YQHC - ECOLI - GREMLIN Contacts

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YQHC - Uncharacterized HTH-type transcriptional regulator YqhC

UniProt:	Q46855	Sequences: MLQNCAQSNCRIIPKKLRDMKREEICRLLADKVNKLKNKENSLSGLLPDVRLLYGETPFARTPVMYEPGIIILFSGHKIGYINERVFRYDANEYLLLTVPLPFECETYATSEVPLAGLRLNVDILQLQELLMDIGEDEHFQPSMAASGINSATLSEEILCAAERLLDVMERPLDARILGKQIIREILYYVLTGPCGGALLALVSRQTHFSLISRVLKRIENKYTENLSVEQLAAEANMSVSAFHHNFKSVTSTSPLQYLKNYRLHKARMMIIHDGMKASAAAMRVGYESASQFSREFKRYFGVTPGEDAARMRAMQGN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13013
Length:	318 (252)
Sequences:	23949 (20183)
Seq/√Len:	1271.4

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
268_R	301_F	3.209	1.00
253_T	261_N	3.107	1.00
220_E	262_Y	3.034	1.00
264_L	301_F	3.026	1.00
276_M	284_R	3.007	1.00
230_E	240_V	2.857	1.00
222_K	225_E	2.711	1.00
266_K	269_M	2.690	1.00
218_R	222_K	2.685	1.00
261_N	300_Y	2.494	1.00
267_A	293_F	2.357	1.00
297_F	308_D	2.310	1.00
270_M	284_R	2.295	1.00
215_V	243_F	2.239	1.00
79_I	86_V	2.168	1.00
247_F	258_Y	2.099	1.00
270_M	285_V	1.994	1.00
79_I	88_R	1.994	1.00
219_I	259_L	1.988	1.00
303_V	311_R	1.954	1.00
223_Y	262_Y	1.934	1.00
276_M	280_A	1.913	1.00
228_S	231_Q	1.897	1.00
256_L	260_K	1.858	1.00
81_Y	86_V	1.852	1.00
212_I	251_T	1.849	1.00
216_L	251_T	1.810	1.00
215_V	236_A	1.805	1.00
218_R	235_E	1.800	1.00
232_L	255_P	1.752	1.00
90_D	93_E	1.739	1.00
270_M	276_M	1.739	1.00
264_L	300_Y	1.730	1.00
229_V	244_H	1.721	1.00
77_H	88_R	1.717	1.00
74_F	118_L	1.714	1.00
75_S	116_A	1.695	1.00
271_I	278_A	1.679	1.00
296_E	299_R	1.661	1.00
277_K	280_A	1.653	1.00
220_E	258_Y	1.641	1.00
182_I	185_E	1.623	1.00
290_A	294_S	1.614	1.00
253_T	257_Q	1.606	1.00
242_A	246_N	1.587	1.00
268_R	308_D	1.576	1.00
262_Y	266_K	1.576	1.00
217_K	221_N	1.561	1.00
218_R	227_L	1.559	1.00
77_H	90_D	1.558	1.00
243_F	255_P	1.548	1.00
79_I	106_E	1.527	1.00
306_G	310_A	1.519	1.00
83_N	101_L	1.516	1.00
223_Y	266_K	1.515	1.00
279_S	290_A	1.512	1.00
255_P	259_L	1.511	1.00
81_Y	104_E	1.510	1.00
292_Q	296_E	1.495	1.00
280_A	284_R	1.476	1.00
303_V	307_E	1.474	1.00
269_M	273_H	1.464	1.00
219_I	262_Y	1.453	1.00
241_S	245_H	1.445	1.00
159_L	163_E	1.441	1.00
281_A	285_V	1.428	1.00
224_T	284_R	1.427	1.00
242_A	245_H	1.426	1.00
230_E	234_A	1.412	1.00
266_K	270_M	1.404	1.00
266_K	285_V	1.384	1.00
280_A	283_M	1.380	1.00
209_F	250_V	1.375	1.00
231_Q	235_E	1.370	1.00
267_A	285_V	1.362	1.00
238_M	242_A	1.360	1.00
244_H	255_P	1.354	1.00
287_Y	296_E	1.351	1.00
