MLRA - ECOLI - GREMLIN Contacts

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MLRA - HTH-type transcriptional regulator MlrA

UniProt:	P33358	Sequences: MALYTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNENVDVQNGWRDQQETLLTYLQSGNLHSLRTWIKERGQDYPAQTLTTHLFIPLRRRLQCQQPTLQALLAILDGVLINYIAICLASARKKQGKDALVVGWNIQDTTRLWLEGWIASQQGWRIDVLAHSLNQLRPELFEGRTLLVWCGENRTSAQQQQLTSWQEQGHDIFPLGI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12008
Length:	243 (224)
Sequences:	1196 (869)
Seq/√Len:	58.1

ECOLI - MLRA BLUR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
167_V	178_L	4.069	1.00
4_Y	44_D	3.834	1.00
9_V	47_I	3.772	1.00
12_L	51_R	3.419	1.00
140_A	174_D	2.912	1.00
129_Q	132_Q	2.869	1.00
9_V	50_I	2.837	1.00
9_V	13_C	2.549	1.00
129_Q	174_D	2.540	1.00
140_A	200_N	2.456	1.00
139_L	174_D	2.448	1.00
129_Q	139_L	2.440	1.00
174_D	177_R	2.229	1.00
84_Q	107_R	2.121	1.00
139_L	143_D	2.105	1.00
48_D	51_R	2.101	1.00
147_I	175_T	2.094	1.00
143_D	174_D	2.045	1.00
165_A	185_A	2.030	1.00
10_A	17_P	2.028	1.00
43_N	46_D	1.993	1.00
22_A	25_R	1.947	1.00
16_N	19_T	1.907	1.00
139_L	196_A	1.906	1.00
53_I	63_V	1.883	1.00
165_A	190_W	1.850	1.00
24_Q	34_R	1.827	0.99
21_R	26_R	1.800	0.99
112_P	116_L	1.792	0.99
129_Q	177_R	1.781	0.99
35_T	38_G	1.733	0.99
6_I	32_P	1.722	0.99
92_L	100_L	1.698	0.99
29_L	53_I	1.669	0.99
132_Q	139_L	1.638	0.99
54_K	58_D	1.597	0.99
9_V	30_L	1.595	0.99
132_Q	140_A	1.592	0.99
53_I	66_V	1.575	0.98
10_A	22_A	1.554	0.98
24_Q	32_P	1.547	0.98
204_P	209_G	1.542	0.98
34_R	38_G	1.523	0.98
132_Q	196_A	1.521	0.98
108_G	149_Y	1.513	0.98
132_Q	177_R	1.505	0.98
13_C	50_I	1.480	0.98
129_Q	140_A	1.476	0.98
76_D	219_N	1.466	0.98
174_D	200_N	1.455	0.97
6_I	24_Q	1.448	0.97
174_D	196_A	1.430	0.97
22_A	41_L	1.417	0.97
105_K	109_Q	1.416	0.97
181_E	184_I	1.416	0.97
129_Q	196_A	1.415	0.97
105_K	149_Y	1.414	0.97
66_V	70_L	1.412	0.97
164_D	191_R	1.409	0.97
165_A	169_G	1.406	0.97
6_I	34_R	1.403	0.97
137_A	140_A	1.383	0.96
112_P	115_T	1.376	0.96
140_A	177_R	1.375	0.96
107_R	120_L	1.357	0.96
62_Q	100_L	1.351	0.96
125_R	132_Q	1.341	0.96
5_T	8_E	1.305	0.95
97_L	209_G	1.291	0.95
111_Y	120_L	1.277	0.94
108_G	116_L	1.267	0.94
22_A	30_L	1.263	0.94
15_I	20_L	1.241	0.94
140_A	143_D	1.216	0.93
53_I	56_W	1.211	0.93
132_Q	174_D	1.211	0.93
105_K	152_I	1.211	0.93
49_R	71_S	1.202	0.92
140_A	172_I	1.200	0.92
139_L	172_I	1.196	0.92
129_Q	143_D	1.189	0.92
26_R	42_F	1.182	0.92
99_S	103_W	1.163	0.91
94_S	99_S	1.161	0.91
52_E	56_W	1.161	0.91
21_R	27_Y	1.136	0.90
101_R	105_K	1.136	0.90
217_G	220_R	1.127	0.90
147_I	179_W	1.115	0.89
125_R	142_L	1.114	0.89
113_A	170_W	1.108	0.89
149_Y	152_I	1.106	0.89
167_V	185_A	1.103	0.89
88_L	100_L	1.094	0.88
158_R	186_S	1.093	0.88
96_N	99_S	1.089	0.88
33_Q	36_D	1.076	0.88
53_I	67_K	1.076	0.88
95_G	141_I	1.073	0.87
103_W	107_R	1.065	0.87
53_I	70_L	1.058	0.87
29_L	67_K	1.057	0.87
