MODE - ECOLI - GREMLIN Contacts

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MODE - Transcriptional regulator ModE

UniProt:	P0A9G8	Sequences: MQAEILLTLKLQQKLFADPRRISLLKHIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGAVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQTSARNQWFGTITARDHDDVQQHVDVLLADGKTRLKVAITAQSGARLGLDEGKEVLILLKAPWVGITQDEAVAQNADNQLPGIISHIERGAEQCEVLMALPDGQTLCATVPVNEATSLQQGQNVTAYFNADSVIIATLC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13227
Length:	262 (245)
Sequences:	388 (251)
Seq/√Len:	16.0

ECOLI - MODE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_K	90_D	5.354	1.00
221_M	247_V	4.477	1.00
149_V	180_I	4.163	1.00
145_Q	167_G	3.579	1.00
29_A	83_Q	3.515	0.99
125_T	181_L	2.728	0.97
189_I	247_V	2.651	0.96
133_G	149_V	2.512	0.95
14_K	82_G	2.393	0.93
90_D	93_A	2.351	0.93
131_W	182_L	2.322	0.92
149_V	178_V	2.316	0.92
215_E	234_P	2.267	0.91
96_Q	99_A	2.262	0.91
158_L	251_F	2.239	0.91
205_G	221_M	2.196	0.90
162_I	258_I	2.170	0.89
135_I	162_I	2.165	0.89
180_I	256_V	2.145	0.89
221_M	249_A	2.107	0.88
135_I	174_E	2.077	0.87
251_F	256_V	2.067	0.87
86_I	240_S	2.037	0.86
21_R	51_A	2.033	0.86
213_G	217_C	2.014	0.85
53_N	66_R	2.009	0.85
207_I	219_V	1.977	0.84
203_L	223_L	1.976	0.84
125_T	166_S	1.968	0.84
154_G	203_L	1.957	0.84
63_L	66_R	1.954	0.84
133_G	253_A	1.875	0.81
27_H	72_G	1.857	0.80
66_R	186_W	1.856	0.80
78_L	86_I	1.830	0.79
234_P	250_Y	1.750	0.76
138_R	174_E	1.723	0.75
188_G	198_N	1.697	0.74
28_I	63_L	1.641	0.71
198_N	234_P	1.641	0.71
141_D	247_V	1.619	0.70
47_S	51_A	1.606	0.69
205_G	249_A	1.591	0.69
151_L	154_G	1.578	0.68
70_G	73_G	1.577	0.68
134_T	150_L	1.566	0.67
70_G	74_G	1.556	0.67
138_R	167_G	1.555	0.67
233_V	239_T	1.551	0.67
16_F	55_M	1.543	0.66
143_V	213_G	1.540	0.66
50_D	71_K	1.533	0.66
24_L	127_A	1.494	0.64
50_D	127_A	1.489	0.63
118_I	158_L	1.483	0.63
139_D	247_V	1.462	0.62
148_D	157_R	1.458	0.62
85_L	112_N	1.445	0.61
143_V	257_I	1.444	0.61
210_I	219_V	1.444	0.61
191_Q	245_Q	1.432	0.60
57_Q	254_D	1.417	0.59
37_G	76_A	1.412	0.59
138_R	145_Q	1.393	0.58
28_I	223_L	1.393	0.58
143_V	232_T	1.392	0.58
20_R	86_I	1.391	0.58
71_K	183_K	1.380	0.57
146_H	200_D	1.378	0.57
19_P	96_Q	1.374	0.57
216_Q	239_T	1.335	0.55
86_I	89_Y	1.327	0.54
18_D	86_I	1.320	0.54
160_V	180_I	1.315	0.54
156_T	249_A	1.308	0.53
154_G	219_V	1.308	0.53
131_W	229_L	1.297	0.52
