YCXD - BACSU - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

YCXD - Uncharacterized HTH-type transcriptional regulator YcxD

UniProt:	Q08792	Sequences: MEKYMSLLTRIEEMMQSTSYQEGDRLPSIRQLSARYQVSKSTVIRALQELEKRHLIYSVPKSGYYIVKKSGKSKSGQPGPIDFATSAPDPDVFPYLDFQHCINKAIDTYKNDLFIYGTPKGLPSLIRVLRKLLATQQVFADERHIFITSGVQQALSLLCAMPFPNGKEKIAIEQPGYHLMVEQLETLGIPAIGVKRTEEGLDIAKVERLFQTESIKFFYTMPRFHNPLGCSLSERDKQELVRLAEAYDVYLVEDDYLGDLEENKKADPLYAYDLSSHVIYLKSFSKMMFPGLRVGAAVLPEALTDTFYAYKKLNDIDCSMISQAALEIYLKSGMYGRHKEKIRDSYKERSLRLHQAIRTHRQLGSGRFTFSSGQAPCMHTHLVLPQDLPASRVIHRLEKQGVLLEAIDRHYLSDYPKENLLKINISNVKTEDIERGVKLLMSHL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	444 (350)
Sequences:	33314 (22972)
Seq/√Len:	1227.9

ECOLI - YDCR YJIR YBDL AVTA ALAC ALAA MALY HIS8
BACSU - YCXD YISV YDFD GABR YDEL YHDI YDEF MTNE PATA AAT2 YUGH AAT1 CBL AAT3 HIS8
HALSA - Q9HQK2 Q9HRM6 Q9HRX4 Q9HQW2 HIS8 Q9HPL0
SULSO - Y104 Q97TY7 AAT 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
103_N	107_D	3.581	1.00
348_E	430_T	3.237	1.00
347_K	351_L	2.999	1.00
169_K	190_P	2.907	1.00
134_A	139_F	2.873	1.00
352_R	434_E	2.766	1.00
207_E	246_A	2.677	1.00
234_E	238_Q	2.622	1.00
163_F	189_I	2.605	1.00
148_T	154_A	2.469	1.00
369_T	383_V	2.453	1.00
435_R	439_L	2.378	1.00
128_V	331_K	2.336	1.00
124_S	327_E	2.316	1.00
168_E	216_K	2.290	1.00
396_R	399_K	2.258	1.00
96_L	100_H	2.228	1.00
356_A	437_V	2.059	1.00
299_L	304_T	1.992	1.00
130_R	142_E	1.989	1.00
354_H	372_S	1.954	1.00
356_A	438_K	1.939	1.00
352_R	430_T	1.935	1.00
354_H	358_R	1.930	1.00
156_S	160_A	1.919	1.00
123_P	127_R	1.898	1.00
233_S	236_D	1.893	1.00
205_K	209_L	1.880	1.00
104_K	328_I	1.866	1.00
244_A	251_L	1.854	1.00
203_I	239_E	1.846	1.00
131_K	331_K	1.821	1.00
83_F	436_G	1.818	1.00
122_L	324_A	1.814	1.00
174_Q	193_G	1.814	1.00
169_K	192_I	1.809	1.00
248_D	277_H	1.807	1.00
197_T	236_D	1.807	1.00
429_K	432_D	1.793	1.00
389_P	392_R	1.754	1.00
127_R	142_E	1.734	1.00
158_L	279_I	1.731	1.00
128_V	131_K	1.721	1.00
252_V	281_L	1.718	1.00
238_Q	242_R	1.709	1.00
355_Q	359_T	1.704	1.00
435_R	438_K	1.682	1.00
356_A	359_T	1.682	1.00
345_S	430_T	1.654	1.00
100_H	104_K	1.652	1.00
127_R	131_K	1.648	1.00
99_Q	103_N	1.644	1.00
234_E	267_D	1.637	1.00
356_A	441_M	1.628	1.00
352_R	356_A	1.619	1.00
239_E	242_R	1.614	1.00
