TRMBR - HALSA - GREMLIN Contacts

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TRMBR - HTH-type sugar sensing transcriptional regulator TrmB

UniProt:	Q9HPW0	Sequences: MSDEDLRGTVEQVGRGFNLGEYEVEAYLTVLRHGELTASDIADRTDIPQPRVYDTVRSLGDRGLVELRESRPMKIVALSPEDAFAGLQEDFQEMVGALEAEYTQPARNTEAVSLVKSRSTIVRYFGDVIAEADFELVCSLTPSLLERFADDLAAAVDRGVSVDVVVSPARNAPNPDAFDYAAATTAARGRRGITTPVIAVADGRYSVYATQDAVRDDSDRYGVIFDQSALGFLVSGFFDTVLWSTATESLYDPATELSLPRTYAAIRRCVRDLQSVDESVYATVTGRDVLTGADRRIQGRIVETRFEESGEVATIIVYTENGDRVEVGGRVAALEDVEAHEIAVARDAPPAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	352 (286)
Sequences:	1023 (801)
Seq/√Len:	47.4

HALSA - TRMBR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
91_F	95_V	5.488	1.00
139_S	242_L	3.716	1.00
161_S	186_A	3.685	1.00
23_E	58_S	3.679	1.00
137_V	203_G	3.370	1.00
91_F	94_M	3.365	1.00
30_V	65_V	3.270	1.00
132_A	201_A	3.101	1.00
92_Q	98_L	3.012	1.00
20_G	58_S	3.010	1.00
98_L	102_Y	2.967	1.00
165_V	242_L	2.946	1.00
20_G	23_E	2.618	1.00
135_E	203_G	2.577	1.00
92_Q	96_G	2.553	1.00
163_D	239_D	2.471	1.00
99_E	102_Y	2.449	1.00
95_V	99_E	2.404	1.00
267_R	301_I	2.396	1.00
92_Q	99_E	2.372	1.00
91_F	98_L	2.340	1.00
139_S	193_I	2.280	1.00
95_V	98_L	2.277	1.00
132_A	136_L	2.259	1.00
98_L	101_E	2.237	1.00
270_V	281_Y	2.212	1.00
128_V	205_Y	2.166	1.00
22_Y	51_R	2.131	1.00
127_D	131_E	2.127	1.00
140_L	144_L	2.125	1.00
155_A	158_R	2.070	1.00
56_V	65_V	2.070	1.00
48_P	51_R	2.055	1.00
94_M	98_L	2.053	1.00
152_L	176_D	2.044	1.00
171_N	189_G	2.007	0.99
91_F	99_E	1.970	0.99
130_A	154_A	1.968	0.99
279_S	293_A	1.966	0.99
115_V	224_I	1.940	0.99
277_D	283_T	1.852	0.99
117_S	120_T	1.799	0.99
14_G	18_N	1.793	0.99
228_S	231_G	1.771	0.99
137_V	200_V	1.732	0.98
153_A	183_A	1.726	0.98
153_A	157_D	1.724	0.98
195_T	237_F	1.717	0.98
33_H	44_R	1.717	0.98
139_S	165_V	1.687	0.98
289_V	293_A	1.687	0.98
129_I	162_V	1.682	0.98
279_S	289_V	1.678	0.98
168_P	189_G	1.646	0.98
166_V	187_A	1.631	0.98
36_L	44_R	1.629	0.98
190_R	246_A	1.626	0.98
142_P	197_V	1.608	0.97
203_G	235_S	1.603	0.97
193_I	242_L	1.577	0.97
101_E	104_Q	1.574	0.97
94_M	97_A	1.569	0.97
22_Y	47_I	1.558	0.97
52_V	65_V	1.553	0.97
37_T	40_D	1.547	0.97
148_F	152_L	1.523	0.96
149_A	179_D	1.483	0.96
23_E	62_R	1.472	0.95
200_V	235_S	1.451	0.95
137_V	235_S	1.444	0.95
266_I	295_R	1.418	0.94
94_M	99_E	1.381	0.94
139_S	198_I	1.380	0.94
42_A	52_V	1.368	0.93
149_A	152_L	1.329	0.92
200_V	231_G	1.326	0.92
29_T	41_I	1.321	0.92
289_V	292_G	1.309	0.92
163_D	243_W	1.303	0.92
24_V	28_L	1.284	0.91
97_A	100_A	1.278	0.91
97_A	101_E	1.273	0.91
91_F	102_Y	1.255	0.90
39_S	43_D	1.252	0.90
134_F	203_G	1.246	0.90
223_V	230_L	1.239	0.89
267_R	295_R	1.235	0.89
56_V	75_I	1.234	0.89
91_F	100_A	1.234	0.89
201_A	270_V	1.230	0.89
