YGBI - ECOLI - GREMLIN Contacts

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YGBI - Uncharacterized HTH-type transcriptional regulator YgbI

UniProt:	P52598	Sequences: MIPVERRQIILEMVAEKGIVSIAELTDRMNVSHMTIRRDLQKLEQQGAVVLVSGGVQSPGRVAHEPSHQVKTALAMTQKAAIGKLAASLVQPGSCIYLDAGTTTLAIAQHLIHMESLTVVTNDFVIADYLLDNSNCTIIHTGGAVCRENRSCVGEAAATMLRSLMIDQAFISASSWSVRGISTPAEDKVTVKRAIASASRQRVLVCDATKYGQVATWLALPLSEFDQIITDDGLPESASRALVKQDLSLLVAKNE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13103
Length:	255 (246)
Sequences:	7680 (5611)
Seq/√Len:	357.8

ECOLI - YGBI AGAR YIHW GLPR GATR SGCR YDJF SRLR ULAR DEOR YCIT FUCR
BACSU - GLCR YULB 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_S	168_Q	3.319	1.00
85_L	88_S	3.124	1.00
107_I	205_V	2.940	1.00
137_T	144_A	2.756	1.00
169_A	199_S	2.610	1.00
13_M	28_R	2.354	1.00
99_D	192_K	2.336	1.00
208_A	231_D	2.283	1.00
196_A	220_L	2.256	1.00
109_Q	129_Y	2.242	1.00
162_R	194_A	2.131	1.00
203_V	227_Q	2.121	1.00
91_Q	94_S	2.087	1.00
9_I	12_E	2.054	1.00
168_Q	203_V	2.043	1.00
13_M	17_K	2.023	1.00
84_K	110_H	2.007	1.00
97_Y	166_I	1.999	1.00
80_A	106_A	1.997	1.00
196_A	202_R	1.981	1.00
218_L	221_P	1.969	1.00
234_L	239_S	1.933	1.00
159_T	162_R	1.914	1.00
98_L	104_T	1.913	1.00
168_Q	201_Q	1.887	1.00
97_Y	195_I	1.828	1.00
201_Q	227_Q	1.812	1.00
92_P	115_E	1.781	1.00
106_A	109_Q	1.776	1.00
239_S	243_V	1.761	1.00
120_V	166_I	1.752	1.00
221_P	224_E	1.690	1.00
86_A	170_F	1.679	1.00
159_T	163_S	1.678	1.00
166_I	195_I	1.656	1.00
158_A	190_T	1.608	1.00
140_H	152_C	1.604	1.00
194_A	197_S	1.604	1.00
86_A	205_V	1.599	1.00
167_D	200_R	1.559	1.00
141_T	160_M	1.549	1.00
127_A	140_H	1.545	1.00
107_I	170_F	1.535	1.00
181_I	225_F	1.518	1.00
75_A	209_T	1.509	1.00
240_R	244_K	1.506	1.00
181_I	204_L	1.499	1.00
31_V	36_I	1.495	1.00
87_A	110_H	1.495	1.00
162_R	197_S	1.482	1.00
19_I	57_Q	1.469	1.00
25_L	36_I	1.454	1.00
80_A	110_H	1.446	1.00
7_R	46_Q	1.444	1.00
157_A	191_V	1.444	1.00
13_M	20_V	1.427	1.00
235_P	238_A	1.425	1.00
50_V	59_P	1.422	1.00
83_G	110_H	1.420	1.00
119_V	130_L	1.415	1.00
141_T	152_C	1.412	1.00
89_L	229_I	1.409	1.00
9_I	13_M	1.399	1.00
8_Q	12_E	1.397	1.00
10_I	25_L	1.393	1.00
194_A	198_A	1.391	1.00
75_A	78_Q	1.389	1.00
40_L	56_V	1.388	1.00
17_K	24_E	1.372	1.00
15_A	58_S	1.366	1.00
89_L	203_V	1.365	1.00
204_L	225_F	1.361	1.00
100_A	151_S	1.359	1.00
145_V	152_C	1.358	1.00
208_A	233_G	1.339	1.00
