CODY - BACSU - GREMLIN Contacts

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CODY - GTP-sensing transcriptional pleiotropic repressor CodY

UniProt:	P39779	Sequences: MALLQKTRIINSMLQAAAGKPVNFKEMAETLRDVIDSNIFVVSRRGKLLGYSINQQIENDRMKKMLEDRQFPEEYTKNLFNVPETSSNLDINSEYTAFPVENRDLFQAGLTTIVPIIGGGERLGTLILSRLQDQFNDDDLILAEYGATVVGMEILREKAEEIEEEARSKAVVQMAISSLSYSELEAIEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNNKFLIELENLKSH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	259 (254)
Sequences:	421 (197)
Seq/√Len:	12.4

BACSU - CODY

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
96_T	104_D	4.691	1.00
76_T	80_F	4.640	1.00
59_N	96_T	3.854	0.99
59_N	104_D	3.520	0.99
10_I	149_V	3.224	0.97
32_R	52_S	2.936	0.95
193_E	209_R	2.850	0.95
23_N	27_M	2.342	0.86
35_I	146_G	2.286	0.85
43_S	47_K	2.229	0.83
189_H	210_V	2.210	0.83
215_S	237_M	2.182	0.82
13_M	27_M	2.160	0.81
178_S	224_L	2.108	0.80
251_I	254_E	2.092	0.79
59_N	131_L	2.076	0.79
120_G	149_V	2.062	0.78
168_S	178_S	2.038	0.77
148_T	155_L	2.030	0.77
252_E	255_N	1.995	0.76
190_I	203_A	1.986	0.75
75_Y	111_T	1.968	0.75
10_I	244_V	1.957	0.74
28_A	154_I	1.942	0.74
57_I	96_T	1.938	0.73
171_V	233_R	1.937	0.73
168_S	247_N	1.934	0.73
114_V	143_A	1.908	0.72
96_T	109_G	1.898	0.72
151_G	243_K	1.884	0.71
13_M	174_M	1.881	0.71
67_E	108_A	1.879	0.71
190_I	222_R	1.856	0.70
130_R	233_R	1.826	0.69
24_F	191_F	1.822	0.69
40_F	109_G	1.790	0.67
146_G	241_Y	1.787	0.67
38_N	150_V	1.782	0.67
166_A	170_A	1.771	0.66
22_V	126_L	1.766	0.66
119_G	150_V	1.734	0.65
98_F	150_V	1.718	0.64
189_H	209_R	1.710	0.63
48_L	79_L	1.710	0.63
6_K	31_L	1.691	0.63
185_E	193_E	1.681	0.62
185_E	205_K	1.663	0.61
201_L	208_D	1.642	0.60
125_T	199_G	1.640	0.60
48_L	103_R	1.584	0.57
72_P	98_F	1.583	0.57
37_S	135_F	1.525	0.54
216_V	222_R	1.519	0.54
208_D	211_G	1.517	0.54
181_Y	232_S	1.513	0.54
185_E	189_H	1.501	0.53
244_V	249_F	1.487	0.52
57_I	104_D	1.483	0.52
43_S	161_E	1.446	0.50
59_N	109_G	1.417	0.49
41_V	72_P	1.399	0.48
43_S	243_K	1.386	0.47
17_A	32_R	1.382	0.47
42_V	48_L	1.369	0.46
109_G	131_L	1.366	0.46
122_R	125_T	1.349	0.45
33_D	128_L	1.343	0.45
59_N	129_S	1.331	0.44
23_N	26_E	1.327	0.44
61_R	109_G	1.318	0.44
73_E	256_L	1.306	0.43
24_F	153_E	1.298	0.43
109_G	129_S	1.296	0.43
177_S	187_I	1.295	0.43
119_G	154_I	1.295	0.43
175_A	226_S	1.290	0.42
24_F	157_E	1.285	0.42
91_I	97_A	1.283	0.42
143_A	154_I	1.275	0.42
119_G	160_E	1.270	0.41
76_T	157_E	1.262	0.41
