ALLR - ECOLI - GREMLIN Contacts

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ALLR - HTH-type transcriptional repressor AllR

UniProt:	P0ACN4	Sequences: MTEVRRRGRPGQAEPVAQKGAQALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIGLGVFNVGAAYIHNRDVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRFVSQGELVRDTARDISTALGLKAHP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13616
Length:	271 (247)
Sequences:	12885 (9388)
Seq/√Len:	597.3

ECOLI - ALLR YIAJ ICLR KDGR MHPR RHMR YAGI YJHI
BACSU - KIPR
HALSA - Q9HHM8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_L	27_G	3.310	1.00
112_L	253_L	3.099	1.00
120_A	156_A	2.873	1.00
105_F	257_T	2.840	1.00
25_E	67_A	2.825	1.00
198_Q	202_L	2.609	1.00
32_Q	84_G	2.569	1.00
158_K	195_D	2.398	1.00
170_M	193_L	2.393	1.00
103_G	131_G	2.391	1.00
28_I	69_F	2.359	1.00
158_K	210_E	2.314	1.00
126_E	148_R	2.236	1.00
115_E	241_R	2.142	1.00
34_L	70_V	2.094	1.00
73_D	76_L	2.087	1.00
105_F	260_D	2.082	1.00
29_A	67_A	2.071	1.00
207_D	217_C	2.004	1.00
107_R	133_L	1.994	1.00
164_L	168_E	1.970	1.00
122_R	151_L	1.942	1.00
163_P	223_Y	1.922	1.00
208_K	216_N	1.888	1.00
220_S	254_V	1.872	1.00
105_F	264_A	1.818	1.00
216_N	239_S	1.815	1.00
108_R	260_D	1.789	1.00
220_S	258_A	1.786	1.00
32_Q	67_A	1.776	1.00
71_Y	80_H	1.732	1.00
102_A	261_I	1.727	1.00
110_M	117_V	1.698	1.00
251_G	255_R	1.694	1.00
188_D	191_T	1.683	1.00
189_M	193_L	1.680	1.00
30_I	46_I	1.679	1.00
108_R	112_L	1.676	1.00
33_Y	50_L	1.660	1.00
33_Y	41_S	1.651	1.00
61_L	70_V	1.647	1.00
33_Y	46_I	1.605	1.00
237_G	242_L	1.601	1.00
220_S	255_R	1.597	1.00
209_E	239_S	1.592	1.00
235_I	250_Q	1.585	1.00
61_L	79_W	1.572	1.00
33_Y	49_N	1.541	1.00
165_A	168_E	1.531	1.00
41_S	49_N	1.524	1.00
204_Y	251_G	1.523	1.00
246_R	249_S	1.522	1.00
209_E	214_G	1.520	1.00
40_S	80_H	1.516	1.00
195_D	198_Q	1.504	1.00
42_S	45_D	1.491	1.00
105_F	108_R	1.489	1.00
169_L	193_L	1.482	1.00
46_I	57_T	1.461	1.00
113_S	253_L	1.450	1.00
134_E	140_R	1.444	1.00
52_L	57_T	1.436	1.00
199_A	205_T	1.429	1.00
182_T	185_T	1.429	1.00
40_S	78_W	1.427	1.00
253_L	256_D	1.427	1.00
84_G	87_N	1.425	1.00
127_A	160_L	1.415	1.00
170_M	189_M	1.413	1.00
34_L	40_S	1.400	1.00
99_L	131_G	1.399	1.00
223_Y	262_S	1.397	1.00
127_A	151_L	1.381	1.00
109_L	253_L	1.375	1.00
110_M	133_L	1.363	1.00
34_L	41_S	1.362	1.00
32_Q	69_F	1.355	1.00
65_Q	70_V	1.351	1.00
106_M	119_V	1.314	1.00
