YIDL - ECOLI - GREMLIN Contacts

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YIDL - Uncharacterized HTH-type transcriptional regulator YidL

UniProt:	P31449	Sequences: MNGKLQSSDVKNETPYNIPLLINENVISSGISLISLWHTYADEHYRVIWPRDKKKPLIANSWVAVYTVQGCGKILLKNGEQITLHGNCIIFLKPMDIHSYHCEGLVWEQYWMEFTPTSMMDIPVGQQSVIYNGEIYNQELTEVAELITSPEAIKNNLAVAFLTKIIYQWICLMYADGKKDPQRRQIEKLIATLHASLQQRWSVADMAATIPCSEAWLRRLFLRYTGKTPKEYYLDARLDLALSLLKQQGNSVGEVADTLNFFDSFHFSKAFKHKFGYAPSAVLKNTDQHPTDASPHN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11707
Length:	297 (236)
Sequences:	25983 (22099)
Seq/√Len:	1438.5

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
242_L	275_F	3.160	1.00
250_N	258_T	3.089	1.00
238_L	275_F	3.068	1.00
227_K	235_D	2.970	1.00
194_H	236_A	2.944	1.00
204_A	214_E	2.921	1.00
240_L	243_S	2.710	1.00
196_S	199_Q	2.611	1.00
192_T	196_S	2.523	1.00
235_D	274_K	2.429	1.00
241_A	267_F	2.416	1.00
271_F	282_V	2.373	1.00
244_L	258_T	2.199	1.00
189_L	217_L	2.166	1.00
221_F	232_Y	2.114	1.00
73_K	81_Q	2.030	1.00
250_N	254_E	2.028	1.00
244_L	259_L	1.969	1.00
277_Y	285_N	1.967	1.00
193_L	233_Y	1.918	1.00
202_S	205_D	1.877	1.00
244_L	250_N	1.832	1.00
73_K	83_T	1.788	1.00
238_L	274_K	1.783	1.00
230_K	234_L	1.780	1.00
75_L	81_Q	1.778	1.00
186_I	225_T	1.755	1.00
161_F	164_K	1.742	1.00
197_L	236_A	1.737	1.00
189_L	210_I	1.726	1.00
69_Q	108_E	1.703	1.00
245_L	252_V	1.699	1.00
68_V	110_Y	1.692	1.00
190_I	225_T	1.681	1.00
203_V	218_R	1.672	1.00
192_T	209_T	1.668	1.00
251_S	254_E	1.656	1.00
71_C	83_T	1.634	1.00
264_S	268_S	1.631	1.00
191_A	195_A	1.609	1.00
206_M	229_P	1.608	1.00
242_L	282_V	1.594	1.00
253_G	264_S	1.589	1.00
243_S	247_Q	1.570	1.00
62_W	94_P	1.565	1.00
270_A	273_H	1.557	1.00
216_W	220_L	1.539	1.00
85_H	88_C	1.530	1.00
229_P	233_Y	1.530	1.00
217_L	229_P	1.526	1.00
236_A	240_L	1.520	1.00
77_K	96_D	1.508	1.00
227_K	231_E	1.502	1.00
240_L	244_L	1.497	1.00
192_T	201_W	1.490	1.00
216_W	219_R	1.486	1.00
194_H	232_Y	1.472	1.00
254_E	258_T	1.465	1.00
212_C	216_W	1.449	1.00
261_F	270_A	1.444	1.00
75_L	99_S	1.442	1.00
160_A	167_Y	1.431	1.00
197_L	240_L	1.429	1.00
71_C	85_H	1.422	1.00
266_H	270_A	1.421	1.00
253_G	257_D	1.400	1.00
214_E	218_R	1.397	1.00
164_K	168_Q	1.393	1.00
73_K	101_H	1.381	1.00
280_S	284_K	1.372	1.00
265_F	268_S	1.369	1.00
277_Y	281_A	1.362	1.00
183_R	224_Y	1.359	1.00
