YDEF - BACSU - GREMLIN Contacts

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YDEF - Uncharacterized HTH-type transcriptional regulator YdeF

UniProt:	P96663	Sequences: MPINSFENYPMSWKPSIDKAEKPIYKALAGQLEQDILNGVLLPGTKLPPQRELADYLDLNVSTISKAFKVCELKGLLSATVGSGTFVSYDALSNAYLLEDTKPTHLIEMGAILPDHASYEPLLYQLKNMVHEEDYEKWFSYGRAGESLWQKDAAVKLIQRGGFETSVDHILFANGGQNAIAATLASLCKPGDRIGVDHHTYPGLKTVASLLSVQIVPIKSENDEMSPESLEYACKNENIKGLYLIPDYHNPTTSFMSVENRRMVADIVKKYNLFVIEDASYHLLNKNPLPALASFAPQQVIHIASLSKSLAPGLRLAYVAVPRQYKEPISKALYNLNITVSPLLAELTARTIVSNQFEVLIESHREQTIRRNQLVNRYVAGYTCLGVETGIFRWLLLPGKMSGAEFEELAARLGVQVYAAERFVVGNSCPERAVRVSVCAPKTLEELEQGLMILRRLLDDLT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	462 (354)
Sequences:	25810 (17551)
Seq/√Len:	932.8

ECOLI - YDCR YJIR YBDL ALAC AVTA ALAA MALY HIS8
BACSU - YDEF YISV YDFD YHDI GABR YDEL YCXD PATA MTNE AAT2 YUGH AAT3 CBL AAT1 HIS8
HALSA - Q9HQK2 Q9HRX4 Q9HRM6 Q9HQW2 HIS8 Q9HPL0
SULSO - Y104 AAT Q97TY7 Q97YX5 HIS8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
370_R	444_L	3.381	1.00
231_E	270_K	3.335	1.00
127_K	131_H	3.198	1.00
369_I	373_Q	3.124	1.00
258_V	262_R	2.796	1.00
413_L	456_R	2.718	1.00
193_R	214_Q	2.637	1.00
383_T	396_L	2.571	1.00
221_E	260_N	2.486	1.00
159_Q	164_E	2.477	1.00
449_Q	453_I	2.438	1.00
173_A	179_A	2.397	1.00
188_C	213_V	2.389	1.00
192_D	240_K	2.242	1.00
374_L	448_E	2.231	1.00
272_N	299_Q	2.202	1.00
120_E	124_Y	2.130	1.00
155_V	167_V	2.076	1.00
449_Q	452_M	2.070	1.00
268_V	275_V	2.063	1.00
378_Y	451_L	2.059	1.00
181_A	185_A	2.031	1.00
378_Y	452_M	2.003	1.00
443_T	446_E	1.970	1.00
153_A	353_V	1.962	1.00
149_W	349_A	1.947	1.00
402_S	405_E	1.946	1.00
405_E	409_L	1.888	1.00
321_V	326_K	1.866	1.00
109_M	450_G	1.861	1.00
262_R	266_D	1.857	1.00
147_S	346_E	1.831	1.00
152_D	156_K	1.804	1.00
156_K	353_V	1.800	1.00
228_E	263_M	1.787	1.00
148_L	152_D	1.777	1.00
124_Y	128_N	1.768	1.00
219_K	229_S	1.747	1.00
183_T	301_I	1.739	1.00
374_L	444_L	1.737	1.00
231_E	263_M	1.728	1.00
241_G	276_I	1.720	1.00
306_L	348_T	1.698	1.00
266_D	270_K	1.666	1.00
375_V	451_L	1.653	1.00
269_K	297_P	1.651	1.00
380_A	384_C	1.650	1.00
229_S	232_Y	1.647	1.00
227_P	267_I	1.623	1.00
376_N	386_G	1.620	1.00
229_S	233_A	1.617	1.00
158_I	320_A	1.611	1.00
374_L	378_Y	1.606	1.00
145_G	151_K	1.595	1.00
169_H	323_R	1.589	1.00
