ALR2 - ECOLI - GREMLIN Contacts

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ALR2 - Alanine racemase, catabolic

UniProt:	P29012	Sequences: MTRPIQASLDLQALKQNLSIVRQAATHARVWSVVKANAYGHGIERIWSAIGATDGFALLNLEEAITLRERGWKGPILMLEGFFHAQDLEIYDQHRLTTCVHSNWQLKALQNARLKAPLDIYLKVNSGMNRLGFQPDRVLTVWQQLRAMANVGEMTLMSHFAEAEHPDGISGAMARIEQAAEGLECRRSLSNSAATLWHPEAHFDWVRPGIILYGASPSGQWRDIANTGLRPVMTLSSEIIGVQTLKAGERVGYGGRYTARDEQRIGIVAAGYADGYPRHAPTGTPVLVDGVRTMTVGTVSMDMLAVDLTPCPQAGIGTPVELWGKEIKIDDVAAAAGTVGYELMCALALRVPVVTV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11408
Length:	356 (346)
Sequences:	4892 (3623)
Seq/√Len:	194.8

ECOLI - ALR2 ALR1
BACSU - ALR1 ALR2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_L	232_V	3.433	1.00
158_S	189_L	3.389	1.00
285_P	292_R	3.135	1.00
250_R	255_G	2.907	1.00
244_T	264_R	2.832	1.00
177_E	203_F	2.782	1.00
266_G	308_L	2.762	1.00
16_Q	230_R	2.729	1.00
239_I	266_G	2.697	1.00
65_I	94_H	2.680	1.00
192_S	211_I	2.677	1.00
250_R	258_T	2.675	1.00
246_K	262_E	2.663	1.00
292_R	331_D	2.576	1.00
321_E	326_E	2.517	1.00
236_S	319_P	2.508	1.00
265_I	296_V	2.478	1.00
64_A	96_L	2.456	1.00
21_V	211_I	2.415	1.00
244_T	262_E	2.390	1.00
29_R	54_D	2.259	1.00
10_D	13_A	2.253	1.00
91_Y	98_T	2.252	1.00
256_R	298_T	2.232	1.00
293_T	311_C	2.226	1.00
8_S	236_S	2.217	1.00
252_G	300_S	2.174	1.00
257_Y	263_Q	2.171	1.00
129_N	249_E	2.171	1.00
31_W	205_W	2.093	1.00
125_N	129_N	2.080	1.00
245_L	259_A	2.077	1.00
286_V	306_V	2.050	1.00
237_S	268_V	2.038	1.00
235_L	270_A	2.034	1.00
33_V	57_A	2.030	1.00
239_I	314_A	2.011	1.00
173_M	201_A	2.005	1.00
171_G	175_R	1.970	1.00
247_A	262_E	1.950	1.00
119_D	152_G	1.940	1.00
215_A	340_G	1.940	1.00
215_A	344_M	1.934	1.00
261_D	310_P	1.928	1.00
180_A	187_R	1.923	1.00
289_D	318_T	1.895	1.00
347_L	351_V	1.868	1.00
276_Y	322_L	1.845	1.00
20_I	23_Q	1.831	1.00
329_I	344_M	1.822	1.00
37_N	349_L	1.807	1.00
44_E	70_R	1.803	1.00
162_E	255_G	1.798	1.00
16_Q	20_I	1.792	1.00
182_G	185_C	1.783	1.00
99_C	157_M	1.763	1.00
133_F	141_V	1.757	1.00
15_K	49_A	1.736	1.00
32_S	212_L	1.731	1.00
315_G	318_T	1.715	1.00
6_Q	236_S	1.656	1.00
246_K	249_E	1.626	1.00
97_T	154_M	1.623	1.00
246_K	259_A	1.601	1.00
174_A	178_Q	1.598	1.00
173_M	203_F	1.582	1.00
107_K	144_Q	1.578	1.00
18_L	212_L	1.563	1.00
15_K	51_G	1.558	1.00
242_V	308_L	1.542	1.00
43_I	66_T	1.533	1.00
110_Q	148_M	1.522	1.00
277_P	346_A	1.520	1.00
195_T	208_P	1.520	1.00
121_Y	188_S	1.515	1.00
330_D	340_G	1.498	1.00
31_W	57_A	1.497	1.00
124_V	179_A	1.492	1.00
187_R	204_D	1.487	1.00
288_V	306_V	1.470	1.00
267_I	305_A	1.461	1.00
162_E	169_I	1.456	1.00
288_V	293_T	1.446	1.00
