YIJO - ECOLI - GREMLIN Contacts

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YIJO - Uncharacterized HTH-type transcriptional regulator YijO

UniProt:	P32677	Sequences: MYHDVSYLLSRLINGPLSLRQIYFASSNGPVPDLAYQVDFPRLEIVLEGEFVDTGAGATLVPGDVLYVPAGGWNFPQWQAPATTFSVLFGKQQLGFSVVQWDGKQYQNLAKQHVARRGPRIGSFLLQTLNEMQMQPQEQQTARLIVASLLSHCRDLLGSQIQTASRSQALFEAIRDYIDERYASALTRESVAQAFYISPNYLSHLFQKTGAIGFNEYLNHTRLEHAKTLLKGYDLKVKEVAHACGFVDSNYFCRLFRKNTERSPSEYRRQYHSQLTEKPTTPE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11913
Length:	283 (238)
Sequences:	34381 (29566)
Seq/√Len:	1916.5

ECOLI - YIJO YPDC YQHC MELR YEAM RHAR RHAS YDIP ARAC YIDL YBCM CHBR RCLR EUTR APPY FEAR GADX YDEO ADIY ENVY GADW MARA YKGA SOXS ROB XYLR
BACSU - YISR YFIF YDEC YBFI BTR YOBQ YTDP YESS ADAA YDEE YESN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
227_K	260_T	3.215	1.00
212_I	220_H	3.186	1.00
235_L	243_A	2.981	1.00
223_L	260_T	2.964	1.00
179_D	221_T	2.952	1.00
189_E	199_P	2.848	1.00
225_H	228_T	2.777	1.00
177_Y	181_R	2.767	1.00
220_H	259_N	2.641	1.00
181_R	184_S	2.608	1.00
256_F	267_Y	2.577	1.00
229_L	243_A	2.304	1.00
226_A	252_F	2.292	1.00
174_I	202_L	2.269	1.00
206_F	217_Y	2.096	1.00
229_L	244_C	2.091	1.00
262_R	270_Q	2.042	1.00
187_T	190_S	2.022	1.00
235_L	239_E	1.979	1.00
182_Y	221_T	1.908	1.00
52_V	57_G	1.873	1.00
177_Y	194_A	1.867	1.00
178_I	218_L	1.853	1.00
223_L	259_N	1.823	1.00
229_L	235_L	1.815	1.00
215_N	219_N	1.798	1.00
175_R	210_G	1.796	1.00
174_I	195_F	1.787	1.00
171_F	210_G	1.783	1.00
236_K	239_E	1.726	1.00
52_V	59_T	1.707	1.00
249_S	253_C	1.683	1.00
201_Y	205_L	1.675	1.00
227_K	267_Y	1.674	1.00
188_R	203_S	1.670	1.00
191_V	214_F	1.669	1.00
47_L	85_F	1.643	1.00
48_E	83_T	1.626	1.00
255_L	258_K	1.622	1.00
61_V	64_D	1.622	1.00
238_K	249_S	1.587	1.00
176_D	180_E	1.581	1.00
145_I	148_S	1.570	1.00
225_H	229_L	1.556	1.00
230_L	237_V	1.542	1.00
50_E	59_T	1.538	1.00
199_P	203_S	1.526	1.00
202_L	214_F	1.514	1.00
212_I	216_E	1.511	1.00
179_D	217_Y	1.497	1.00
221_T	225_H	1.471	1.00
228_T	232_G	1.471	1.00
182_Y	225_H	1.460	1.00
144_L	151_S	1.457	1.00
214_F	218_L	1.448	1.00
177_Y	186_L	1.446	1.00
41_P	70_A	1.441	1.00
201_Y	204_H	1.440	1.00
168_Q	209_T	1.440	1.00
239_E	243_A	1.440	1.00
251_Y	255_L	1.432	1.00
262_R	266_E	1.427	1.00
238_K	242_H	1.418	1.00
239_E	242_H	1.414	1.00
197_I	201_Y	1.409	1.00
265_S	269_R	1.381	1.00
240_V	244_C	1.372	1.00
