DEGA - BACSU - GREMLIN Contacts

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DEGA - HTH-type transcriptional regulator DegA

UniProt:	P37947	Sequences: MKTTIYDVAKAAGVSITTVSRVINNTGRISDKTRQKVMNVMNEMAYTPNVHAAALTGKRTNMIALVAPDISNPFYGELAKSIEERADELGFQMLICSTDYDPKKETKYFSVLKQKKVDGIIFATGIESHDSMSALEEIASEQIPIAMISQDKPLLPMDIVVIDDVRGGYEAAKHLLSLGHTNIACIIGDGSTTGEKNRIKGFRQAMEEAGVPIDESLIIQTRFSLESGKEEAGKLLDRNAPTAIFAFNDVLACAAIQAARIRGIKVPDDLSIIGFDNTILAEMAAPPLTTVAQPIKEMGAERHRTAGRSNRGKRKAKQKIVLPPELVVRHSTSPLNT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	337 (323)
Sequences:	37040 (26721)
Seq/√Len:	1486.8

ECOLI - GALR GALS CYTR PURR LACI YCJW IDNR ASCG CRA GNTR RBSR MALI EBGR TRER TORT YTFQ ALSB XYLF RBSB YPHF ARAF LSRB DGAL XYLR
BACSU - DEGA CCPA KDGR RBSR EXUR NTDR MSMR YKVZ GANR YVDE ARAR CCPB RBSB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
165_V	204_Q	3.276	1.00
180_H	242_T	3.045	1.00
11_A	43_E	3.042	1.00
265_K	268_D	2.977	1.00
199_I	203_R	2.597	1.00
119_G	306_A	2.597	1.00
171_A	273_I	2.557	1.00
180_H	271_S	2.419	1.00
277_N	292_A	2.350	1.00
158_D	309_S	2.330	1.00
169_Y	208_E	2.245	1.00
31_D	35_Q	2.238	1.00
39_N	43_E	2.203	1.00
233_G	262_R	2.152	1.00
229_K	261_I	2.150	1.00
35_Q	39_N	2.134	1.00
85_R	88_E	2.121	1.00
173_K	205_A	2.105	1.00
233_G	258_A	2.088	1.00
85_R	304_R	2.084	1.00
169_Y	205_A	2.065	1.00
176_L	209_A	2.055	1.00
166_R	170_E	2.050	1.00
169_Y	204_Q	2.027	1.00
22_V	37_V	2.008	1.00
301_E	304_R	1.992	1.00
86_A	303_H	1.936	1.00
85_R	300_A	1.913	1.00
178_L	332_T	1.895	1.00
165_V	200_K	1.882	1.00
6_Y	16_I	1.879	1.00
34_R	38_M	1.871	1.00
23_I	41_M	1.866	1.00
175_L	243_A	1.849	1.00
167_G	275_F	1.841	1.00
168_G	172_A	1.812	1.00
11_A	40_V	1.798	1.00
172_A	202_F	1.773	1.00
292_A	325_E	1.764	1.00
81_S	299_G	1.761	1.00
237_D	262_R	1.761	1.00
173_K	177_S	1.758	1.00
12_A	40_V	1.747	1.00
168_G	245_F	1.747	1.00
173_K	209_A	1.739	1.00
301_E	320_I	1.734	1.00
184_A	241_P	1.733	1.00
259_A	270_L	1.717	1.00
169_Y	173_K	1.689	1.00
308_R	313_K	1.687	1.00
84_E	296_K	1.679	1.00
228_G	254_A	1.675	1.00
232_A	255_A	1.671	1.00
229_K	258_A	1.655	1.00
64_A	117_V	1.653	1.00
246_A	255_A	1.650	1.00
85_R	89_L	1.629	1.00
258_A	262_R	1.623	1.00
185_C	247_F	1.621	1.00
81_S	296_K	1.618	1.00
264_I	269_D	1.610	1.00
294_P	297_E	1.609	1.00
182_N	214_D	1.602	1.00
170_E	324_P	1.586	1.00
174_H	178_L	1.583	1.00
148_I	302_R	1.570	1.00
265_K	269_D	1.550	1.00
174_H	177_S	1.545	1.00
166_R	169_Y	1.541	1.00
287_P	330_H	1.536	1.00
260_R	285_A	1.517	1.00
