YBFP - BACSU - GREMLIN Contacts

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YBFP - Uncharacterized HTH-type transcriptional regulator YbfP

UniProt:	O31456	Sequences: MYYEKAVQKTINWIESHLHEQISNEDIVNVSSFSKFHFHRIFQKEVGMSVASYIRLRRLANAAAALLYTDHRIIDIALYYQFESQEAFTRTFKKMYHMPPGAYRTFMKRFTSKKEESYMEKKMKGWVLSGSHPFQFEMGIDRENVHQGKASGYLKSTMVQDIGEFATMMQQFKADRYLGKRLRLSSFIKTKGVQHFASLWMRVDSAADDVLQFDNMSNRPITGTTNWNHYAIVLDVPENSAVISFGVQLSGPGQVWMDHVVFEEVDESVPSTNLEMPGELLDEPVNLSFEEELQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	295 (242)
Sequences:	1034 (809)
Seq/√Len:	52.0

BACSU - YBFP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_H	20_E	5.277	1.00
14_I	54_I	3.898	1.00
155_K	158_M	3.509	1.00
199_L	202_R	3.426	1.00
10_T	38_F	3.190	1.00
154_L	158_M	2.942	1.00
126_W	231_A	2.841	1.00
59_L	95_M	2.756	1.00
65_A	80_Y	2.734	1.00
182_L	185_S	2.686	1.00
65_A	79_Y	2.621	1.00
162_I	166_A	2.491	1.00
26_D	29_N	2.411	1.00
103_Y	110_F	2.406	1.00
154_L	157_T	2.385	1.00
71_H	76_I	2.351	1.00
65_A	71_H	2.287	1.00
242_V	246_G	2.266	1.00
89_T	99_P	2.218	1.00
136_F	220_P	2.211	1.00
182_L	186_S	2.206	1.00
78_L	85_Q	2.188	1.00
199_L	203_V	2.090	1.00
237_P	241_A	2.061	1.00
182_L	187_F	1.999	1.00
185_S	189_K	1.990	1.00
183_R	187_F	1.985	1.00
5_K	9_K	1.922	0.99
72_R	75_D	1.915	0.99
121_K	125_G	1.855	0.99
62_A	88_F	1.842	0.99
69_T	104_R	1.747	0.99
183_R	186_S	1.744	0.99
166_A	171_Q	1.717	0.99
141_D	198_S	1.715	0.99
23_S	26_D	1.707	0.99
73_I	76_I	1.683	0.99
71_H	79_Y	1.670	0.98
151_S	155_K	1.644	0.98
25_E	35_K	1.626	0.98
235_D	239_N	1.624	0.98
45_E	117_S	1.616	0.98
202_R	207_A	1.613	0.98
70_D	76_I	1.612	0.98
197_A	202_R	1.606	0.98
197_A	203_V	1.606	0.98
116_E	120_E	1.601	0.98
202_R	206_A	1.600	0.98
244_S	248_Q	1.581	0.98
202_R	205_S	1.579	0.98
13_W	17_H	1.537	0.97
185_S	188_I	1.513	0.97
201_M	204_D	1.511	0.97
153_Y	157_T	1.501	0.97
12_N	115_E	1.495	0.97
149_K	154_L	1.484	0.97
72_R	85_Q	1.472	0.97
73_I	104_R	1.460	0.96
136_F	218_N	1.456	0.96
197_A	201_M	1.450	0.96
162_I	167_T	1.439	0.96
203_V	207_A	1.439	0.96
74_I	85_Q	1.427	0.96
181_R	185_S	1.427	0.96
162_I	165_F	1.422	0.96
161_D	165_F	1.404	0.96
167_T	170_Q	1.359	0.95
76_I	104_R	1.346	0.94
195_H	199_L	1.346	0.94
178_L	185_S	1.342	0.94
200_W	205_S	1.341	0.94
199_L	207_A	1.336	0.94
166_A	169_M	1.332	0.94
213_F	216_M	1.327	0.94
112_S	115_E	1.284	0.93