218_R	229_P	1.358	1.00
240_L	259_L	1.357	1.00
193_L	236_A	1.354	1.00
241_A	259_L	1.346	1.00
255_V	259_L	1.341	1.00
254_E	257_D	1.331	1.00
198_Q	258_T	1.327	1.00
215_A	219_R	1.326	1.00
204_A	208_A	1.324	1.00
205_D	209_T	1.310	1.00
268_S	278_A	1.279	1.00
212_C	217_L	1.264	1.00
57_L	98_H	1.262	1.00
248_Q	283_L	1.262	1.00
63_V	98_H	1.230	1.00
236_A	239_D	1.219	1.00
228_T	231_E	1.216	1.00
268_S	280_S	1.215	1.00
213_S	216_W	1.207	1.00
189_L	206_M	1.204	1.00
150_P	154_K	1.201	1.00
160_A	164_K	1.196	1.00
234_L	270_A	1.187	1.00
141_T	145_E	1.178	1.00
235_D	239_D	1.168	1.00
69_Q	86_G	1.167	1.00
93_K	96_D	1.166	1.00
199_Q	205_D	1.155	1.00
59_A	98_H	1.144	1.00
160_A	163_T	1.139	1.00
185_Q	212_C	1.138	1.00
56_P	97_I	1.123	1.00
68_V	108_E	1.122	1.00
190_I	194_H	1.115	1.00
242_L	246_K	1.110	1.00
281_A	284_K	1.100	1.00
157_L	164_K	1.070	1.00
146_L	150_P	1.062	1.00
201_W	206_M	1.057	1.00
142_E	146_L	1.051	1.00
157_L	161_F	1.042	1.00
203_V	229_P	1.035	1.00
280_S	283_L	1.028	1.00
220_L	223_R	1.026	1.00
206_M	209_T	1.021	1.00
205_D	208_A	1.013	1.00
200_R	205_D	1.010	1.00
163_T	167_Y	1.008	1.00
126_Q	129_V	1.003	1.00
138_Q	142_E	1.000	1.00
220_L	224_Y	0.997	1.00
239_D	242_L	0.995	1.00
185_Q	220_L	0.992	1.00
263_D	269_K	0.984	1.00
193_L	229_P	0.983	1.00
184_R	188_K	0.981	1.00
72_G	107_W	0.976	1.00
269_K	273_H	0.971	1.00
250_N	255_V	0.970	1.00
278_A	281_A	0.962	1.00
248_Q	255_V	0.954	1.00
185_Q	210_I	0.950	1.00
187_E	191_A	0.949	1.00
192_T	210_I	0.948	1.00
198_Q	240_L	0.942	1.00
167_Y	171_C	0.940	1.00
246_K	286_T	0.940	1.00
207_A	214_E	0.939	1.00
203_V	214_E	0.938	1.00
234_L	273_H	0.936	1.00
138_Q	141_T	0.925	1.00
270_A	274_K	0.925	1.00
59_A	63_V	0.920	1.00
192_T	206_M	0.920	1.00
281_A	285_N	0.919	1.00
268_S	272_K	0.909	1.00
190_I	232_Y	0.908	1.00
128_S	132_N	0.906	1.00
238_L	270_A	0.894	1.00
210_I	217_L	0.892	1.00
62_W	91_F	0.887	1.00
67_T	72_G	0.886	1.00
188_K	209_T	0.885	1.00
186_I	189_L	0.880	1.00
76_L	80_E	0.879	1.00
72_G	84_L	0.876	1.00
231_E	234_L	0.869	1.00
230_K	266_H	0.863	1.00
197_L	233_Y	0.861	1.00
159_V	163_T	0.859	1.00
215_A	218_R	0.854	1.00
132_N	136_Y	0.854	1.00
237_R	259_L	0.851	1.00
71_C	103_E	0.850	1.00
244_L	255_V	0.848	1.00
242_L	271_F	0.847	1.00
188_K	191_A	0.841	1.00
116_P	120_M	0.840	1.00
200_R	262_F	0.838	1.00
188_K	210_I	0.833	1.00
