YBGA - BACSU - GREMLIN Contacts

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YBGA - Uncharacterized HTH-type transcriptional regulator YbgA

UniProt:	O31459	Sequences: MTALYSVIKFKIIELIKSGKYQANDQLPTESEFCEQYDVSRTTVRLALQQLELEGYIKRIQGKGTFVSAAKIQTPIPHKITSFAEQMRGLRSESKVLELVVIPADHSIAELLKMKENEPVNKLVRVRYAEGEPLQYHTSYIPWKAAPGLAQEECTGSLFELLRTKYNIEISRGTESIEPILTDETISGHLLTNVGAPAFLSESLTYDKNEEVVEYAQIITRGDRTKFTVEQSYHS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	235 (193)
Sequences:	22233 (16949)
Seq/√Len:	1220.0

ECOLI - MNGR YIHL YIDP PHNF FRLR YEGW
BACSU - YBGA YYDK GMUR TRER YURK YVOA YMFC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_Q	25_D	3.890	1.00
15_L	20_K	3.759	1.00
13_I	54_E	3.298	1.00
118_E	175_E	3.185	1.00
15_L	36_Q	3.109	1.00
9_K	50_Q	2.970	1.00
58_K	68_S	2.741	1.00
103_P	183_D	2.624	1.00
8_I	39_V	2.477	1.00
30_E	41_R	2.464	1.00
178_E	181_L	2.440	1.00
60_I	63_K	2.426	1.00
125_R	168_I	2.367	1.00
11_K	15_L	2.350	1.00
59_R	65_T	2.334	1.00
26_Q	66_F	2.186	1.00
14_E	18_S	2.096	1.00
8_I	37_Y	2.092	1.00
9_K	54_E	2.059	1.00
63_K	66_F	1.922	1.00
11_K	37_Y	1.874	1.00
89_G	152_E	1.816	1.00
52_E	59_R	1.785	1.00
9_K	13_I	1.741	1.00
113_K	150_A	1.715	1.00
46_L	49_Q	1.703	1.00
96_V	100_V	1.696	1.00
13_I	17_K	1.668	1.00
107_S	179_P	1.649	1.00
183_D	186_I	1.627	1.00
48_L	57_I	1.600	1.00
32_E	36_Q	1.557	1.00
57_I	65_T	1.554	1.00
13_I	56_Y	1.549	1.00
11_K	14_E	1.525	1.00
183_D	187_S	1.516	1.00
95_K	191_L	1.492	1.00
33_F	44_V	1.481	1.00
52_E	57_I	1.477	1.00
109_A	114_M	1.462	1.00
7_V	11_K	1.455	1.00
130_E	133_P	1.455	1.00
124_V	138_T	1.452	1.00
31_S	35_E	1.434	1.00
15_L	21_Y	1.423	1.00
29_T	32_E	1.415	1.00
49_Q	59_R	1.409	1.00
16_I	67_V	1.385	1.00
114_M	175_E	1.379	1.00
110_E	113_K	1.362	1.00
30_E	45_R	1.350	1.00
166_Y	192_T	1.340	1.00
122_K	138_T	1.338	1.00
108_I	140_Y	1.336	1.00
4_L	7_V	1.333	1.00
39_V	44_V	1.320	1.00
181_L	185_T	1.315	1.00
147_P	155_T	1.312	1.00
93_E	128_Y	1.312	1.00
15_L	19_G	1.311	1.00
181_L	197_P	1.310	1.00
23_A	69_A	1.298	1.00
105_D	108_I	1.285	1.00
95_K	99_L	1.280	1.00
21_Y	67_V	1.279	1.00
184_E	188_G	1.256	1.00
116_E	144_K	1.253	1.00
32_E	35_E	1.248	1.00
144_K	147_P	1.241	1.00
60_I	66_F	1.240	1.00
115_K	118_E	1.235	1.00
58_K	66_F	1.222	1.00
120_V	137_H	1.195	1.00
109_A	177_I	1.188	1.00
49_Q	53_L	1.183	1.00
103_P	179_P	1.180	1.00
49_Q	52_E	1.176	1.00
121_N	171_S	1.173	1.00
136_Y	186_I	1.158	1.00
17_K	56_Y	1.149	1.00
173_G	181_L	1.145	1.00
50_Q	53_L	1.131	1.00
118_E	171_S	1.106	1.00
92_S	108_I	1.091	1.00
123_L	140_Y	1.084	1.00
168_I	172_R	1.084	1.00