128_N	350_R	1.588	1.00
126_L	130_V	1.578	1.00
226_S	229_S	1.575	1.00
417_V	434_V	1.574	1.00
257_S	260_N	1.568	1.00
409_L	412_R	1.566	1.00
152_D	167_V	1.565	1.00
263_M	266_D	1.560	1.00
208_A	213_V	1.554	1.00
280_S	305_S	1.550	1.00
198_H	217_P	1.548	1.00
376_N	380_A	1.547	1.00
149_W	353_V	1.536	1.00
409_L	457_L	1.532	1.00
276_I	303_I	1.531	1.00
367_Q	444_L	1.530	1.00
258_V	290_P	1.527	1.00
176_G	303_I	1.522	1.00
413_L	453_I	1.510	1.00
227_P	263_M	1.503	1.00
403_G	421_E	1.495	1.00
319_V	329_I	1.494	1.00
266_D	269_K	1.490	1.00
128_N	132_E	1.486	1.00
376_N	393_R	1.486	1.00
231_E	271_Y	1.478	1.00
316_L	348_T	1.468	1.00
375_V	393_R	1.468	1.00
145_G	330_S	1.462	1.00
193_R	216_V	1.459	1.00
373_Q	377_R	1.458	1.00
234_C	267_I	1.452	1.00
355_N	359_V	1.451	1.00
268_V	273_L	1.439	1.00
333_L	337_N	1.437	1.00
452_M	456_R	1.430	1.00
378_Y	455_R	1.419	1.00
402_S	431_E	1.419	1.00
154_A	172_F	1.418	1.00
367_Q	370_R	1.417	1.00
193_R	238_N	1.413	1.00
231_E	235_K	1.401	1.00
394_W	420_A	1.391	1.00
165_T	320_A	1.388	1.00
104_T	414_G	1.383	1.00
341_S	344_L	1.380	1.00
267_I	273_L	1.379	1.00
259_E	262_R	1.375	1.00
198_H	219_K	1.369	1.00
194_I	208_A	1.366	1.00
258_V	295_F	1.362	1.00
123_L	131_H	1.358	1.00
153_A	156_K	1.353	1.00
380_A	386_G	1.352	1.00
125_Q	129_M	1.346	1.00
362_E	365_R	1.346	1.00
160_R	358_E	1.326	1.00
396_L	433_A	1.326	1.00
376_N	384_C	1.326	1.00
183_T	276_I	1.320	1.00
378_Y	448_E	1.317	1.00
123_L	127_K	1.310	1.00
151_K	155_V	1.308	1.00
410_A	454_L	1.307	1.00
168_D	323_R	1.302	1.00
123_L	130_V	1.296	1.00
195_G	218_I	1.281	1.00
406_F	409_L	1.278	1.00
444_L	448_E	1.278	1.00
366_E	369_I	1.270	1.00
195_G	239_I	1.269	1.00
267_I	271_Y	1.263	1.00
122_L	125_Q	1.254	1.00
301_I	321_V	1.252	1.00
187_L	241_G	1.249	1.00
194_I	241_G	1.245	1.00
184_L	208_A	1.244	1.00
362_E	366_E	1.239	1.00
155_V	170_I	1.224	1.00
125_Q	350_R	1.221	1.00
292_L	300_V	1.208	1.00
372_N	376_N	1.203	1.00
367_Q	371_R	1.201	1.00
408_E	412_R	1.195	1.00
446_E	449_Q	1.194	1.00
153_A	349_A	1.193	1.00
350_R	354_S	1.190	1.00
234_C	273_L	1.189	1.00
291_A	294_S	1.186	1.00
190_P	212_S	1.183	1.00
401_M	405_E	1.180	1.00
259_E	263_M	1.178	1.00
275_V	292_L	1.175	1.00
123_L	129_M	1.173	1.00
403_G	407_E	1.173	1.00
170_I	320_A	1.165	1.00
260_N	263_M	1.162	1.00
146_E	151_K	1.161	1.00
166_S	323_R	1.159	1.00
188_C	194_I	1.148	1.00