175_R	179_D	1.365	1.00
50_E	61_V	1.364	1.00
183_A	243_A	1.355	1.00
226_A	244_C	1.354	1.00
200_N	204_H	1.353	1.00
52_V	77_Q	1.352	1.00
246_F	255_L	1.348	1.00
174_I	191_V	1.345	1.00
54_T	57_G	1.337	1.00
148_S	152_H	1.334	1.00
250_N	253_C	1.333	1.00
178_I	221_T	1.327	1.00
144_L	148_S	1.321	1.00
225_H	244_C	1.319	1.00
213_G	216_E	1.303	1.00
203_S	214_F	1.277	1.00
190_S	194_A	1.264	1.00
197_I	202_L	1.263	1.00
220_H	224_E	1.261	1.00
219_N	255_L	1.253	1.00
189_E	193_Q	1.249	1.00
54_T	75_F	1.240	1.00
184_S	190_S	1.229	1.00
221_T	224_E	1.226	1.00
143_R	147_A	1.222	1.00
253_C	263_S	1.215	1.00
233_Y	268_R	1.212	1.00
253_C	265_S	1.208	1.00
198_S	201_Y	1.191	1.00
48_E	62_P	1.171	1.00
144_L	147_A	1.168	1.00
69_P	72_G	1.164	1.00
227_K	231_K	1.138	1.00
36_Y	74_N	1.134	1.00
122_G	132_M	1.122	1.00
170_L	197_I	1.116	1.00
127_Q	131_E	1.116	1.00
126_L	132_M	1.106	1.00
254_R	258_K	1.104	1.00
47_L	83_T	1.086	1.00
147_A	151_S	1.085	1.00
235_L	240_V	1.077	1.00
224_E	227_K	1.066	1.00
263_S	266_E	1.063	1.00
188_R	214_F	1.059	1.00
205_L	208_K	1.057	1.00
186_L	191_V	1.042	1.00
266_E	269_R	1.040	1.00
192_A	199_P	1.035	1.00
124_F	127_Q	1.034	1.00
123_S	127_Q	1.033	1.00
183_A	225_H	1.029	1.00
177_Y	195_F	1.028	1.00
170_L	205_L	1.025	1.00
51_F	82_A	1.018	1.00
35_A	73_W	1.014	1.00
169_A	173_A	1.012	1.00
132_M	135_Q	1.009	1.00
38_V	74_N	1.009	1.00
141_T	145_I	1.005	1.00
205_L	209_T	1.000	1.00
219_N	258_K	0.997	1.00
172_E	176_D	0.993	1.00
185_A	190_S	0.992	1.00
170_L	195_F	0.992	1.00
131_E	135_Q	0.991	1.00
200_N	203_S	0.990	1.00
151_S	155_D	0.990	1.00
265_S	268_R	0.990	1.00
38_V	42_R	0.989	1.00
42_R	74_N	0.984	1.00
248_D	254_R	0.983	1.00
185_A	247_V	0.979	1.00
216_E	219_N	0.975	1.00
229_L	240_V	0.956	1.00
188_R	199_P	0.951	1.00
190_S	193_Q	0.951	1.00
148_S	151_S	0.946	1.00
173_A	194_A	0.945	1.00
177_Y	191_V	0.927	1.00
191_V	194_A	0.922	1.00
46_V	51_F	0.920	1.00
126_L	130_N	0.918	1.00
195_F	202_L	0.916	1.00
255_L	259_N	0.911	1.00
106_Y	109_L	0.906	1.00
237_V	240_V	0.905	1.00
253_C	257_R	0.901	1.00
171_F	205_L	0.900	1.00
122_G	128_T	0.893	1.00
175_R	217_Y	0.892	1.00
141_T	148_S	0.890	1.00
260_T	267_Y	0.887	1.00
251_Y	254_R	0.882	1.00
110_A	113_H	0.878	1.00
140_Q	147_A	0.873	1.00
227_K	256_F	0.870	1.00
266_E	270_Q	0.870	1.00
182_Y	186_L	0.867	1.00
197_I	205_L	0.865	1.00
222_R	244_C	0.861	1.00
257_R	263_S	0.860	1.00
129_L	132_M	0.859	1.00
178_I	214_F	0.858	1.00