34_V	47_W	1.426	1.00
162_E	165_H	1.422	1.00
13_A	230_R	1.414	1.00
190_S	201_A	1.402	1.00
287_L	327_I	1.402	1.00
287_L	321_E	1.389	1.00
14_L	46_I	1.387	1.00
25_A	28_A	1.385	1.00
7_A	351_V	1.384	1.00
44_E	66_T	1.383	1.00
300_S	305_A	1.382	1.00
263_Q	307_D	1.375	1.00
263_Q	309_T	1.372	1.00
268_V	304_L	1.371	1.00
56_F	74_G	1.363	1.00
47_W	67_L	1.351	1.00
284_T	295_T	1.350	1.00
302_D	350_R	1.344	1.00
233_M	323_W	1.344	1.00
29_R	55_G	1.334	1.00
95_R	116_A	1.333	1.00
173_M	177_E	1.315	1.00
117_P	152_G	1.278	1.00
287_L	326_E	1.276	1.00
256_R	282_T	1.275	1.00
259_A	263_Q	1.261	1.00
268_V	320_V	1.259	1.00
119_D	154_M	1.256	1.00
103_N	144_Q	1.253	1.00
45_R	48_S	1.251	1.00
103_N	107_K	1.250	1.00
190_S	202_H	1.247	1.00
249_E	259_A	1.246	1.00
5_I	270_A	1.230	1.00
41_H	233_M	1.226	1.00
170_S	200_E	1.225	1.00
31_W	55_G	1.221	1.00
242_V	316_I	1.218	1.00
163_A	193_A	1.217	1.00
32_S	53_T	1.215	1.00
16_Q	228_G	1.207	1.00
135_P	178_Q	1.185	1.00
7_A	235_L	1.175	1.00
18_L	53_T	1.174	1.00
45_R	355_T	1.154	1.00
110_Q	144_Q	1.146	1.00
11_L	355_T	1.146	1.00
173_M	189_L	1.133	1.00
18_L	30_V	1.132	1.00
265_I	305_A	1.131	1.00
170_S	174_A	1.130	1.00
260_R	263_Q	1.126	1.00
5_I	237_S	1.124	1.00
276_Y	332_V	1.124	1.00
107_K	111_N	1.123	1.00
69_E	94_H	1.122	1.00
190_S	194_A	1.116	1.00
21_V	208_P	1.115	1.00
256_R	281_P	1.115	1.00
171_G	174_A	1.113	1.00
245_L	251_V	1.112	1.00
36_A	273_A	1.102	1.00
14_L	50_I	1.100	1.00
323_W	329_I	1.098	1.00
175_R	178_Q	1.095	1.00
235_L	351_V	1.094	1.00
177_E	181_E	1.090	1.00
287_L	292_R	1.086	1.00
104_W	316_I	1.084	1.00
20_I	24_A	1.075	1.00
139_L	182_G	1.073	1.00
165_H	168_G	1.072	1.00
65_I	69_E	1.069	1.00
238_E	319_P	1.065	1.00
211_I	229_L	1.064	1.00
239_I	242_V	1.063	1.00
90_I	94_H	1.060	1.00
285_P	294_M	1.056	1.00
22_R	54_D	1.053	1.00
50_I	212_L	1.052	1.00
270_A	322_L	1.050	1.00
308_L	314_A	1.048	1.00
67_L	72_W	1.047	1.00
78_M	96_L	1.036	1.00
299_V	304_L	1.036	1.00
276_Y	295_T	1.035	1.00
110_Q	150_N	1.032	1.00
97_T	119_D	1.025	1.00
75_P	97_T	1.024	1.00
55_G	97_T	1.023	1.00
89_E	93_Q	1.022	1.00
134_Q	249_E	1.019	1.00
261_D	309_T	1.017	1.00
286_V	304_L	1.015	1.00
125_N	243_Q	1.013	1.00
169_I	198_H	1.011	1.00
106_L	145_L	1.011	1.00
336_A	343_L	1.000	1.00
11_L	49_A	0.999	1.00
25_A	202_H	0.989	1.00
239_I	308_L	0.989	1.00
199_P	202_H	0.977	0.99
7_A	233_M	0.970	0.99
30_V	208_P	0.967	0.99
236_S	321_E	0.965	0.99
195_T	206_V	0.962	0.99
324_G	327_I	0.961	0.99
177_E	200_E	0.960	0.99
123_K	131_L	0.960	0.99
18_L	50_I	0.955	0.99
328_K	331_D	0.954	0.99
138_V	179_A	0.953	0.99
44_E	48_S	0.949	0.99
285_P	335_A	0.947	0.99
241_G	316_I	0.947	0.99