144_H	301_E	1.613	1.00
358_R	370_F	1.607	1.00
202_D	205_K	1.602	1.00
205_K	208_R	1.601	1.00
390_A	408_D	1.599	1.00
207_E	239_E	1.590	1.00
120_K	308_Y	1.570	1.00
356_A	360_H	1.557	1.00
404_L	421_L	1.535	1.00
256_Y	283_S	1.534	1.00
356_A	434_E	1.529	1.00
284_F	326_L	1.526	1.00
333_G	337_R	1.520	1.00
353_L	380_T	1.518	1.00
217_F	252_V	1.518	1.00
184_L	189_I	1.515	1.00
242_R	246_A	1.510	1.00
353_L	437_V	1.509	1.00
392_R	396_R	1.506	1.00
165_N	188_G	1.499	1.00
133_L	298_V	1.499	1.00
174_Q	195_K	1.497	1.00
195_K	205_K	1.495	1.00
204_A	239_E	1.488	1.00
169_K	214_S	1.480	1.00
297_A	307_F	1.477	1.00
319_S	322_S	1.471	1.00
140_A	298_V	1.451	1.00
100_H	103_N	1.450	1.00
104_K	108_T	1.449	1.00
354_H	370_F	1.446	1.00
294_V	326_L	1.445	1.00
124_S	331_K	1.428	1.00
430_T	434_E	1.426	1.00
101_C	328_I	1.425	1.00
345_S	348_E	1.425	1.00
210_F	243_L	1.424	1.00
78_P	401_G	1.418	1.00
395_H	398_E	1.412	1.00
360_H	441_M	1.410	1.00
203_I	243_L	1.405	1.00
351_L	355_Q	1.402	1.00
171_A	215_I	1.399	1.00
354_H	380_T	1.399	1.00
327_E	331_K	1.390	1.00
400_Q	439_L	1.387	1.00
207_E	211_Q	1.386	1.00
207_E	247_Y	1.382	1.00
102_I	325_A	1.382	1.00
128_V	327_E	1.381	1.00
120_K	126_I	1.378	1.00
102_I	106_I	1.369	1.00
197_T	200_G	1.362	1.00
159_C	184_L	1.358	1.00
123_P	142_E	1.353	1.00
244_A	249_V	1.340	1.00
392_R	395_H	1.339	1.00
359_T	441_M	1.339	1.00
181_V	185_E	1.339	1.00
328_I	332_S	1.334	1.00
151_V	281_L	1.329	1.00
243_L	249_V	1.325	1.00
235_R	238_Q	1.325	1.00
242_R	245_E	1.319	1.00
171_A	194_V	1.319	1.00
101_C	104_K	1.319	1.00
129_L	296_A	1.318	1.00
243_L	247_Y	1.311	1.00
383_V	420_L	1.310	1.00
170_I	184_L	1.308	1.00
360_H	438_K	1.297	1.00
234_E	272_Y	1.287	1.00
358_R	372_S	1.274	1.00
170_I	217_F	1.259	1.00
238_Q	272_Y	1.255	1.00
236_D	239_E	1.247	1.00
99_Q	107_D	1.246	1.00
282_K	296_A	1.245	1.00
135_T	336_G	1.245	1.00
210_F	249_V	1.241	1.00
263_N	375_A	1.238	1.00
235_R	239_E	1.236	1.00
432_D	435_R	1.232	1.00
381_H	407_I	1.219	1.00
245_E	275_S	1.217	1.00
344_D	347_K	1.210	1.00
169_K	215_I	1.200	1.00
391_S	408_D	1.198	1.00
340_E	344_D	1.195	1.00
218_F	249_V	1.185	1.00
164_P	168_E	1.184	1.00
124_S	324_A	1.181	1.00
143_R	301_E	1.180	1.00
276_S	300_P	1.175	1.00
211_Q	247_Y	1.168	1.00
126_I	130_R	1.164	1.00
350_S	425_I	1.158	1.00
340_E	343_R	1.154	1.00