38_M	42_N	1.516	1.00
258_A	261_I	1.506	1.00
297_E	301_E	1.497	1.00
219_I	234_K	1.490	1.00
89_L	307_G	1.480	1.00
174_H	328_V	1.470	1.00
176_L	205_A	1.468	1.00
200_K	204_Q	1.449	1.00
307_G	311_R	1.438	1.00
163_D	166_R	1.421	1.00
273_I	289_T	1.418	1.00
38_M	41_M	1.414	1.00
22_V	41_M	1.410	1.00
8_V	40_V	1.403	1.00
205_A	208_E	1.403	1.00
203_R	207_E	1.400	1.00
61_N	118_D	1.389	1.00
167_G	324_P	1.363	1.00
197_N	200_K	1.361	1.00
297_E	300_A	1.354	1.00
214_D	217_L	1.350	1.00
182_N	242_T	1.348	1.00
11_A	44_M	1.344	1.00
277_N	329_R	1.341	1.00
259_A	264_I	1.340	1.00
229_K	257_Q	1.337	1.00
229_K	233_G	1.336	1.00
85_R	303_H	1.315	1.00
222_R	227_S	1.305	1.00
233_G	261_I	1.283	1.00
40_V	43_E	1.279	1.00
6_Y	10_K	1.276	1.00
31_D	34_R	1.275	1.00
36_K	40_V	1.273	1.00
172_A	205_A	1.269	1.00
172_A	176_L	1.265	1.00
121_I	302_R	1.264	1.00
233_G	237_D	1.263	1.00
165_V	169_Y	1.260	1.00
172_A	201_G	1.254	1.00
61_N	91_F	1.251	1.00
7_D	10_K	1.248	1.00
21_R	26_T	1.238	1.00
184_A	235_L	1.235	1.00
170_E	173_K	1.234	1.00
174_H	332_T	1.231	1.00
30_S	33_T	1.226	1.00
168_G	201_G	1.218	1.00
63_I	86_A	1.212	1.00
232_A	244_I	1.207	1.00
96_C	108_Y	1.201	1.00
304_R	308_R	1.200	1.00
86_A	93_M	1.193	1.00
33_T	36_K	1.189	1.00
232_A	259_A	1.187	1.00
64_A	112_L	1.184	1.00
205_A	209_A	1.184	1.00
40_V	44_M	1.183	1.00
201_G	205_A	1.181	1.00
256_I	272_I	1.177	1.00
173_K	208_E	1.174	1.00
5_I	16_I	1.171	1.00
82_I	303_H	1.169	1.00
180_H	243_A	1.159	1.00
234_K	238_R	1.159	1.00
181_T	242_T	1.151	1.00
296_K	300_A	1.148	1.00
8_V	12_A	1.148	1.00
8_V	44_M	1.147	1.00
136_E	140_S	1.144	1.00
96_C	112_L	1.142	1.00
231_E	234_K	1.141	1.00
62_M	92_Q	1.140	1.00
202_F	206_M	1.138	1.00
65_L	82_I	1.137	1.00
22_V	29_I	1.125	1.00
35_Q	38_M	1.116	1.00
305_T	320_I	1.111	1.00
165_V	197_N	1.102	1.00
89_L	304_R	1.092	1.00
62_M	94_L	1.092	1.00
301_E	305_T	1.087	1.00
185_C	199_I	1.086	1.00
165_V	201_G	1.080	1.00
110_S	137_E	1.080	1.00
83_E	87_D	1.080	1.00
271_S	332_T	1.079	1.00
39_N	42_N	1.078	1.00
171_A	245_F	1.069	1.00
82_I	121_I	1.065	1.00
224_S	227_S	1.064	1.00
25_N	34_R	1.057	1.00
204_Q	208_E	1.052	1.00
226_E	230_E	1.050	1.00
183_I	206_M	1.047	1.00
254_A	258_A	1.045	1.00
299_G	303_H	1.040	1.00
244_I	255_A	1.037	1.00
182_N	240_A	1.034	1.00
186_I	255_A	1.033	1.00
200_K	203_R	1.031	1.00
65_L	93_M	1.030	1.00
106_T	110_S	1.029	1.00
292_A	327_V	1.028	1.00
176_L	211_V	1.024	1.00
249_D	290_T	1.021	1.00
91_F	307_G	1.021	1.00
219_I	231_E	1.016	1.00
300_A	304_R	1.016	1.00
