YULB - BACSU - GREMLIN Contacts

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YULB - Uncharacterized HTH-type transcriptional regulator YulB

UniProt:	O05261	Sequences: MLVAERQQKIVEIVNMRSSIRVSELSDIFSVTEETIRRDLEKLEKEHKLSRSHGGAVSIQQKESEIHFSEREITNVIEKKAIAHEAAKYVKSGDRIILDASTTAWYMAKILPDIELTVITNSMKAAIELSNKENISVISTGGILLEKSLSFAGPLAERSLETYHVNKTFLSCKGFDVHNGMSDSNEWQALLKKRMIERSDQTILMADSSKWGNREFSHIASLQDVSRLITDSGLDPASVKALEDKKVKVTAVPLSKRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	258 (247)
Sequences:	7694 (5630)
Seq/√Len:	358.3

ECOLI - YGBI AGAR YIHW GLPR SGCR SRLR GATR YDJF ULAR DEOR YCIT FUCR
BACSU - YULB GLCR IOLR FRUR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_D	167_K	3.334	1.00
85_E	88_K	3.042	1.00
107_M	205_M	2.970	1.00
136_S	143_I	2.739	1.00
168_T	199_S	2.610	1.00
99_D	192_K	2.463	1.00
13_I	28_I	2.312	1.00
208_S	231_D	2.246	1.00
109_K	128_E	2.209	1.00
196_I	220_A	2.209	1.00
227_R	250_T	2.154	1.00
203_I	227_R	2.084	1.00
167_K	203_I	2.050	1.00
91_K	94_D	2.050	1.00
161_E	194_R	2.034	1.00
9_K	12_E	2.028	1.00
13_I	17_R	2.004	1.00
97_I	165_V	2.003	1.00
80_K	106_Y	1.965	1.00
84_H	110_I	1.955	1.00
196_I	202_T	1.953	1.00
218_H	221_S	1.950	1.00
234_L	239_V	1.942	1.00
98_L	104_A	1.908	1.00
158_R	161_E	1.903	1.00
167_K	201_Q	1.861	1.00
92_S	114_I	1.840	1.00
97_I	195_M	1.837	1.00
119_I	165_V	1.787	1.00
201_Q	227_R	1.752	1.00
106_Y	109_K	1.751	1.00
239_V	243_E	1.739	1.00
86_A	169_F	1.718	1.00
165_V	195_M	1.707	1.00
85_E	250_T	1.687	1.00
221_S	224_D	1.654	1.00
158_R	162_T	1.641	1.00
86_A	205_M	1.629	1.00
157_E	190_L	1.576	1.00
139_S	151_F	1.576	1.00
166_N	200_D	1.568	1.00
140_T	159_S	1.540	1.00
194_R	197_E	1.540	1.00
75_N	209_S	1.533	1.00
107_M	169_F	1.527	1.00
126_A	139_S	1.523	1.00
181_M	225_V	1.516	1.00
240_K	244_D	1.502	1.00
161_E	197_E	1.500	1.00
87_A	110_I	1.499	1.00
31_V	36_I	1.493	1.00
181_M	204_L	1.482	1.00
25_L	36_I	1.478	1.00
19_S	57_V	1.463	1.00
83_A	110_I	1.450	1.00
156_A	191_L	1.425	1.00
10_I	25_L	1.424	1.00
7_Q	46_E	1.422	1.00
140_T	151_F	1.417	1.00
40_L	56_A	1.416	1.00
235_D	238_S	1.415	1.00
13_I	20_I	1.406	1.00
8_Q	12_E	1.402	1.00
80_K	110_I	1.397	1.00
118_V	129_L	1.391	1.00
17_R	24_E	1.383	1.00
194_R	198_R	1.375	1.00
50_S	59_I	1.373	1.00
75_N	78_E	1.372	1.00
9_K	13_I	1.372	1.00
204_L	225_V	1.361	1.00
89_Y	203_I	1.353	1.00
100_A	150_S	1.347	1.00
52_S	55_G	1.347	1.00
208_S	233_G	1.346	1.00