102_A	119_V	1.307	1.00
73_D	80_H	1.304	1.00
28_I	67_A	1.303	1.00
65_Q	72_Q	1.277	1.00
258_A	262_S	1.266	1.00
125_N	175_Q	1.260	1.00
109_L	257_T	1.258	1.00
53_P	56_T	1.257	1.00
166_E	193_L	1.243	1.00
153_A	185_T	1.238	1.00
37_S	49_N	1.229	1.00
58_F	62_K	1.228	1.00
37_S	41_S	1.225	1.00
46_I	61_L	1.219	1.00
166_E	170_M	1.214	1.00
256_D	260_D	1.214	1.00
174_L	189_M	1.209	1.00
163_P	221_A	1.208	1.00
103_G	107_R	1.206	1.00
47_S	57_T	1.191	1.00
186_L	195_D	1.177	1.00
196_L	199_A	1.174	1.00
223_Y	229_V	1.165	1.00
43_V	58_F	1.163	1.00
255_R	259_R	1.157	1.00
120_A	127_A	1.157	1.00
162_Y	199_A	1.147	1.00
113_S	250_Q	1.142	1.00
153_A	181_F	1.139	1.00
220_S	251_G	1.134	1.00
119_V	231_A	1.117	1.00
25_E	66_A	1.110	1.00
163_P	229_V	1.098	1.00
122_R	125_N	1.096	1.00
44_S	48_L	1.087	1.00
184_T	209_E	1.086	1.00
123_N	148_R	1.085	1.00
107_R	111_L	1.085	1.00
169_L	200_R	1.084	1.00
121_I	231_A	1.073	1.00
42_S	78_W	1.072	1.00
85_V	92_Y	1.071	1.00
122_R	164_L	1.069	1.00
106_M	117_V	1.066	1.00
224_D	228_S	1.064	1.00
119_V	222_I	1.064	1.00
173_I	189_M	1.057	1.00
21_A	63_V	1.057	1.00
35_E	38_G	1.056	1.00
113_S	235_I	1.054	1.00
166_E	197_E	1.054	1.00
166_E	169_L	1.053	1.00
233_I	261_I	1.037	1.00
156_A	232_A	1.037	1.00
25_E	63_V	1.023	1.00
152_H	185_T	1.019	1.00
45_D	48_L	1.019	1.00
154_S	157_G	1.013	1.00
43_V	47_S	1.005	1.00
260_D	264_A	1.005	1.00
252_E	256_D	0.998	1.00
69_F	88_V	0.982	1.00
22_Q	26_R	0.982	1.00
170_M	174_L	0.977	1.00
112_L	256_D	0.976	1.00
98_V	231_A	0.971	1.00
199_A	202_L	0.953	1.00
259_R	263_T	0.949	1.00
108_R	257_T	0.948	1.00
44_S	54_L	0.948	1.00
183_P	213_V	0.948	1.00
168_E	171_S	0.938	1.00
120_A	129_L	0.934	1.00
180_Q	187_V	0.933	1.00
31_L	85_V	0.930	1.00
181_F	185_T	0.923	1.00
194_K	197_E	0.921	1.00
155_G	217_C	0.915	1.00
197_E	201_E	0.915	1.00
40_S	73_D	0.914	1.00
103_G	133_L	0.911	1.00
128_V	148_R	0.911	1.00
243_T	246_R	0.909	1.00
106_M	131_G	0.897	1.00
194_K	198_Q	0.897	1.00
221_A	229_V	0.896	1.00
30_I	50_L	0.894	1.00
36_K	49_N	0.891	1.00
20_G	66_A	0.888	1.00
159_A	163_P	0.888	1.00
248_V	252_E	0.883	1.00
218_I	251_G	0.877	1.00
26_R	56_T	0.877	1.00
161_L	192_L	0.875	1.00
171_S	175_Q	0.869	1.00
55_S	58_F	0.865	1.00
159_A	229_V	0.865	1.00
118_N	236_S	0.863	1.00
117_V	235_I	0.858	1.00
219_A	234_S	0.857	1.00
45_D	49_N	0.850	1.00
101_V	264_A	0.842	1.00
208_K	239_S	0.841	1.00
181_F	211_H	0.841	1.00
156_A	234_S	0.841	1.00
