YJIE - ECOLI - GREMLIN Contacts

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YJIE - HTH-type transcriptional regulator YjiE

UniProt:	P39376	Sequences: MDDCGAILHNIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPPLFTWAIEAIDVDEAVDKLREGQSDCIFSFHDEDLLEAPFDHIRLFESQLFPVCASDEHGEALFNLAQPHFPLLNYSRNSYMGRLINRTLTRHSELSFSTFFVSSMSELLKQVALDGCGIAWLPEYAIQQEIRSGKLVVLNRDELVIPIQAYAYRMNTRMNPVAERFWRELRELEIVLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12566
Length:	303 (281)
Sequences:	79234 (57698)
Seq/√Len:	3442.0

ECOLI - YJIE OXYR YDCI TDCA ABGR YHAJ NAC LEUO XAPR LYSR CYSB YBDO CYNR DSDC HCAR YBHD NHAR YIDZ PGRR YNEJ YEEY YFER YBEF TTDR YAHB LRHA CBL ALLS YFIE YAFC AAER YDHB ILVY DMLR METR YNFL YGFI YEIE YHJC YIAU YCAN ICIA GCVA HDFR PERR
BACSU - CYSL YWBI ALSR GLTC YYBE YCGK GLTR CITR YOFA YUST BSDA YKUM YWQM YVBU YTLI CZCR YRAN YOAU YXJO

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
80_H	84_Q	3.764	1.00
25_C	34_S	3.419	1.00
21_T	34_S	2.744	1.00
77_Q	91_E	2.616	1.00
167_I	296_R	2.602	1.00
168_R	274_Q	2.481	1.00
55_V	70_Q	2.360	1.00
20_L	79_R	2.317	1.00
106_A	148_S	2.312	1.00
168_R	171_E	2.268	1.00
175_F	249_E	2.265	1.00
171_E	274_Q	2.252	1.00
20_L	24_K	2.221	1.00
102_K	130_A	2.220	1.00
18_D	45_R	2.177	1.00
77_Q	84_Q	2.169	1.00
21_T	25_C	2.135	1.00
102_K	128_T	2.037	1.00
239_L	260_K	2.014	1.00
238_A	245_A	2.011	1.00
175_F	263_V	2.004	1.00
171_E	272_P	1.997	1.00
104_K	130_A	1.982	1.00
122_Q	294_E	1.974	1.00
173_Q	249_E	1.959	1.00
182_E	195_F	1.952	1.00
23_E	67_L	1.944	1.00
21_T	24_K	1.911	1.00
81_L	85_L	1.893	1.00
75_H	79_R	1.892	1.00
18_D	42_F	1.861	1.00
23_E	75_H	1.859	1.00
235_K	255_E	1.843	1.00
30_Q	33_V	1.831	1.00
239_L	255_E	1.828	1.00
20_L	75_H	1.818	1.00
77_Q	80_H	1.768	1.00
24_K	79_R	1.768	1.00
73_I	91_E	1.757	1.00
196_P	225_F	1.755	1.00
166_H	276_Y	1.735	1.00
178_C	264_L	1.731	1.00
25_C	30_Q	1.695	1.00
142_K	147_Q	1.689	1.00
198_L	243_G	1.663	1.00
59_N	66_Q	1.648	1.00
27_N	30_Q	1.642	1.00
167_I	279_R	1.594	1.00
74_F	88_N	1.589	1.00
279_R	292_W	1.584	1.00
15_W	52_A	1.548	1.00
113_L	232_E	1.544	1.00
165_D	281_N	1.543	1.00
84_Q	87_S	1.542	1.00
61_Q	66_Q	1.536	1.00
20_L	78_I	1.528	1.00
77_Q	87_S	1.510	1.00
15_W	48_A	1.505	1.00
15_W	45_R	1.488	1.00
141_D	145_E	1.479	1.00
292_W	296_R	1.477	1.00
38_S	41_A	1.471	1.00
24_K	34_S	1.469	1.00
165_D	279_R	1.466	1.00
21_T	35_R	1.460	1.00
139_A	151_I	1.449	1.00
142_K	148_S	1.437	1.00
28_F	46_I	1.424	1.00
153_S	278_Y	1.421	1.00
76_S	80_H	1.413	1.00
56_E	59_N	1.400	1.00
207_G	211_N	1.397	1.00
104_K	132_E	1.393	1.00
81_L	88_N	1.375	1.00
155_H	276_Y	1.370	1.00
123_M	291_F	1.370	1.00
284_M	288_A	1.363	1.00
12_E	15_W	1.363	1.00
143_L	151_I	1.344	1.00
29_S	39_Q	1.340	1.00
277_A	292_W	1.338	1.00