5_I	19_V	1.014	1.00
87_D	104_K	1.012	1.00
246_A	251_L	1.009	1.00
166_R	323_P	1.001	1.00
196_K	200_K	0.999	1.00
104_K	107_K	0.997	1.00
158_D	305_T	0.994	1.00
178_L	328_V	0.983	1.00
260_R	287_P	0.981	1.00
41_M	44_M	0.980	1.00
202_F	245_F	0.974	1.00
301_E	322_L	0.973	1.00
178_L	271_S	0.970	1.00
193_T	197_N	0.969	1.00
51_H	54_A	0.968	1.00
246_A	252_A	0.968	1.00
177_S	209_A	0.965	1.00
190_G	220_Q	0.964	1.00
306_A	310_N	0.962	1.00
213_I	216_S	0.962	1.00
183_I	243_A	0.961	1.00
206_M	211_V	0.960	1.00
12_A	19_V	0.958	1.00
132_M	136_E	0.957	1.00
49_N	55_L	0.956	1.00
89_L	311_R	0.954	1.00
230_E	234_K	0.952	1.00
294_P	325_E	0.949	1.00
79_A	83_E	0.948	1.00
174_H	289_T	0.947	1.00
227_S	230_E	0.946	1.00
249_D	274_G	0.944	1.00
232_A	236_L	0.940	1.00
225_L	257_Q	0.938	1.00
25_N	38_M	0.923	1.00
110_S	114_Q	0.918	1.00
256_I	266_V	0.912	1.00
256_I	284_A	0.911	1.00
121_I	306_A	0.911	1.00
228_G	232_A	0.910	1.00
80_K	84_E	0.910	1.00
325_E	328_V	0.909	1.00
172_A	206_M	0.906	1.00
88_E	300_A	0.906	1.00
159_I	319_K	0.906	1.00
171_A	291_V	0.895	1.00
280_L	283_M	0.890	1.00
244_I	270_L	0.877	1.00
305_T	308_R	0.872	1.00
203_R	213_I	0.871	1.00
182_N	217_L	0.870	1.00
176_L	181_T	0.869	1.00
74_F	295_I	0.858	1.00
82_I	299_G	0.858	1.00
22_V	38_M	0.856	1.00
48_P	53_A	0.856	1.00
161_V	319_K	0.852	1.00
163_D	321_V	0.850	1.00
264_I	270_L	0.848	1.00
49_N	52_A	0.846	1.00
181_T	211_V	0.845	1.00
78_L	148_I	0.837	1.00
52_A	55_L	0.832	1.00
230_E	233_G	0.829	1.00
166_R	324_P	0.828	1.00
238_R	241_P	0.828	1.00
164_D	198_R	0.828	1.00
84_E	300_A	0.826	1.00
158_D	318_Q	0.825	1.00
236_L	258_A	0.825	1.00
162_I	294_P	0.822	1.00
161_V	321_V	0.820	1.00
160_V	305_T	0.817	1.00
249_D	277_N	0.814	1.00
217_L	238_R	0.814	1.00
232_A	258_A	0.811	1.00
277_N	327_V	0.810	1.00
191_S	196_K	0.807	1.00
63_I	121_I	0.807	1.00
62_M	115_K	0.802	1.00
162_I	324_P	0.802	1.00
328_V	332_T	0.802	1.00
227_S	231_E	0.802	1.00
187_I	199_I	0.801	1.00
204_Q	207_E	0.800	1.00
199_I	218_I	0.798	1.00
184_A	244_I	0.797	1.00
14_V	37_V	0.797	1.00
79_A	95_I	0.796	1.00
84_E	88_E	0.795	1.00
294_P	322_L	0.794	1.00
188_G	223_F	0.793	1.00
303_H	307_G	0.792	1.00
232_A	235_L	0.792	1.00
119_G	310_N	0.791	1.00
259_A	272_I	0.791	1.00
65_L	79_A	0.789	1.00
17_T	21_R	0.788	1.00
81_S	85_R	0.788	1.00
162_I	293_Q	0.780	1.00
32_K	35_Q	0.780	1.00
151_D	319_K	0.779	1.00
50_V	53_A	0.770	1.00
182_N	239_N	0.769	1.00
82_I	93_M	0.761	1.00
113_K	141_E	0.760	1.00
186_I	246_A	0.759	1.00
81_S	300_A	0.756	1.00
137_E	140_S	0.756	1.00