106_F	209_R	1.256	0.41
22_V	247_N	1.250	0.40
106_F	111_T	1.249	0.40
186_A	212_I	1.246	0.40
189_H	229_V	1.216	0.39
182_S	203_A	1.197	0.38
119_G	158_K	1.190	0.38
61_R	96_T	1.185	0.37
231_E	243_K	1.181	0.37
221_L	242_I	1.177	0.37
201_L	212_I	1.173	0.37
130_R	243_K	1.170	0.37
20_K	32_R	1.165	0.36
27_M	174_M	1.159	0.36
188_E	244_V	1.158	0.36
12_S	224_L	1.156	0.36
181_Y	190_I	1.141	0.35
190_I	232_S	1.141	0.35
202_V	229_V	1.138	0.35
19_G	209_R	1.134	0.35
210_V	224_L	1.130	0.35
165_E	246_N	1.126	0.35
169_K	229_V	1.117	0.34
149_V	244_V	1.108	0.34
24_F	170_A	1.104	0.34
197_N	254_E	1.103	0.33
6_K	33_D	1.103	0.33
48_L	174_M	1.100	0.33
15_Q	135_F	1.098	0.33
21_P	44_R	1.090	0.33
201_L	224_L	1.070	0.32
186_A	201_L	1.065	0.32
5_Q	87_S	1.064	0.32
157_E	178_S	1.058	0.31
168_S	224_L	1.057	0.31
64_K	106_F	1.053	0.31
26_E	156_R	1.047	0.31
107_Q	130_R	1.043	0.31
96_T	131_L	1.032	0.30
5_Q	127_I	1.030	0.30
61_R	99_P	1.030	0.30
154_I	250_L	1.027	0.30
121_E	158_K	1.027	0.30
122_R	230_I	1.025	0.30
53_I	178_S	1.024	0.30
204_S	237_M	1.023	0.30
181_Y	224_L	1.022	0.30
57_I	111_T	1.016	0.30
59_N	65_M	1.014	0.30
196_G	209_R	1.013	0.30
32_R	35_I	1.010	0.29
91_I	96_T	0.999	0.29
61_R	65_M	0.986	0.28
42_V	121_E	0.983	0.28
28_A	32_R	0.978	0.28
19_G	28_A	0.978	0.28
73_E	77_K	0.973	0.28
30_T	78_N	0.970	0.28
28_A	174_M	0.966	0.28
76_T	79_L	0.960	0.27
181_Y	253_L	0.956	0.27
116_I	151_G	0.950	0.27
6_K	128_L	0.942	0.27
81_N	256_L	0.940	0.27
47_K	161_E	0.940	0.27
169_K	205_K	0.938	0.26
45_R	161_E	0.936	0.26
207_A	216_V	0.935	0.26
204_S	215_S	0.932	0.26
58_E	243_K	0.931	0.26
24_F	56_Q	0.929	0.26
185_E	210_V	0.926	0.26
37_S	40_F	0.923	0.26
130_R	133_D	0.922	0.26
185_E	200_L	0.919	0.26
65_M	104_D	0.919	0.26
52_S	62_M	0.918	0.26
40_F	129_S	0.917	0.26
9_I	41_V	0.916	0.26
77_K	116_I	0.914	0.25
123_L	253_L	0.909	0.25
75_Y	140_L	0.904	0.25
139_D	148_T	0.903	0.25
12_S	177_S	0.897	0.25
37_S	60_D	0.888	0.24
232_S	253_L	0.885	0.24
140_L	250_L	0.883	0.24
28_A	152_M	0.880	0.24
230_I	252_E	0.879	0.24
128_L	173_Q	0.879	0.24
42_V	151_G	0.875	0.24
73_E	197_N	0.870	0.24
24_F	47_K	0.869	0.24
224_L	249_F	0.864	0.24
56_Q	90_D	0.863	0.24
11_N	15_Q	0.861	0.23
6_K	48_L	0.858	0.23
65_M	96_T	0.856	0.23
38_N	98_F	0.851	0.23
27_M	32_R	0.841	0.23
225_E	230_I	0.841	0.23
157_E	224_L	0.837	0.23
28_A	35_I	0.836	0.23
162_I	166_A	0.832	0.22
91_I	94_E	0.832	0.22
98_F	159_A	0.828	0.22
190_I	220_A	0.827	0.22
27_M	119_G	0.827	0.22
