ARAR - BACSU - GREMLIN Contacts

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ARAR - Arabinose metabolism transcriptional repressor

UniProt:	P96711	Sequences: MLPKYAQVKEEISSWINQGKILPDQKIPTENELMQQFGVSRHTIRKAIGDLVSQGLLYSVQGGGTFVASRSAKSALHSNKTIGVLTTYISDYIFPSIIRGIESYLSEQGYSMLLTSTNNNPDNERRGLENLLSQHIDGLIVEPTKSALQTPNIGYYLNLEKNGIPFAMINASYAELAAPSFTLDDVKGGMMAAEHLLSLGHTHMMGIFKADDTQGVKRMNGFIQAHRERELFPSPDMIVTFTTEEKESKLLEKVKATLEKNSKHMPTAILCYNDEIALKVIDMLREMDLKVPEDMSIVGYDDSHFAQISEVKLTSVKHPKSVLGKAAAKYVIDCLEHKKPKQEDVIFEPELIIRQSARKLNE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	362 (321)
Sequences:	31954 (23812)
Seq/√Len:	1329.1

ECOLI - CYTR GALS GALR PURR GNTR MALI LACI IDNR ASCG RBSR CRA YCJW EBGR TRER YTFQ ALSB ARAF TORT RBSB LSRB DGAL XYLF YPHF XYLR
BACSU - ARAR KDGR DEGA CCPA NTDR RBSR MSMR EXUR YKVZ GANR YVDE 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
186_V	224_Q	3.446	1.00
201_H	267_T	3.356	1.00
290_K	293_E	3.212	1.00
192_A	298_V	2.849	1.00
201_H	296_S	2.664	1.00
302_D	317_K	2.600	1.00
219_M	223_I	2.599	1.00
179_P	334_C	2.520	1.00
190_M	228_E	2.431	1.00
138_G	331_V	2.428	1.00
54_Q	58_Y	2.337	1.00
251_L	286_E	2.265	1.00
255_K	287_M	2.207	1.00
58_Y	62_G	2.175	1.00
104_Y	107_E	2.152	1.00
104_Y	329_K	2.137	1.00
197_L	229_R	2.134	1.00
47_A	60_V	2.105	1.00
326_A	329_K	2.079	1.00
57_L	61_Q	2.037	1.00
187_K	191_M	2.033	1.00
255_K	283_M	2.029	1.00
194_E	225_A	2.014	1.00
48_I	64_G	2.003	1.00
105_L	328_A	1.997	1.00
190_M	224_Q	1.993	1.00
199_L	357_A	1.985	1.00
194_E	198_S	1.980	1.00
190_M	225_A	1.971	1.00
100_G	324_G	1.965	1.00
189_G	193_A	1.945	1.00
284_L	295_M	1.936	1.00
31_N	41_R	1.930	1.00
250_L	279_K	1.906	1.00
186_V	220_N	1.877	1.00
189_G	270_L	1.872	1.00
188_G	300_Y	1.868	1.00
317_K	350_E	1.861	1.00
259_E	287_M	1.842	1.00
194_E	229_R	1.805	1.00
36_Q	63_G	1.797	1.00
193_A	222_F	1.794	1.00
37_F	63_G	1.779	1.00
104_Y	325_K	1.779	1.00
326_A	345_V	1.755	1.00
285_R	310_E	1.749	1.00
312_K	355_Q	1.724	1.00
251_L	283_M	1.721	1.00
190_M	194_E	1.715	1.00
254_V	280_V	1.706	1.00
196_L	268_A	1.706	1.00
206_G	272_Y	1.705	1.00
103_S	321_S	1.701	1.00
333_D	338_K	1.696	1.00
191_M	349_P	1.696	1.00
100_G	321_S	1.674	1.00
319_P	322_V	1.671	1.00
289_L	294_D	1.654	1.00
271_C	280_V	1.649	1.00
33_L	63_G	1.646	1.00
290_K	294_D	1.638	1.00
83_G	136_I	1.636	1.00
47_A	64_G	1.598	1.00
283_M	287_M	1.591	1.00
205_M	266_P	1.575	1.00
169_I	327_A	1.542	1.00
104_Y	108_Q	1.516	1.00
61_Q	64_G	1.515	1.00
239_V	256_A	1.510	1.00
184_D	187_K	1.510	1.00