182_G	186_R	0.942	0.99
100_V	120_I	0.942	0.99
52_A	74_G	0.940	0.99
239_I	288_V	0.938	0.99
90_I	93_Q	0.938	0.99
6_Q	354_V	0.934	0.99
333_A	338_T	0.931	0.99
263_Q	296_V	0.928	0.99
293_T	309_T	0.927	0.99
248_G	259_A	0.916	0.99
308_L	311_C	0.913	0.99
89_E	113_R	0.908	0.99
19_S	51_G	0.906	0.99
233_M	347_L	0.904	0.99
32_S	50_I	0.902	0.99
168_G	197_W	0.901	0.99
268_V	286_V	0.901	0.99
268_V	306_V	0.896	0.99
131_L	267_I	0.895	0.99
68_R	76_I	0.894	0.99
100_V	106_L	0.894	0.99
8_S	354_V	0.892	0.99
245_L	249_E	0.881	0.99
293_T	306_V	0.879	0.99
279_H	337_G	0.873	0.99
210_I	341_Y	0.867	0.99
237_S	269_A	0.865	0.99
135_P	175_R	0.863	0.99
187_R	203_F	0.862	0.99
55_G	75_P	0.859	0.99
277_P	336_A	0.856	0.99
55_G	205_W	0.851	0.99
92_D	118_L	0.848	0.98
131_L	303_M	0.843	0.98
6_Q	238_E	0.842	0.98
162_E	168_G	0.842	0.98
5_I	351_V	0.841	0.98
95_R	119_D	0.836	0.98
279_H	336_A	0.835	0.98
276_Y	284_T	0.834	0.98
184_E	187_R	0.833	0.98
327_I	331_D	0.832	0.98
160_F	189_L	0.831	0.98
162_E	254_G	0.830	0.98
15_K	19_S	0.829	0.98
42_G	355_T	0.828	0.98
264_R	313_Q	0.827	0.98
158_S	203_F	0.825	0.98
261_D	307_D	0.825	0.98
143_Q	147_A	0.824	0.98
48_S	70_R	0.823	0.98
289_D	315_G	0.820	0.98
252_G	305_A	0.819	0.98
306_V	320_V	0.812	0.98
156_L	180_A	0.808	0.98
288_V	320_V	0.806	0.98
160_F	194_A	0.805	0.98
289_D	314_A	0.804	0.98
155_T	188_S	0.804	0.98
208_P	211_I	0.803	0.98
291_V	311_C	0.802	0.98
18_L	51_G	0.802	0.98
106_L	141_V	0.802	0.98
129_N	134_Q	0.802	0.98
11_L	45_R	0.801	0.98
195_T	202_H	0.801	0.98
293_T	310_P	0.801	0.98
251_V	305_A	0.801	0.98
68_R	95_R	0.799	0.98
46_I	50_I	0.797	0.98
251_V	263_Q	0.795	0.98
121_Y	155_T	0.792	0.98
193_A	217_P	0.791	0.98
215_A	329_I	0.789	0.98
280_A	335_A	0.788	0.98
7_A	347_L	0.787	0.98
46_I	232_V	0.787	0.98
176_I	187_R	0.786	0.97
124_V	138_V	0.785	0.97
170_S	198_H	0.785	0.97
314_A	318_T	0.782	0.97
248_G	262_E	0.782	0.97
240_I	269_A	0.782	0.97
19_S	52_A	0.782	0.97
291_V	310_P	0.781	0.97
7_A	41_H	0.779	0.97
21_V	30_V	0.767	0.97
143_Q	186_R	0.766	0.97
164_E	254_G	0.765	0.97
67_L	76_I	0.764	0.97
210_I	215_A	0.762	0.97
120_I	151_V	0.761	0.97
77_L	121_Y	0.756	0.97
34_V	56_F	0.752	0.97
251_V	265_I	0.751	0.97
9_L	232_V	0.746	0.97
219_G	334_A	0.742	0.96
250_R	259_A	0.742	0.96
144_Q	148_M	0.742	0.96
288_V	314_A	0.742	0.96
129_N	245_L	0.742	0.96
33_V	79_L	0.738	0.96
20_I	228_G	0.735	0.96
278_R	342_E	0.734	0.96
216_S	227_T	0.733	0.96
137_R	140_T	0.733	0.96
234_T	321_E	0.732	0.96
173_M	190_S	0.731	0.96
100_V	109_L	0.730	0.96
104_W	107_K	0.730	0.96
270_A	304_L	0.729	0.96
286_V	322_L	0.727	0.96
247_A	260_R	0.727	0.96
78_M	91_Y	0.726	0.96