160_E	164_T	1.080	1.00
26_Q	64_G	1.071	1.00
5_Y	50_Q	1.065	1.00
171_S	175_E	1.061	1.00
143_W	147_P	1.047	1.00
15_L	37_Y	1.044	1.00
48_L	65_T	1.040	1.00
104_A	108_I	1.016	1.00
149_L	155_T	1.009	1.00
120_V	140_Y	1.003	1.00
101_V	119_P	0.999	1.00
95_K	187_S	0.997	1.00
60_I	64_G	0.995	1.00
50_Q	54_E	0.995	1.00
102_I	122_K	0.989	1.00
99_L	183_D	0.989	1.00
46_L	50_Q	0.989	1.00
103_P	180_I	0.974	1.00
95_K	128_Y	0.972	1.00
21_Y	25_D	0.968	1.00
118_E	122_K	0.960	1.00
138_T	142_P	0.957	1.00
121_N	168_I	0.955	1.00
24_N	58_K	0.949	1.00
193_N	196_A	0.932	1.00
10_F	13_I	0.931	1.00
101_V	143_W	0.928	1.00
114_M	171_S	0.925	1.00
92_S	104_A	0.924	1.00
117_N	144_K	0.919	1.00
122_K	125_R	0.905	1.00
182_T	192_T	0.898	1.00
140_Y	144_K	0.895	1.00
114_M	118_E	0.892	1.00
99_L	187_S	0.888	1.00
90_L	130_E	0.888	1.00
100_V	103_P	0.887	1.00
114_M	177_I	0.884	1.00
187_S	191_L	0.884	1.00
133_P	136_Y	0.882	1.00
109_A	148_G	0.882	1.00
179_P	183_D	0.881	1.00
172_R	176_S	0.878	1.00
127_R	137_H	0.875	1.00
124_V	185_T	0.873	1.00
6_S	10_F	0.872	1.00
109_A	113_K	0.870	1.00
180_I	186_I	0.853	1.00
118_E	168_I	0.849	1.00
102_I	186_I	0.848	1.00
98_E	124_V	0.846	1.00
120_V	144_K	0.841	1.00
119_P	123_L	0.841	1.00
6_S	50_Q	0.839	1.00
83_F	87_M	0.836	1.00
62_G	65_T	0.827	1.00
123_L	137_H	0.818	1.00
4_L	43_T	0.816	1.00
98_E	122_K	0.815	1.00
123_L	126_V	0.813	1.00
84_A	87_M	0.812	1.00
48_L	52_E	0.811	1.00
116_E	119_P	0.805	1.00
123_L	127_R	0.804	1.00
142_P	145_A	0.793	1.00
116_E	147_P	0.790	1.00
40_S	43_T	0.790	1.00
12_I	33_F	0.787	1.00
144_K	148_G	0.784	1.00
161_L	166_Y	0.778	1.00
30_E	59_R	0.777	1.00
8_I	44_V	0.772	1.00
136_Y	140_Y	0.771	1.00
145_A	174_T	0.765	1.00
8_I	11_K	0.763	1.00
169_E	185_T	0.760	1.00
109_A	174_T	0.759	1.00
102_I	106_H	0.758	1.00
80_I	83_F	0.752	1.00
142_P	167_N	0.750	1.00
33_F	48_L	0.750	1.00
181_L	184_E	0.742	1.00
23_A	68_S	0.737	1.00
116_E	120_V	0.735	1.00
12_I	21_Y	0.735	1.00
99_L	103_P	0.735	1.00
102_I	108_I	0.732	1.00
96_V	154_C	0.732	1.00
48_L	59_R	0.729	1.00
26_Q	29_T	0.727	1.00
172_R	175_E	0.722	1.00
161_L	165_K	0.709	1.00
192_T	196_A	0.708	1.00
109_A	117_N	0.706	1.00
141_I	171_S	0.706	1.00
122_K	140_Y	0.700	1.00
34_C	44_V	0.698	1.00
121_N	125_R	0.697	1.00
118_E	144_K	0.694	1.00
10_F	14_E	0.691	1.00
100_V	183_D	0.690	1.00
111_L	177_I	0.690	1.00
21_Y	27_L	0.686	1.00
100_V	104_A	0.682	1.00
170_I	186_I	0.676	1.00
24_N	69_A	0.674	1.00
143_W	156_G	0.673	1.00
176_S	181_L	0.666	1.00
27_L	57_I	0.666	1.00
89_G	92_S	0.666	1.00
73_Q	77_P	0.665	1.00
93_E	153_E	0.664	1.00
94_S	127_R	0.661	1.00
35_E	38_D	0.661	1.00