231_E	274_K	0.833	1.00
231_E	235_D	0.825	1.00
234_L	274_K	0.819	1.00
66_Y	89_I	0.817	1.00
252_V	255_V	0.813	1.00
139_E	142_E	0.802	1.00
73_K	103_E	0.801	1.00
197_L	259_L	0.800	1.00
275_F	282_V	0.795	1.00
75_L	101_H	0.792	1.00
74_I	90_I	0.789	1.00
164_K	167_Y	0.788	1.00
134_E	137_N	0.786	1.00
221_F	225_T	0.786	1.00
75_L	78_N	0.781	1.00
212_C	220_L	0.779	1.00
63_V	113_E	0.779	1.00
128_S	131_Y	0.778	1.00
156_N	160_A	0.778	1.00
218_R	228_T	0.777	1.00
56_P	99_S	0.776	1.00
65_V	111_W	0.775	1.00
77_K	80_E	0.773	1.00
145_E	149_S	0.764	1.00
186_I	220_L	0.764	1.00
221_F	229_P	0.761	1.00
266_H	269_K	0.760	1.00
245_L	283_L	0.757	1.00
147_I	150_P	0.753	1.00
238_L	267_F	0.751	1.00
187_E	190_I	0.751	1.00
130_I	136_Y	0.750	1.00
257_D	262_F	0.749	1.00
72_G	83_T	0.748	1.00
230_K	233_Y	0.748	1.00
245_L	255_V	0.746	1.00
272_K	281_A	0.746	1.00
196_S	205_D	0.744	1.00
168_Q	172_L	0.742	1.00
206_M	217_L	0.731	1.00
67_T	109_Q	0.730	1.00
127_Q	131_Y	0.729	1.00
157_L	167_Y	0.729	1.00
255_V	283_L	0.728	1.00
197_L	201_W	0.728	1.00
241_A	244_L	0.725	1.00
193_L	232_Y	0.725	1.00
189_L	192_T	0.724	1.00
189_L	229_P	0.723	1.00
58_I	97_I	0.723	1.00
65_V	109_Q	0.720	1.00
61_S	113_E	0.720	1.00
155_N	159_V	0.718	1.00
246_K	282_V	0.718	1.00
67_T	70_G	0.715	1.00
84_L	90_I	0.710	1.00
182_Q	223_R	0.708	1.00
238_L	261_F	0.706	1.00
69_Q	106_V	0.706	1.00
186_I	224_Y	0.700	1.00
142_E	145_E	0.700	1.00
272_K	278_A	0.698	1.00
189_L	221_F	0.698	1.00
133_G	137_N	0.697	1.00
263_D	266_H	0.693	1.00
72_G	100_Y	0.689	1.00
92_L	98_H	0.687	1.00
139_E	147_I	0.687	1.00
252_V	280_S	0.686	1.00
262_F	266_H	0.683	1.00
251_S	255_V	0.682	1.00
271_F	277_Y	0.678	1.00
232_Y	236_A	0.678	1.00
118_S	121_D	0.676	1.00
277_Y	282_V	0.674	1.00
256_A	264_S	0.673	1.00
156_N	159_V	0.670	1.00
125_G	128_S	0.664	1.00
241_A	255_V	0.662	1.00
139_E	143_V	0.660	1.00
218_R	222_L	0.657	1.00
154_K	158_A	0.656	1.00
157_L	160_A	0.656	1.00
64_A	89_I	0.655	1.00
74_I	100_Y	0.654	1.00
143_V	146_L	0.653	1.00
227_K	232_Y	0.647	1.00
183_R	220_L	0.646	1.00
201_W	237_R	0.646	1.00
153_I	156_N	0.645	1.00
265_F	278_A	0.644	1.00
142_E	164_K	0.640	1.00
233_Y	237_R	0.638	1.00
65_V	90_I	0.632	1.00
139_E	146_L	0.631	1.00
157_L	171_C	0.629	1.00
132_N	135_I	0.628	1.00
158_A	161_F	0.626	1.00
64_A	91_F	0.622	1.00
196_S	209_T	0.622	1.00
203_V	230_K	0.622	1.00
107_W	111_W	0.621	1.00