130_R	248_K	0.821	0.22
192_E	197_N	0.820	0.22
186_A	206_I	0.814	0.22
91_I	141_I	0.814	0.22
47_K	160_E	0.814	0.22
126_L	149_V	0.812	0.22
77_K	82_V	0.809	0.22
222_R	232_S	0.805	0.21
173_Q	177_S	0.794	0.21
58_E	141_I	0.793	0.21
138_D	141_I	0.793	0.21
50_G	124_G	0.788	0.21
165_E	170_A	0.787	0.21
24_F	76_T	0.786	0.21
161_E	243_K	0.780	0.21
229_V	256_L	0.779	0.21
32_R	101_E	0.779	0.21
75_Y	96_T	0.774	0.20
146_G	246_N	0.774	0.20
108_A	132_Q	0.770	0.20
15_Q	200_L	0.765	0.20
121_E	256_L	0.764	0.20
168_S	246_N	0.761	0.20
61_R	89_L	0.759	0.20
172_V	196_G	0.756	0.20
20_K	149_V	0.751	0.20
37_S	55_Q	0.749	0.20
42_V	250_L	0.745	0.20
10_I	19_G	0.745	0.20
48_L	61_R	0.743	0.19
100_V	103_R	0.740	0.19
8_R	221_L	0.738	0.19
15_Q	118_G	0.735	0.19
166_A	210_V	0.734	0.19
191_F	253_L	0.733	0.19
11_N	113_I	0.733	0.19
78_N	95_Y	0.731	0.19
18_A	146_G	0.730	0.19
189_H	245_L	0.729	0.19
13_M	149_V	0.729	0.19
130_R	174_M	0.728	0.19
30_T	146_G	0.725	0.19
49_L	123_L	0.722	0.19
2_A	108_A	0.718	0.19
71_F	77_K	0.718	0.19
193_E	225_E	0.715	0.19
85_T	212_I	0.714	0.19
141_I	165_E	0.713	0.19
153_E	242_I	0.712	0.18
198_E	243_K	0.710	0.18
210_V	230_I	0.710	0.18
153_E	205_K	0.707	0.18
56_Q	128_L	0.706	0.18
168_S	206_I	0.705	0.18
9_I	152_M	0.704	0.18
9_I	94_E	0.697	0.18
51_Y	111_T	0.695	0.18
48_L	105_L	0.693	0.18
87_S	110_L	0.693	0.18
89_L	93_S	0.693	0.18
38_N	130_R	0.690	0.18
12_S	48_L	0.688	0.18
209_R	222_R	0.686	0.18
13_M	145_Y	0.685	0.18
30_T	165_E	0.685	0.18
39_I	48_L	0.681	0.18
59_N	111_T	0.679	0.17
24_F	45_R	0.679	0.17
35_I	56_Q	0.678	0.17
170_A	210_V	0.677	0.17
175_A	213_T	0.677	0.17
10_I	16_A	0.676	0.17
48_L	177_S	0.676	0.17
50_G	123_L	0.675	0.17
37_S	120_G	0.673	0.17
33_D	185_E	0.670	0.17
216_V	226_S	0.666	0.17
179_L	226_S	0.666	0.17
35_I	87_S	0.663	0.17
10_I	91_I	0.663	0.17
247_N	255_N	0.660	0.17
24_F	161_E	0.660	0.17
130_R	224_L	0.656	0.17
7_T	10_I	0.655	0.17
72_P	129_S	0.655	0.17
172_V	201_L	0.653	0.17
149_V	160_E	0.651	0.17
222_R	233_R	0.644	0.16
138_D	161_E	0.643	0.16
116_I	177_S	0.643	0.16
153_E	156_R	0.642	0.16
163_E	235_L	0.637	0.16
76_T	97_A	0.637	0.16
48_L	106_F	0.635	0.16
10_I	21_P	0.635	0.16
172_V	190_I	0.634	0.16
42_V	125_T	0.631	0.16
184_L	252_E	0.630	0.16
5_Q	244_V	0.627	0.16
172_V	182_S	0.623	0.16
181_Y	203_A	0.622	0.16
27_M	59_N	0.620	0.16
86_S	251_I	0.619	0.16
105_L	152_M	0.616	0.16
82_V	168_S	0.615	0.16
37_S	152_M	0.614	0.16
87_S	158_K	0.611	0.16
89_L	127_I	0.606	0.15
