0.8566	100	0.285	Contact Map
1hw1A	2	0.8566	100	0.294	Contact Map
3ic7A	2	0.4302	99.9	0.568	Contact Map
3by6A	2	0.469	99.9	0.568	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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