322_V	326_A	1.486	1.00
220_N	224_Q	1.478	1.00
197_L	225_A	1.478	1.00
188_G	349_P	1.477	1.00
283_M	286_E	1.469	1.00
298_V	314_T	1.466	1.00
302_D	354_R	1.464	1.00
195_H	353_I	1.461	1.00
203_H	265_M	1.437	1.00
108_Q	332_I	1.431	1.00
203_H	234_S	1.424	1.00
80_K	137_D	1.409	1.00
187_K	190_M	1.402	1.00
82_I	105_L	1.381	1.00
322_V	325_K	1.380	1.00
284_L	289_L	1.375	1.00
217_K	220_N	1.371	1.00
193_A	221_G	1.370	1.00
33_L	37_F	1.366	1.00
195_H	199_L	1.360	1.00
195_H	198_S	1.359	1.00
31_N	35_Q	1.358	1.00
104_Y	328_A	1.352	1.00
46_K	51_L	1.340	1.00
195_H	357_A	1.339	1.00
254_V	269_I	1.333	1.00
32_E	35_Q	1.332	1.00
223_I	227_R	1.331	1.00
80_K	110_Y	1.330	1.00
193_A	225_A	1.328	1.00
189_G	221_G	1.326	1.00
234_S	237_M	1.325	1.00
225_A	228_E	1.309	1.00
59_S	63_G	1.306	1.00
194_E	228_E	1.300	1.00
255_K	286_E	1.299	1.00
193_A	197_L	1.298	1.00
53_S	56_L	1.291	1.00
255_K	259_E	1.286	1.00
201_H	268_A	1.286	1.00
54_Q	57_L	1.278	1.00
30_E	41_R	1.275	1.00
329_K	333_D	1.270	1.00
254_V	284_L	1.263	1.00
251_L	255_K	1.260	1.00
205_M	257_T	1.258	1.00
221_G	225_A	1.237	1.00
281_I	297_I	1.233	1.00
105_L	112_M	1.230	1.00
203_H	267_T	1.220	1.00
296_S	357_A	1.200	1.00
115_T	127_G	1.199	1.00
251_L	282_D	1.199	1.00
47_A	52_V	1.198	1.00
101_I	140_I	1.197	1.00
191_M	194_E	1.195	1.00
186_V	217_K	1.189	1.00
84_V	101_I	1.186	1.00
256_A	260_K	1.184	1.00
56_L	59_S	1.183	1.00
140_I	327_A	1.170	1.00
50_D	57_L	1.169	1.00
263_K	266_P	1.166	1.00
157_L	161_K	1.166	1.00
186_V	190_M	1.165	1.00
274_D	315_S	1.161	1.00
332_I	336_E	1.159	1.00
207_I	280_V	1.156	1.00
115_T	131_L	1.151	1.00
83_G	131_L	1.150	1.00
204_M	226_H	1.147	1.00
321_S	325_K	1.141	1.00
101_I	328_A	1.139	1.00
279_K	283_M	1.126	1.00
222_F	226_H	1.121	1.00
269_I	280_V	1.117	1.00
330_Y	345_V	1.112	1.00
84_V	112_M	1.107	1.00
198_S	229_R	1.103	1.00
30_E	44_I	1.102	1.00
106_S	123_N	1.099	1.00
224_Q	228_E	1.084	1.00
253_K	256_A	1.078	1.00
108_Q	329_K	1.078	1.00
203_H	264_H	1.076	1.00
324_G	328_A	1.076	1.00
225_A	229_R	1.074	1.00
108_Q	336_E	1.071	1.00
226_H	231_L	1.065	1.00
102_E	106_S	1.056	1.00
271_C	277_A	1.056	1.00
326_A	330_Y	1.055	1.00
274_D	299_G	1.055	1.00
206_G	219_M	1.043	1.00
186_V	221_G	1.038	1.00
199_L	353_I	1.038	1.00
202_T	267_T	1.032	1.00
69_S	72_A	1.030	1.00
325_K	329_K	1.026	1.00
125_R	129_E	1.018	1.00
58_Y	61_Q	1.016	1.00
242_T	249_K	1.011	1.00
197_L	231_L	1.011	1.00
37_F	44_I	1.009	1.00
71_S	74_S	1.008	1.00
317_K	352_I	1.006	1.00
81_T	113_L	1.005	1.00
220_N	223_I	1.002	1.00