77_Q	88_N	1.337	1.00
172_S	250_Y	1.336	1.00
74_F	89_L	1.332	1.00
98_Y	126_L	1.331	1.00
236_Q	239_L	1.326	1.00
168_R	276_Y	1.323	1.00
37_V	41_A	1.314	1.00
255_E	260_K	1.312	1.00
19_F	75_H	1.311	1.00
234_L	245_A	1.308	1.00
290_R	293_R	1.306	1.00
13_T	85_L	1.299	1.00
180_S	262_V	1.291	1.00
100_Q	126_L	1.290	1.00
73_I	77_Q	1.285	1.00
20_L	82_L	1.283	1.00
44_R	48_A	1.282	1.00
150_C	277_A	1.282	1.00
18_D	37_V	1.280	1.00
123_M	127_F	1.280	1.00
144_R	163_P	1.264	1.00
69_E	72_K	1.262	1.00
73_I	76_S	1.238	1.00
195_F	244_I	1.233	1.00
124_P	225_F	1.231	1.00
178_C	244_I	1.228	1.00
118_S	240_D	1.224	1.00
121_S	240_D	1.219	1.00
249_E	263_V	1.215	1.00
187_L	192_Q	1.212	1.00
150_C	288_A	1.209	1.00
180_S	260_K	1.198	1.00
263_V	266_R	1.193	1.00
80_H	87_S	1.177	1.00
19_F	23_E	1.174	1.00
249_E	253_Q	1.169	1.00
167_I	292_W	1.162	1.00
166_H	278_Y	1.161	1.00
124_P	196_P	1.154	1.00
16_L	78_I	1.154	1.00
19_F	58_F	1.149	1.00
52_A	89_L	1.149	1.00
236_Q	240_D	1.135	1.00
44_R	47_R	1.129	1.00
21_T	31_A	1.117	1.00
72_K	76_S	1.116	1.00
132_E	142_K	1.116	1.00
183_H	195_F	1.110	1.00
81_L	84_Q	1.103	1.00
208_R	211_N	1.102	1.00
45_R	48_A	1.100	1.00
235_K	239_L	1.081	1.00
85_L	89_L	1.078	1.00
144_R	161_E	1.076	1.00
196_P	223_S	1.075	1.00
189_N	267_D	1.071	1.00
173_Q	272_P	1.063	1.00
83_Q	87_S	1.054	1.00
177_V	263_V	1.053	1.00
28_F	65_L	1.051	1.00
254_Q	258_S	1.048	1.00
289_E	293_R	1.045	1.00
47_R	51_Q	1.040	1.00
89_L	93_R	1.038	1.00
179_A	241_G	1.036	1.00
199_N	224_T	1.030	1.00
130_A	227_V	1.022	1.00
123_M	294_E	1.012	1.00
103_I	291_F	1.011	1.00
43_S	47_R	1.007	1.00
293_R	296_R	1.004	1.00
70_Q	73_I	1.001	1.00
80_H	83_Q	0.999	1.00
253_Q	257_R	0.998	1.00
208_R	212_R	0.989	1.00
74_F	78_I	0.985	1.00
294_E	297_E	0.981	1.00
48_A	51_Q	0.977	1.00
280_M	283_R	0.974	1.00
165_D	168_R	0.971	1.00
14_K	17_Y	0.965	1.00
182_E	185_E	0.963	1.00
30_Q	34_S	0.963	1.00
31_A	42_F	0.960	1.00
22_L	31_A	0.959	1.00
22_L	28_F	0.958	1.00
26_R	66_Q	0.946	1.00
188_F	262_V	0.944	1.00
239_L	258_S	0.941	1.00
73_I	95_G	0.941	1.00
198_L	234_L	0.938	1.00
19_F	49_L	0.933	1.00
142_K	145_E	0.933	1.00
86_E	89_L	0.925	1.00
17_Y	86_E	0.923	1.00
228_S	234_L	0.922	1.00
23_E	58_F	0.921	1.00
67_L	71_G	0.919	1.00
286_P	290_R	0.914	1.00
119_I	295_L	0.911	1.00
87_S	91_E	0.910	1.00
177_V	252_I	0.909	1.00
19_F	57_L	0.906	1.00
176_P	244_I	0.905	1.00
178_C	182_E	0.901	1.00
37_V	42_F	0.899	1.00
121_S	242_C	0.897	1.00
14_K	45_R	0.896	1.00
285_N	288_A	0.893	1.00
18_D	35_R	0.892	1.00
61_Q	64_P	0.890	1.00
85_L	88_N	0.887	1.00
109_H	230_M	0.884	1.00
29_S	33_V	0.882	1.00
76_S	79_R	0.879	1.00
119_I	294_E	0.878	1.00
25_C	31_A	0.878	1.00
17_Y	21_T	0.875	1.00
157_E	161_E	0.873	1.00
155_H	274_Q	0.872	1.00
19_F	67_L	0.871	1.00
124_P	242_C	0.869	1.00