131_S	224_T	1.282	0.93
6_A	9_K	1.256	0.92
184_L	187_F	1.250	0.92
200_W	203_V	1.246	0.92
131_S	226_N	1.234	0.91
203_V	206_A	1.231	0.91
197_A	200_W	1.210	0.90
238_E	242_V	1.206	0.90
201_M	207_A	1.204	0.90
201_M	205_S	1.194	0.90
15_E	57_R	1.189	0.90
244_S	247_V	1.189	0.90
198_S	202_R	1.183	0.89
185_S	190_T	1.177	0.89
98_M	103_Y	1.172	0.89
22_I	27_I	1.136	0.87
186_S	189_K	1.127	0.87
84_S	90_R	1.124	0.87
186_S	191_K	1.122	0.87
22_I	54_I	1.120	0.87
135_Q	221_I	1.120	0.87
175_D	178_L	1.114	0.86
90_R	94_K	1.114	0.86
180_K	183_R	1.109	0.86
242_V	245_F	1.109	0.86
14_I	27_I	1.093	0.85
215_N	222_T	1.093	0.85
195_H	204_D	1.092	0.85
56_L	95_M	1.091	0.85
216_M	222_T	1.090	0.85
199_L	206_A	1.090	0.85
70_D	73_I	1.087	0.85
177_Y	182_L	1.086	0.85
175_D	180_K	1.086	0.85
237_P	240_S	1.060	0.84
181_R	184_L	1.058	0.83
199_L	204_D	1.042	0.82
132_H	135_Q	1.036	0.82
2_Y	5_K	1.034	0.82
43_Q	50_V	1.029	0.82
26_D	30_V	1.024	0.81
47_G	245_F	1.020	0.81
243_I	246_G	1.018	0.81
56_L	113_K	1.017	0.81
182_L	188_I	1.013	0.81
199_L	205_S	1.011	0.80
60_A	115_E	1.008	0.80
161_D	164_E	1.004	0.80
237_P	247_V	1.000	0.80
236_V	239_N	0.997	0.80
166_A	170_Q	0.996	0.79
5_K	65_A	0.991	0.79
34_S	87_A	0.981	0.78
134_F	220_P	0.977	0.78
137_E	228_N	0.964	0.77
188_I	191_K	0.956	0.77
138_M	205_S	0.955	0.77
160_Q	169_M	0.953	0.76
177_Y	181_R	0.952	0.76
138_M	216_M	0.951	0.76
161_D	166_A	0.950	0.76
59_L	94_K	0.949	0.76
9_K	16_S	0.934	0.75
177_Y	185_S	0.927	0.74
228_N	247_V	0.914	0.73
163_G	168_M	0.909	0.73
178_L	187_F	0.908	0.73
82_F	103_Y	0.904	0.72
153_Y	156_S	0.898	0.72
187_F	190_T	0.898	0.72
121_K	129_S	0.897	0.72
176_R	180_K	0.894	0.72
14_I	17_H	0.892	0.71
232_I	236_V	0.889	0.71
27_I	118_Y	0.889	0.71
177_Y	180_K	0.882	0.71
181_R	187_F	0.879	0.70
169_M	172_F	0.873	0.70
232_I	243_I	0.869	0.69
59_L	89_T	0.868	0.69
200_W	204_D	0.868	0.69
243_I	247_V	0.862	0.69
75_D	129_S	0.857	0.68
19_H	76_I	0.853	0.68
184_L	193_V	0.848	0.68
178_L	182_L	0.846	0.67
82_F	96_Y	0.844	0.67
150_A	241_A	0.838	0.67
66_L	73_I	0.837	0.67
165_F	169_M	0.836	0.66
234_L	237_P	0.832	0.66
112_S	127_V	0.827	0.66
40_R	63_A	0.827	0.66
243_I	248_Q	0.826	0.66
161_D	169_M	0.807	0.64
24_N	27_I	0.800	0.63
38_F	91_T	0.798	0.63
160_Q	165_F	0.796	0.63
49_S	67_L	0.796	0.63
152_G	155_K	0.792	0.62
18_L	61_N	0.791	0.62
141_D	200_W	0.790	0.62
12_N	16_S	0.788	0.62