281_I	291_V	1.001	1.00
331_V	335_L	1.001	1.00
326_A	347_F	0.999	1.00
250_L	254_V	0.997	1.00
192_A	270_L	0.996	1.00
187_K	348_E	0.990	1.00
50_D	61_Q	0.985	1.00
180_S	344_D	0.978	1.00
204_M	268_A	0.968	1.00
271_C	276_I	0.966	1.00
123_N	126_R	0.965	1.00
216_V	220_N	0.962	1.00
211_D	240_T	0.960	1.00
199_L	296_S	0.959	1.00
203_H	237_M	0.958	1.00
84_V	98_I	0.958	1.00
223_I	233_P	0.957	1.00
110_Y	332_I	0.954	1.00
222_F	270_L	0.951	1.00
197_L	202_T	0.950	1.00
183_L	319_P	0.949	1.00
129_E	158_N	0.947	1.00
193_A	226_H	0.946	1.00
260_K	263_K	0.945	1.00
252_E	256_A	0.938	1.00
281_I	309_S	0.932	1.00
202_T	231_L	0.927	1.00
107_E	325_K	0.924	1.00
129_E	133_S	0.923	1.00
350_E	353_I	0.922	1.00
319_P	347_F	0.919	1.00
254_V	258_L	0.917	1.00
192_A	316_V	0.917	1.00
47_A	61_Q	0.915	1.00
187_K	349_P	0.907	1.00
68_A	73_K	0.902	1.00
269_I	295_M	0.897	1.00
81_T	111_S	0.894	1.00
29_T	32_E	0.892	1.00
195_H	314_T	0.891	1.00
179_P	330_Y	0.891	1.00
184_D	346_I	0.889	1.00
182_T	346_I	0.886	1.00
99_R	103_S	0.883	1.00
328_A	332_I	0.881	1.00
299_G	315_S	0.879	1.00
179_P	343_E	0.879	1.00
140_I	331_V	0.877	1.00
103_S	325_K	0.877	1.00
213_T	217_K	0.875	1.00
319_P	350_E	0.875	1.00
182_T	344_D	0.875	1.00
82_I	140_I	0.874	1.00
183_L	349_P	0.871	1.00
101_I	324_G	0.869	1.00
246_K	252_E	0.867	1.00
249_K	252_E	0.862	1.00
184_D	348_E	0.862	1.00
181_F	330_Y	0.856	1.00
79_N	137_D	0.855	1.00
239_V	253_K	0.851	1.00
330_Y	333_D	0.850	1.00
244_E	249_K	0.846	1.00
289_L	295_M	0.842	1.00
353_I	357_A	0.837	1.00
258_L	283_M	0.835	1.00
205_M	269_I	0.831	1.00
183_L	318_H	0.829	1.00
302_D	352_I	0.827	1.00
196_L	298_V	0.825	1.00
185_D	218_R	0.819	1.00
43_T	46_K	0.819	1.00
239_V	260_K	0.817	1.00
265_M	289_L	0.810	1.00
226_H	233_P	0.808	1.00
237_M	260_K	0.806	1.00
274_D	302_D	0.804	1.00
39_V	60_V	0.803	1.00
55_G	58_Y	0.803	1.00
217_K	221_G	0.802	1.00
254_V	283_M	0.802	1.00
42_H	46_K	0.798	1.00
195_H	351_L	0.797	1.00
97_I	169_I	0.796	1.00
209_K	243_T	0.791	1.00
302_D	306_A	0.786	1.00
78_S	137_D	0.785	1.00
206_G	270_L	0.785	1.00
191_M	316_V	0.785	1.00
233_P	236_D	0.783	1.00
270_L	298_V	0.782	1.00
258_L	287_M	0.780	1.00
224_Q	227_R	0.778	1.00
284_L	297_I	0.775	1.00
252_E	255_K	0.773	1.00
100_G	104_Y	0.773	1.00
78_S	336_E	0.773	1.00
254_V	257_T	0.768	1.00
301_D	318_H	0.766	1.00
120_N	123_N	0.765	1.00
96_S	321_S	0.765	1.00
274_D	277_A	0.764	1.00
93_I	320_K	0.760	1.00
278_L	309_S	0.759	1.00
47_A	57_L	0.759	1.00
314_T	357_A	0.757	1.00
267_T	296_S	0.756	1.00
138_G	335_L	0.754	1.00