23_A	33_H	1.335	1.00
78_Q	231_D	1.331	1.00
7_R	42_K	1.328	1.00
92_P	114_M	1.322	1.00
94_S	167_D	1.320	1.00
76_M	106_A	1.320	1.00
52_V	55_G	1.319	1.00
144_A	187_D	1.317	1.00
11_L	48_A	1.289	1.00
119_V	136_C	1.289	1.00
176_W	211_Y	1.288	1.00
92_P	116_S	1.287	1.00
220_L	224_E	1.281	1.00
79_K	102_T	1.280	1.00
21_S	24_E	1.269	1.00
3_P	7_R	1.246	1.00
93_G	116_S	1.244	1.00
236_E	240_R	1.242	1.00
141_T	157_A	1.239	1.00
90_V	111_L	1.238	1.00
201_Q	226_D	1.236	1.00
9_I	28_R	1.232	1.00
80_A	109_Q	1.228	1.00
85_L	89_L	1.221	1.00
118_T	139_I	1.200	1.00
197_S	224_E	1.193	1.00
34_M	38_R	1.192	1.00
240_R	243_V	1.184	1.00
9_I	29_M	1.183	1.00
77_T	80_A	1.177	1.00
97_Y	198_A	1.173	1.00
14_V	49_V	1.159	1.00
41_Q	45_Q	1.159	1.00
108_A	130_L	1.156	1.00
173_A	206_C	1.143	1.00
76_M	80_A	1.142	1.00
227_Q	248_S	1.132	1.00
158_A	191_V	1.129	1.00
170_F	203_V	1.124	1.00
17_K	28_R	1.121	1.00
156_A	160_M	1.114	1.00
91_Q	168_Q	1.114	1.00
12_E	16_E	1.111	1.00
211_Y	234_L	1.109	1.00
78_Q	208_A	1.105	1.00
118_T	137_T	1.099	1.00
50_V	57_Q	1.097	1.00
173_A	219_A	1.091	1.00
11_L	14_V	1.088	1.00
202_R	225_F	1.065	1.00
203_V	229_I	1.060	1.00
14_V	58_S	1.060	1.00
139_I	144_A	1.044	1.00
22_I	40_L	1.042	1.00
42_K	46_Q	1.030	1.00
49_V	56_V	1.026	1.00
120_V	164_L	1.020	1.00
175_S	182_S	1.017	1.00
238_A	241_A	1.017	1.00
26_T	33_H	1.013	1.00
3_P	42_K	1.012	1.00
89_L	227_Q	1.011	1.00
86_A	107_I	1.007	1.00
87_A	90_V	0.991	1.00
141_T	161_L	0.990	1.00
90_V	170_F	0.985	1.00
78_Q	82_I	0.984	1.00
5_E	9_I	0.980	1.00
68_H	102_T	0.980	1.00
211_Y	228_I	0.978	1.00
156_A	164_L	0.976	1.00
87_A	107_I	0.972	1.00
98_L	107_I	0.965	1.00
104_T	126_I	0.964	1.00
176_W	206_C	0.960	1.00
223_S	245_Q	0.957	1.00
41_Q	44_E	0.953	1.00
83_G	87_A	0.950	1.00
80_A	84_K	0.950	1.00
108_A	129_Y	0.937	1.00
174_S	183_T	0.936	1.00
101_G	104_T	0.935	1.00
190_T	193_R	0.934	1.00
13_M	16_E	0.934	1.00
177_S	214_V	0.930	1.00
79_K	103_T	0.924	1.00
189_V	217_W	0.921	1.00
79_K	210_K	0.919	1.00
158_A	194_A	0.916	1.00
169_A	195_I	0.916	1.00
82_I	103_T	0.911	1.00
107_I	110_H	0.911	1.00
24_E	28_R	0.910	1.00
42_K	45_Q	0.906	1.00
173_A	204_L	0.905	1.00
103_T	207_D	0.903	1.00
163_S	193_R	0.899	1.00
125_V	150_R	0.893	1.00
75_A	207_D	0.889	1.00
239_S	249_L	0.885	1.00
165_M	200_R	0.884	1.00
83_G	107_I	0.883	1.00
138_I	145_V	0.875	1.00
26_T	36_I	0.874	1.00
20_V	56_V	0.874	1.00
103_T	210_K	0.873	1.00