193_R	239_I	1.134	1.00
377_R	448_E	1.131	1.00
262_R	295_F	1.129	1.00
149_W	346_E	1.125	1.00
169_H	326_K	1.120	1.00
186_S	332_A	1.116	1.00
154_A	318_Y	1.115	1.00
448_E	452_M	1.112	1.00
304_A	318_Y	1.111	1.00
148_L	151_K	1.109	1.00
148_L	167_V	1.108	1.00
349_A	353_V	1.104	1.00
174_N	178_N	1.097	1.00
178_N	333_L	1.093	1.00
415_V	454_L	1.091	1.00
186_S	329_I	1.089	1.00
242_L	273_L	1.089	1.00
407_E	417_V	1.087	1.00
126_L	347_L	1.084	1.00
150_Q	172_F	1.081	1.00
244_L	264_V	1.073	1.00
225_M	260_N	1.072	1.00
405_E	408_E	1.070	1.00
171_L	326_K	1.069	1.00
204_L	243_Y	1.065	1.00
372_N	438_V	1.064	1.00
125_Q	128_N	1.063	1.00
147_S	349_A	1.060	1.00
350_R	353_V	1.059	1.00
171_L	329_I	1.055	1.00
179_A	303_I	1.048	1.00
223_D	260_N	1.045	1.00
189_K	192_D	1.043	1.00
138_W	346_E	1.043	1.00
184_L	188_C	1.040	1.00
154_A	170_I	1.037	1.00
333_L	340_V	1.036	1.00
178_N	337_N	1.036	1.00
309_S	357_F	1.032	1.00
208_A	215_I	1.031	1.00
185_A	211_L	1.029	1.00
221_E	226_S	1.027	1.00
109_M	447_L	1.025	1.00
403_G	406_F	1.024	1.00
114_P	368_T	1.024	1.00
163_F	293_A	1.023	1.00
235_K	271_Y	1.021	1.00
321_V	329_I	1.017	1.00
269_K	299_Q	1.006	1.00
398_P	432_R	1.006	1.00
395_L	436_V	1.004	1.00
183_T	329_I	1.000	1.00
105_H	446_E	0.999	1.00
327_E	331_K	0.997	1.00
225_M	242_L	0.993	1.00
375_V	447_L	0.991	1.00
269_K	298_Q	0.986	1.00
303_I	319_V	0.980	1.00
404_A	421_E	0.976	1.00
124_Y	127_K	0.975	1.00
195_G	230_L	0.975	1.00
366_E	370_R	0.974	1.00
413_L	457_L	0.968	1.00
410_A	417_V	0.963	1.00
265_A	275_V	0.959	1.00
193_R	235_K	0.958	1.00
121_P	350_R	0.957	1.00
301_I	325_Y	0.951	1.00
124_Y	131_H	0.949	1.00
274_F	299_Q	0.947	1.00
98_L	102_K	0.946	1.00
157_L	283_L	0.943	1.00
265_A	300_V	0.943	1.00
198_H	426_G	0.943	1.00
205_K	209_S	0.940	1.00
223_D	257_S	0.936	1.00
156_K	159_Q	0.935	1.00
328_P	331_K	0.934	1.00
157_L	161_G	0.934	1.00
235_K	239_I	0.934	1.00
373_Q	386_G	0.934	1.00
374_L	377_R	0.931	1.00
410_A	457_L	0.931	1.00
157_L	358_E	0.931	1.00
153_A	352_I	0.926	1.00
293_A	302_H	0.919	1.00
226_S	260_N	0.918	1.00
404_A	408_E	0.918	1.00
326_K	330_S	0.917	1.00
285_N	388_E	0.914	1.00
227_P	260_N	0.909	1.00
401_M	406_F	0.906	1.00
149_W	152_D	0.904	1.00
157_L	160_R	0.899	1.00
195_G	233_A	0.898	1.00
197_D	249_H	0.892	1.00
166_S	169_H	0.891	1.00
420_A	433_A	0.886	1.00
265_A	295_F	0.884	1.00