152_H	156_L	0.855	1.00
122_G	126_L	0.848	1.00
216_E	220_H	0.842	1.00
223_L	255_L	0.839	1.00
219_N	259_N	0.838	1.00
215_N	218_L	0.834	1.00
173_A	176_D	0.830	1.00
127_Q	130_N	0.828	1.00
215_N	251_Y	0.828	1.00
182_Y	218_L	0.822	1.00
51_F	60_L	0.820	1.00
217_Y	221_T	0.815	1.00
171_F	174_I	0.814	1.00
206_F	210_G	0.810	1.00
181_R	194_A	0.802	1.00
128_T	132_M	0.791	1.00
119_P	122_G	0.789	1.00
262_R	267_Y	0.787	1.00
173_A	195_F	0.784	1.00
45_I	65_V	0.782	1.00
140_Q	143_R	0.780	1.00
171_F	209_T	0.778	1.00
230_L	268_R	0.777	1.00
223_L	252_F	0.777	1.00
41_P	67_Y	0.776	1.00
181_R	190_S	0.772	1.00
172_E	175_R	0.769	1.00
42_R	88_L	0.769	1.00
206_F	214_F	0.768	1.00
46_V	49_G	0.767	1.00
139_Q	143_R	0.766	1.00
216_E	259_N	0.763	1.00
233_Y	240_V	0.763	1.00
91_K	95_G	0.762	1.00
226_A	229_L	0.759	1.00
230_L	240_V	0.758	1.00
112_Q	115_A	0.756	1.00
140_Q	144_L	0.755	1.00
191_V	202_L	0.747	1.00
44_E	86_S	0.745	1.00
120_R	123_S	0.744	1.00
257_R	266_E	0.743	1.00
174_I	177_Y	0.743	1.00
128_T	131_E	0.743	1.00
167_S	208_K	0.740	1.00
231_K	267_Y	0.732	1.00
171_F	175_R	0.731	1.00
35_A	75_F	0.731	1.00
82_A	86_S	0.730	1.00
132_M	136_P	0.728	1.00
153_C	157_L	0.728	1.00
138_E	142_A	0.726	1.00
105_Q	108_N	0.721	1.00
241_A	249_S	0.719	1.00
182_Y	244_C	0.717	1.00
186_L	190_S	0.716	1.00
174_I	206_F	0.715	1.00
178_I	217_Y	0.708	1.00
242_H	247_V	0.708	1.00
124_F	131_E	0.705	1.00
204_H	208_K	0.705	1.00
48_E	81_P	0.700	1.00
122_G	125_L	0.698	1.00
203_S	207_Q	0.695	1.00
168_Q	205_L	0.694	1.00
46_V	84_T	0.693	1.00
130_N	134_M	0.689	1.00
49_G	52_V	0.689	1.00
68_V	74_N	0.688	1.00
203_S	213_G	0.688	1.00
51_F	59_T	0.687	1.00
248_D	251_Y	0.686	1.00
123_S	126_L	0.681	1.00
40_F	88_L	0.676	1.00
175_R	206_F	0.672	1.00
107_Q	111_K	0.671	1.00
174_I	214_F	0.671	1.00
247_V	251_Y	0.669	1.00
37_Q	73_W	0.666	1.00
182_Y	222_R	0.665	1.00
118_G	121_I	0.662	1.00
170_L	173_A	0.658	1.00
212_I	217_Y	0.654	1.00
223_L	246_F	0.654	1.00
236_K	240_V	0.648	1.00
117_R	121_I	0.647	1.00
111_K	114_V	0.642	1.00
219_N	251_Y	0.639	1.00
135_Q	138_E	0.638	1.00
60_L	66_L	0.637	1.00
188_R	215_N	0.636	1.00
54_T	77_Q	0.635	1.00
167_S	170_L	0.634	1.00
203_S	215_N	0.632	1.00
133_Q	136_P	0.631	1.00
141_T	151_S	0.630	1.00
179_D	225_H	0.629	1.00
224_E	260_T	0.627	1.00
192_A	195_F	0.627	1.00
240_V	268_R	0.624	1.00
252_F	256_F	0.619	1.00
44_E	84_T	0.619	1.00
249_S	252_F	0.619	1.00
95_G	99_V	0.618	1.00