166_Y	189_H	0.657	1.00
5_Y	9_K	0.657	1.00
95_K	194_V	0.655	1.00
180_I	183_D	0.654	1.00
184_E	187_S	0.652	1.00
185_T	188_G	0.649	1.00
186_I	189_H	0.647	1.00
104_A	109_A	0.644	1.00
137_H	140_Y	0.642	1.00
122_K	126_V	0.640	1.00
11_K	36_Q	0.638	1.00
131_G	134_L	0.633	1.00
37_Y	44_V	0.633	1.00
104_A	120_V	0.632	1.00
120_V	123_L	0.629	1.00
126_V	133_P	0.626	1.00
93_E	131_G	0.625	1.00
28_P	36_Q	0.623	1.00
102_I	105_D	0.623	1.00
103_P	106_H	0.620	1.00
20_K	36_Q	0.617	1.00
170_I	185_T	0.614	1.00
180_I	184_E	0.606	1.00
26_Q	63_K	0.602	1.00
113_K	148_G	0.598	1.00
87_M	129_A	0.595	1.00
113_K	116_E	0.595	1.00
182_T	196_A	0.587	1.00
96_V	99_L	0.585	1.00
101_V	146_A	0.583	1.00
150_A	153_E	0.583	1.00
99_L	150_A	0.581	1.00
31_S	34_C	0.579	1.00
15_L	18_S	0.579	1.00
125_R	129_A	0.576	1.00
115_K	119_P	0.571	1.00
103_P	119_P	0.571	1.00
93_E	97_L	0.565	1.00
182_T	195_G	0.565	1.00
168_I	171_S	0.564	1.00
44_V	47_A	0.563	1.00
106_H	179_P	0.562	1.00
117_N	120_V	0.561	1.00
182_T	187_S	0.560	1.00
181_L	196_A	0.560	1.00
105_D	148_G	0.560	1.00
97_L	126_V	0.559	1.00
21_Y	28_P	0.557	1.00
42_T	46_L	0.557	1.00
82_S	86_Q	0.556	1.00
123_L	133_P	0.556	1.00
9_K	47_A	0.553	1.00
185_T	189_H	0.552	1.00
138_T	186_I	0.550	1.00
5_Y	46_L	0.550	1.00
33_F	37_Y	0.546	1.00
44_V	57_I	0.545	1.00
14_E	17_K	0.545	1.00
117_N	148_G	0.545	1.00
159_F	163_R	0.544	1.00
43_T	47_A	0.544	1.00
34_C	37_Y	0.542	1.00
71_K	75_P	0.542	1.00
136_Y	189_H	0.535	1.00
105_D	109_A	0.533	1.00
34_C	42_T	0.532	1.00
61_Q	64_G	0.532	1.00
29_T	44_V	0.531	1.00
111_L	115_K	0.531	1.00
102_I	140_Y	0.530	1.00
79_K	82_S	0.530	1.00
81_T	85_E	0.526	1.00
186_I	190_L	0.525	1.00
124_V	136_Y	0.522	1.00
95_K	190_L	0.521	1.00
81_T	84_A	0.519	1.00
108_I	112_L	0.516	1.00
52_E	65_T	0.515	1.00
187_S	195_G	0.512	1.00
103_P	107_S	0.511	1.00
106_H	116_E	0.506	1.00
188_G	192_T	0.506	1.00
105_D	140_Y	0.505	1.00
140_Y	143_W	0.503	1.00
173_G	178_E	0.502	1.00
169_E	181_L	0.501	1.00
119_P	143_W	0.500	1.00
99_L	102_I	0.500	1.00
101_V	121_N	0.500	1.00
146_A	149_L	0.500	1.00

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
4u0wA	2	0.9915	100	0.124	Contact Map
3bwgA	2	0.9745	100	0.142	Contact Map
3edpA	2	0.9362	100	0.145	Contact Map
3f8mA	2	0.966	100	0.151	Contact Map
2ra5A	2	0.6298	100	0.161	Contact Map
3eetA	2	0.9745	100	0.181	Contact Map
3f8lA	2	0.6809	100	0.437	Contact Map
2di3A	2	0.8468	99.9	0.504	Contact Map
1hw1A	2	0.8298	99.9	0.506	Contact Map
4p96A	2	0.9021	99.9	0.518	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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