SRLR - ECOLI - GREMLIN Contacts

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SRLR - Glucitol operon repressor

UniProt:	P15082	Sequences: MKPRQRQAAILEYLQKQGKCSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTYGGVVLNKEESDPPIDHKTLINTHKKELIAEAAVSFIHDGDSIILDAGSTVLQMVPLLSRFNNITVMTNSLHIVNALSELDNEQTILMPGGTFRKKSASFHGQLAENAFEHFTFDKLFMGTDGIDLNAGVTTFNEVYTVSKAMCNAAREVILMADSSKFGRKSPNVVCSLESVDKLITDAGIDPAFRQALEEKGIDVIITGESNE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10974
Length:	257 (247)
Sequences:	7681 (5642)
Seq/√Len:	359.0

ECOLI - SRLR GATR YIHW AGAR GLPR YGBI SGCR 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
93_D	168_K	3.281	1.00
84_A	87_S	3.055	1.00
106_M	205_M	2.994	1.00
137_T	144_T	2.692	1.00
169_L	199_A	2.562	1.00
13_Y	28_Y	2.373	1.00
98_D	192_S	2.244	1.00
227_K	250_I	2.218	1.00
108_P	128_A	2.215	1.00
196_C	220_C	2.203	1.00
208_S	231_D	2.198	1.00
162_E	194_A	2.123	1.00
90_H	93_D	2.120	1.00
203_I	227_K	2.068	1.00
13_Y	17_Q	2.062	1.00
168_K	203_I	2.049	1.00
9_A	12_E	2.034	1.00
83_E	109_L	1.996	1.00
79_E	105_Q	1.989	1.00
196_C	202_V	1.956	1.00
96_I	166_F	1.950	1.00
218_V	221_S	1.916	1.00
97_L	103_V	1.885	1.00
168_K	201_E	1.881	1.00
159_N	162_E	1.871	1.00
234_I	239_R	1.852	1.00
96_I	195_M	1.846	1.00
91_D	114_N	1.775	1.00
105_Q	108_P	1.774	1.00
201_E	227_K	1.771	1.00
239_R	243_E	1.767	1.00
84_A	250_I	1.747	1.00
119_M	166_F	1.716	1.00
85_A	170_F	1.645	1.00
221_S	224_S	1.640	1.00
166_F	195_M	1.635	1.00
159_N	163_H	1.621	1.00
194_A	197_N	1.617	1.00
85_A	205_M	1.587	1.00
140_M	152_F	1.580	1.00
126_V	140_M	1.574	1.00
167_D	200_R	1.547	1.00
141_P	160_A	1.547	1.00
106_M	170_F	1.537	1.00
74_N	209_S	1.490	1.00
31_T	36_I	1.478	1.00
162_E	197_N	1.477	1.00
86_V	109_L	1.477	1.00
182_V	204_L	1.476	1.00
19_K	57_V	1.473	1.00
118_V	129_L	1.472	1.00
182_V	225_V	1.462	1.00
25_L	36_I	1.457	1.00
240_Q	244_E	1.447	1.00
79_E	109_L	1.436	1.00
157_A	191_V	1.431	1.00
7_Q	46_A	1.429	1.00
141_P	152_F	1.422	1.00
74_N	77_K	1.421	1.00
50_I	59_N	1.418	1.00
82_A	109_L	1.414	1.00
15_Q	58_L	1.407	1.00
10_I	25_L	1.399	1.00
13_Y	20_C	1.394	1.00
9_A	13_Y	1.387	1.00
204_L	225_V	1.386	1.00
40_L	56_V	1.385	1.00
194_A	198_A	1.383	1.00
88_F	229_I	1.377	1.00
77_K	231_D	1.361	1.00
8_A	12_E	1.359	1.00
93_D	167_D	1.358	1.00
99_A	151_S	1.354	1.00
17_Q	24_E	1.350	1.00
208_S	233_G	1.348	1.00
88_F	203_I	1.345	1.00
145_F	152_F	1.335	1.00