94_D	166_N	1.344	1.00
144_L	151_F	1.344	1.00
89_Y	229_I	1.326	1.00
15_N	58_S	1.325	1.00
143_I	187_W	1.324	1.00
78_E	231_D	1.323	1.00
23_S	33_E	1.316	1.00
92_S	115_E	1.312	1.00
76_V	106_Y	1.293	1.00
118_V	135_I	1.289	1.00
7_Q	42_K	1.284	1.00
34_E	38_R	1.271	1.00
93_G	115_E	1.268	1.00
79_K	102_T	1.265	1.00
140_T	156_A	1.263	1.00
90_V	111_L	1.260	1.00
11_V	48_K	1.257	1.00
220_A	224_D	1.244	1.00
21_R	24_E	1.242	1.00
236_P	240_K	1.240	1.00
175_F	211_W	1.230	1.00
85_E	89_Y	1.228	1.00
3_V	7_Q	1.226	1.00
9_K	28_I	1.224	1.00
112_P	132_K	1.213	1.00
201_Q	226_S	1.212	1.00
80_K	109_K	1.196	1.00
117_T	138_I	1.195	1.00
197_E	224_D	1.191	1.00
89_Y	250_T	1.182	1.00
240_K	243_E	1.162	1.00
9_K	29_F	1.153	1.00
172_C	206_A	1.152	1.00
108_A	129_L	1.146	1.00
211_W	234_L	1.142	1.00
176_D	179_N	1.135	1.00
14_V	49_L	1.134	1.00
97_I	198_R	1.131	1.00
169_F	203_I	1.130	1.00
12_E	16_M	1.123	1.00
77_I	80_K	1.115	1.00
14_V	58_S	1.111	1.00
41_E	45_K	1.108	1.00
91_K	167_K	1.108	1.00
11_V	14_V	1.106	1.00
78_E	208_S	1.097	1.00
157_E	191_L	1.095	1.00
76_V	80_K	1.092	1.00
17_R	28_I	1.081	1.00
117_T	136_S	1.081	1.00
174_G	182_S	1.077	1.00
155_L	159_S	1.077	1.00
50_S	57_V	1.070	1.00
227_R	248_K	1.069	1.00
203_I	229_I	1.067	1.00
172_C	219_I	1.064	1.00
202_T	225_V	1.061	1.00
90_V	169_F	1.016	1.00
22_V	40_L	1.012	1.00
138_I	143_I	1.011	1.00
49_L	56_A	1.007	1.00
87_A	90_V	1.007	1.00
42_K	46_E	1.004	1.00
87_A	107_M	0.999	1.00
26_S	33_E	0.983	1.00
140_T	160_L	0.983	1.00
119_I	163_Y	0.977	1.00
86_A	107_M	0.976	1.00
238_S	241_A	0.975	1.00
78_E	82_I	0.971	1.00
3_V	42_K	0.970	1.00
98_L	107_M	0.968	1.00
173_K	183_D	0.963	1.00
155_L	163_Y	0.963	1.00
5_E	9_K	0.956	1.00
108_A	128_E	0.954	1.00
68_F	102_T	0.953	1.00
211_W	228_L	0.949	1.00
175_F	206_A	0.949	1.00
101_S	104_A	0.942	1.00
41_E	44_E	0.934	1.00
103_T	207_D	0.934	1.00
80_K	84_H	0.932	1.00
79_K	103_T	0.930	1.00
104_A	125_A	0.929	1.00
168_T	195_M	0.928	1.00
172_C	204_L	0.925	1.00
107_M	110_I	0.922	1.00
190_L	193_K	0.920	1.00
83_A	87_A	0.919	1.00
89_Y	227_R	0.917	1.00
157_E	194_R	0.912	1.00
13_I	16_M	0.910	1.00
42_K	45_K	0.908	1.00
79_K	210_K	0.907	1.00
239_V	249_V	0.907	1.00
223_Q	245_K	0.906	1.00
162_T	193_K	0.897	1.00
189_A	217_S	0.895	1.00
176_D	214_R	0.895	1.00
164_H	200_D	0.890	1.00
26_S	36_I	0.890	1.00
104_A	107_M	0.883	1.00
24_E	28_I	0.883	1.00
164_H	179_N	0.880	1.00
82_I	103_T	0.878	1.00
103_T	210_K	0.878	1.00