228_E	232_Y	0.883	1.00
401_M	409_L	0.882	1.00
396_L	432_R	0.882	1.00
301_I	319_V	0.881	1.00
445_E	448_E	0.879	1.00
306_L	318_Y	0.870	1.00
176_G	305_S	0.869	1.00
274_F	301_I	0.868	1.00
285_N	372_N	0.864	1.00
375_V	378_Y	0.860	1.00
179_A	319_V	0.860	1.00
258_V	288_P	0.854	1.00
406_F	434_V	0.852	1.00
187_L	274_F	0.849	1.00
125_Q	131_H	0.848	1.00
375_V	436_V	0.842	1.00
174_N	341_S	0.842	1.00
158_I	302_H	0.841	1.00
184_L	243_Y	0.833	1.00
177_Q	203_G	0.832	1.00
265_A	292_L	0.832	1.00
158_I	318_Y	0.828	1.00
407_E	419_A	0.826	1.00
372_N	387_V	0.822	1.00
231_E	267_I	0.821	1.00
121_P	124_Y	0.820	1.00
290_P	295_F	0.819	1.00
220_S	249_H	0.814	1.00
230_L	267_I	0.814	1.00
118_S	367_Q	0.811	1.00
121_P	354_S	0.811	1.00
364_H	368_T	0.810	1.00
120_E	123_L	0.806	1.00
155_V	165_T	0.801	1.00
265_A	296_A	0.801	1.00
218_I	225_M	0.796	1.00
115_D	371_R	0.793	1.00
204_L	208_A	0.792	1.00
408_E	411_A	0.791	1.00
129_M	347_L	0.791	1.00
239_I	273_L	0.790	1.00
181_A	336_L	0.788	1.00
127_K	130_V	0.787	1.00
196_V	215_I	0.785	1.00
403_G	419_A	0.784	1.00
383_T	398_P	0.783	1.00
296_A	299_Q	0.781	1.00
123_L	126_L	0.780	1.00
224_E	260_N	0.775	1.00
206_T	209_S	0.773	1.00
281_Y	392_F	0.772	1.00
316_L	340_V	0.769	1.00
293_A	296_A	0.768	1.00
118_S	122_L	0.764	1.00
415_V	453_I	0.761	1.00
323_R	327_E	0.759	1.00
172_F	316_L	0.757	1.00
382_Y	397_L	0.756	1.00
105_H	414_G	0.755	1.00
196_V	208_A	0.754	1.00
152_D	353_V	0.752	1.00
363_S	366_E	0.752	1.00
195_G	242_L	0.745	1.00
169_H	297_P	0.743	1.00
403_G	432_R	0.741	1.00
184_L	241_G	0.737	1.00
176_G	280_S	0.737	1.00
209_S	215_I	0.736	1.00
359_V	363_S	0.736	1.00
371_R	444_L	0.734	1.00
175_G	315_R	0.733	1.00
415_V	450_G	0.733	1.00
269_K	296_A	0.731	1.00
188_C	192_D	0.726	1.00
107_I	453_I	0.725	1.00
188_C	241_G	0.723	1.00
161_G	282_H	0.723	1.00
198_H	424_V	0.721	1.00
279_A	282_H	0.721	1.00
397_L	434_V	0.718	1.00
354_S	358_E	0.718	1.00
256_M	261_R	0.717	1.00
358_E	362_E	0.716	1.00
377_R	380_A	0.716	1.00
258_V	294_S	0.715	1.00
128_N	131_H	0.714	1.00
230_L	242_L	0.714	1.00
406_F	457_L	0.712	1.00
174_N	340_V	0.712	1.00
121_P	360_L	0.712	1.00
374_L	447_L	0.711	1.00
155_V	166_S	0.711	1.00
394_W	433_A	0.709	1.00
291_A	302_H	0.706	1.00
405_E	411_A	0.705	1.00
298_Q	322_P	0.705	1.00
286_K	369_I	0.704	1.00
151_K	167_V	0.698	1.00
218_I	233_A	0.697	1.00
228_E	231_E	0.697	1.00