144_H	275_S	1.151	1.00
306_T	309_A	1.145	1.00
159_C	163_F	1.145	1.00
160_A	187_L	1.141	1.00
345_S	349_R	1.140	1.00
158_L	252_V	1.133	1.00
394_I	404_L	1.131	1.00
385_P	419_N	1.129	1.00
251_L	269_L	1.123	1.00
434_E	438_K	1.118	1.00
311_K	315_D	1.089	1.00
352_R	355_Q	1.087	1.00
169_K	211_Q	1.085	1.00
269_L	278_V	1.073	1.00
268_P	271_A	1.071	1.00
162_P	217_F	1.068	1.00
350_S	354_H	1.064	1.00
146_F	304_T	1.061	1.00
328_I	331_K	1.061	1.00
125_L	147_I	1.058	1.00
113_L	324_A	1.048	1.00
149_S	153_Q	1.048	1.00
132_L	135_T	1.047	1.00
305_D	309_A	1.045	1.00
141_D	144_H	1.037	1.00
163_F	170_I	1.034	1.00
299_L	307_F	1.034	1.00
261_E	266_A	1.033	1.00
144_H	304_T	1.027	1.00
130_R	145_I	1.024	1.00
104_K	107_D	1.020	1.00
245_E	277_H	1.015	1.00
337_R	341_K	1.004	1.00
159_C	219_Y	1.003	1.00
351_L	372_S	0.998	1.00
129_L	147_I	0.998	1.00
153_Q	311_K	0.997	1.00
402_V	440_L	0.996	1.00
391_S	395_H	0.990	1.00
245_E	276_S	0.989	1.00
355_Q	434_E	0.982	1.00
207_E	243_L	0.980	1.00
161_M	310_Y	0.977	1.00
383_V	419_N	0.976	1.00
389_P	418_E	0.976	1.00
141_D	301_E	0.973	1.00
122_L	327_E	0.971	1.00
96_L	99_Q	0.969	1.00
234_E	271_A	0.969	1.00
172_I	191_A	0.967	1.00
382_L	423_I	0.966	1.00
279_I	299_L	0.964	1.00
204_A	208_R	0.964	1.00
360_H	437_V	0.960	1.00
200_G	236_D	0.957	1.00
281_L	297_A	0.956	1.00
181_V	193_G	0.954	1.00
99_Q	106_I	0.953	1.00
145_I	298_V	0.953	1.00
100_H	107_D	0.952	1.00
171_A	209_L	0.951	1.00
132_L	259_D	0.951	1.00
123_P	126_I	0.948	1.00
184_L	191_A	0.947	1.00
101_C	105_A	0.945	1.00
163_F	217_F	0.944	1.00
336_G	340_E	0.935	1.00
135_T	259_D	0.933	1.00
124_S	127_R	0.929	1.00
324_A	327_E	0.929	1.00
241_V	278_V	0.929	1.00
79_G	401_G	0.927	1.00
304_T	308_Y	0.924	1.00
97_D	328_I	0.921	1.00
151_V	283_S	0.920	1.00
199_E	236_D	0.918	1.00
131_K	134_A	0.917	1.00
341_K	344_D	0.915	1.00
211_Q	215_I	0.914	1.00
185_E	191_A	0.914	1.00
279_I	303_L	0.911	1.00
220_T	240_L	0.910	1.00
250_Y	277_H	0.899	1.00
180_M	219_Y	0.899	1.00
97_D	332_S	0.899	1.00
261_E	264_K	0.895	1.00
171_A	206_V	0.893	1.00
129_L	145_I	0.892	1.00
344_D	348_E	0.891	1.00
154_A	281_L	0.889	1.00
396_R	400_Q	0.888	1.00
154_A	297_A	0.885	1.00
196_R	225_H	0.885	1.00
355_Q	358_R	0.882	1.00
138_V	270_Y	0.880	1.00
270_Y	280_Y	0.879	1.00
162_P	250_Y	0.878	1.00