75_N	207_D	0.876	1.00
124_K	149_L	0.875	1.00
83_A	107_M	0.862	1.00
20_I	25_L	0.858	1.00
20_I	56_A	0.855	1.00
43_L	48_K	0.855	1.00
83_A	106_Y	0.849	1.00
137_V	144_L	0.847	1.00
241_A	244_D	0.841	1.00
200_D	214_R	0.836	1.00
122_S	125_A	0.836	1.00
130_S	149_L	0.834	1.00
108_A	125_A	0.832	1.00
163_Y	186_E	0.830	1.00
11_V	15_N	0.826	1.00
160_L	195_M	0.821	1.00
164_H	218_H	0.814	1.00
86_A	229_I	0.813	1.00
155_L	162_T	0.809	1.00
148_S	173_K	0.809	1.00
169_F	205_M	0.805	1.00
183_D	189_A	0.803	1.00
5_E	8_Q	0.794	1.00
112_P	128_E	0.792	1.00
12_E	15_N	0.788	1.00
132_K	135_I	0.786	1.00
202_T	226_S	0.781	1.00
164_H	214_R	0.779	1.00
81_A	84_H	0.778	1.00
24_E	27_D	0.778	1.00
75_N	208_S	0.774	1.00
71_R	173_K	0.774	1.00
186_E	217_S	0.769	1.00
41_E	51_R	0.765	1.00
160_L	194_R	0.765	1.00
179_N	214_R	0.764	1.00
128_E	131_N	0.762	1.00
145_L	188_Q	0.759	1.00
5_E	19_S	0.756	1.00
175_F	181_M	0.755	1.00
115_E	134_N	0.753	1.00
234_L	249_V	0.753	1.00
182_S	214_R	0.752	1.00
97_I	160_L	0.751	1.00
104_A	205_M	0.749	1.00
172_C	181_M	0.748	1.00
98_L	108_A	0.740	1.00
162_T	218_H	0.738	1.00
98_L	118_V	0.737	1.00
234_L	238_S	0.732	1.00
141_G	156_A	0.729	1.00
126_A	151_F	0.723	0.99
105_W	128_E	0.720	0.99
127_I	149_L	0.719	0.99
102_T	210_K	0.719	0.99
164_H	198_R	0.714	0.99
106_Y	110_I	0.711	0.99
77_I	81_A	0.709	0.99
67_H	70_E	0.707	0.99
183_D	219_I	0.706	0.99
183_D	188_Q	0.702	0.99
7_Q	11_V	0.701	0.99
196_I	219_I	0.698	0.99
181_M	219_I	0.694	0.99
18_S	58_S	0.692	0.99
126_A	144_L	0.692	0.99
100_A	148_S	0.690	0.99
121_N	195_M	0.688	0.99
165_V	199_S	0.688	0.99
168_T	202_T	0.687	0.99
31_V	34_E	0.680	0.99
145_L	152_A	0.679	0.99
84_H	88_K	0.677	0.99
175_F	222_L	0.677	0.99
193_K	197_E	0.676	0.99
207_D	210_K	0.670	0.99
206_A	228_L	0.669	0.99
141_G	159_S	0.666	0.99
95_R	119_I	0.665	0.99
23_S	27_D	0.663	0.99
40_L	51_R	0.662	0.99
81_A	85_E	0.660	0.99
153_G	156_A	0.659	0.99
52_S	57_V	0.649	0.99
44_E	51_R	0.647	0.99
11_V	43_L	0.646	0.99
25_L	40_L	0.645	0.99
236_P	239_V	0.644	0.99
22_V	36_I	0.641	0.99
82_I	205_M	0.641	0.99
201_Q	248_K	0.641	0.99
96_I	118_V	0.641	0.99
123_M	151_F	0.640	0.99
131_N	149_L	0.639	0.99
96_I	167_K	0.636	0.99
170_L	199_S	0.636	0.99
34_E	122_S	0.634	0.99
14_V	20_I	0.634	0.99
203_I	226_S	0.633	0.99
161_E	198_R	0.633	0.99
237_A	241_A	0.629	0.99
158_R	190_L	0.627	0.99
65_E	71_R	0.627	0.99
72_E	105_W	0.626	0.99
105_W	124_K	0.624	0.99
154_P	158_R	0.622	0.98