56_Q	168_S	0.604	0.15
114_V	250_L	0.603	0.15
113_I	157_E	0.601	0.15
41_V	80_F	0.601	0.15
174_M	233_R	0.599	0.15
2_A	137_D	0.598	0.15
146_G	174_M	0.597	0.15
176_I	191_F	0.596	0.15
97_A	132_Q	0.592	0.15
86_S	89_L	0.590	0.15
55_Q	80_F	0.589	0.15
41_V	47_K	0.589	0.15
123_L	182_S	0.587	0.15
200_L	229_V	0.586	0.15
51_Y	98_F	0.585	0.15
37_S	108_A	0.583	0.15
156_R	160_E	0.583	0.15
113_I	132_Q	0.579	0.15
174_M	209_R	0.578	0.15
38_N	193_E	0.576	0.15
19_G	95_Y	0.575	0.15
204_S	207_A	0.574	0.15
204_S	213_T	0.571	0.15
176_I	210_V	0.570	0.15
4_L	8_R	0.569	0.14
17_A	26_E	0.568	0.14
19_G	106_F	0.567	0.14
107_Q	134_Q	0.567	0.14
120_G	241_Y	0.565	0.14
64_K	188_E	0.564	0.14
203_A	233_R	0.562	0.14
61_R	100_V	0.561	0.14
113_I	133_D	0.558	0.14
63_K	70_Q	0.557	0.14
36_D	116_I	0.556	0.14
63_K	131_L	0.554	0.14
42_V	142_L	0.549	0.14
53_I	185_E	0.548	0.14
82_V	195_D	0.548	0.14
116_I	198_E	0.548	0.14
61_R	69_R	0.547	0.14
9_I	27_M	0.545	0.14
40_F	59_N	0.545	0.14
38_N	55_Q	0.543	0.14
26_E	76_T	0.542	0.14
59_N	101_E	0.540	0.14
194_L	215_S	0.539	0.14
158_K	249_F	0.538	0.14
179_L	213_T	0.538	0.14
52_S	134_Q	0.537	0.14
41_V	176_I	0.535	0.14
59_N	174_M	0.534	0.14
14_L	137_D	0.534	0.14
44_R	47_K	0.533	0.14
171_V	206_I	0.531	0.14
146_G	244_V	0.530	0.14
91_I	174_M	0.529	0.13
59_N	94_E	0.527	0.13
82_V	247_N	0.527	0.13
84_E	137_D	0.526	0.13
167_R	181_Y	0.526	0.13
30_T	158_K	0.526	0.13
29_E	74_E	0.524	0.13
210_V	245_L	0.524	0.13
179_L	216_V	0.523	0.13
128_L	154_I	0.521	0.13
6_K	28_A	0.521	0.13
174_M	243_K	0.520	0.13
36_D	133_D	0.519	0.13
207_A	226_S	0.518	0.13
13_M	192_E	0.517	0.13
83_P	157_E	0.517	0.13
62_M	65_M	0.516	0.13
54_N	59_N	0.515	0.13
87_S	112_T	0.513	0.13
116_I	256_L	0.511	0.13
174_M	248_K	0.510	0.13
29_E	149_V	0.510	0.13
152_M	241_Y	0.507	0.13
110_L	138_D	0.507	0.13
64_K	247_N	0.505	0.13
130_R	188_E	0.504	0.13
113_I	254_E	0.501	0.13
18_A	152_M	0.500	0.13

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
2gx5A	2	0.6178	100	0.485	Contact Map
2w1rA	2	0.444	99	0.895	Contact Map
2b0lA	4	0.3784	98.2	0.919	Contact Map
3vv4A	2	0.5714	97.4	0.931	Contact Map
3e0yA	2	0.5676	97.4	0.932	Contact Map
2vxzA	1	0.3012	97.4	0.932	Contact Map
3trcA	2	0.6139	97.2	0.934	Contact Map
4g3vA	2	0.5598	97.1	0.935	Contact Map
2zmfA	2	0.6293	97.1	0.935	Contact Map
3k2nA	2	0.6293	96.8	0.938	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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