92_L	111_L	1.281	0.52
29_A	78_L	1.277	0.51
174_E	258_I	1.272	0.51
51_A	59_S	1.242	0.49
24_L	89_Y	1.226	0.48
43_I	258_I	1.216	0.48
160_V	256_V	1.215	0.48
198_N	215_E	1.212	0.48
215_E	239_T	1.186	0.46
42_G	76_A	1.181	0.46
131_W	151_L	1.174	0.45
204_P	248_T	1.165	0.45
229_L	249_A	1.160	0.45
46_K	257_I	1.157	0.44
188_G	252_N	1.155	0.44
146_H	215_E	1.152	0.44
18_D	88_L	1.140	0.43
19_P	89_Y	1.130	0.43
47_S	125_T	1.124	0.42
153_D	156_T	1.122	0.42
140_H	164_A	1.121	0.42
49_W	184_A	1.112	0.42
158_L	173_D	1.112	0.42
192_D	197_Q	1.106	0.41
91_L	122_S	1.102	0.41
159_K	212_R	1.061	0.39
28_I	76_A	1.051	0.38
215_E	252_N	1.050	0.38
141_D	215_E	1.044	0.38
134_T	177_E	1.038	0.38
61_H	81_Y	1.037	0.38
214_A	235_V	1.033	0.37
164_A	167_G	1.032	0.37
88_L	130_Q	1.025	0.37
189_I	221_M	1.025	0.37
171_G	178_V	1.021	0.37
189_I	258_I	1.016	0.37
114_L	122_S	1.015	0.36
157_R	245_Q	1.014	0.36
26_K	31_S	1.013	0.36
30_L	166_S	1.009	0.36
194_A	240_S	1.006	0.36
200_D	252_N	1.003	0.36
35_S	125_T	0.992	0.35
31_S	52_I	0.990	0.35
142_D	198_N	0.986	0.35
51_A	64_V	0.985	0.35
35_S	39_K	0.981	0.35
32_G	73_G	0.981	0.35
209_H	255_S	0.980	0.35
52_I	164_A	0.978	0.34
27_H	120_R	0.977	0.34
59_S	63_L	0.974	0.34
39_K	133_G	0.973	0.34
125_T	229_L	0.967	0.34
35_S	103_L	0.965	0.34
170_L	179_L	0.962	0.34
26_K	87_Q	0.961	0.34
89_Y	127_A	0.961	0.34
97_Q	153_D	0.956	0.33
20_R	42_G	0.956	0.33
51_A	135_I	0.953	0.33
241_L	247_V	0.952	0.33
28_I	43_I	0.945	0.33
151_L	256_V	0.945	0.33
177_E	184_A	0.941	0.33
174_E	197_Q	0.940	0.33
26_K	98_K	0.938	0.32
30_L	86_I	0.936	0.32
54_E	88_L	0.936	0.32
135_I	164_A	0.933	0.32
102_V	115_L	0.923	0.32
23_S	27_H	0.921	0.32
123_L	188_G	0.916	0.31
198_N	213_G	0.916	0.31
246_N	250_Y	0.902	0.31
96_Q	130_Q	0.896	0.30
185_P	257_I	0.894	0.30
28_I	44_S	0.886	0.30
138_R	182_L	0.881	0.30
182_L	186_W	0.873	0.29
35_S	76_A	0.868	0.29
39_K	71_K	0.867	0.29
234_P	254_D	0.866	0.29
196_A	253_A	0.863	0.29
117_A	167_G	0.855	0.28
139_D	146_H	0.847	0.28
220_L	230_C	0.843	0.28
202_Q	250_Y	0.841	0.28
35_S	259_A	0.837	0.27
199_A	228_T	0.833	0.27
36_Q	39_K	0.832	0.27
189_I	207_I	0.831	0.27
48_A	79_T	0.831	0.27
142_D	215_E	0.828	0.27
127_A	231_A	0.823	0.27
214_A	243_Q	0.821	0.27
56_N	127_A	0.806	0.26
89_Y	169_R	0.802	0.26
76_A	99_A	0.796	0.26
27_H	249_A	0.790	0.25
18_D	89_Y	0.787	0.25
72_G	76_A	0.787	0.25
137_A	159_K	0.787	0.25
120_R	130_Q	0.787	0.25