101_R	287_V	0.867	1.00
228_S	237_V	0.867	1.00
72_K	75_H	0.858	1.00
84_Q	88_N	0.858	1.00
26_R	64_P	0.857	1.00
24_K	75_H	0.855	1.00
255_E	258_S	0.853	1.00
55_V	92_L	0.849	1.00
70_Q	95_G	0.847	1.00
23_E	26_R	0.847	1.00
86_E	90_A	0.843	1.00
17_Y	20_L	0.841	1.00
58_F	65_L	0.838	1.00
209_L	213_T	0.834	1.00
237_V	242_C	0.832	1.00
181_D	241_G	0.826	1.00
22_L	58_F	0.825	1.00
290_R	294_E	0.825	1.00
284_M	289_E	0.824	1.00
70_Q	92_L	0.823	1.00
252_I	255_E	0.820	1.00
35_R	42_F	0.819	1.00
39_Q	43_S	0.812	1.00
140_V	144_R	0.809	1.00
132_E	148_S	0.808	1.00
88_N	92_L	0.807	1.00
184_G	195_F	0.807	1.00
148_S	151_I	0.806	1.00
105_I	150_C	0.802	1.00
79_R	83_Q	0.802	1.00
138_E	141_D	0.798	1.00
212_R	216_R	0.797	1.00
196_P	224_T	0.795	1.00
107_A	112_S	0.793	1.00
106_A	151_I	0.792	1.00
106_A	153_S	0.792	1.00
22_L	42_F	0.791	1.00
206_M	210_I	0.789	1.00
173_Q	270_V	0.788	1.00
146_G	280_M	0.783	1.00
230_M	233_L	0.780	1.00
185_E	262_V	0.780	1.00
213_T	216_R	0.778	1.00
211_N	215_T	0.778	1.00
13_T	82_L	0.775	1.00
22_L	46_I	0.773	1.00
113_L	236_Q	0.773	1.00
28_F	42_F	0.771	1.00
78_I	81_L	0.771	1.00
19_F	74_F	0.764	1.00
178_C	262_V	0.761	1.00
47_R	56_E	0.758	1.00
17_Y	82_L	0.757	1.00
128_T	223_S	0.757	1.00
123_M	290_R	0.754	1.00
19_F	71_G	0.751	1.00
69_E	73_I	0.750	1.00
127_F	287_V	0.749	1.00
118_S	121_S	0.745	1.00
26_R	72_K	0.745	1.00
59_N	68_S	0.744	1.00
178_C	183_H	0.744	1.00
15_W	18_D	0.743	1.00
179_A	182_E	0.742	1.00
164_F	278_Y	0.740	1.00
144_R	164_F	0.739	1.00
214_L	220_L	0.739	1.00
179_A	242_C	0.737	1.00
186_A	196_P	0.737	1.00
176_P	246_W	0.736	1.00
183_H	188_F	0.733	1.00
149_D	288_A	0.731	1.00
177_V	247_L	0.727	1.00
138_E	142_K	0.718	1.00
209_L	212_R	0.716	1.00
116_L	119_I	0.714	1.00
173_Q	265_N	0.714	1.00
213_T	218_S	0.712	1.00
77_Q	81_L	0.711	1.00
23_E	71_G	0.708	1.00
201_S	227_V	0.708	1.00
104_K	149_D	0.706	1.00
150_C	291_F	0.701	1.00
191_A	267_D	0.699	1.00
67_L	72_K	0.696	1.00
23_E	72_K	0.693	1.00
188_F	191_A	0.693	1.00
210_I	213_T	0.689	1.00
177_V	245_A	0.686	1.00
33_V	36_N	0.686	1.00
74_F	92_L	0.686	1.00
252_I	256_I	0.684	1.00
93_R	96_S	0.681	1.00
70_Q	74_F	0.680	1.00
256_I	259_G	0.679	1.00
177_V	256_I	0.672	1.00
193_P	220_L	0.670	1.00
14_K	48_A	0.668	1.00
41_A	45_R	0.665	1.00
82_L	86_E	0.664	1.00
286_P	289_E	0.659	1.00
163_P	281_N	0.651	1.00
59_N	64_P	0.650	1.00
226_F	237_V	0.649	1.00
248_P	251_A	0.644	1.00
210_I	214_L	0.642	1.00
106_A	139_A	0.642	1.00
154_F	273_I	0.642	1.00
53_I	74_F	0.640	1.00
293_R	297_E	0.639	1.00
66_Q	72_K	0.639	1.00
205_Y	208_R	0.638	1.00
182_E	186_A	0.634	1.00
87_S	90_A	0.633	1.00
104_K	148_S	0.632	1.00
197_L	222_F	0.626	1.00
128_T	227_V	0.626	1.00
228_S	233_L	0.622	1.00
178_C	184_G	0.621	1.00
287_V	290_R	0.618	1.00
200_Y	234_L	0.617	1.00