314_T	351_L	0.753	1.00
208_F	219_M	0.753	1.00
67_V	133_S	0.750	1.00
207_I	271_C	0.748	1.00
219_M	238_I	0.746	1.00
83_G	139_L	0.745	1.00
282_D	312_K	0.739	1.00
70_R	73_K	0.739	1.00
82_I	328_A	0.738	1.00
28_P	63_G	0.738	1.00
55_G	59_S	0.737	1.00
158_N	161_K	0.730	1.00
81_T	134_Q	0.730	1.00
284_L	291_V	0.729	1.00
102_E	112_M	0.728	1.00
239_V	257_T	0.725	1.00
249_K	253_K	0.724	1.00
212_D	216_V	0.723	1.00
132_L	162_N	0.720	1.00
126_R	129_E	0.718	1.00
204_M	267_T	0.717	1.00
100_G	325_K	0.714	1.00
197_L	226_H	0.713	1.00
87_T	94_F	0.711	1.00
282_D	310_E	0.711	1.00
256_A	259_E	0.708	1.00
241_F	276_I	0.706	1.00
103_S	107_E	0.705	1.00
219_M	240_T	0.704	1.00
309_S	312_K	0.703	1.00
333_D	337_H	0.703	1.00
101_I	112_M	0.701	1.00
168_M	173_Y	0.699	1.00
98_I	114_L	0.690	1.00
172_S	344_D	0.689	1.00
282_D	285_R	0.688	1.00
260_K	264_H	0.684	1.00
52_V	57_L	0.684	1.00
282_D	286_E	0.680	1.00
222_F	233_P	0.677	1.00
250_L	253_K	0.673	1.00
28_P	65_T	0.670	1.00
260_K	266_P	0.670	1.00
138_G	167_A	0.669	1.00
160_E	178_A	0.666	1.00
160_E	166_F	0.665	1.00
260_K	265_M	0.665	1.00
206_G	222_F	0.663	1.00
99_R	102_E	0.660	1.00
122_D	126_R	0.658	1.00
333_D	343_E	0.658	1.00
102_E	116_S	0.657	1.00
96_S	320_K	0.656	1.00
33_L	44_I	0.655	1.00
168_M	178_A	0.654	1.00
166_F	178_A	0.654	1.00
39_V	56_L	0.653	1.00
140_I	169_I	0.652	1.00
204_M	222_F	0.652	1.00
312_K	354_R	0.650	1.00
159_L	166_F	0.649	1.00
44_I	64_G	0.646	1.00
190_M	221_G	0.645	1.00
113_L	136_I	0.643	1.00
254_V	279_K	0.643	1.00
337_H	340_P	0.641	1.00
191_M	195_H	0.638	1.00
118_N	123_N	0.638	1.00
209_K	215_G	0.632	1.00
321_S	324_G	0.630	1.00
67_V	129_E	0.630	1.00
99_R	118_N	0.628	1.00
205_M	237_M	0.627	1.00
46_K	52_V	0.623	1.00
190_M	193_A	0.621	1.00
99_R	321_S	0.621	1.00
273_N	301_D	0.620	1.00
31_N	75_A	0.620	1.00
208_F	240_T	0.618	1.00
157_L	160_E	0.618	1.00
105_L	332_I	0.617	1.00
300_Y	318_H	0.617	1.00
179_P	342_Q	0.613	1.00
308_I	311_V	0.613	1.00
97_I	320_K	0.610	1.00
170_N	185_D	0.610	1.00
245_E	282_D	0.608	1.00
170_N	214_Q	0.607	1.00
281_I	285_R	0.607	1.00
284_L	287_M	0.605	1.00
330_Y	334_C	0.602	1.00
196_L	270_L	0.601	1.00
298_V	357_A	0.600	1.00
44_I	47_A	0.600	1.00
91_D	94_F	0.600	1.00
203_H	232_F	0.600	1.00
100_G	320_K	0.599	1.00
160_E	177_A	0.598	1.00
278_L	303_S	0.598	1.00
277_A	299_G	0.597	1.00
316_V	349_P	0.597	1.00
125_R	155_Y	0.594	1.00
132_L	164_I	0.593	1.00
241_F	249_K	0.591	1.00
138_G	327_A	0.586	1.00
110_Y	137_D	0.586	1.00
167_A	181_F	0.585	1.00
93_I	97_I	0.584	1.00
42_H	51_L	0.583	1.00