174_I	178_I	0.617	1.00
124_F	128_T	0.614	1.00
226_A	240_V	0.612	1.00
168_Q	172_E	0.612	1.00
207_Q	213_G	0.610	1.00
186_L	222_R	0.610	1.00
46_V	60_L	0.610	1.00
133_Q	137_Q	0.606	1.00
250_N	263_S	0.603	1.00
50_E	80_A	0.602	1.00
119_P	123_S	0.601	1.00
229_L	232_G	0.597	1.00
174_I	194_A	0.596	1.00
121_I	128_T	0.595	1.00
256_F	262_R	0.595	1.00
210_G	217_Y	0.587	1.00
51_F	76_P	0.583	1.00
78_W	82_A	0.583	1.00
167_S	209_T	0.582	1.00
125_L	129_L	0.581	1.00
104_K	107_Q	0.580	1.00
43_L	65_V	0.580	1.00
76_P	84_T	0.578	1.00
118_G	124_F	0.578	1.00
112_Q	116_R	0.577	1.00
224_E	259_N	0.572	1.00
121_I	132_M	0.571	1.00
252_F	264_P	0.569	1.00
154_R	158_G	0.568	1.00
185_A	222_R	0.568	1.00
44_E	68_V	0.566	1.00
141_T	152_H	0.566	1.00
191_V	195_F	0.564	1.00
121_I	124_F	0.563	1.00
237_V	265_S	0.562	1.00
44_E	66_L	0.561	1.00
115_A	118_G	0.557	1.00
167_S	201_Y	0.556	1.00
177_Y	190_S	0.554	1.00
125_L	128_T	0.553	1.00
193_Q	196_Y	0.552	1.00
142_A	146_V	0.552	1.00
250_N	254_R	0.547	1.00
178_I	186_L	0.544	1.00
157_L	161_I	0.544	1.00
171_F	202_L	0.543	1.00
227_K	262_R	0.541	1.00
141_T	155_D	0.540	1.00
246_F	251_Y	0.540	1.00
176_D	179_D	0.539	1.00
218_L	222_R	0.538	1.00
104_K	108_N	0.537	1.00
93_Q	96_F	0.536	1.00
165_S	168_Q	0.534	1.00
241_A	246_F	0.533	1.00
120_R	124_F	0.533	1.00
65_V	68_V	0.533	1.00
43_L	67_Y	0.532	1.00
107_Q	110_A	0.531	1.00
130_N	133_Q	0.530	1.00
141_T	144_L	0.529	1.00
138_E	155_D	0.529	1.00
91_K	94_L	0.528	1.00
218_L	221_T	0.525	1.00
219_N	223_L	0.524	1.00
140_Q	151_S	0.524	1.00
64_D	116_R	0.523	1.00
92_Q	95_G	0.521	1.00
39_D	90_G	0.520	1.00
146_V	153_C	0.518	1.00
195_F	199_P	0.515	1.00
51_F	78_W	0.513	1.00
248_D	258_K	0.512	1.00
188_R	200_N	0.508	1.00
230_L	267_Y	0.508	1.00
181_R	186_L	0.508	1.00
228_T	231_K	0.507	1.00
121_I	126_L	0.506	1.00
255_L	260_T	0.502	1.00
107_Q	112_Q	0.502	1.00
117_R	122_G	0.501	1.00
186_L	218_L	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
3gbgA	1	0.8728	100	0.244	Contact Map
3oouA	1	0.371	100	0.472	Contact Map
3oioA	1	0.3958	100	0.472	Contact Map
3w6vA	1	0.3922	100	0.474	Contact Map
1bl0A	1	0.4099	100	0.475	Contact Map
3mn2A	1	0.3746	100	0.476	Contact Map
3mklA	1	0.3922	100	0.476	Contact Map
2k9sA	1	0.3746	100	0.483	Contact Map
3lsgA	2	0.3604	100	0.492	Contact Map
1d5yA	1	0.4134	99.9	0.505	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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