104_T	107_I	0.872	1.00
83_G	106_A	0.864	1.00
11_L	15_A	0.860	1.00
165_M	179_R	0.860	1.00
156_A	163_S	0.858	1.00
20_V	25_L	0.857	1.00
43_L	48_A	0.856	1.00
131_L	150_R	0.853	1.00
200_R	214_V	0.848	1.00
179_R	214_V	0.845	1.00
241_A	244_K	0.841	1.00
112_I	133_N	0.838	1.00
149_N	174_S	0.836	1.00
108_A	126_I	0.826	1.00
164_L	186_E	0.824	1.00
123_D	126_I	0.818	1.00
112_I	129_Y	0.816	1.00
161_L	195_I	0.813	1.00
165_M	218_L	0.813	1.00
170_F	205_V	0.810	1.00
165_M	214_V	0.806	1.00
183_T	189_V	0.805	1.00
202_R	226_D	0.801	1.00
12_E	15_A	0.801	1.00
81_A	84_K	0.799	1.00
5_E	8_Q	0.796	1.00
176_W	181_I	0.784	1.00
86_A	229_I	0.779	1.00
161_L	194_A	0.778	1.00
129_Y	132_D	0.777	1.00
97_Y	161_L	0.776	1.00
24_E	27_D	0.772	1.00
104_T	205_V	0.770	1.00
75_A	208_A	0.767	1.00
234_L	238_A	0.763	1.00
41_Q	51_L	0.763	1.00
112_I	115_E	0.761	1.00
186_E	217_W	0.761	1.00
71_K	174_S	0.758	1.00
163_S	218_L	0.752	1.00
182_S	214_V	0.749	1.00
102_T	210_K	0.749	1.00
165_M	198_A	0.746	1.00
173_A	181_I	0.743	1.00
116_S	135_N	0.741	1.00
105_L	129_Y	0.739	1.00
128_D	150_R	0.737	1.00
5_E	19_I	0.735	1.00
234_L	249_L	0.733	1.00
67_S	70_V	0.732	1.00
77_T	81_A	0.729	1.00
183_T	219_A	0.726	1.00
146_C	188_K	0.725	1.00
98_L	108_A	0.724	0.99
98_L	119_V	0.719	0.99
196_A	219_A	0.719	0.99
18_G	58_S	0.716	0.99
127_A	145_V	0.709	0.99
146_C	153_V	0.707	0.99
176_W	222_L	0.704	0.99
106_A	110_H	0.701	0.99
178_V	241_A	0.701	0.99
7_R	11_L	0.699	0.99
11_L	43_L	0.691	0.99
65_E	71_K	0.688	0.99
127_A	152_C	0.688	0.99
95_C	120_V	0.686	0.99
142_G	160_M	0.684	0.99
206_C	228_I	0.684	0.99
133_N	136_C	0.683	0.99
72_T	105_L	0.683	0.99
100_A	149_N	0.683	0.99
169_A	202_R	0.683	0.99
207_D	210_K	0.681	0.99
40_L	51_L	0.680	0.99
154_G	157_A	0.679	0.99
166_I	199_S	0.676	0.99
181_I	219_A	0.676	0.99
81_A	85_L	0.673	0.99
23_A	27_D	0.672	0.99
142_G	157_A	0.671	0.99
132_D	150_R	0.669	0.99
236_E	239_S	0.669	0.99
115_E	135_N	0.666	0.99
84_K	88_S	0.665	0.99
193_R	197_S	0.665	0.99
96_I	119_V	0.665	0.99
237_S	241_A	0.664	0.99
31_V	34_M	0.660	0.99
241_A	245_Q	0.657	0.99
52_V	57_Q	0.655	0.99
113_H	133_N	0.655	0.99
162_R	198_A	0.654	0.99
155_E	159_T	0.650	0.99
4_V	7_R	0.648	0.99
159_T	190_T	0.648	0.99
96_I	168_Q	0.646	0.99
25_L	40_L	0.645	0.99
155_E	190_T	0.640	0.99
82_I	205_V	0.638	0.99
183_T	188_K	0.637	0.99
105_L	125_V	0.632	0.99
171_I	199_S	0.630	0.99
22_I	36_I	0.629	0.99
44_E	51_L	0.628	0.99
121_T	127_A	0.626	0.99