360_L	363_S	0.695	1.00
95_A	98_L	0.695	1.00
409_L	413_L	0.695	1.00
360_L	364_H	0.694	1.00
287_N	388_E	0.693	1.00
222_N	383_T	0.693	1.00
234_C	271_Y	0.693	1.00
249_H	252_T	0.693	1.00
182_A	333_L	0.693	1.00
194_I	213_V	0.693	1.00
261_R	295_F	0.690	1.00
171_L	321_V	0.687	1.00
160_R	283_L	0.684	1.00
452_M	455_R	0.682	1.00
248_Y	389_T	0.681	1.00
182_A	329_I	0.680	1.00
221_E	229_S	0.680	1.00
184_L	213_V	0.679	1.00
449_Q	456_R	0.674	1.00
185_A	336_L	0.674	1.00
147_S	342_P	0.673	1.00
370_R	373_Q	0.672	1.00
372_N	386_G	0.672	1.00
363_S	367_Q	0.669	1.00
112_I	392_F	0.668	1.00
142_G	339_T	0.662	1.00
172_F	345_A	0.660	1.00
261_R	277_E	0.660	1.00
225_M	230_L	0.659	1.00
151_K	168_D	0.654	1.00
122_L	126_L	0.653	1.00
157_L	282_H	0.653	1.00
234_C	239_I	0.653	1.00
184_L	211_L	0.651	1.00
142_G	342_P	0.647	1.00
103_P	414_G	0.645	1.00
346_E	349_A	0.645	1.00
343_L	347_L	0.644	1.00
105_H	453_I	0.643	1.00
285_N	369_I	0.640	1.00
122_L	131_H	0.639	1.00
250_N	281_Y	0.639	1.00
109_M	436_V	0.639	1.00
382_Y	395_L	0.639	1.00
242_L	268_V	0.637	1.00
453_I	456_R	0.636	1.00
290_P	294_S	0.635	1.00
379_V	395_L	0.635	1.00
374_L	451_L	0.633	1.00
247_D	279_A	0.632	1.00
165_T	293_A	0.632	1.00
327_E	330_S	0.631	1.00
230_L	264_V	0.631	1.00
183_T	303_I	0.627	1.00
273_L	299_Q	0.624	1.00
417_V	436_V	0.622	1.00
173_A	319_V	0.622	1.00
99_E	104_T	0.618	1.00
193_R	237_E	0.618	1.00
177_Q	201_Y	0.617	1.00
420_A	424_V	0.616	1.00
105_H	449_Q	0.615	1.00
283_L	309_S	0.613	1.00
420_A	423_F	0.610	1.00
378_Y	447_L	0.610	1.00
321_V	325_Y	0.609	1.00
370_R	374_L	0.608	1.00
171_L	330_S	0.608	1.00
178_N	182_A	0.608	1.00
172_F	340_V	0.607	1.00
279_A	291_A	0.607	1.00
310_L	348_T	0.606	1.00
242_L	267_I	0.605	1.00
440_A	446_E	0.605	1.00
180_I	207_V	0.604	1.00
185_A	332_A	0.603	1.00
112_I	281_Y	0.603	1.00
279_A	302_H	0.603	1.00
177_Q	338_I	0.600	1.00
379_V	384_C	0.600	1.00
293_A	300_V	0.600	1.00
375_V	438_V	0.598	1.00
324_Q	327_E	0.597	1.00
268_V	272_N	0.596	1.00
277_E	302_H	0.595	1.00
316_L	344_L	0.594	1.00
132_E	350_R	0.589	1.00
173_A	317_A	0.588	1.00
296_A	300_V	0.588	1.00
182_A	332_A	0.587	1.00
307_S	315_R	0.585	1.00
411_A	416_Q	0.583	1.00
122_L	129_M	0.582	1.00
142_G	147_S	0.580	1.00
274_F	325_Y	0.577	1.00
284_L	365_R	0.577	1.00
268_V	271_Y	0.576	1.00
125_Q	347_L	0.575	1.00
197_D	218_I	0.573	1.00