18_V	38_G	1.050	0.86
32_P	41_L	1.049	0.86
23_W	26_R	1.044	0.86
44_D	48_D	1.040	0.86
140_A	196_A	1.034	0.85
21_R	42_F	1.033	0.85
97_L	141_I	1.024	0.85
26_R	32_P	1.023	0.85
168_V	196_A	1.022	0.85
165_A	211_T	1.021	0.85
21_R	32_P	1.020	0.85
6_I	18_V	1.011	0.84
17_P	39_H	1.011	0.84
15_I	19_T	1.001	0.83
29_L	57_I	1.001	0.83
53_I	57_I	0.998	0.83
158_R	178_L	0.993	0.83
121_F	146_L	0.984	0.82
102_T	202_L	0.979	0.82
81_W	119_H	0.979	0.82
19_T	39_H	0.978	0.82
154_L	183_W	0.970	0.82
173_Q	198_S	0.955	0.80
6_I	21_R	0.952	0.80
22_A	70_L	0.951	0.80
172_I	178_L	0.946	0.80
129_Q	172_I	0.946	0.80
154_L	182_G	0.942	0.80
13_C	32_P	0.942	0.80
218_E	221_T	0.940	0.79
46_D	67_K	0.939	0.79
179_W	194_V	0.938	0.79
102_T	105_K	0.932	0.79
132_Q	143_D	0.927	0.78
18_V	25_R	0.926	0.78
195_L	199_L	0.924	0.78
50_I	158_R	0.923	0.78
93_Q	131_Q	0.922	0.78
104_I	121_F	0.919	0.78
13_C	66_V	0.915	0.78
80_G	83_D	0.904	0.77
143_D	177_R	0.904	0.77
22_A	32_P	0.900	0.76
11_L	167_V	0.900	0.76
132_Q	200_N	0.899	0.76
18_V	35_T	0.898	0.76
35_T	39_H	0.896	0.76
20_L	213_L	0.888	0.75
76_D	102_T	0.884	0.75
29_L	35_T	0.874	0.74
8_E	11_L	0.871	0.74
142_L	194_V	0.871	0.74
16_N	63_V	0.869	0.74
70_L	74_N	0.861	0.73
93_Q	119_H	0.857	0.73
139_L	177_R	0.852	0.72
125_R	139_L	0.844	0.72
33_Q	109_Q	0.842	0.71
18_V	34_R	0.842	0.71
6_I	42_F	0.840	0.71
9_V	16_N	0.840	0.71
87_T	94_S	0.838	0.71
23_W	42_F	0.836	0.71
168_V	214_V	0.830	0.70
140_A	199_L	0.826	0.70
50_I	80_G	0.824	0.70
52_E	55_R	0.820	0.69
105_K	141_I	0.816	0.69
76_D	210_R	0.812	0.69
29_L	46_D	0.807	0.68
43_N	94_S	0.806	0.68
18_V	56_W	0.798	0.67
83_D	208_E	0.797	0.67
115_T	119_H	0.797	0.67
132_Q	172_I	0.796	0.67
205_E	225_Q	0.796	0.67
20_L	25_R	0.795	0.67
125_R	143_D	0.794	0.67
75_V	79_N	0.777	0.65
113_A	180_L	0.773	0.65
141_I	145_V	0.769	0.64
165_A	171_N	0.767	0.64
100_L	145_V	0.766	0.64
8_E	13_C	0.764	0.64
23_W	40_R	0.760	0.64
24_Q	27_Y	0.755	0.63
86_E	127_R	0.753	0.63
169_G	174_D	0.751	0.63
33_Q	46_D	0.746	0.62
47_I	137_A	0.746	0.62
164_D	210_R	0.745	0.62
177_R	196_A	0.745	0.62
29_L	59_N	0.743	0.62
182_G	192_I	0.738	0.61
37_G	57_I	0.736	0.61
139_L	169_G	0.734	0.61
114_Q	188_Q	0.729	0.60
188_Q	222_S	0.726	0.60
18_V	22_A	0.725	0.60
13_C	22_A	0.724	0.60
162_G	191_R	0.723	0.60
48_D	94_S	0.723	0.60
212_L	223_A	0.722	0.60
158_R	185_A	0.718	0.59
5_T	47_I	0.711	0.58
90_T	176_T	0.711	0.58
22_A	34_R	0.707	0.58
210_R	219_N	0.705	0.58
125_R	174_D	0.701	0.57
88_L	124_L	0.696	0.57
42_F	50_I	0.695	0.57
18_V	39_H	0.694	0.57
143_D	196_A	0.693	0.56
144_G	194_V	0.691	0.56
20_L	92_L	0.690	0.56
140_A	197_H	0.689	0.56
166_L	170_W	0.688	0.56
61_V	66_V	0.687	0.56
7_G	18_V	0.686	0.56
72_N	89_L	0.682	0.55
59_N	66_V	0.682	0.55
43_N	85_Q	0.681	0.55
26_R	60_G	0.681	0.55
32_P	42_F	0.677	0.55
182_G	194_V	0.676	0.55
36_D	120_L	0.675	0.54
109_Q	156_S	0.673	0.54
176_T	197_H	0.673	0.54
54_K	57_I	0.672	0.54