240_V	244_H	1.349	1.00
279_S	283_M	1.337	1.00
185_E	189_Y	1.331	1.00
254_S	257_Q	1.329	1.00
211_L	238_M	1.325	1.00
181_Q	188_Y	1.304	1.00
68_P	99_V	1.301	1.00
294_S	304_T	1.292	1.00
238_M	243_F	1.289	1.00
75_S	91_A	1.281	1.00
225_E	231_Q	1.270	1.00
215_V	232_L	1.255	1.00
291_S	294_S	1.255	1.00
294_S	306_G	1.255	1.00
148_G	151_S	1.251	1.00
239_S	242_A	1.229	1.00
274_D	309_A	1.224	1.00
261_N	265_H	1.220	1.00
276_M	281_A	1.220	1.00
260_K	296_E	1.216	1.00
262_Y	265_H	1.214	1.00
98_T	101_L	1.207	1.00
74_F	116_A	1.189	1.00
246_N	249_S	1.165	1.00
216_L	220_E	1.152	1.00
307_E	310_A	1.152	1.00
295_R	299_R	1.149	1.00
181_Q	184_R	1.145	1.00
219_I	255_P	1.143	1.00
181_Q	185_E	1.142	1.00
160_C	163_E	1.140	1.00
218_R	236_A	1.134	1.00
265_H	268_R	1.127	1.00
224_T	266_K	1.110	1.00
233_A	240_V	1.099	1.00
306_G	309_A	1.087	1.00
188_Y	192_T	1.086	1.00
178_L	185_E	1.085	1.00
229_V	255_P	1.083	1.00
172_P	175_A	1.082	1.00
211_L	236_A	1.080	1.00
268_R	272_I	1.059	1.00
210_S	214_R	1.058	1.00
65_M	103_F	1.042	1.00
184_R	188_Y	1.034	1.00
69_G	103_F	1.029	1.00
304_T	307_E	1.028	1.00
63_P	103_F	1.027	1.00
232_L	235_E	1.020	1.00
231_Q	234_A	1.017	1.00
157_E	189_Y	1.002	1.00
163_E	167_D	1.000	1.00
226_N	288_E	0.999	1.00
178_L	182_I	0.998	1.00
214_R	235_E	0.996	1.00
164_R	182_I	0.994	1.00
246_N	250_V	0.992	1.00
160_C	164_R	0.986	1.00
81_Y	106_E	0.985	1.00
268_R	297_F	0.983	1.00
211_L	246_N	0.971	1.00
256_L	292_Q	0.970	1.00
216_L	258_Y	0.966	1.00
152_A	155_S	0.964	1.00
294_S	298_K	0.961	1.00
157_E	160_C	0.957	1.00
296_E	300_Y	0.955	1.00
257_Q	261_N	0.950	1.00
236_A	243_F	0.949	1.00
241_S	244_H	0.944	1.00
263_R	285_V	0.939	1.00
62_T	102_P	0.936	1.00
278_A	281_A	0.925	1.00
72_I	94_Y	0.924	1.00
289_S	295_R	0.924	1.00
223_Y	259_L	0.919	1.00
307_E	311_R	0.915	1.00
270_M	281_A	0.914	1.00
78_K	89_Y	0.910	1.00
71_I	119_R	0.902	1.00
73_L	78_K	0.893	1.00
227_L	232_L	0.892	1.00
223_Y	227_L	0.888	1.00
260_K	299_R	0.888	1.00
212_I	246_N	0.886	1.00
164_R	185_E	0.881	1.00
218_R	232_L	0.881	1.00
292_Q	295_R	0.878	1.00
65_M	69_G	0.875	1.00
68_P	96_L	0.868	1.00
264_L	296_E	0.867	1.00
256_L	259_L	0.867	1.00
274_D	281_A	0.865	1.00
282_A	290_A	0.861	1.00
75_S	114_P	0.860	1.00
212_I	215_V	0.858	1.00
301_F	308_D	0.858	1.00
271_I	309_A	0.855	1.00
238_M	246_N	0.854	1.00
214_R	236_A	0.853	1.00
208_H	249_S	0.851	1.00
223_Y	285_V	0.848	1.00
271_I	281_A	0.847	1.00
147_S	151_S	0.845	1.00
214_R	217_K	0.845	1.00
226_N	231_Q	0.842	1.00
148_G	152_A	0.841	1.00