278_R	339_V	0.726	0.96
237_S	304_L	0.725	0.96
210_I	340_G	0.723	0.96
9_L	355_T	0.720	0.96
103_N	137_R	0.720	0.96
277_P	343_L	0.719	0.96
10_D	234_T	0.719	0.96
176_I	189_L	0.718	0.96
11_L	46_I	0.717	0.96
77_L	97_T	0.716	0.96
47_W	72_W	0.715	0.96
311_C	314_A	0.715	0.96
259_A	262_E	0.713	0.96
64_A	94_H	0.713	0.96
280_A	336_A	0.713	0.96
126_S	172_A	0.710	0.95
138_V	142_W	0.709	0.95
142_W	183_L	0.709	0.95
61_L	91_Y	0.706	0.95
193_A	210_I	0.706	0.95
85_A	108_A	0.706	0.95
124_V	156_L	0.704	0.95
196_L	227_T	0.703	0.95
57_A	205_W	0.702	0.95
245_L	265_I	0.699	0.95
87_D	90_I	0.699	0.95
37_N	43_I	0.694	0.95
84_H	87_D	0.694	0.95
230_R	325_K	0.693	0.95
323_W	343_L	0.693	0.95
304_L	322_L	0.693	0.95
22_R	30_V	0.692	0.95
281_P	284_T	0.692	0.95
92_D	112_A	0.692	0.95
139_L	143_Q	0.690	0.95
276_Y	304_L	0.690	0.95
4_P	238_E	0.689	0.95
331_D	334_A	0.687	0.95
286_V	320_V	0.687	0.95
82_F	101_H	0.687	0.95
83_F	98_T	0.684	0.94
319_P	326_E	0.683	0.94
44_E	72_W	0.676	0.94
329_I	340_G	0.675	0.94
12_Q	15_K	0.675	0.94
235_L	347_L	0.673	0.94
13_A	16_Q	0.673	0.94
73_K	95_R	0.672	0.94
13_A	229_L	0.665	0.94
106_L	148_M	0.665	0.94
8_S	234_T	0.664	0.94
50_I	56_F	0.661	0.93
241_G	267_I	0.659	0.93
283_G	335_A	0.656	0.93
29_R	205_W	0.654	0.93
101_H	241_G	0.652	0.93
66_T	349_L	0.651	0.93
189_L	203_F	0.649	0.93
145_L	153_E	0.643	0.92
43_I	273_A	0.642	0.92
293_T	314_A	0.640	0.92
104_W	108_A	0.639	0.92
103_N	140_T	0.639	0.92
61_L	64_A	0.638	0.92
197_W	218_S	0.637	0.92
285_P	331_D	0.637	0.92
264_R	310_P	0.637	0.92
291_V	313_Q	0.636	0.92
134_Q	243_Q	0.636	0.92
251_V	296_V	0.634	0.92
235_L	323_W	0.634	0.92
178_Q	181_E	0.633	0.92
140_T	143_Q	0.633	0.92
134_Q	137_R	0.633	0.92
293_T	308_L	0.630	0.92
280_A	284_T	0.627	0.91
10_D	325_K	0.625	0.91
28_A	206_V	0.624	0.91
284_T	335_A	0.623	0.91
55_G	77_L	0.623	0.91
32_S	56_F	0.619	0.91
34_V	213_Y	0.617	0.91
76_I	96_L	0.616	0.91
65_I	90_I	0.615	0.91
183_L	186_R	0.614	0.91
274_D	350_R	0.613	0.91
144_Q	147_A	0.612	0.90
242_V	264_R	0.611	0.90
168_G	198_H	0.611	0.90
19_S	22_R	0.611	0.90
141_V	145_L	0.610	0.90
160_F	201_A	0.610	0.90
340_G	344_M	0.610	0.90
16_Q	19_S	0.609	0.90
251_V	259_A	0.608	0.90
30_V	206_V	0.607	0.90
181_E	184_E	0.604	0.90
57_A	79_L	0.600	0.90
260_R	294_M	0.599	0.90
330_D	334_A	0.599	0.90
338_T	343_L	0.598	0.89
289_D	313_Q	0.598	0.89
20_I	227_T	0.597	0.89
264_R	308_L	0.597	0.89
240_I	303_M	0.595	0.89
295_T	306_V	0.595	0.89
289_D	311_C	0.595	0.89
46_I	49_A	0.594	0.89
13_A	232_V	0.593	0.89
53_T	56_F	0.593	0.89
321_E	324_G	0.591	0.89
140_T	144_Q	0.590	0.89
66_T	70_R	0.590	0.89
59_L	302_D	0.586	0.88
244_T	263_Q	0.586	0.88