175_L	273_I	0.756	1.00
174_H	326_L	0.750	1.00
219_I	238_R	0.750	1.00
274_G	290_T	0.750	1.00
101_D	104_K	0.748	1.00
289_T	332_T	0.746	1.00
163_D	323_P	0.742	1.00
59_R	118_D	0.742	1.00
257_Q	260_R	0.742	1.00
18_T	21_R	0.740	1.00
32_K	36_K	0.739	1.00
252_A	274_G	0.739	1.00
94_L	117_V	0.733	1.00
107_K	110_S	0.731	1.00
77_E	296_K	0.730	1.00
104_K	108_Y	0.729	1.00
139_A	157_M	0.729	1.00
289_T	326_L	0.729	1.00
197_N	201_G	0.728	1.00
185_C	245_F	0.728	1.00
206_M	213_I	0.727	1.00
170_E	291_V	0.724	1.00
280_L	284_A	0.721	1.00
236_L	262_R	0.719	1.00
80_K	83_E	0.717	1.00
21_R	27_G	0.717	1.00
139_A	156_P	0.713	1.00
60_T	118_D	0.708	1.00
259_A	266_V	0.707	1.00
21_R	28_R	0.707	1.00
99_D	104_K	0.706	1.00
121_I	148_I	0.703	1.00
221_T	251_L	0.699	1.00
94_L	115_K	0.696	1.00
68_P	75_Y	0.695	1.00
47_T	114_Q	0.694	1.00
22_V	34_R	0.694	1.00
169_Y	201_G	0.692	1.00
83_E	97_S	0.690	1.00
281_A	284_A	0.688	1.00
136_E	139_A	0.685	1.00
219_I	235_L	0.683	1.00
308_R	312_G	0.682	1.00
234_K	237_D	0.681	1.00
257_Q	287_P	0.681	1.00
64_A	120_I	0.680	1.00
66_V	108_Y	0.680	1.00
145_I	157_M	0.678	1.00
253_C	284_A	0.678	1.00
139_A	145_I	0.675	1.00
83_E	93_M	0.669	1.00
257_Q	261_I	0.669	1.00
14_V	33_T	0.667	1.00
35_Q	42_N	0.666	1.00
147_M	152_K	0.665	1.00
63_I	303_H	0.662	1.00
277_N	281_A	0.658	1.00
185_C	202_F	0.655	1.00
138_I	145_I	0.655	1.00
221_T	227_S	0.651	1.00
195_E	223_F	0.650	1.00
119_G	146_A	0.649	1.00
203_R	218_I	0.648	1.00
176_L	206_M	0.648	1.00
170_E	174_H	0.648	1.00
240_A	264_I	0.647	1.00
245_F	273_I	0.646	1.00
276_D	293_Q	0.642	1.00
183_I	242_T	0.637	1.00
228_G	231_E	0.637	1.00
256_I	260_R	0.636	1.00
47_T	110_S	0.634	1.00
120_I	143_I	0.634	1.00
134_A	137_E	0.633	1.00
199_I	220_Q	0.632	1.00
146_A	309_S	0.632	1.00
103_K	107_K	0.630	1.00
60_T	92_Q	0.628	1.00
241_P	264_I	0.627	1.00
249_D	252_A	0.626	1.00
312_G	315_K	0.622	1.00
59_R	311_R	0.619	1.00
106_T	134_A	0.618	1.00
175_L	245_F	0.617	1.00
77_E	295_I	0.616	1.00
202_F	213_I	0.616	1.00
223_F	247_F	0.616	1.00
242_T	271_S	0.611	1.00
80_K	296_K	0.610	1.00
36_K	39_N	0.607	1.00
146_A	306_A	0.607	1.00
147_M	157_M	0.602	1.00
146_A	160_V	0.600	1.00
119_G	302_R	0.600	1.00
28_R	33_T	0.599	1.00
81_S	295_I	0.598	1.00
248_N	251_L	0.598	1.00
109_F	120_I	0.598	1.00
149_S	164_D	0.598	1.00
158_D	317_K	0.595	1.00
19_V	41_M	0.594	1.00
169_Y	172_A	0.592	1.00
149_S	194_G	0.592	1.00
113_K	143_I	0.592	1.00
72_N	250_V	0.591	1.00
86_A	91_F	0.587	1.00
63_I	310_N	0.586	1.00
257_Q	285_A	0.584	1.00