156_N	163_T	0.614	1.00
201_W	205_D	0.614	1.00
182_Q	224_Y	0.612	1.00
197_L	237_R	0.610	1.00
88_C	131_Y	0.606	1.00
218_R	230_K	0.606	1.00
186_I	190_I	0.602	1.00
67_T	84_L	0.602	1.00
185_Q	188_K	0.600	1.00
142_E	161_F	0.600	1.00
161_F	168_Q	0.599	1.00
222_L	228_T	0.596	1.00
182_Q	185_Q	0.595	1.00
88_C	129_V	0.592	1.00
234_L	266_H	0.589	1.00
138_Q	145_E	0.589	1.00
152_A	155_N	0.588	1.00
219_R	223_R	0.586	1.00
267_F	279_P	0.585	1.00
190_I	221_F	0.585	1.00
189_L	209_T	0.582	1.00
146_L	171_C	0.581	1.00
117_T	120_M	0.581	1.00
67_T	107_W	0.581	1.00
143_V	147_I	0.581	1.00
189_L	193_L	0.579	1.00
144_A	148_T	0.578	1.00
137_N	141_T	0.577	1.00
124_V	128_S	0.577	1.00
76_L	92_L	0.576	1.00
74_I	92_L	0.576	1.00
62_W	65_V	0.575	1.00
126_Q	130_I	0.572	1.00
129_V	132_N	0.568	1.00
203_V	215_A	0.568	1.00
249_G	255_V	0.568	1.00
265_F	269_K	0.562	1.00
60_N	115_T	0.560	1.00
186_I	217_L	0.560	1.00
77_K	97_I	0.559	1.00
68_V	141_T	0.556	1.00
217_L	220_L	0.553	1.00
66_Y	140_L	0.552	1.00
157_L	168_Q	0.552	1.00
194_H	240_L	0.552	1.00
233_Y	236_A	0.549	1.00
264_S	267_F	0.547	1.00
180_D	183_R	0.547	1.00
117_T	121_D	0.546	1.00
200_R	237_R	0.545	1.00
256_A	261_F	0.545	1.00
65_V	92_L	0.544	1.00
129_V	136_Y	0.544	1.00
239_D	274_K	0.543	1.00
263_D	273_H	0.540	1.00
124_V	136_Y	0.539	1.00
170_I	173_M	0.538	1.00
193_L	201_W	0.537	1.00
78_N	81_Q	0.537	1.00
60_N	95_M	0.532	1.00
53_K	101_H	0.529	1.00
267_F	271_F	0.528	1.00
244_L	247_Q	0.522	1.00
201_W	233_Y	0.521	1.00
62_W	93_K	0.521	1.00
63_V	92_L	0.520	1.00
261_F	266_H	0.520	1.00
153_I	157_L	0.519	1.00
119_M	122_I	0.517	1.00
102_C	107_W	0.517	1.00
206_M	210_I	0.513	1.00
208_A	211_P	0.512	1.00
158_A	169_W	0.507	1.00
196_S	201_W	0.507	1.00
192_T	205_D	0.505	1.00
243_S	246_K	0.504	1.00
65_V	100_Y	0.503	1.00
131_Y	136_Y	0.502	1.00
130_I	133_G	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	0.8316	100	0.291	Contact Map
1bl0A	1	0.3872	100	0.503	Contact Map
3w6vA	1	0.3737	100	0.504	Contact Map
3oouA	1	0.3535	100	0.505	Contact Map
3oioA	1	0.3771	100	0.505	Contact Map
3mklA	1	0.3737	100	0.511	Contact Map
3mn2A	1	0.3569	100	0.511	Contact Map
2k9sA	1	0.3569	100	0.517	Contact Map
3lsgA	2	0.3434	100	0.521	Contact Map
1d5yA	1	0.3906	99.9	0.531	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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