197_L	244_I	0.615	1.00
12_E	52_A	0.615	1.00
50_E	60_R	0.613	1.00
256_I	263_V	0.612	1.00
181_D	184_G	0.609	1.00
191_A	268_E	0.605	1.00
133_A	229_S	0.605	1.00
101_R	127_F	0.604	1.00
207_G	213_T	0.603	1.00
150_C	292_W	0.602	1.00
181_D	185_E	0.601	1.00
121_S	124_P	0.600	1.00
14_K	18_D	0.597	1.00
187_L	190_L	0.591	1.00
117_P	121_S	0.591	1.00
83_Q	86_E	0.589	1.00
279_R	289_E	0.587	1.00
254_Q	257_R	0.586	1.00
143_L	164_F	0.586	1.00
91_E	94_G	0.586	1.00
144_R	147_Q	0.586	1.00
212_R	215_T	0.585	1.00
103_I	150_C	0.583	1.00
22_L	27_N	0.582	1.00
100_Q	128_T	0.581	1.00
155_H	166_H	0.578	1.00
137_D	141_D	0.578	1.00
211_N	214_L	0.578	1.00
182_E	196_P	0.578	1.00
90_A	94_G	0.577	1.00
107_A	131_I	0.577	1.00
180_S	259_G	0.575	1.00
53_I	56_E	0.575	1.00
115_L	119_I	0.575	1.00
55_V	59_N	0.571	1.00
73_I	92_L	0.571	1.00
118_S	122_Q	0.571	1.00
28_F	39_Q	0.569	1.00
184_G	187_L	0.569	1.00
201_S	229_S	0.567	1.00
31_A	35_R	0.567	1.00
186_A	189_N	0.566	1.00
291_F	295_L	0.563	1.00
208_R	213_T	0.561	1.00
207_G	227_V	0.561	1.00
206_M	209_L	0.559	1.00
26_R	65_L	0.558	1.00
214_L	222_F	0.550	1.00
288_A	292_W	0.549	1.00
174_L	246_W	0.547	1.00
53_I	92_L	0.547	1.00
99_A	126_L	0.546	1.00
20_L	86_E	0.545	1.00
88_N	91_E	0.545	1.00
279_R	284_M	0.543	1.00
56_E	70_Q	0.543	1.00
90_A	93_R	0.542	1.00
58_F	67_L	0.542	1.00
183_H	187_L	0.541	1.00
289_E	292_W	0.541	1.00
181_D	262_V	0.540	1.00
232_E	236_Q	0.538	1.00
260_K	263_V	0.537	1.00
169_L	277_A	0.533	1.00
247_L	252_I	0.533	1.00
94_G	99_A	0.530	1.00
48_A	52_A	0.530	1.00
172_S	273_I	0.530	1.00
46_I	50_E	0.530	1.00
16_L	74_F	0.530	1.00
234_L	238_A	0.529	1.00
40_P	43_S	0.528	1.00
78_I	82_L	0.526	1.00
40_P	44_R	0.526	1.00
37_V	45_R	0.526	1.00
178_C	185_E	0.525	1.00
107_A	116_L	0.525	1.00
53_I	89_L	0.524	1.00
182_E	244_I	0.524	1.00
143_L	278_Y	0.522	1.00
172_S	248_P	0.521	1.00
41_A	44_R	0.521	1.00
12_E	48_A	0.520	1.00
101_R	126_L	0.518	1.00
106_A	132_E	0.512	1.00
55_V	96_S	0.511	1.00
113_L	230_M	0.510	1.00
231_S	248_P	0.509	1.00
118_S	236_Q	0.508	1.00
128_T	225_F	0.508	1.00
193_P	221_S	0.507	1.00
111_L	115_L	0.506	1.00
141_D	147_Q	0.505	1.00
157_E	160_L	0.502	1.00
81_L	89_L	0.501	1.00
18_D	46_I	0.501	1.00
183_H	186_A	0.501	1.00
38_S	44_R	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
3fxqA	3	0.9571	100	0.14	Contact Map
2esnA	3	0.9703	100	0.146	Contact Map
1uthA	2	0.7195	100	0.15	Contact Map
3fzvA	4	0.9307	100	0.152	Contact Map
2h98A	2	0.6568	100	0.154	Contact Map
1ixcA	4	0.9439	100	0.156	Contact Map
2h9bA	2	0.6568	100	0.159	Contact Map
4x6gA	4	0.9736	100	0.16	Contact Map
1al3A	1	0.6766	100	0.166	Contact Map
3szpA	3	0.934	100	0.182	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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