8_V	19_V	0.583	1.00
225_L	254_A	0.582	1.00
6_Y	56_T	0.582	1.00
96_C	111_V	0.581	1.00
63_I	119_G	0.580	1.00
309_S	312_G	0.578	1.00
248_N	276_D	0.575	1.00
19_V	22_V	0.575	1.00
184_A	217_L	0.574	1.00
91_F	310_N	0.574	1.00
151_D	159_I	0.574	1.00
21_R	29_I	0.573	1.00
291_V	324_P	0.572	1.00
133_S	136_E	0.571	1.00
147_M	159_I	0.571	1.00
42_N	45_A	0.570	1.00
182_N	241_P	0.569	1.00
226_E	229_K	0.569	1.00
188_G	195_E	0.568	1.00
187_I	220_Q	0.568	1.00
213_I	217_L	0.568	1.00
241_P	244_I	0.568	1.00
305_T	309_S	0.566	1.00
253_C	278_T	0.566	1.00
102_P	106_T	0.564	1.00
74_F	78_L	0.564	1.00
164_D	197_N	0.561	1.00
91_F	118_D	0.559	1.00
110_S	113_K	0.557	1.00
287_P	329_R	0.555	1.00
245_F	275_F	0.554	1.00
47_T	51_H	0.552	1.00
259_A	262_R	0.551	1.00
174_H	273_I	0.550	1.00
260_R	265_K	0.549	1.00
171_A	243_A	0.549	1.00
146_A	302_R	0.549	1.00
63_I	91_F	0.549	1.00
182_N	212_P	0.548	1.00
78_L	295_I	0.547	1.00
75_Y	123_A	0.546	1.00
223_F	251_L	0.546	1.00
195_E	247_F	0.543	1.00
260_R	286_P	0.540	1.00
133_S	137_E	0.539	1.00
255_A	259_A	0.537	1.00
229_K	232_A	0.536	1.00
308_R	318_Q	0.535	1.00
232_A	254_A	0.535	1.00
146_A	305_T	0.533	1.00
137_E	141_E	0.531	1.00
86_A	307_G	0.530	1.00
281_A	288_L	0.530	1.00
199_I	213_I	0.530	1.00
81_S	84_E	0.529	1.00
29_I	34_R	0.528	1.00
183_I	202_F	0.524	1.00
231_E	235_L	0.523	1.00
225_L	250_V	0.523	1.00
160_V	301_E	0.521	1.00
80_K	99_D	0.520	1.00
257_Q	282_E	0.520	1.00
62_M	118_D	0.518	1.00
26_T	29_I	0.517	1.00
282_E	287_P	0.516	1.00
249_D	278_T	0.515	1.00
246_A	274_G	0.514	1.00
229_K	254_A	0.513	1.00
301_E	308_R	0.512	1.00
14_V	19_V	0.512	1.00
321_V	324_P	0.511	1.00
298_M	322_L	0.511	1.00
7_D	11_A	0.510	1.00
111_V	114_Q	0.508	1.00
73_P	250_V	0.508	1.00
164_D	194_G	0.507	1.00
25_N	28_R	0.506	1.00
273_I	332_T	0.506	1.00
112_L	117_V	0.505	1.00
53_A	57_G	0.505	1.00
82_I	86_A	0.505	1.00
187_I	218_I	0.504	1.00
106_T	137_E	0.504	1.00
186_I	231_E	0.502	1.00
266_V	269_D	0.502	1.00
144_P	309_S	0.501	1.00
296_K	299_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
2hsgA	1	0.9674	100	0.063	Contact Map
2o20A	2	0.816	100	0.072	Contact Map
3bilA	2	0.7596	100	0.076	Contact Map
3dbiA	2	0.819	100	0.08	Contact Map
1qpzA	2	0.9852	100	0.082	Contact Map
3e3mA	2	0.7923	100	0.092	Contact Map
4o5aA	2	0.7953	100	0.092	Contact Map
3kjxA	2	0.9822	100	0.094	Contact Map
3jvdA	2	0.7745	100	0.094	Contact Map
3ctpA	2	0.7893	100	0.096	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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