124_I	128_Q	0.835	1.00
180_K	184_R	0.834	1.00
213_S	217_K	0.831	1.00
78_K	115_L	0.829	1.00
213_S	216_L	0.825	1.00
232_L	243_F	0.825	1.00
247_F	255_P	0.824	1.00
82_I	85_R	0.823	1.00
67_E	121_N	0.822	1.00
257_Q	260_K	0.822	1.00
219_I	258_Y	0.819	1.00
257_Q	300_Y	0.816	1.00
128_Q	132_M	0.816	1.00
78_K	88_R	0.809	1.00
264_L	293_F	0.809	1.00
229_V	240_V	0.806	1.00
69_G	121_N	0.806	1.00
222_K	231_Q	0.806	1.00
73_L	76_G	0.805	1.00
168_V	192_T	0.798	1.00
258_Y	262_Y	0.797	1.00
166_L	170_E	0.796	1.00
62_T	104_E	0.795	1.00
215_V	255_P	0.790	1.00
71_I	117_G	0.789	1.00
244_H	254_S	0.789	1.00
298_K	307_E	0.785	1.00
298_K	304_T	0.783	1.00
177_I	180_K	0.782	1.00
80_G	95_L	0.781	1.00
212_I	250_V	0.778	1.00
189_Y	193_G	0.778	1.00
247_F	251_T	0.776	1.00
222_K	235_E	0.775	1.00
81_Y	84_E	0.773	1.00
89_Y	95_L	0.766	1.00
151_S	155_S	0.765	1.00
215_V	218_R	0.763	1.00
73_L	89_Y	0.762	1.00
303_V	308_D	0.759	1.00
267_A	270_M	0.754	1.00
283_M	288_E	0.753	1.00
244_H	248_K	0.750	1.00
278_A	306_G	0.749	1.00
260_K	300_Y	0.748	1.00
71_I	97_L	0.736	1.00
289_S	292_Q	0.734	1.00
156_E	160_C	0.732	1.00
245_H	249_S	0.731	1.00
178_L	188_Y	0.727	1.00
223_Y	263_R	0.726	1.00
78_K	105_C	0.726	1.00
97_L	103_F	0.725	1.00
211_L	214_R	0.725	1.00
73_L	117_G	0.723	1.00
72_I	162_A	0.723	1.00
176_R	180_K	0.722	1.00
281_A	309_A	0.715	1.00
215_V	247_F	0.713	1.00
175_A	179_G	0.711	1.00
264_L	287_Y	0.709	1.00
227_L	263_R	0.703	1.00
157_E	161_A	0.696	1.00
150_N	154_L	0.695	1.00
70_I	96_L	0.691	1.00
178_L	192_T	0.691	1.00
297_F	303_V	0.686	1.00
272_I	308_D	0.685	1.00
212_I	243_F	0.678	1.00
215_V	235_E	0.678	1.00
155_S	159_L	0.676	1.00
157_E	164_R	0.675	1.00
229_V	256_L	0.673	1.00
161_A	182_I	0.673	1.00
215_V	219_I	0.673	1.00
71_I	80_G	0.672	1.00
147_S	150_N	0.670	1.00
116_A	119_R	0.669	1.00
288_E	292_Q	0.669	1.00
168_V	178_L	0.669	1.00
126_Q	129_E	0.666	1.00
59_F	106_E	0.664	1.00
291_S	304_T	0.664	1.00
82_I	97_L	0.663	1.00
64_V	102_P	0.662	1.00
293_F	305_P	0.662	1.00
77_H	113_V	0.659	1.00
156_E	159_L	0.658	1.00
150_N	153_T	0.656	1.00
267_A	281_A	0.654	1.00
227_L	231_Q	0.654	1.00
160_C	167_D	0.651	1.00
129_E	132_M	0.650	1.00
167_D	171_R	0.650	1.00
179_G	182_I	0.647	1.00
178_L	181_Q	0.645	1.00
71_I	95_L	0.639	1.00
164_R	168_V	0.636	1.00
216_L	247_F	0.635	1.00
177_I	184_R	0.635	1.00
253_T	258_Y	0.634	1.00
129_E	133_D	0.630	1.00
291_S	295_R	0.630	1.00
212_I	216_L	0.629	1.00
115_L	119_R	0.622	1.00
74_F	163_E	0.621	1.00
220_E	266_K	0.620	1.00
151_S	154_L	0.618	1.00