99_L	103_G	0.840	1.00
106_M	233_I	0.837	1.00
191_T	195_D	0.837	1.00
209_E	213_V	0.836	1.00
191_T	194_K	0.832	1.00
159_A	199_A	0.831	1.00
193_L	197_E	0.828	1.00
169_L	196_L	0.826	1.00
43_V	61_L	0.814	1.00
65_Q	79_W	0.813	1.00
202_L	251_G	0.809	1.00
195_D	202_L	0.809	1.00
195_D	199_A	0.804	1.00
115_E	137_S	0.800	1.00
30_I	60_L	0.795	1.00
168_E	172_I	0.794	1.00
254_V	258_A	0.793	1.00
217_C	236_S	0.791	1.00
50_L	57_T	0.789	1.00
34_L	39_G	0.788	1.00
224_D	230_V	0.786	1.00
118_N	143_A	0.785	1.00
247_F	252_E	0.785	1.00
81_I	85_V	0.783	1.00
238_P	241_R	0.780	1.00
198_Q	201_E	0.777	1.00
105_F	261_I	0.775	1.00
123_N	128_V	0.774	1.00
31_L	69_F	0.774	1.00
160_L	232_A	0.774	1.00
169_L	172_I	0.770	1.00
34_L	37_S	0.766	1.00
155_G	219_A	0.762	1.00
217_C	234_S	0.760	1.00
137_S	241_R	0.760	1.00
257_T	260_D	0.755	1.00
20_G	25_E	0.744	1.00
247_F	251_G	0.741	1.00
122_R	168_E	0.740	1.00
186_L	191_T	0.740	1.00
98_V	102_A	0.736	1.00
23_A	27_G	0.736	1.00
118_N	132_Q	0.736	1.00
186_L	192_L	0.734	1.00
85_V	89_G	0.730	1.00
30_I	57_T	0.730	1.00
153_A	211_H	0.728	1.00
72_Q	77_G	0.723	1.00
85_V	88_V	0.716	1.00
172_I	176_T	0.716	1.00
162_Y	196_L	0.707	1.00
43_V	54_L	0.705	1.00
97_D	100_S	0.705	1.00
52_L	56_T	0.705	1.00
106_M	133_L	0.702	1.00
166_E	200_R	0.699	1.00
252_E	255_R	0.693	1.00
249_S	253_L	0.693	1.00
41_S	46_I	0.691	1.00
223_Y	230_V	0.688	1.00
158_K	199_A	0.686	1.00
62_K	65_Q	0.685	1.00
206_V	247_F	0.678	1.00
24_L	60_L	0.677	1.00
71_Y	82_G	0.677	1.00
249_S	252_E	0.677	1.00
257_T	261_I	0.674	1.00
47_S	50_L	0.673	1.00
208_K	244_E	0.673	1.00
122_R	160_L	0.670	1.00
43_V	57_T	0.668	1.00
72_Q	76_L	0.668	1.00
125_N	172_I	0.664	1.00
169_L	197_E	0.663	1.00
43_V	79_W	0.660	1.00
218_I	247_F	0.657	1.00
24_L	28_I	0.656	1.00
259_R	262_S	0.656	1.00
154_S	217_C	0.652	1.00
256_D	259_R	0.650	1.00
233_I	258_A	0.649	1.00
108_R	111_L	0.648	1.00
62_K	66_A	0.648	1.00
89_G	92_Y	0.648	1.00
111_L	136_K	0.644	1.00
110_M	135_C	0.644	1.00
164_L	169_L	0.642	1.00
161_L	196_L	0.640	1.00
71_Y	83_L	0.630	1.00
35_E	88_V	0.628	1.00
109_L	113_S	0.627	1.00
160_L	164_L	0.625	1.00
197_E	200_R	0.624	1.00
246_R	250_Q	0.624	1.00
118_N	217_C	0.621	1.00
121_I	130_I	0.620	1.00
32_Q	87_N	0.620	1.00
26_R	52_L	0.619	1.00
169_L	173_I	0.616	1.00
109_L	235_I	0.615	1.00
260_D	263_T	0.615	1.00
182_T	186_L	0.610	1.00
255_R	258_A	0.607	1.00
23_A	60_L	0.607	1.00