149_K	158_M	0.784	0.61
144_N	153_Y	0.783	0.61
70_D	78_L	0.780	0.61
166_A	172_F	0.780	0.61
14_I	73_I	0.778	0.61
138_M	207_A	0.774	0.60
151_S	154_L	0.773	0.60
44_K	50_V	0.772	0.60
200_W	207_A	0.771	0.60
189_K	192_G	0.762	0.59
130_G	229_H	0.761	0.59
168_M	172_F	0.760	0.59
164_E	167_T	0.760	0.59
66_L	76_I	0.759	0.59
38_F	75_D	0.759	0.59
90_R	95_M	0.754	0.58
138_M	141_D	0.753	0.58
14_I	21_Q	0.753	0.58
7_V	27_I	0.748	0.58
149_K	156_S	0.742	0.57
11_I	192_G	0.737	0.57
235_D	238_E	0.736	0.57
87_A	96_Y	0.734	0.56
3_Y	41_I	0.734	0.56
50_V	114_K	0.728	0.56
84_S	114_K	0.726	0.56
219_R	244_S	0.725	0.55
61_N	97_H	0.723	0.55
34_S	135_Q	0.723	0.55
48_M	113_K	0.721	0.55
236_V	240_S	0.721	0.55
188_I	194_Q	0.717	0.55
76_I	136_F	0.715	0.54
179_G	214_D	0.715	0.54
111_T	126_W	0.711	0.54
58_R	63_A	0.704	0.53
195_H	200_W	0.704	0.53
197_A	204_D	0.701	0.53
234_L	240_S	0.697	0.53
168_M	225_T	0.697	0.53
85_Q	96_Y	0.695	0.52
217_S	222_T	0.694	0.52
49_S	106_F	0.694	0.52
245_F	248_Q	0.692	0.52
54_I	79_Y	0.691	0.52
160_Q	164_E	0.691	0.52
39_H	46_V	0.690	0.52
111_T	124_K	0.681	0.51
236_V	241_A	0.680	0.51
196_F	206_A	0.680	0.51
137_E	145_V	0.680	0.51
184_L	188_I	0.679	0.51
41_I	248_Q	0.678	0.51
9_K	27_I	0.677	0.50
23_S	105_T	0.676	0.50
167_T	171_Q	0.674	0.50
178_L	186_S	0.672	0.50
60_A	231_A	0.671	0.50
160_Q	168_M	0.668	0.50
7_V	70_D	0.668	0.50
212_Q	215_N	0.666	0.49
178_L	181_R	0.664	0.49
145_V	152_G	0.663	0.49
165_F	171_Q	0.662	0.49
105_T	134_F	0.662	0.49
48_M	56_L	0.659	0.49
27_I	31_S	0.658	0.48
239_N	245_F	0.657	0.48
234_L	239_N	0.654	0.48
41_I	44_K	0.654	0.48
66_L	103_Y	0.653	0.48
2_Y	59_L	0.652	0.48
162_I	171_Q	0.651	0.48
164_E	168_M	0.649	0.48
46_V	50_V	0.647	0.47
176_R	182_L	0.646	0.47
241_A	244_S	0.644	0.47
47_G	83_E	0.641	0.47
180_K	185_S	0.639	0.47
234_L	241_A	0.633	0.46
241_A	246_G	0.632	0.46
175_D	185_S	0.630	0.46
50_V	54_I	0.624	0.45
67_L	106_F	0.624	0.45
168_M	171_Q	0.623	0.45
178_L	184_L	0.621	0.45
185_S	193_V	0.621	0.45
122_K	125_G	0.619	0.44
13_W	30_V	0.615	0.44
241_A	247_V	0.614	0.44
66_L	228_N	0.612	0.44
163_G	166_A	0.610	0.44
26_D	94_K	0.609	0.43
142_R	161_D	0.609	0.43
164_E	170_Q	0.609	0.43
5_K	75_D	0.608	0.43
176_R	185_S	0.608	0.43
35_K	122_K	0.607	0.43
176_R	186_S	0.607	0.43
58_R	86_E	0.598	0.42
241_A	245_F	0.598	0.42
37_H	228_N	0.596	0.42
22_I	26_D	0.594	0.42
67_L	107_M	0.593	0.42