80_G	105_C	0.618	1.00
260_K	264_L	0.614	1.00
208_H	211_L	0.609	1.00
218_R	231_Q	0.609	1.00
244_H	256_L	0.606	1.00
177_I	181_Q	0.604	1.00
209_F	213_S	0.602	1.00
209_F	246_N	0.599	1.00
77_H	110_T	0.598	1.00
164_R	167_D	0.598	1.00
275_G	281_A	0.597	1.00
161_A	164_R	0.595	1.00
219_I	227_L	0.594	1.00
154_L	157_E	0.594	1.00
161_A	165_L	0.592	1.00
161_A	189_Y	0.592	1.00
248_K	254_S	0.590	1.00
229_V	241_S	0.590	1.00
265_H	300_Y	0.590	1.00
222_K	227_L	0.587	1.00
166_L	169_M	0.585	1.00
93_E	151_S	0.584	1.00
290_A	293_F	0.584	1.00
260_K	292_Q	0.584	1.00
232_L	236_A	0.583	1.00
259_L	262_Y	0.578	1.00
206_Q	209_F	0.574	1.00
243_F	246_N	0.574	1.00
251_T	258_Y	0.573	1.00
289_S	299_R	0.572	1.00
138_E	141_Q	0.572	1.00
212_I	236_A	0.571	1.00
218_R	223_Y	0.571	1.00
157_E	167_D	0.568	1.00
86_V	106_E	0.568	1.00
243_F	251_T	0.563	1.00
259_L	263_R	0.561	1.00
69_G	97_L	0.559	1.00
73_L	77_H	0.552	1.00
234_A	237_N	0.552	1.00
236_A	240_V	0.550	1.00
72_I	155_S	0.549	1.00
80_G	97_L	0.548	1.00
245_H	248_K	0.548	1.00
168_V	172_P	0.547	1.00
248_K	251_T	0.545	1.00
277_K	281_A	0.544	1.00
283_M	290_A	0.541	1.00
161_A	186_I	0.538	1.00
189_Y	192_T	0.538	1.00
215_V	238_M	0.534	1.00
185_E	188_Y	0.533	1.00
73_L	115_L	0.532	1.00
118_L	166_L	0.530	1.00
145_A	148_G	0.530	1.00
265_H	301_F	0.527	1.00
263_R	286_G	0.527	1.00
273_H	276_M	0.526	1.00
208_H	250_V	0.524	1.00
174_D	192_T	0.524	1.00
226_N	263_R	0.524	1.00
70_I	94_Y	0.522	1.00
167_D	170_E	0.520	1.00
125_L	128_Q	0.519	1.00
66_Y	123_D	0.518	1.00
169_M	179_G	0.518	1.00
105_C	119_R	0.518	1.00
68_P	124_I	0.518	1.00
178_L	189_Y	0.517	1.00
68_P	71_I	0.517	1.00
211_L	215_V	0.516	1.00
158_I	161_A	0.515	1.00
271_I	308_D	0.515	1.00
68_P	98_T	0.514	1.00
227_L	259_L	0.513	1.00
66_Y	100_P	0.512	1.00
293_F	297_F	0.512	1.00
163_E	166_L	0.512	1.00
61_R	104_E	0.509	1.00
156_E	163_E	0.508	1.00
77_H	91_A	0.507	1.00
260_K	287_Y	0.504	1.00
73_L	95_L	0.504	1.00
229_V	233_A	0.502	1.00
287_Y	292_Q	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	0.8019	100	0.289	Contact Map
1bl0A	1	0.3491	100	0.515	Contact Map
3w6vA	1	0.3459	100	0.517	Contact Map
3oouA	1	0.3302	100	0.518	Contact Map
3oioA	1	0.3522	100	0.519	Contact Map
3mklA	1	0.3491	100	0.523	Contact Map
3mn2A	1	0.3333	100	0.524	Contact Map
2k9sA	1	0.3333	100	0.529	Contact Map
3lsgA	2	0.3208	100	0.537	Contact Map
1d5yA	1	0.3491	99.9	0.543	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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