153_Q	315_D	0.876	1.00
338_H	341_K	0.876	1.00
194_V	209_L	0.875	1.00
182_E	185_E	0.875	1.00
384_L	421_L	0.864	1.00
250_Y	279_I	0.863	1.00
263_N	347_K	0.863	1.00
350_S	373_G	0.862	1.00
173_E	194_V	0.860	1.00
368_F	384_L	0.860	1.00
161_M	307_F	0.859	1.00
390_A	419_N	0.859	1.00
349_R	430_T	0.858	1.00
132_L	336_G	0.856	1.00
394_I	406_A	0.854	1.00
130_R	141_D	0.854	1.00
201_L	236_D	0.848	1.00
353_L	356_A	0.844	1.00
395_H	399_K	0.843	1.00
368_F	382_L	0.841	1.00
369_T	385_P	0.836	1.00
132_L	136_Q	0.831	1.00
393_V	421_L	0.830	1.00
279_I	297_A	0.828	1.00
146_F	307_F	0.827	1.00
133_L	296_A	0.827	1.00
121_G	126_I	0.823	1.00
294_V	318_C	0.823	1.00
206_V	218_F	0.822	1.00
301_E	305_D	0.820	1.00
83_F	433_I	0.814	1.00
215_I	249_V	0.810	1.00
72_K	76_G	0.804	1.00
173_E	201_L	0.803	1.00
157_L	307_F	0.800	1.00
128_V	330_L	0.796	1.00
404_L	423_I	0.794	1.00
337_R	340_E	0.792	1.00
206_V	243_L	0.792	1.00
427_N	432_D	0.791	1.00
88_P	346_Y	0.791	1.00
149_S	319_S	0.790	1.00
97_D	338_H	0.784	1.00
203_I	236_D	0.784	1.00
250_Y	303_L	0.783	1.00
108_T	328_I	0.782	1.00
241_V	272_Y	0.780	1.00
97_D	100_H	0.780	1.00
341_K	345_S	0.780	1.00
353_L	425_I	0.779	1.00
350_S	372_S	0.777	1.00
197_T	202_D	0.769	1.00
77_Q	401_G	0.769	1.00
263_N	350_S	0.766	1.00
342_I	346_Y	0.761	1.00
245_E	274_L	0.755	1.00
348_E	352_R	0.755	1.00
159_C	217_F	0.753	1.00
156_S	314_N	0.753	1.00
79_G	432_D	0.751	1.00
158_L	307_F	0.750	1.00
130_R	140_A	0.749	1.00
390_A	418_E	0.745	1.00
225_H	228_L	0.745	1.00
267_D	271_A	0.743	1.00
136_Q	258_G	0.742	1.00
194_V	205_K	0.738	1.00
431_E	434_E	0.738	1.00
201_L	218_F	0.737	1.00
359_T	434_E	0.736	1.00
171_A	218_F	0.734	1.00
203_I	207_E	0.734	1.00
126_I	142_E	0.734	1.00
79_G	435_R	0.731	1.00
348_E	351_L	0.728	1.00
173_E	225_H	0.726	1.00
408_D	418_E	0.724	1.00
311_K	318_C	0.724	1.00
241_V	251_L	0.723	1.00
360_H	364_G	0.723	1.00
390_A	394_I	0.721	1.00
397_L	440_L	0.718	1.00
210_F	247_Y	0.716	1.00
353_L	433_I	0.715	1.00
152_Q	179_L	0.714	1.00
89_D	349_R	0.711	1.00
390_A	406_A	0.711	1.00
105_A	325_A	0.709	1.00
151_V	256_Y	0.707	1.00
339_K	343_R	0.706	1.00
351_L	354_H	0.701	1.00
402_V	439_L	0.701	1.00
381_H	420_L	0.699	1.00
391_S	406_A	0.698	1.00
172_I	184_L	0.696	1.00
133_L	280_Y	0.695	1.00
170_I	189_I	0.693	1.00
353_L	423_I	0.689	1.00
320_M	324_A	0.684	1.00