9_K	12_N	0.591	0.42
27_I	38_F	0.589	0.41
201_M	206_A	0.588	0.41
182_L	189_K	0.588	0.41
195_H	206_A	0.587	0.41
66_L	69_T	0.586	0.41
6_A	32_S	0.584	0.41
45_E	132_H	0.584	0.41
19_H	80_Y	0.583	0.41
22_I	64_A	0.581	0.41
15_E	82_F	0.580	0.40
134_F	224_T	0.579	0.40
153_Y	158_M	0.577	0.40
175_D	182_L	0.575	0.40
151_S	156_S	0.573	0.40
142_R	157_T	0.571	0.40
24_N	90_R	0.571	0.40
240_S	244_S	0.569	0.39
178_L	189_K	0.568	0.39
35_K	39_H	0.567	0.39
37_H	86_E	0.566	0.39
96_Y	103_Y	0.566	0.39
232_I	244_S	0.559	0.38
110_F	227_W	0.559	0.38
13_W	207_A	0.558	0.38
33_F	86_E	0.558	0.38
163_G	170_Q	0.557	0.38
50_V	117_S	0.557	0.38
37_H	90_R	0.556	0.38
152_G	156_S	0.555	0.38
198_S	205_S	0.555	0.38
86_E	89_T	0.551	0.38
37_H	40_R	0.551	0.38
74_I	78_L	0.546	0.37
49_S	110_F	0.546	0.37
239_N	243_I	0.546	0.37
69_T	130_G	0.546	0.37
200_W	206_A	0.544	0.37
233_V	247_V	0.541	0.37
133_P	224_T	0.540	0.36
168_M	202_R	0.539	0.36
179_G	186_S	0.539	0.36
180_K	190_T	0.537	0.36
219_R	222_T	0.537	0.36
49_S	233_V	0.536	0.36
11_I	231_A	0.535	0.36
190_T	193_V	0.535	0.36
180_K	186_S	0.534	0.36
161_D	170_Q	0.532	0.36
196_F	207_A	0.532	0.36
76_I	164_E	0.531	0.36
80_Y	222_T	0.528	0.35
9_K	22_I	0.527	0.35
150_A	153_Y	0.526	0.35
185_S	192_G	0.526	0.35
17_H	30_V	0.526	0.35
33_F	103_Y	0.525	0.35
121_K	127_V	0.525	0.35
73_I	79_Y	0.524	0.35
49_S	65_A	0.524	0.35
32_S	133_P	0.522	0.35
64_A	67_L	0.520	0.35
103_Y	108_K	0.519	0.34
30_V	50_V	0.519	0.34
197_A	205_S	0.518	0.34
63_A	96_Y	0.518	0.34
77_A	121_K	0.517	0.34
119_M	126_W	0.515	0.34
117_S	121_K	0.511	0.34
13_W	26_D	0.511	0.34
186_S	190_T	0.511	0.34
31_S	180_K	0.510	0.34
38_F	242_V	0.509	0.34
55_R	96_Y	0.509	0.34
4_E	8_Q	0.508	0.33
14_I	61_N	0.507	0.33
178_L	183_R	0.507	0.33
61_N	96_Y	0.504	0.33
157_T	201_M	0.502	0.33
71_H	75_D	0.500	0.33
46_V	87_A	0.500	0.33

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
1d5yA	1	0.9254	100	0.606	Contact Map
3gbgA	1	0.3695	99.9	0.755	Contact Map
4fe7A	2	0.3695	99.9	0.761	Contact Map
3oioA	1	0.3763	99.9	0.764	Contact Map
2k9sA	1	0.3593	99.9	0.765	Contact Map
3mn2A	1	0.3593	99.9	0.765	Contact Map
3w6vA	1	0.3763	99.9	0.765	Contact Map
1bl0A	1	0.3932	99.9	0.768	Contact Map
3lsgA	2	0.3458	99.9	0.768	Contact Map
3oouA	1	0.3559	99.9	0.768	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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