ENVR - ECOLI - GREMLIN Contacts

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ENVR - Probable acrEF/envCD operon repressor

UniProt:	P0ACT2	Sequences: MAKRTKAEALKTRQELIETAIAQFAQHGVSKTTLNDIADAANVTRGAIYWHFENKTQLFNEMWLQQPSLRELIQEHLTAGLEHDPFQQLREKLIVGLQYIAKIPRQQALLKILYHKCEFNDEMLAEGVIREKMGFNPQTLREVLQACQQQGCVANNLDLDVVMIIIDGAFSGIVQNWLMNMAGYDLYKQAPALVDNVLRMFMPDENITKLIHQTNELSVM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11741
Length:	220 (188)
Sequences:	45576 (36169)
Seq/√Len:	2637.9

ECOLI - ENVR ACRR UIDR RUTR SLMA FABR NEMR COMR BETI BDCR YBIH YJDC RCDA
BACSU - YVDT YFIR FADR PKSA YHGD BSCR YVKB YDGC YDES YEZE YTTP LMRA YXAF YVAF YCNC YOBS YUXN YERO
HALSA - Q9HRF3
SULSO - Q97VV1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_N	45_R	3.993	1.00
27_H	36_D	3.957	1.00
22_A	40_A	3.543	1.00
53_E	57_Q	2.727	1.00
24_F	32_T	2.417	1.00
54_N	57_Q	2.247	1.00
38_A	48_I	2.147	1.00
141_R	160_D	2.097	1.00
23_Q	40_A	2.041	1.00
26_Q	40_A	2.004	1.00
13_R	61_E	1.971	1.00
14_Q	65_Q	1.964	1.00
23_Q	36_D	1.941	1.00
23_Q	32_T	1.926	1.00
23_Q	27_H	1.901	1.00
12_T	15_E	1.880	1.00
84_D	87_Q	1.870	1.00
19_T	40_A	1.843	1.00
15_E	19_T	1.842	1.00
88_Q	146_A	1.840	1.00
141_R	145_Q	1.832	1.00
35_N	39_D	1.822	1.00
21_I	65_Q	1.714	1.00
19_T	22_A	1.669	1.00
145_Q	159_L	1.641	1.00
44_T	47_A	1.629	1.00
145_Q	149_Q	1.623	1.00
14_Q	18_E	1.579	1.00
20_A	24_F	1.576	1.00
17_I	61_E	1.542	1.00
34_L	49_Y	1.529	1.00
61_E	64_L	1.525	1.00
21_I	66_Q	1.524	1.00
22_A	26_Q	1.516	1.00
161_V	192_A	1.505	1.00
13_R	51_H	1.504	1.00
145_Q	148_Q	1.503	1.00
34_L	45_R	1.502	1.00
36_D	39_D	1.483	1.00
33_T	36_D	1.476	1.00
36_D	40_A	1.454	1.00
90_R	191_P	1.429	1.00
32_T	37_I	1.426	1.00
74_Q	139_T	1.419	1.00
147_C	153_V	1.365	1.00
165_I	169_A	1.362	1.00
146_A	150_Q	1.356	1.00
65_Q	68_S	1.344	1.00
28_G	32_T	1.339	1.00
21_I	62_M	1.339	1.00
94_I	190_A	1.336	1.00
60_N	64_L	1.335	1.00
52_F	61_E	1.328	1.00
20_A	58_L	1.325	1.00
18_E	65_Q	1.304	1.00
11_K	15_E	1.284	1.00
86_F	198_L	1.269	1.00
34_L	48_I	1.248	1.00
47_A	50_W	1.247	1.00
94_I	191_P	1.241	1.00
27_H	31_K	1.231	1.00
148_Q	155_N	1.220	1.00
90_R	94_I	1.219	1.00
64_L	128_V	1.215	1.00
87_Q	91_E	1.215	1.00
19_T	23_Q	1.197	1.00
94_I	187_Y	1.179	1.00
196_N	200_M	1.175	1.00
137_P	164_I	1.172	1.00
195_D	199_R	1.168	1.00
24_F	29_V	1.168	1.00
45_R	49_Y	1.164	1.00
86_F	90_R	1.161	1.00
72_L	95_V	1.157	1.00
44_T	50_W	1.154	1.00
158_D	161_V	1.145	1.00
147_C	152_C	1.134	1.00
57_Q	61_E	1.130	1.00
116_K	120_N	1.113	1.00
90_R	194_V	1.108	1.00