99_E	103_T	1.224	0.89
143_S	197_V	1.223	0.89
292_G	296_R	1.204	0.88
94_M	102_Y	1.199	0.88
165_V	227_Q	1.195	0.88
225_F	230_L	1.192	0.87
152_L	156_V	1.191	0.87
38_A	52_V	1.184	0.87
26_A	47_I	1.180	0.87
64_L	83_A	1.179	0.87
228_S	232_F	1.176	0.87
111_A	226_D	1.170	0.86
30_V	36_L	1.169	0.86
95_V	102_Y	1.148	0.85
124_Y	226_D	1.138	0.85
277_D	293_A	1.137	0.85
88_Q	293_A	1.129	0.84
149_A	153_A	1.120	0.84
33_H	36_L	1.115	0.84
227_Q	232_F	1.109	0.83
138_C	162_V	1.108	0.83
67_L	280_V	1.101	0.83
27_Y	31_L	1.101	0.83
166_V	281_Y	1.095	0.82
29_T	44_R	1.092	0.82
26_A	52_V	1.088	0.82
136_L	201_A	1.086	0.82
299_G	304_T	1.073	0.81
121_I	222_G	1.072	0.81
140_L	197_V	1.060	0.80
125_F	201_A	1.056	0.80
129_I	149_A	1.052	0.80
31_L	76_V	1.045	0.79
41_I	52_V	1.037	0.79
303_E	306_F	1.035	0.79
96_G	134_F	1.029	0.78
238_F	243_W	1.028	0.78
278_E	294_D	1.020	0.78
273_L	281_Y	1.018	0.78
125_F	197_V	1.004	0.77
160_V	202_D	1.003	0.77
129_I	201_A	0.998	0.76
18_N	84_F	0.997	0.76
26_A	232_F	0.993	0.76
201_A	295_R	0.990	0.76
137_V	227_Q	0.988	0.75
37_T	75_I	0.979	0.75
25_E	102_Y	0.978	0.75
144_L	197_V	0.959	0.73
190_R	242_L	0.956	0.73
40_D	43_D	0.952	0.73
92_Q	95_V	0.946	0.72
65_V	75_I	0.943	0.72
278_E	290_L	0.943	0.72
62_R	90_D	0.943	0.72
26_A	41_I	0.938	0.72
136_L	182_A	0.935	0.71
113_S	224_I	0.932	0.71
271_R	276_V	0.928	0.71
109_T	199_A	0.926	0.71
205_Y	226_D	0.924	0.70
125_F	129_I	0.917	0.70
263_Y	267_R	0.916	0.70
48_P	52_V	0.915	0.70
156_V	185_T	0.914	0.70
36_L	65_V	0.914	0.70
39_S	175_P	0.914	0.70
174_N	208_Y	0.911	0.69
14_G	24_V	0.909	0.69
181_A	187_A	0.902	0.69
76_V	299_G	0.894	0.68
267_R	287_R	0.888	0.67
47_I	52_V	0.888	0.67
96_G	99_E	0.887	0.67
137_V	156_V	0.887	0.67
136_L	162_V	0.887	0.67
168_P	171_N	0.885	0.67
64_L	290_L	0.883	0.67
280_V	292_G	0.879	0.67
293_A	306_F	0.878	0.66
136_L	173_P	0.875	0.66
191_R	265_A	0.874	0.66
34_G	196_P	0.873	0.66
95_V	208_Y	0.870	0.66
140_L	187_A	0.869	0.66
270_V	295_R	0.868	0.66
142_P	167_S	0.867	0.65
113_S	124_Y	0.863	0.65
196_P	233_L	0.862	0.65
269_C	272_D	0.860	0.65
167_S	197_V	0.853	0.64
107_R	208_Y	0.851	0.64
96_G	131_E	0.848	0.64
283_T	302_V	0.847	0.64
30_V	83_A	0.847	0.64
39_S	50_P	0.845	0.63
48_P	55_T	0.837	0.63
138_C	199_A	0.834	0.62
141_T	171_N	0.829	0.62
139_S	227_Q	0.829	0.62
291_T	294_D	0.829	0.62
39_S	49_Q	0.827	0.62
198_I	234_V	0.823	0.61
167_S	295_R	0.820	0.61
277_D	292_G	0.820	0.61
97_A	186_A	0.819	0.61
230_L	268_R	0.818	0.61
17_F	217_D	0.815	0.61
150_D	179_D	0.814	0.61
126_G	130_A	0.812	0.60
300_R	303_E	0.811	0.60
132_A	155_A	0.806	0.60
302_V	306_F	0.804	0.60
162_V	187_A	0.795	0.59
112_V	230_L	0.793	0.59
139_S	195_T	0.793	0.59
80_P	282_A	0.791	0.58
35_E	130_A	0.789	0.58
127_D	269_C	0.786	0.58
31_L	174_N	0.782	0.57
41_I	68_R	0.772	0.56