154_A	306_L	0.572	1.00
361_I	365_R	0.571	1.00
223_D	259_E	0.571	1.00
377_R	386_G	0.571	1.00
165_T	169_H	0.567	1.00
400_K	458_L	0.565	1.00
427_N	431_E	0.564	1.00
265_A	269_K	0.563	1.00
385_L	396_L	0.562	1.00
216_V	233_A	0.561	1.00
342_P	346_E	0.558	1.00
227_P	231_E	0.558	1.00
155_V	159_Q	0.557	1.00
227_P	264_V	0.557	1.00
129_M	350_R	0.556	1.00
106_L	414_G	0.556	1.00
219_K	226_S	0.555	1.00
402_S	421_E	0.555	1.00
150_Q	154_A	0.555	1.00
256_M	260_N	0.555	1.00
197_D	225_M	0.552	1.00
216_V	239_I	0.551	1.00
453_I	457_L	0.550	1.00
188_C	240_K	0.549	1.00
407_E	411_A	0.548	1.00
322_P	325_Y	0.548	1.00
202_P	422_R	0.546	1.00
107_I	449_Q	0.546	1.00
373_Q	376_N	0.546	1.00
218_I	229_S	0.544	1.00
356_Q	359_V	0.543	1.00
292_L	295_F	0.539	1.00
222_N	385_L	0.539	1.00
355_N	358_E	0.537	1.00
108_E	111_A	0.535	1.00
180_I	276_I	0.533	1.00
308_K	315_R	0.532	1.00
394_W	435_R	0.531	1.00
200_T	205_K	0.531	1.00
347_L	350_R	0.531	1.00
368_T	439_C	0.531	1.00
147_S	345_A	0.529	1.00
192_D	238_N	0.529	1.00
247_D	255_F	0.529	1.00
159_Q	162_G	0.528	1.00
395_L	433_A	0.527	1.00
179_A	317_A	0.527	1.00
244_L	256_M	0.526	1.00
247_D	261_R	0.524	1.00
397_L	400_K	0.523	1.00
379_V	382_Y	0.522	1.00
108_E	416_Q	0.522	1.00
200_T	245_I	0.522	1.00
196_V	205_K	0.521	1.00
201_Y	338_I	0.518	1.00
379_V	451_L	0.518	1.00
381_G	398_P	0.515	1.00
217_P	425_V	0.513	1.00
189_K	240_K	0.512	1.00
406_F	411_A	0.512	1.00
359_V	362_E	0.510	1.00
97_L	100_D	0.510	1.00
256_M	264_V	0.510	1.00
346_E	350_R	0.509	1.00
110_G	416_Q	0.508	1.00
268_V	299_Q	0.508	1.00
117_A	123_L	0.508	1.00
159_Q	163_F	0.507	1.00
103_P	106_L	0.507	1.00
380_A	383_T	0.505	1.00
310_L	358_E	0.504	1.00
121_P	125_Q	0.503	1.00
222_N	260_N	0.502	1.00
384_C	393_R	0.502	1.00
265_A	268_V	0.502	1.00
403_G	434_V	0.501	1.00
216_V	235_K	0.500	1.00
129_M	132_E	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
4tv7A	2	0.9416	100	0.318	Contact Map
3pplA	2	0.8225	100	0.383	Contact Map
3f6tA	2	0.868	100	0.401	Contact Map
3qguA	2	0.829	100	0.41	Contact Map
3ez1A	2	0.8009	100	0.413	Contact Map
2x5fA	2	0.8485	100	0.427	Contact Map
3d6kA	2	0.8074	100	0.439	Contact Map
2r2nA	2	0.8398	100	0.451	Contact Map
1vp4A	2	0.8506	100	0.46	Contact Map
4je5A	2	0.8463	100	0.466	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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