7_Q	42_I	1.327	1.00
91_D	113_F	1.325	1.00
23_E	33_G	1.322	1.00
111_S	132_L	1.317	1.00
235_D	238_F	1.314	1.00
144_T	188_V	1.308	1.00
118_V	136_Q	1.307	1.00
75_T	105_Q	1.303	1.00
91_D	115_N	1.294	1.00
220_C	224_S	1.294	1.00
52_T	55_G	1.292	1.00
11_L	48_T	1.280	1.00
176_I	211_F	1.280	1.00
92_G	115_N	1.264	1.00
21_S	24_E	1.262	1.00
89_I	110_L	1.262	1.00
79_E	108_P	1.250	1.00
3_P	7_Q	1.247	1.00
84_A	88_F	1.245	1.00
201_E	226_D	1.244	1.00
78_K	101_S	1.238	1.00
9_A	28_Y	1.228	1.00
141_P	157_A	1.217	1.00
236_P	240_Q	1.216	1.00
88_F	250_I	1.194	1.00
117_T	139_L	1.192	1.00
96_I	198_A	1.188	1.00
14_L	49_V	1.179	1.00
9_A	29_F	1.178	1.00
34_T	38_K	1.167	1.00
173_T	206_A	1.166	1.00
75_T	79_E	1.162	1.00
197_N	224_S	1.154	1.00
41_V	45_H	1.154	1.00
240_Q	243_E	1.152	1.00
156_L	160_A	1.136	1.00
77_K	208_S	1.134	1.00
107_V	129_L	1.133	1.00
211_F	234_I	1.128	1.00
117_T	137_T	1.126	1.00
227_K	248_D	1.121	1.00
170_F	203_I	1.116	1.00
17_Q	28_Y	1.113	1.00
11_L	14_L	1.110	1.00
14_L	58_L	1.107	1.00
90_H	168_K	1.105	1.00
76_H	79_E	1.104	1.00
158_E	191_V	1.104	1.00
12_E	16_K	1.093	1.00
173_T	219_V	1.092	1.00
202_V	225_V	1.069	1.00
50_I	57_V	1.066	1.00
49_V	56_V	1.042	1.00
203_I	229_I	1.041	1.00
42_I	46_A	1.040	1.00
139_L	144_T	1.036	1.00
119_M	164_F	1.033	1.00
86_V	89_I	1.029	1.00
85_A	106_M	1.026	1.00
82_A	86_V	1.025	1.00
176_I	206_A	1.023	1.00
22_V	40_L	1.019	1.00
175_G	183_T	1.015	1.00
141_P	161_F	1.010	1.00
67_I	101_S	1.004	1.00
238_F	241_A	0.998	1.00
26_A	33_G	0.995	1.00
89_I	170_F	0.990	1.00
88_F	227_K	0.988	1.00
211_F	228_L	0.986	1.00
77_K	81_I	0.979	1.00
158_E	194_A	0.978	1.00
5_Q	9_A	0.970	1.00
97_L	106_M	0.968	1.00
100_G	103_V	0.966	1.00
156_L	164_F	0.957	1.00
13_Y	16_K	0.956	1.00
86_V	106_M	0.945	1.00
3_P	42_I	0.944	1.00
103_V	125_I	0.928	1.00
173_T	204_L	0.925	1.00
177_D	180_A	0.923	1.00
107_V	128_A	0.921	1.00
169_L	195_M	0.921	1.00
74_N	207_D	0.921	1.00
223_E	245_K	0.918	1.00
124_H	150_A	0.911	1.00
79_E	83_E	0.909	1.00
138_I	145_F	0.908	1.00
41_V	44_E	0.907	1.00
177_D	214_K	0.906	1.00
174_D	184_T	0.906	1.00
81_I	102_T	0.904	1.00
106_M	109_L	0.903	1.00
163_H	193_K	0.897	1.00
20_C	56_V	0.896	1.00
239_R	249_V	0.892	1.00
102_T	207_D	0.890	1.00
20_C	25_L	0.890	1.00
42_I	45_H	0.884	1.00
184_T	190_T	0.881	1.00
78_K	210_K	0.878	1.00
103_V	106_M	0.877	1.00
24_E	28_Y	0.874	1.00
190_T	217_N	0.867	1.00
26_A	36_I	0.864	1.00