388_L	396_R	0.684	1.00
393_V	396_R	0.683	1.00
294_V	322_S	0.682	1.00
96_L	107_D	0.680	1.00
127_R	130_R	0.679	1.00
108_T	113_L	0.678	1.00
163_F	168_E	0.676	1.00
338_H	342_I	0.673	1.00
160_A	310_Y	0.672	1.00
192_I	209_L	0.672	1.00
194_V	201_L	0.671	1.00
262_E	347_K	0.671	1.00
174_Q	411_Y	0.670	1.00
199_E	233_S	0.669	1.00
305_D	308_Y	0.666	1.00
267_D	272_Y	0.665	1.00
169_K	213_E	0.662	1.00
324_A	328_I	0.661	1.00
146_F	308_Y	0.659	1.00
273_D	276_S	0.655	1.00
352_R	437_V	0.653	1.00
372_S	375_A	0.653	1.00
204_A	207_E	0.647	1.00
269_L	272_Y	0.644	1.00
259_D	287_M	0.642	1.00
347_K	350_S	0.639	1.00
241_V	245_E	0.639	1.00
232_L	237_K	0.638	1.00
332_S	336_G	0.638	1.00
407_I	420_L	0.638	1.00
265_K	375_A	0.638	1.00
438_K	441_M	0.637	1.00
302_A	305_D	0.634	1.00
388_L	392_R	0.633	1.00
122_L	320_M	0.632	1.00
92_V	98_F	0.631	1.00
237_K	272_Y	0.630	1.00
201_L	206_V	0.630	1.00
230_C	375_A	0.630	1.00
127_R	331_K	0.628	1.00
154_A	295_G	0.627	1.00
180_M	184_L	0.622	1.00
258_G	282_K	0.622	1.00
244_A	248_D	0.622	1.00
370_F	380_T	0.620	1.00
255_D	258_G	0.620	1.00
245_E	273_D	0.619	1.00
91_D	99_Q	0.619	1.00
105_A	328_I	0.618	1.00
147_I	294_V	0.618	1.00
169_K	216_K	0.617	1.00
153_Q	157_L	0.617	1.00
73_S	78_P	0.616	1.00
284_F	296_A	0.616	1.00
224_F	376_P	0.616	1.00
149_S	318_C	0.616	1.00
352_R	433_I	0.615	1.00
105_A	108_T	0.615	1.00
206_V	240_L	0.614	1.00
178_H	409_R	0.613	1.00
382_L	420_L	0.613	1.00
159_C	187_L	0.612	1.00
92_V	345_S	0.611	1.00
218_F	244_A	0.611	1.00
157_L	311_K	0.607	1.00
160_A	314_N	0.605	1.00
173_E	218_F	0.605	1.00
333_G	336_G	0.604	1.00
270_Y	273_D	0.604	1.00
218_F	243_L	0.602	1.00
195_K	202_D	0.601	1.00
132_L	258_G	0.601	1.00
202_D	236_D	0.600	1.00
103_N	106_I	0.598	1.00
172_I	193_G	0.598	1.00
117_G	122_L	0.598	1.00
156_S	187_L	0.597	1.00
146_F	299_L	0.597	1.00
203_I	240_L	0.596	1.00
117_G	317_D	0.596	1.00
210_F	215_I	0.595	1.00
394_I	421_L	0.595	1.00
81_I	439_L	0.594	1.00
174_Q	416_P	0.594	1.00
97_D	101_C	0.592	1.00
117_G	320_M	0.591	1.00
262_E	425_I	0.591	1.00
148_T	297_A	0.590	1.00
105_A	324_A	0.589	1.00
402_V	436_G	0.588	1.00
84_A	403_L	0.587	1.00
241_V	269_L	0.585	1.00
164_P	216_K	0.585	1.00
147_I	318_C	0.584	1.00
102_I	321_I	0.583	1.00
166_G	190_P	0.583	1.00
237_K	269_L	0.581	1.00
97_D	333_G	0.581	1.00