23_E	55_T	0.767	0.56
18_N	24_V	0.767	0.56
195_T	233_L	0.765	0.56
165_V	254_A	0.764	0.56
26_A	55_T	0.758	0.55
26_A	65_V	0.752	0.55
49_Q	53_Y	0.751	0.54
165_V	241_V	0.750	0.54
166_V	184_T	0.750	0.54
270_V	292_G	0.745	0.54
14_G	75_I	0.744	0.54
231_G	235_S	0.743	0.54
185_T	197_V	0.739	0.53
148_F	169_A	0.739	0.53
21_E	25_E	0.737	0.53
17_F	21_E	0.736	0.53
190_R	284_V	0.735	0.53
133_D	260_P	0.729	0.52
280_V	283_T	0.727	0.52
81_E	166_V	0.727	0.52
126_G	191_R	0.727	0.52
274_Q	296_R	0.726	0.52
92_Q	102_Y	0.720	0.51
162_V	185_T	0.715	0.51
200_V	206_S	0.714	0.51
14_G	85_A	0.710	0.50
129_I	152_L	0.708	0.50
36_L	121_I	0.707	0.50
176_D	180_Y	0.707	0.50
144_L	187_A	0.703	0.50
177_A	187_A	0.702	0.50
163_D	278_E	0.702	0.50
67_L	227_Q	0.700	0.49
123_R	127_D	0.698	0.49
188_R	243_W	0.692	0.49
99_E	104_Q	0.691	0.48
155_A	164_V	0.690	0.48
104_Q	121_I	0.690	0.48
187_A	286_G	0.686	0.48
124_Y	127_D	0.685	0.48
129_I	155_A	0.682	0.48
94_M	203_G	0.682	0.48
43_D	101_E	0.680	0.47
26_A	115_V	0.679	0.47
31_L	293_A	0.678	0.47
136_L	281_Y	0.678	0.47
266_I	292_G	0.677	0.47
199_A	209_A	0.677	0.47
19_L	238_F	0.676	0.47
19_L	283_T	0.675	0.47
42_A	82_D	0.675	0.47
246_A	282_A	0.674	0.47
183_A	279_S	0.673	0.47
208_Y	223_V	0.671	0.46
89_E	292_G	0.671	0.46
122_V	125_F	0.671	0.46
51_R	55_T	0.670	0.46
141_T	306_F	0.669	0.46
164_V	242_L	0.668	0.46
131_E	207_V	0.668	0.46
93_E	97_A	0.667	0.46
84_F	170_R	0.666	0.46
19_L	273_L	0.663	0.46
166_V	185_T	0.662	0.46
115_V	296_R	0.661	0.45
121_I	174_N	0.659	0.45
281_Y	292_G	0.655	0.45
124_Y	209_A	0.654	0.45
196_P	209_A	0.654	0.45
134_F	204_R	0.653	0.45
83_A	282_A	0.653	0.45
126_G	175_P	0.651	0.44
167_S	293_A	0.648	0.44
50_P	205_Y	0.648	0.44
134_F	161_S	0.646	0.44
113_S	226_D	0.646	0.44
39_S	134_F	0.645	0.44
187_A	270_V	0.644	0.44
53_Y	57_R	0.644	0.44
209_A	221_Y	0.643	0.44
88_Q	95_V	0.642	0.44
27_Y	80_P	0.642	0.44
302_V	305_R	0.640	0.43
76_V	155_A	0.640	0.43
94_M	101_E	0.634	0.43
163_D	188_R	0.634	0.43
152_L	162_V	0.633	0.43
130_A	136_L	0.633	0.43
152_L	185_T	0.631	0.43
50_P	71_R	0.630	0.42
277_D	280_V	0.628	0.42
126_G	154_A	0.627	0.42
23_E	235_S	0.627	0.42
56_V	118_R	0.627	0.42
43_D	49_Q	0.625	0.42
31_L	135_E	0.624	0.42
151_D	173_P	0.623	0.42
139_S	277_D	0.623	0.42
146_E	149_A	0.623	0.42
129_I	185_T	0.622	0.42
277_D	284_V	0.622	0.42
35_E	74_K	0.621	0.42
157_D	183_A	0.621	0.42
138_C	200_V	0.620	0.41
93_E	109_T	0.619	0.41
70_S	73_M	0.616	0.41
285_T	290_L	0.616	0.41
77_A	198_I	0.614	0.41
139_S	234_V	0.613	0.41
23_E	64_L	0.613	0.41
93_E	112_V	0.610	0.40
152_L	187_A	0.610	0.40
267_R	298_Q	0.608	0.40
231_G	290_L	0.606	0.40
78_L	171_N	0.606	0.40
225_F	305_R	0.602	0.40
68_R	76_V	0.601	0.40
206_S	231_G	0.599	0.39
154_A	157_D	0.599	0.39
156_V	184_T	0.598	0.39
121_I	232_F	0.598	0.39