156_L	163_H	0.863	1.00
130_S	150_A	0.861	1.00
82_A	106_M	0.861	1.00
82_A	105_Q	0.859	1.00
11_L	15_Q	0.854	1.00
78_K	102_T	0.853	1.00
241_A	244_E	0.850	1.00
122_S	125_I	0.849	1.00
107_V	125_I	0.845	1.00
149_S	174_D	0.845	1.00
165_T	200_R	0.843	1.00
170_F	205_M	0.843	1.00
43_L	48_T	0.838	1.00
200_R	214_K	0.829	1.00
111_S	128_A	0.824	1.00
161_F	194_A	0.816	1.00
164_F	187_E	0.807	1.00
102_T	210_K	0.805	1.00
80_L	83_E	0.804	1.00
5_Q	8_A	0.804	1.00
165_T	180_A	0.804	1.00
187_E	217_N	0.797	1.00
161_F	195_M	0.797	1.00
202_V	226_D	0.796	1.00
165_T	218_V	0.792	1.00
12_E	15_Q	0.791	1.00
103_V	205_M	0.786	1.00
165_T	214_K	0.783	1.00
178_L	181_G	0.777	1.00
85_A	229_I	0.776	1.00
128_A	131_E	0.772	1.00
41_V	51_R	0.765	1.00
127_N	150_A	0.761	1.00
132_L	136_Q	0.754	1.00
180_A	214_K	0.753	1.00
96_I	161_F	0.750	1.00
104_L	128_A	0.750	1.00
24_E	27_Q	0.749	1.00
178_L	241_A	0.747	1.00
183_T	214_K	0.747	1.00
97_L	107_V	0.745	1.00
173_T	182_V	0.743	1.00
165_T	198_A	0.741	1.00
163_H	218_V	0.741	1.00
5_Q	19_K	0.739	1.00
146_R	153_H	0.738	1.00
18_G	58_L	0.737	1.00
70_K	174_D	0.736	1.00
74_N	208_S	0.734	1.00
66_P	69_H	0.731	1.00
196_C	219_V	0.726	1.00
40_L	51_R	0.723	0.99
234_I	249_V	0.723	0.99
76_H	80_L	0.719	0.99
166_F	199_A	0.717	0.99
111_S	114_N	0.716	0.99
7_Q	11_L	0.712	0.99
234_I	238_F	0.707	0.99
182_V	219_V	0.705	0.99
105_Q	109_L	0.704	0.99
101_S	210_K	0.704	0.99
176_I	182_V	0.701	0.99
97_L	118_V	0.700	0.99
206_A	228_L	0.699	0.99
146_R	189_Y	0.699	0.99
126_V	145_F	0.697	0.99
131_E	150_A	0.688	0.99
176_I	222_L	0.686	0.99
95_I	118_V	0.686	0.99
11_L	43_L	0.685	0.99
193_K	197_N	0.684	0.99
99_A	149_S	0.681	0.99
94_S	119_M	0.681	0.99
142_G	160_A	0.681	0.99
23_E	27_Q	0.679	0.99
241_A	245_K	0.678	0.99
81_I	205_M	0.675	0.99
169_L	202_V	0.675	0.99
83_E	87_S	0.672	0.99
52_T	57_V	0.672	0.99
236_P	239_R	0.670	0.99
71_T	104_L	0.666	0.99
184_T	189_Y	0.666	0.99
133_D	136_Q	0.666	0.99
142_G	157_A	0.663	0.99
126_V	152_F	0.661	0.99
154_G	157_A	0.661	0.99
184_T	219_V	0.661	0.99
64_D	70_K	0.658	0.99
80_L	84_A	0.657	0.99
203_I	226_D	0.654	0.99
95_I	168_K	0.648	0.99
162_E	198_A	0.647	0.99
25_L	40_L	0.644	0.99
155_Q	159_N	0.642	0.99
237_A	241_A	0.639	0.99
44_E	51_R	0.637	0.99
31_T	34_T	0.636	0.99
4_R	7_Q	0.634	0.99
164_F	217_N	0.632	0.99
14_L	20_C	0.630	0.99
22_V	36_I	0.626	0.99
44_E	49_V	0.625	0.99
207_D	210_K	0.622	0.98
123_L	140_M	0.619	0.98