208_R	211_Q	0.581	1.00
241_V	273_D	0.580	1.00
81_I	435_R	0.578	1.00
176_G	221_M	0.577	1.00
86_S	379_H	0.574	1.00
98_F	329_Y	0.573	1.00
273_D	278_V	0.573	1.00
255_D	268_P	0.570	1.00
80_P	403_L	0.570	1.00
237_K	253_E	0.568	1.00
357_I	437_V	0.568	1.00
260_L	343_R	0.568	1.00
357_I	382_L	0.567	1.00
273_D	277_H	0.567	1.00
150_G	293_R	0.566	1.00
241_V	274_L	0.566	1.00
223_R	231_S	0.565	1.00
241_V	244_A	0.563	1.00
95_Y	99_Q	0.563	1.00
159_C	189_I	0.562	1.00
101_C	325_A	0.561	1.00
262_E	350_S	0.560	1.00
98_F	289_F	0.559	1.00
157_L	310_Y	0.559	1.00
343_R	347_K	0.558	1.00
140_A	144_H	0.558	1.00
244_A	247_Y	0.558	1.00
284_F	330_L	0.558	1.00
211_Q	246_A	0.557	1.00
155_L	183_Q	0.557	1.00
163_F	216_K	0.555	1.00
232_L	236_D	0.555	1.00
261_E	265_K	0.553	1.00
244_A	277_H	0.550	1.00
108_T	112_D	0.550	1.00
158_L	281_L	0.548	1.00
172_I	181_V	0.547	1.00
299_L	303_L	0.547	1.00
104_K	332_S	0.542	1.00
397_L	404_L	0.542	1.00
276_S	302_A	0.541	1.00
97_D	337_R	0.541	1.00
80_P	401_G	0.541	1.00
158_L	162_P	0.537	1.00
300_P	303_L	0.531	1.00
325_A	328_I	0.530	1.00
140_A	270_Y	0.530	1.00
223_R	255_D	0.528	1.00
156_S	183_Q	0.528	1.00
193_G	412_L	0.527	1.00
134_A	137_Q	0.526	1.00
371_S	383_V	0.524	1.00
356_A	433_I	0.522	1.00
253_E	269_L	0.521	1.00
336_G	339_K	0.521	1.00
287_M	339_K	0.519	1.00
82_D	403_L	0.517	1.00
232_L	240_L	0.517	1.00
255_D	280_Y	0.516	1.00
257_L	379_H	0.515	1.00
192_I	215_I	0.515	1.00
87_A	115_I	0.514	1.00
388_L	393_V	0.511	1.00
108_T	324_A	0.511	1.00
268_P	280_Y	0.511	1.00
168_E	214_S	0.510	1.00
160_A	186_T	0.510	1.00
147_I	323_Q	0.510	1.00
125_L	327_E	0.509	1.00
285_S	293_R	0.508	1.00
253_E	280_Y	0.507	1.00
137_Q	271_A	0.504	1.00
152_Q	177_Y	0.504	1.00
398_E	403_L	0.504	1.00
134_A	138_V	0.503	1.00
262_E	346_Y	0.501	1.00
230_C	236_D	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	0.9617	100	0.255	Contact Map
3pplA	2	0.8671	100	0.327	Contact Map
3f6tA	2	0.8851	100	0.363	Contact Map
3qguA	2	0.8671	100	0.369	Contact Map
3ez1A	2	0.8514	100	0.371	Contact Map
3d6kA	2	0.8559	100	0.392	Contact Map
2x5fA	2	0.8874	100	0.396	Contact Map
2r2nA	2	0.8829	100	0.399	Contact Map
1vp4A	2	0.8896	100	0.405	Contact Map
4je5A	2	0.8941	100	0.416	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.

Page generated in 0.0117 seconds.