310_P	314_A	0.586	0.88
89_E	112_A	0.584	0.88
19_S	23_Q	0.583	0.88
331_D	335_A	0.583	0.88
295_T	299_V	0.583	0.88
38_A	43_I	0.582	0.88
277_P	280_A	0.580	0.88
31_W	77_L	0.580	0.88
106_L	110_Q	0.579	0.88
284_T	332_V	0.579	0.88
105_Q	109_L	0.578	0.88
139_L	142_W	0.576	0.88
54_D	74_G	0.575	0.88
36_A	350_R	0.573	0.87
194_A	198_H	0.573	0.87
92_D	114_L	0.572	0.87
288_V	308_L	0.570	0.87
332_V	343_L	0.569	0.87
321_E	327_I	0.569	0.87
124_V	183_L	0.569	0.87
323_W	347_L	0.564	0.87
28_A	202_H	0.563	0.86
138_V	141_V	0.563	0.86
323_W	332_V	0.562	0.86
72_W	75_P	0.558	0.86
307_D	311_C	0.557	0.86
295_T	304_L	0.556	0.86
47_W	56_F	0.553	0.85
216_S	330_D	0.553	0.85
82_F	91_Y	0.553	0.85
38_A	48_S	0.551	0.85
257_Y	296_V	0.551	0.85
126_S	161_A	0.548	0.85
82_F	98_T	0.547	0.85
21_V	195_T	0.546	0.85
12_Q	16_Q	0.546	0.85
5_I	235_L	0.546	0.85
164_E	298_T	0.546	0.85
121_Y	154_M	0.545	0.85
210_I	344_M	0.544	0.85
251_V	257_Y	0.544	0.85
25_A	206_V	0.543	0.84
164_E	278_R	0.543	0.84
54_D	75_P	0.543	0.84
10_D	230_R	0.541	0.84
157_M	300_S	0.540	0.84
208_P	212_L	0.540	0.84
176_I	180_A	0.538	0.84
216_S	228_G	0.538	0.84
322_L	332_V	0.538	0.84
55_G	74_G	0.536	0.84
158_S	169_I	0.535	0.84
173_M	198_H	0.535	0.84
93_Q	116_A	0.534	0.83
44_E	47_W	0.534	0.83
36_A	302_D	0.532	0.83
61_L	65_I	0.532	0.83
18_L	56_F	0.529	0.83
292_R	327_I	0.528	0.83
341_Y	345_C	0.528	0.83
133_F	138_V	0.527	0.83
20_I	230_R	0.526	0.83
195_T	211_I	0.526	0.83
44_E	69_E	0.521	0.82
135_P	179_A	0.521	0.82
146_R	153_E	0.520	0.82
274_D	302_D	0.519	0.82
77_L	99_C	0.517	0.81
284_T	299_V	0.516	0.81
126_S	175_R	0.515	0.81
273_A	348_A	0.515	0.81
134_Q	246_K	0.514	0.81
122_L	142_W	0.514	0.81
145_L	151_V	0.512	0.81
148_M	151_V	0.511	0.81
26_T	202_H	0.510	0.81
273_A	302_D	0.510	0.81
161_A	172_A	0.509	0.80
189_L	194_A	0.508	0.80
334_A	337_G	0.508	0.80
14_L	212_L	0.508	0.80
267_I	303_M	0.507	0.80
247_A	261_D	0.507	0.80
46_I	51_G	0.505	0.80
290_G	326_E	0.505	0.80
14_L	213_Y	0.504	0.80
98_T	118_L	0.503	0.80
177_E	187_R	0.502	0.80
107_K	140_T	0.502	0.80
273_A	350_R	0.501	0.79
279_H	342_E	0.501	0.79
11_L	15_K	0.500	0.79

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
1bd0A	2	0.986	100	0.24	Contact Map
3hurA	4	0.9803	100	0.248	Contact Map
3e5pA	2	0.986	100	0.253	Contact Map
2rjgA	2	0.9944	100	0.254	Contact Map
4bhyA	2	0.9494	100	0.256	Contact Map
2vd8A	2	0.9438	100	0.263	Contact Map
1rcqA	2	0.9888	100	0.264	Contact Map
4a3qA	2	0.9213	100	0.268	Contact Map
3co8A	2	0.9831	100	0.272	Contact Map
3s46A	2	0.9831	100	0.273	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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