123_N	127_G	0.582	1.00
37_F	47_A	0.581	1.00
128_L	139_L	0.581	1.00
185_D	217_K	0.579	1.00
199_L	267_T	0.579	1.00
117_T	124_E	0.577	1.00
91_D	275_E	0.576	1.00
154_G	157_L	0.573	1.00
307_Q	312_K	0.572	1.00
110_Y	335_L	0.571	1.00
167_A	327_A	0.568	1.00
167_A	331_V	0.566	1.00
129_E	132_L	0.564	1.00
59_S	62_G	0.562	1.00
286_E	310_E	0.562	1.00
233_P	238_I	0.562	1.00
28_P	36_Q	0.561	1.00
219_M	233_P	0.561	1.00
82_I	335_L	0.560	1.00
67_V	71_S	0.559	1.00
270_L	300_Y	0.557	1.00
323_L	347_F	0.555	1.00
231_L	234_S	0.554	1.00
203_H	266_P	0.553	1.00
51_L	57_L	0.553	1.00
285_R	290_K	0.552	1.00
172_S	180_S	0.552	1.00
280_V	284_L	0.552	1.00
139_L	164_I	0.550	1.00
195_H	298_V	0.545	1.00
307_Q	311_V	0.542	1.00
167_A	330_Y	0.542	1.00
155_Y	158_N	0.541	1.00
44_I	60_V	0.541	1.00
282_D	307_Q	0.540	1.00
82_I	110_Y	0.540	1.00
215_G	272_Y	0.540	1.00
192_A	268_A	0.540	1.00
306_A	315_S	0.540	1.00
167_A	334_C	0.539	1.00
73_K	76_L	0.538	1.00
278_L	305_F	0.534	1.00
88_Y	99_R	0.533	1.00
82_I	138_G	0.532	1.00
181_F	326_A	0.532	1.00
326_A	333_D	0.531	1.00
85_L	127_G	0.531	1.00
251_L	254_V	0.530	1.00
32_E	36_Q	0.529	1.00
236_D	260_K	0.528	1.00
39_V	44_I	0.528	1.00
98_I	102_E	0.528	1.00
45_R	49_G	0.527	1.00
190_M	229_R	0.526	1.00
310_E	355_Q	0.526	1.00
30_E	64_G	0.525	1.00
37_F	60_V	0.525	1.00
34_M	37_F	0.524	1.00
266_P	269_I	0.524	1.00
48_I	51_L	0.522	1.00
47_A	51_L	0.522	1.00
94_F	142_E	0.522	1.00
251_L	279_K	0.518	1.00
113_L	134_Q	0.517	1.00
271_C	299_G	0.516	1.00
334_C	337_H	0.516	1.00
57_L	60_V	0.516	1.00
194_E	197_L	0.515	1.00
169_I	323_L	0.513	1.00
249_K	276_I	0.513	1.00
186_V	189_G	0.511	1.00
79_N	110_Y	0.510	1.00
30_E	46_K	0.510	1.00
273_N	276_I	0.510	1.00
258_L	284_L	0.509	1.00
319_P	323_L	0.509	1.00
183_L	300_Y	0.508	1.00
314_T	353_I	0.506	1.00
90_S	96_S	0.504	1.00
303_S	315_S	0.502	1.00
119_N	171_A	0.502	1.00
182_T	185_D	0.502	1.00
265_M	294_D	0.501	1.00
274_D	303_S	0.501	1.00
60_V	63_G	0.501	1.00
106_S	126_R	0.500	1.00
121_P	125_R	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	0.884	100	0.176	Contact Map
2o20A	2	0.7541	100	0.177	Contact Map
3e3mA	2	0.7376	100	0.178	Contact Map
4o5aA	2	0.7431	100	0.179	Contact Map
3dbiA	2	0.7624	100	0.182	Contact Map
3kjxA	2	0.9006	100	0.184	Contact Map
3h5oA	2	0.7459	100	0.187	Contact Map
1qpzA	2	0.9006	100	0.188	Contact Map
3bilA	2	0.7044	100	0.19	Contact Map
3ctpA	2	0.732	100	0.203	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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