214_A	224_P	0.785	0.25
51_A	58_L	0.785	0.25
43_I	120_R	0.782	0.25
161_A	187_V	0.779	0.25
171_G	242_Q	0.777	0.25
67_A	248_T	0.775	0.25
35_S	114_L	0.773	0.25
29_A	235_V	0.771	0.25
131_W	225_D	0.768	0.24
60_E	63_L	0.767	0.24
154_G	158_L	0.764	0.24
100_F	186_W	0.761	0.24
35_S	51_A	0.760	0.24
115_L	251_F	0.758	0.24
99_A	103_L	0.755	0.24
37_G	251_F	0.752	0.24
120_R	210_I	0.749	0.24
55_M	81_Y	0.748	0.24
23_S	42_G	0.747	0.24
33_S	75_G	0.745	0.23
163_T	183_K	0.743	0.23
55_M	66_R	0.740	0.23
128_R	166_S	0.737	0.23
128_R	163_T	0.735	0.23
76_A	259_A	0.733	0.23
192_D	248_T	0.733	0.23
24_L	50_D	0.731	0.23
36_Q	139_D	0.728	0.23
96_Q	186_W	0.728	0.23
43_I	212_R	0.726	0.23
62_I	162_I	0.725	0.23
146_H	260_T	0.725	0.23
55_M	79_T	0.724	0.23
41_A	113_S	0.723	0.23
75_G	130_Q	0.723	0.23
151_L	203_L	0.719	0.22
20_R	90_D	0.712	0.22
37_G	49_W	0.711	0.22
29_A	191_Q	0.710	0.22
239_T	258_I	0.702	0.22
109_L	158_L	0.700	0.22
91_L	176_K	0.698	0.22
39_K	257_I	0.696	0.21
156_T	253_A	0.694	0.21
77_V	139_D	0.690	0.21
111_L	170_L	0.689	0.21
24_L	56_N	0.689	0.21
28_I	59_S	0.687	0.21
188_G	199_A	0.687	0.21
91_L	97_Q	0.686	0.21
28_I	90_D	0.685	0.21
71_K	127_A	0.684	0.21
52_I	125_T	0.683	0.21
189_I	231_A	0.680	0.21
241_L	250_Y	0.679	0.21
97_Q	101_D	0.678	0.21
55_M	121_F	0.676	0.21
32_G	70_G	0.675	0.21
122_S	135_I	0.668	0.20
41_A	123_L	0.667	0.20
103_L	259_A	0.664	0.20
53_N	168_A	0.664	0.20
42_G	226_G	0.662	0.20
136_T	245_Q	0.657	0.20
62_I	221_M	0.654	0.20
41_A	96_Q	0.653	0.20
33_S	45_Y	0.652	0.20
228_T	238_A	0.651	0.20
135_I	229_L	0.651	0.20
19_P	169_R	0.648	0.20
89_Y	96_Q	0.648	0.20
141_D	144_Q	0.647	0.20
61_H	231_A	0.644	0.20
83_Q	242_Q	0.644	0.20
50_D	166_S	0.643	0.19
59_S	149_V	0.641	0.19
17_A	76_A	0.640	0.19
163_T	166_S	0.639	0.19
123_L	252_N	0.638	0.19
171_G	192_D	0.637	0.19
63_L	147_V	0.637	0.19
224_P	246_N	0.635	0.19
161_A	185_P	0.631	0.19
76_A	125_T	0.627	0.19
17_A	96_Q	0.623	0.19
143_V	146_H	0.623	0.19
198_N	233_V	0.620	0.19
158_L	260_T	0.617	0.19
139_D	168_A	0.616	0.19
28_I	82_G	0.616	0.19
153_D	189_I	0.612	0.18
29_A	158_L	0.611	0.18
202_Q	225_D	0.611	0.18
143_V	253_A	0.611	0.18
96_Q	185_P	0.608	0.18
44_S	122_S	0.608	0.18
207_I	221_M	0.607	0.18
232_T	244_G	0.606	0.18
64_V	213_G	0.606	0.18
147_V	256_V	0.605	0.18
224_P	258_I	0.605	0.18
127_A	133_G	0.604	0.18
245_Q	248_T	0.603	0.18
76_A	81_Y	0.603	0.18
171_G	244_G	0.601	0.18