203_V	226_D	0.625	0.99
14_V	20_V	0.624	0.99
238_A	242_L	0.622	0.98
122_N	195_I	0.621	0.98
6_R	39_D	0.621	0.98
174_S	215_A	0.620	0.98
164_L	217_W	0.618	0.98
201_Q	248_S	0.614	0.98
124_F	152_C	0.614	0.98
29_M	36_I	0.612	0.98
199_S	202_R	0.609	0.98
125_V	128_D	0.607	0.98
44_E	49_V	0.604	0.98
116_S	137_T	0.599	0.98
187_D	190_T	0.597	0.98
34_M	123_D	0.597	0.98
208_A	234_L	0.596	0.98
220_L	225_F	0.596	0.98
90_V	107_I	0.595	0.98
124_F	140_H	0.595	0.98
155_E	158_A	0.593	0.98
146_C	185_A	0.592	0.98
189_V	219_A	0.591	0.98
177_S	182_S	0.591	0.98
81_A	232_D	0.583	0.98
69_Q	72_T	0.582	0.98
158_A	162_R	0.580	0.98
174_S	188_K	0.579	0.98
178_V	238_A	0.578	0.98
124_F	128_D	0.577	0.98
157_A	160_M	0.576	0.98
72_T	106_A	0.576	0.98
120_V	216_T	0.575	0.97
184_P	215_A	0.570	0.97
99_D	104_T	0.568	0.97
101_G	172_S	0.563	0.97
155_E	187_D	0.563	0.97
181_I	220_L	0.560	0.97
171_I	219_A	0.560	0.97
95_C	216_T	0.560	0.97
96_I	170_F	0.559	0.97
65_E	146_C	0.559	0.97
71_K	188_K	0.555	0.97
192_K	219_A	0.555	0.97
34_M	174_S	0.550	0.97
191_V	194_A	0.548	0.97
171_I	196_A	0.547	0.97
96_I	107_I	0.547	0.97
120_V	139_I	0.546	0.97
79_K	207_D	0.546	0.97
233_G	239_S	0.545	0.97
174_S	184_P	0.542	0.96
38_R	176_W	0.540	0.96
97_Y	169_A	0.538	0.96
78_Q	233_G	0.538	0.96
171_I	202_R	0.537	0.96
211_Y	230_T	0.535	0.96
211_Y	238_A	0.534	0.96
202_R	224_E	0.532	0.96
152_C	160_M	0.532	0.96
78_Q	81_A	0.530	0.96
151_S	188_K	0.527	0.96
183_T	192_K	0.525	0.96
159_T	193_R	0.524	0.96
236_E	243_V	0.524	0.96
101_G	174_S	0.523	0.96
175_S	213_Q	0.523	0.96
98_L	126_I	0.520	0.95
22_I	26_T	0.519	0.95
123_D	188_K	0.519	0.95
175_S	215_A	0.516	0.95
180_G	221_P	0.516	0.95
172_S	183_T	0.515	0.95
27_D	30_N	0.515	0.95
156_A	159_T	0.512	0.95
208_A	232_D	0.512	0.95
113_H	135_N	0.511	0.95
71_K	102_T	0.506	0.95
97_Y	120_V	0.504	0.95
82_I	230_T	0.503	0.95
212_G	238_A	0.502	0.95
26_T	32_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	0.9451	100	0.516	Contact Map
3rrlB	1	0.6706	100	0.538	Contact Map
2w48A	3	0.9216	100	0.572	Contact Map
2o0mA	1	0.6941	100	0.614	Contact Map
3l7oA	2	0.6039	100	0.617	Contact Map
1o8bA	2	0.5922	100	0.626	Contact Map
1m0sA	2	0.6157	100	0.63	Contact Map
1lk5A	4	0.6118	100	0.631	Contact Map
3ixqA	4	0.6275	100	0.631	Contact Map
4io1A	2	0.6157	100	0.631	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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