89_I	106_M	0.619	0.98
121_N	195_M	0.618	0.98
123_L	152_F	0.618	0.98
6_R	39_D	0.617	0.98
174_D	215_S	0.616	0.98
199_A	202_V	0.612	0.98
29_F	36_I	0.608	0.98
120_T	126_V	0.606	0.98
123_L	127_N	0.606	0.98
34_T	122_S	0.600	0.98
220_C	225_V	0.598	0.98
171_M	199_A	0.596	0.98
157_A	160_A	0.594	0.98
124_H	127_N	0.593	0.98
133_D	147_K	0.593	0.98
208_S	234_I	0.592	0.98
201_E	248_D	0.589	0.98
191_V	194_A	0.588	0.98
146_R	186_N	0.587	0.98
77_K	233_G	0.586	0.98
104_L	124_H	0.586	0.98
119_M	216_P	0.584	0.98
114_N	134_N	0.583	0.98
115_N	134_N	0.581	0.98
238_F	242_L	0.580	0.98
94_S	216_P	0.580	0.98
171_M	196_C	0.579	0.98
71_T	105_Q	0.572	0.97
182_V	220_C	0.570	0.97
80_L	232_A	0.570	0.97
174_D	185_F	0.568	0.97
112_R	132_L	0.565	0.97
156_L	159_N	0.564	0.97
119_M	139_L	0.564	0.97
98_D	103_V	0.560	0.97
115_N	137_T	0.559	0.97
158_E	162_E	0.557	0.97
70_K	189_Y	0.552	0.97
211_F	230_T	0.552	0.97
171_M	202_V	0.551	0.97
171_M	219_V	0.551	0.97
100_G	172_G	0.550	0.97
38_K	176_I	0.549	0.97
175_G	213_R	0.549	0.97
96_I	169_L	0.546	0.97
175_G	215_S	0.546	0.97
95_I	170_F	0.545	0.97
233_G	239_R	0.545	0.97
34_T	174_D	0.544	0.97
192_S	219_V	0.542	0.96
126_V	138_I	0.539	0.96
155_Q	188_V	0.538	0.96
22_V	26_A	0.536	0.96
155_Q	158_E	0.536	0.96
68_D	71_T	0.535	0.96
152_F	160_A	0.534	0.96
211_F	238_F	0.530	0.96
122_S	189_Y	0.530	0.96
172_G	184_T	0.524	0.96
185_F	215_S	0.524	0.96
202_V	224_S	0.523	0.96
236_P	243_E	0.523	0.96
177_D	183_T	0.521	0.96
151_S	189_Y	0.519	0.95
95_I	106_M	0.515	0.95
77_K	80_L	0.513	0.95
243_E	248_D	0.512	0.95
97_L	125_I	0.511	0.95
26_A	32_T	0.510	0.95
212_G	238_F	0.510	0.95
156_L	187_E	0.509	0.95
70_K	101_S	0.507	0.95
96_I	119_M	0.505	0.95
190_T	219_V	0.505	0.95
99_A	189_Y	0.505	0.95
229_I	250_I	0.504	0.95
174_D	189_Y	0.503	0.95
178_L	238_F	0.502	0.95
67_I	150_A	0.501	0.95
174_D	192_S	0.501	0.95
70_K	98_D	0.501	0.95
139_L	156_L	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	0.9416	100	0.512	Contact Map
3rrlB	1	0.6732	100	0.533	Contact Map
2w48A	3	0.9144	100	0.569	Contact Map
3l7oA	2	0.607	100	0.612	Contact Map
2o0mA	1	0.6848	100	0.614	Contact Map
1o8bA	2	0.5953	100	0.625	Contact Map
1lk5A	4	0.6148	100	0.627	Contact Map
1uj6A	2	0.6148	100	0.628	Contact Map
1m0sA	2	0.6187	100	0.63	Contact Map
3uw1A	2	0.6265	100	0.63	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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