107_R	131_G	0.605	1.00
161_L	169_L	0.605	1.00
187_V	191_T	0.602	1.00
38_G	49_N	0.602	1.00
45_D	78_W	0.601	1.00
152_H	178_L	0.597	1.00
101_V	104_P	0.597	1.00
72_Q	79_W	0.596	1.00
220_S	262_S	0.595	1.00
132_Q	145_L	0.593	1.00
109_L	117_V	0.592	1.00
120_A	154_S	0.590	1.00
208_K	247_F	0.589	1.00
115_E	237_G	0.588	1.00
34_L	38_G	0.585	1.00
233_I	257_T	0.581	1.00
129_L	143_A	0.580	1.00
69_F	84_G	0.579	1.00
209_E	216_N	0.577	1.00
117_V	133_L	0.573	1.00
42_S	54_L	0.570	1.00
253_L	257_T	0.570	1.00
184_T	213_V	0.568	1.00
129_L	156_A	0.566	1.00
32_Q	88_V	0.565	1.00
190_P	193_L	0.562	1.00
159_A	219_A	0.562	1.00
127_A	156_A	0.562	1.00
159_A	221_A	0.561	1.00
160_L	231_A	0.560	1.00
47_S	54_L	0.560	1.00
139_V	240_S	0.559	1.00
150_P	153_A	0.558	1.00
144_P	147_S	0.558	1.00
102_A	106_M	0.557	0.99
68_D	84_G	0.556	0.99
203_G	223_Y	0.555	0.99
104_P	264_A	0.555	0.99
73_D	78_W	0.549	0.99
127_A	154_S	0.548	0.99
114_G	136_K	0.547	0.99
24_L	63_V	0.547	0.99
220_S	233_I	0.546	0.99
62_K	72_Q	0.544	0.99
29_A	32_Q	0.543	0.99
40_S	76_L	0.542	0.99
21_A	60_L	0.542	0.99
158_K	207_D	0.541	0.99
26_R	60_L	0.541	0.99
233_I	254_V	0.540	0.99
190_P	194_K	0.539	0.99
184_T	208_K	0.539	0.99
29_A	33_Y	0.539	0.99
134_E	144_P	0.538	0.99
156_A	217_C	0.536	0.99
27_G	60_L	0.535	0.99
132_Q	143_A	0.532	0.99
35_E	81_I	0.532	0.99
115_E	235_I	0.531	0.99
204_Y	255_R	0.531	0.99
180_Q	183_P	0.529	0.99
86_F	93_I	0.529	0.99
250_Q	253_L	0.528	0.99
173_I	177_G	0.527	0.99
127_A	149_L	0.526	0.99
159_A	205_T	0.525	0.99
222_I	231_A	0.525	0.99
192_L	196_L	0.525	0.99
20_G	63_V	0.524	0.99
223_Y	231_A	0.522	0.99
74_S	77_G	0.521	0.99
115_E	246_R	0.517	0.99
125_N	176_T	0.517	0.99
116_T	132_Q	0.513	0.99
22_Q	63_V	0.512	0.99
131_G	145_L	0.509	0.99
130_I	145_L	0.507	0.99
129_L	149_L	0.506	0.99
129_L	154_S	0.505	0.99
178_L	189_M	0.501	0.99
118_N	234_S	0.500	0.99
28_I	63_V	0.500	0.99

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
2ia2A	4	0.9188	100	0.11	Contact Map
3mq0A	2	0.9262	100	0.111	Contact Map
2g7uA	6	0.9262	100	0.12	Contact Map
3r4kA	2	0.9262	100	0.124	Contact Map
1mkmA	4	0.9114	100	0.129	Contact Map
2xrnA	3	0.8893	100	0.148	Contact Map
2o0yA	4	0.941	100	0.17	Contact Map
1ysqA	1	0.6421	100	0.421	Contact Map
1tf1A	1	0.679	100	0.423	Contact Map
1yspA	1	0.6052	100	0.423	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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