241_A	245_K	0.620	0.98
173_K	215_E	0.617	0.98
44_E	49_L	0.617	0.98
119_I	216_F	0.615	0.98
120_T	126_A	0.614	0.98
163_Y	217_S	0.611	0.98
90_V	107_M	0.606	0.98
154_P	190_L	0.606	0.98
113_D	132_K	0.604	0.98
29_F	36_I	0.604	0.98
115_E	136_S	0.602	0.98
6_R	39_D	0.602	0.98
220_A	225_V	0.602	0.98
4_A	7_Q	0.602	0.98
101_S	171_S	0.599	0.98
199_S	202_T	0.596	0.98
122_S	188_Q	0.595	0.98
189_A	219_I	0.586	0.98
184_S	215_E	0.586	0.98
99_D	104_A	0.583	0.98
78_E	233_G	0.583	0.98
123_M	127_I	0.582	0.98
176_D	182_S	0.579	0.98
173_K	188_Q	0.578	0.98
123_M	139_S	0.577	0.98
114_I	132_K	0.576	0.98
154_P	157_E	0.575	0.97
145_L	185_N	0.571	0.97
81_A	232_S	0.571	0.97
150_S	188_Q	0.569	0.97
72_E	106_Y	0.567	0.97
170_L	219_I	0.567	0.97
34_E	173_K	0.566	0.97
101_S	173_K	0.566	0.97
171_S	183_D	0.565	0.97
238_S	242_L	0.564	0.97
211_W	238_S	0.563	0.97
173_K	184_S	0.562	0.97
79_K	207_D	0.561	0.97
177_V	241_A	0.559	0.97
156_A	159_S	0.559	0.97
124_K	127_I	0.556	0.97
95_R	216_F	0.556	0.97
96_I	169_F	0.554	0.97
38_R	175_F	0.553	0.97
208_S	234_L	0.551	0.97
187_W	190_L	0.551	0.97
192_K	219_I	0.550	0.97
119_I	138_I	0.549	0.97
157_E	161_E	0.547	0.97
183_D	192_K	0.546	0.97
158_R	193_K	0.545	0.97
211_W	230_T	0.544	0.97
177_V	238_S	0.544	0.97
173_K	192_K	0.543	0.96
181_M	220_A	0.541	0.96
27_D	30_S	0.541	0.96
191_L	194_R	0.541	0.96
97_I	168_T	0.540	0.96
101_S	122_S	0.540	0.96
69_S	72_E	0.536	0.96
71_R	188_Q	0.536	0.96
170_L	196_I	0.535	0.96
154_P	187_W	0.531	0.96
10_I	29_F	0.528	0.96
96_I	107_M	0.526	0.96
236_P	243_E	0.522	0.96
100_A	188_Q	0.521	0.96
151_F	159_S	0.520	0.95
78_E	81_A	0.519	0.95
202_T	224_D	0.517	0.95
170_L	202_T	0.516	0.95
65_E	145_L	0.514	0.95
97_I	119_I	0.514	0.95
174_G	215_E	0.513	0.95
233_G	239_V	0.512	0.95
20_I	52_S	0.511	0.95
82_I	230_T	0.511	0.95
26_S	32_T	0.510	0.95
129_L	135_I	0.503	0.95
34_E	183_D	0.500	0.94
22_V	26_S	0.500	0.94

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
1stzA	3	0.9419	100	0.521	Contact Map
3rrlB	1	0.6783	100	0.532	Contact Map
2w48A	3	0.9109	100	0.576	Contact Map
3l7oA	2	0.6008	100	0.614	Contact Map
2o0mA	1	0.6822	100	0.618	Contact Map
1o8bA	2	0.593	100	0.623	Contact Map
1uj6A	2	0.6085	100	0.626	Contact Map
1lk5A	4	0.6124	100	0.628	Contact Map
1m0sA	2	0.6163	100	0.63	Contact Map
4io1A	2	0.6163	100	0.634	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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