135_I	192_D	0.600	0.18
28_I	134_T	0.600	0.18
205_G	256_V	0.599	0.18
68_T	118_I	0.599	0.18
158_L	210_I	0.598	0.18
103_L	152_A	0.598	0.18
52_I	228_T	0.597	0.18
168_A	193_E	0.597	0.18
148_D	198_N	0.597	0.18
141_D	198_N	0.596	0.18
150_L	171_G	0.593	0.18
72_G	125_T	0.590	0.18
205_G	233_V	0.588	0.18
190_T	250_Y	0.588	0.18
93_A	233_V	0.587	0.18
68_T	213_G	0.585	0.17
199_A	234_P	0.583	0.17
19_P	232_T	0.583	0.17
137_A	202_Q	0.583	0.17
169_R	230_C	0.583	0.17
164_A	254_D	0.582	0.17
147_V	228_T	0.578	0.17
93_A	212_R	0.578	0.17
188_G	197_Q	0.577	0.17
215_E	250_Y	0.576	0.17
17_A	152_A	0.575	0.17
120_R	259_A	0.575	0.17
77_V	168_A	0.573	0.17
53_N	57_Q	0.572	0.17
199_A	244_G	0.572	0.17
18_D	149_V	0.570	0.17
138_R	147_V	0.570	0.17
124_Q	169_R	0.566	0.17
131_W	245_Q	0.566	0.17
69_G	128_R	0.564	0.17
59_S	130_Q	0.563	0.17
85_L	247_V	0.561	0.17
41_A	230_C	0.561	0.17
159_K	194_A	0.559	0.17
60_E	150_L	0.559	0.17
116_A	170_L	0.557	0.17
182_L	251_F	0.557	0.17
212_R	235_V	0.556	0.16
78_L	216_Q	0.556	0.16
206_I	214_A	0.555	0.16
160_V	181_L	0.555	0.16
71_K	105_D	0.555	0.16
42_G	259_A	0.553	0.16
127_A	185_P	0.550	0.16
66_R	104_S	0.548	0.16
27_H	217_C	0.547	0.16
87_Q	196_A	0.547	0.16
187_V	257_I	0.546	0.16
17_A	41_A	0.543	0.16
217_C	235_V	0.542	0.16
200_D	215_E	0.541	0.16
99_A	259_A	0.539	0.16
120_R	151_L	0.539	0.16
37_G	118_I	0.537	0.16
96_Q	100_F	0.537	0.16
31_S	82_G	0.536	0.16
63_L	133_G	0.535	0.16
121_F	179_L	0.535	0.16
126_S	172_L	0.529	0.16
90_D	95_I	0.523	0.15
142_D	187_V	0.520	0.15
92_L	160_V	0.519	0.15
35_S	82_G	0.518	0.15
60_E	85_L	0.517	0.15
80_R	250_Y	0.514	0.15
135_I	138_R	0.511	0.15
253_A	257_I	0.510	0.15
35_S	91_L	0.509	0.15
78_L	201_N	0.508	0.15
104_S	205_G	0.507	0.15
174_E	224_P	0.505	0.15
234_P	252_N	0.504	0.15
145_Q	164_A	0.503	0.15
83_Q	158_L	0.501	0.15
97_Q	112_N	0.501	0.15
147_V	189_I	0.500	0.15

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
1b9mA	2	0.9771	100	0.619	Contact Map
2ijlA	2	0.4198	99.6	0.823	Contact Map
1fr3A	5	0.2557	99.6	0.823	Contact Map
1gutA	5	0.2557	99.6	0.827	Contact Map
1h9mA	3	0.5267	99.3	0.858	Contact Map
4x6gA	4	0.9084	98.7	0.886	Contact Map
1uthA	2	0.6298	98.6	0.89	Contact Map
3szpA	3	0.874	98.6	0.89	Contact Map
2h98A	2	0.5534	98.6	0.891	Contact Map
3fzvA	4	0.8626	98.5	0.892	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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