43_V	47_A	1.102	1.00
56_T	60_N	1.101	1.00
12_T	51_H	1.096	1.00
120_N	123_M	1.094	1.00
11_K	14_Q	1.093	1.00
18_E	22_A	1.079	1.00
46_G	50_W	1.079	1.00
19_T	41_A	1.077	1.00
185_D	188_K	1.077	1.00
28_G	31_K	1.076	1.00
137_P	141_R	1.070	1.00
20_A	62_M	1.065	1.00
17_I	62_M	1.065	1.00
88_Q	143_V	1.063	1.00
168_G	172_G	1.055	1.00
76_H	95_V	1.051	1.00
37_I	58_L	1.049	1.00
91_E	94_I	1.046	1.00
139_T	142_E	1.043	1.00
161_V	188_K	1.042	1.00
29_V	59_F	1.035	1.00
57_Q	60_N	1.031	1.00
60_N	128_V	1.018	1.00
83_H	91_E	1.018	1.00
21_I	25_A	1.017	1.00
64_L	67_P	1.012	1.00
48_I	58_L	1.007	1.00
107_Q	110_L	1.006	1.00
47_A	51_H	1.004	1.00
27_H	40_A	0.999	1.00
56_T	122_E	0.997	1.00
9_A	50_W	0.991	1.00
82_E	88_Q	0.988	1.00
143_V	147_C	0.987	1.00
17_I	52_F	0.977	1.00
134_G	138_Q	0.970	1.00
61_E	65_Q	0.968	1.00
84_D	152_C	0.958	1.00
90_R	195_D	0.957	1.00
177_W	180_N	0.956	1.00
142_E	146_A	0.951	1.00
22_A	105_R	0.942	1.00
72_L	75_E	0.940	1.00
30_S	116_K	0.936	1.00
94_I	98_Q	0.932	1.00
148_Q	159_L	0.928	1.00
115_H	119_F	0.927	1.00
128_V	131_E	0.926	1.00
67_P	71_E	0.924	1.00
154_A	157_L	0.921	1.00
10_L	14_Q	0.918	1.00
49_Y	54_N	0.914	1.00
141_R	159_L	0.908	1.00
138_Q	142_E	0.906	1.00
87_Q	90_R	0.903	1.00
191_P	195_D	0.901	1.00
70_R	135_F	0.894	1.00
85_P	150_Q	0.889	1.00
7_A	11_K	0.885	1.00
194_V	198_L	0.881	1.00
192_A	195_D	0.880	1.00
160_D	164_I	0.873	1.00
95_V	98_Q	0.870	1.00
141_R	163_M	0.858	1.00
71_E	75_E	0.858	1.00
8_E	11_K	0.855	1.00
12_T	43_V	0.851	1.00
187_Y	191_P	0.848	1.00
94_I	194_V	0.846	1.00
143_V	146_A	0.843	1.00
23_Q	26_Q	0.843	1.00
188_K	192_A	0.841	1.00
38_A	45_R	0.838	1.00
15_E	41_A	0.838	1.00
39_D	45_R	0.837	1.00
137_P	160_D	0.832	1.00
91_E	95_V	0.828	1.00
131_E	135_F	0.826	1.00
90_R	198_L	0.825	1.00
76_H	91_E	0.822	1.00
45_R	50_W	0.820	1.00
148_Q	157_L	0.818	1.00
16_L	48_I	0.816	1.00
56_T	120_N	0.808	1.00
142_E	145_Q	0.798	1.00
182_A	185_D	0.797	1.00
135_F	139_T	0.793	1.00
70_R	74_Q	0.788	1.00
99_Y	103_I	0.786	1.00
17_I	65_Q	0.784	1.00
16_L	41_A	0.781	1.00
83_H	87_Q	0.781	1.00
148_Q	153_V	0.775	1.00
9_A	12_T	0.771	1.00
15_E	18_E	0.765	1.00
176_N	179_M	0.746	1.00
103_I	106_Q	0.743	1.00
148_Q	151_G	0.743	1.00
85_P	147_C	0.742	1.00
104_P	108_A	0.737	1.00
148_Q	156_N	0.728	1.00
128_V	132_K	0.727	1.00
157_L	162_V	0.723	1.00
192_A	196_N	0.722	1.00
82_E	87_Q	0.722	1.00
159_L	163_M	0.718	1.00
27_H	32_T	0.716	1.00
138_Q	141_R	0.713	1.00
190_A	193_L	0.709	1.00
130_R	134_G	0.709	1.00
34_L	55_K	0.707	1.00
146_A	149_Q	0.707	1.00
12_T	47_A	0.702	1.00