226_D	229_A	0.595	0.39
72_P	218_S	0.591	0.39
64_L	206_S	0.591	0.39
242_L	245_T	0.590	0.39
128_V	134_F	0.590	0.39
155_A	201_A	0.589	0.38
90_D	249_S	0.586	0.38
47_I	51_R	0.585	0.38
129_I	164_V	0.584	0.38
225_F	259_L	0.584	0.38
28_L	101_E	0.583	0.38
96_G	199_A	0.582	0.38
32_R	92_Q	0.582	0.38
42_A	65_V	0.582	0.38
197_V	207_V	0.581	0.38
161_S	200_V	0.580	0.38
41_I	296_R	0.580	0.38
132_A	266_I	0.579	0.38
183_A	199_A	0.579	0.38
100_A	301_I	0.578	0.37
66_E	119_S	0.577	0.37
278_E	285_T	0.577	0.37
168_P	190_R	0.576	0.37
58_S	61_D	0.576	0.37
126_G	286_G	0.574	0.37
187_A	227_Q	0.574	0.37
188_R	291_T	0.574	0.37
33_H	40_D	0.573	0.37
91_F	97_A	0.573	0.37
181_A	185_T	0.571	0.37
139_S	237_F	0.571	0.37
288_D	297_I	0.571	0.37
79_S	293_A	0.570	0.37
52_V	109_T	0.569	0.37
184_T	288_D	0.569	0.37
40_D	61_D	0.568	0.37
290_L	294_D	0.568	0.37
108_N	127_D	0.567	0.36
231_G	293_A	0.567	0.36
206_S	234_V	0.566	0.36
50_P	54_D	0.564	0.36
68_R	262_T	0.563	0.36
270_V	283_T	0.563	0.36
110_E	114_L	0.562	0.36
17_F	275_S	0.560	0.36
125_F	207_V	0.559	0.36
82_D	111_A	0.557	0.35
56_V	238_F	0.557	0.35
66_E	76_V	0.557	0.35
167_S	171_N	0.557	0.35
261_R	264_A	0.556	0.35
48_P	250_L	0.555	0.35
14_G	46_D	0.555	0.35
38_A	53_Y	0.554	0.35
78_L	83_A	0.554	0.35
145_L	176_D	0.550	0.35
131_E	223_V	0.550	0.35
22_Y	48_P	0.549	0.35
98_L	103_T	0.548	0.35
78_L	245_T	0.547	0.35
25_E	97_A	0.545	0.34
165_V	263_Y	0.544	0.34
16_G	153_A	0.541	0.34
227_Q	231_G	0.540	0.34
23_E	135_E	0.539	0.34
132_A	140_L	0.535	0.34
172_A	189_G	0.535	0.34
278_E	281_Y	0.534	0.33
47_I	127_D	0.534	0.33
269_C	273_L	0.532	0.33
60_G	121_I	0.532	0.33
138_C	164_V	0.530	0.33
208_Y	233_L	0.529	0.33
122_V	148_F	0.526	0.33
189_G	197_V	0.523	0.32
280_V	296_R	0.522	0.32
93_E	102_Y	0.522	0.32
225_F	234_V	0.521	0.32
284_V	299_G	0.518	0.32
207_V	227_Q	0.516	0.32
60_G	88_Q	0.516	0.32
135_E	156_V	0.516	0.32
162_V	197_V	0.515	0.32
19_L	105_P	0.512	0.31
69_E	182_A	0.511	0.31
41_I	187_A	0.511	0.31
104_Q	264_A	0.510	0.31
122_V	279_S	0.509	0.31
173_P	292_G	0.508	0.31
190_R	245_T	0.508	0.31
271_R	274_Q	0.507	0.31
121_I	127_D	0.506	0.31
78_L	155_A	0.505	0.31
79_S	127_D	0.503	0.31
263_Y	271_R	0.502	0.31
122_V	158_R	0.502	0.31
271_R	278_E	0.500	0.30

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
3qphA	2	0.9233	100	0.404	Contact Map
2f5tX	2	0.6222	100	0.674	Contact Map
1byrA	2	0.4006	99.2	0.841	Contact Map
4ggjA	2	0.4489	99.2	0.844	Contact Map
4urjA	1	0.429	98.5	0.878	Contact Map
4gelA	2	0.4602	98.2	0.888	Contact Map
1qgpA	1	0.2045	98	0.895	Contact Map
1q1hA	1	0.2301	97.9	0.898	Contact Map
1sfxA	3	0.2955	97.8	0.899	Contact Map
4nb5A	4	0.3778	97.7	0.902	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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