12_L	85_Q	0.671	0.54
52_E	74_N	0.669	0.54
20_L	42_F	0.668	0.54
128_L	186_S	0.666	0.53
172_I	196_A	0.665	0.53
137_A	202_L	0.663	0.53
5_T	41_L	0.659	0.53
216_C	221_T	0.658	0.53
116_L	120_L	0.656	0.52
79_N	103_W	0.653	0.52
37_G	67_K	0.648	0.52
4_Y	12_L	0.646	0.51
37_G	92_L	0.644	0.51
128_L	140_A	0.644	0.51
206_L	228_L	0.642	0.51
148_N	151_A	0.639	0.51
202_L	205_E	0.637	0.50
57_I	69_L	0.635	0.50
105_K	165_A	0.635	0.50
11_L	44_D	0.632	0.50
102_T	156_S	0.632	0.50
95_G	206_L	0.630	0.50
46_D	49_R	0.629	0.49
16_N	34_R	0.628	0.49
137_A	200_N	0.628	0.49
104_I	145_V	0.627	0.49
16_N	47_I	0.627	0.49
104_I	152_I	0.627	0.49
169_G	181_E	0.626	0.49
14_D	26_R	0.624	0.49
39_H	66_V	0.622	0.49
6_I	38_G	0.618	0.48
169_G	172_I	0.618	0.48
13_C	37_G	0.616	0.48
206_L	223_A	0.615	0.48
107_R	197_H	0.615	0.48
180_L	184_I	0.612	0.48
66_V	181_E	0.608	0.47
10_A	39_H	0.604	0.47
21_R	24_Q	0.602	0.46
114_Q	187_Q	0.599	0.46
10_A	193_D	0.598	0.46
51_R	58_D	0.597	0.46
101_R	118_T	0.597	0.46
137_A	174_D	0.597	0.46
160_K	163_K	0.596	0.46
165_A	191_R	0.596	0.46
118_T	184_I	0.592	0.45
5_T	39_H	0.592	0.45
24_Q	132_Q	0.591	0.45
127_R	131_Q	0.589	0.45
168_V	171_N	0.589	0.45
84_Q	87_T	0.588	0.45
157_A	199_L	0.585	0.45
56_W	199_L	0.583	0.44
56_W	61_V	0.580	0.44
76_D	94_S	0.579	0.44
166_L	169_G	0.574	0.43
211_T	215_W	0.574	0.43
26_R	34_R	0.573	0.43
5_T	112_P	0.572	0.43
18_V	70_L	0.570	0.43
97_L	124_L	0.570	0.43
58_D	163_K	0.560	0.42
176_T	183_W	0.555	0.41
156_S	165_A	0.555	0.41
18_V	66_V	0.549	0.41
39_H	53_I	0.548	0.41
21_R	60_G	0.546	0.40
82_R	94_S	0.545	0.40
45_A	205_E	0.541	0.40
110_D	155_A	0.535	0.39
221_T	226_Q	0.535	0.39
26_R	40_R	0.534	0.39
45_A	71_S	0.534	0.39
23_W	27_Y	0.533	0.39
145_V	149_Y	0.533	0.39
8_E	213_L	0.531	0.39
108_G	112_P	0.530	0.39
208_E	228_L	0.527	0.38
19_T	23_W	0.526	0.38
17_P	25_R	0.523	0.38
151_A	182_G	0.522	0.38
201_Q	216_C	0.517	0.37
14_D	21_R	0.515	0.37
71_S	226_Q	0.514	0.37
20_L	117_T	0.514	0.37
48_D	167_V	0.513	0.37
126_R	130_C	0.512	0.37
161_Q	166_L	0.512	0.37
59_N	163_K	0.512	0.37
120_L	178_L	0.512	0.37
52_E	67_K	0.511	0.37
76_D	212_L	0.511	0.37
161_Q	167_V	0.510	0.37
76_D	137_A	0.507	0.36
175_T	194_V	0.505	0.36
50_I	224_Q	0.504	0.36
74_N	121_F	0.504	0.36
27_Y	42_F	0.504	0.36
212_L	215_W	0.503	0.36
57_I	61_V	0.502	0.36
87_T	208_E	0.502	0.36
20_L	26_R	0.501	0.36
15_I	54_K	0.500	0.36

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
3whpA	1	0.6626	100	0.428	Contact Map
3ezxA	2	0.6626	99.7	0.724	Contact Map
1y80A	1	0.3498	99.7	0.726	Contact Map
2i2xB	1	0.8107	99.7	0.727	Contact Map
4hh0A	2	0.9095	99.7	0.737	Contact Map
4jgiA	2	0.6543	99.7	0.738	Contact Map
3hh0A	4	0.535	99.7	0.739	Contact Map
3bulA	1	0.6831	99.7	0.739	Contact Map
2zhgA	2	0.4733	99.7	0.74	Contact Map
2dg6A	2	0.7449	99.7	0.741	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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