168_G	171_S	0.699	1.00
17_I	21_I	0.691	1.00
190_A	194_V	0.686	1.00
41_A	44_T	0.683	1.00
116_K	119_F	0.679	1.00
26_Q	36_D	0.677	1.00
71_E	74_Q	0.675	1.00
187_Y	190_A	0.675	1.00
70_R	139_T	0.670	1.00
18_E	21_I	0.667	1.00
144_L	159_L	0.664	1.00
25_A	105_R	0.664	1.00
64_L	132_K	0.663	1.00
189_Q	193_L	0.661	1.00
106_Q	109_L	0.660	1.00
29_V	55_K	0.658	1.00
8_E	12_T	0.655	1.00
7_A	10_L	0.651	1.00
165_I	168_G	0.651	1.00
154_A	199_R	0.646	1.00
135_F	138_Q	0.644	1.00
34_L	38_A	0.643	1.00
98_Q	190_A	0.642	1.00
90_R	93_L	0.638	1.00
122_E	125_A	0.637	1.00
98_Q	187_Y	0.636	1.00
144_L	166_I	0.636	1.00
161_V	164_I	0.635	1.00
93_L	166_I	0.628	1.00
120_N	124_L	0.623	1.00
186_L	189_Q	0.623	1.00
68_S	71_E	0.622	1.00
161_V	165_I	0.622	1.00
35_N	49_Y	0.622	1.00
64_L	131_E	0.620	1.00
176_N	180_N	0.619	1.00
158_D	192_A	0.614	1.00
184_Y	187_Y	0.612	1.00
169_A	193_L	0.611	1.00
120_N	125_A	0.610	1.00
101_A	186_L	0.606	1.00
130_R	133_M	0.605	1.00
29_V	32_T	0.603	1.00
16_L	51_H	0.598	1.00
144_L	148_Q	0.590	1.00
82_E	91_E	0.582	1.00
9_A	51_H	0.581	1.00
197_V	200_M	0.578	1.00
195_D	198_L	0.578	1.00
84_D	88_Q	0.573	1.00
30_S	119_F	0.570	1.00
121_D	124_L	0.569	1.00
168_G	176_N	0.569	1.00
68_S	72_L	0.569	1.00
175_Q	179_M	0.568	1.00
186_L	190_A	0.567	1.00
98_Q	102_K	0.566	1.00
29_V	56_T	0.564	1.00
158_D	162_V	0.560	1.00
184_Y	188_K	0.553	1.00
133_M	137_P	0.549	1.00
99_Y	102_K	0.549	1.00
35_N	44_T	0.548	1.00
139_T	143_V	0.545	1.00
12_T	44_T	0.542	1.00
45_R	48_I	0.539	1.00
189_Q	192_A	0.536	1.00
132_K	136_N	0.535	1.00
72_L	99_Y	0.530	1.00
24_F	59_F	0.530	1.00
191_P	194_V	0.529	1.00
7_A	12_T	0.515	1.00
144_L	147_C	0.514	1.00
93_L	96_G	0.512	1.00
98_Q	186_L	0.512	1.00
38_A	43_V	0.510	1.00
13_R	52_F	0.509	1.00
155_N	158_D	0.508	1.00
10_L	13_R	0.507	1.00
75_E	95_V	0.507	1.00
98_Q	101_A	0.507	1.00
145_Q	160_D	0.506	1.00
183_G	187_Y	0.506	1.00
171_S	175_Q	0.506	1.00
12_T	16_L	0.505	1.00
86_F	152_C	0.504	1.00
166_I	197_V	0.504	1.00
21_I	68_S	0.504	1.00
37_I	41_A	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
2xdnA	2	0.9227	100	0.214	Contact Map
2wuiA	2	0.8909	100	0.244	Contact Map
2w53A	2	0.9045	100	0.247	Contact Map
3lhqA	2	0.9455	100	0.248	Contact Map
2ibdA	2	0.8682	100	0.258	Contact Map
4udsA	2	0.8455	100	0.26	Contact Map
2gfnA	2	0.8682	100	0.263	Contact Map
4cgrA	2	0.8682	100	0.265	Contact Map
3bhqA	2	0.8773	100	0.27	Contact Map
3g1oA	2	0.8636	100	0.273	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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