PATA - BACSU - GREMLIN Contacts

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PATA - Putative N-acetyl-LL-diaminopimelate aminotransferase

UniProt:	P16524	Sequences: MEHLLNPKAREIEISGIRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTTSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYSELTYDRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDVVKPSGAFYIFPSIKSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRLELFVLKKREAMQTINNGV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	393 (347)
Sequences:	43411 (29777)
Seq/√Len:	1598.5

ECOLI - YBDL ALAC ALAA AVTA YDCR YJIR MALY HIS8
BACSU - PATA YUGH AAT2 MTNE AAT1 YISV YDFD AAT3 YDEF GABR YHDI CBL YCXD YDEL HIS8
HALSA - Q9HQK2 Q9HRM6 Q9HRX4 Q9HQW2 HIS8 Q9HPL0
SULSO - AAT Y104 Q97TY7 Q97YX5 HIS8 Q97ZX4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
95_T	101_A	3.114	1.00
51_K	55_D	3.029	1.00
155_E	192_G	3.003	1.00
339_A	377_L	2.965	1.00
115_E	136_K	2.905	1.00
291_K	295_D	2.780	1.00
114_D	163_K	2.761	1.00
180_E	184_K	2.732	1.00
296_Y	369_R	2.730	1.00
307_D	320_S	2.683	1.00
370_E	374_R	2.608	1.00
334_A	338_D	2.574	1.00
73_A	277_T	2.551	1.00
292_K	365_M	2.523	1.00
110_L	135_A	2.469	1.00
44_H	48_A	2.372	1.00
245_A	250_A	2.364	1.00
79_K	85_N	2.306	1.00
69_E	273_L	2.248	1.00
103_D	107_R	2.180	1.00
300_R	372_L	2.142	1.00
240_I	272_A	2.109	1.00
179_S	182_E	2.068	1.00
370_E	373_D	2.068	1.00
184_K	188_A	2.065	1.00
327_T	330_D	1.988	1.00
152_R	185_S	1.942	1.00
143_T	182_E	1.925	1.00
48_A	52_K	1.912	1.00
72_Q	76_L	1.895	1.00
130_I	135_A	1.882	1.00
194_N	222_Q	1.851	1.00
300_R	303_S	1.847	1.00
115_E	138_V	1.841	1.00
76_L	277_T	1.820	1.00
33_L	371_G	1.818	1.00
299_D	303_S	1.816	1.00
155_E	185_S	1.776	1.00
153_L	157_A	1.773	1.00
72_Q	88_A	1.744	1.00
190_L	197_V	1.737	1.00
298_Y	302_V	1.733	1.00
105_A	224_I	1.719	1.00
300_R	373_D	1.716	1.00
295_D	299_D	1.712	1.00
302_V	308_V	1.706	1.00
75_Q	88_A	1.693	1.00
115_E	162_T	1.685	1.00
202_I	228_G	1.682	1.00
198_L	226_I	1.669	1.00
296_Y	300_R	1.665	1.00
300_R	376_E	1.659	1.00
164_C	198_L	1.647	1.00
115_E	159_T	1.634	1.00
298_Y	310_K	1.619	1.00
52_K	274_E	1.611	1.00
68_L	72_Q	1.603	1.00
120_G	139_I	1.599	1.00
98_A	226_I	1.591	1.00
105_A	198_L	1.589	1.00
297_V	317_I	1.581	1.00
300_R	304_M	1.578	1.00
91_E	247_K	1.571	1.00
115_E	161_N	1.554	1.00
150_T	153_L	1.535	1.00
185_S	188_A	1.534	1.00
116_V	130_I	1.525	1.00
148_K	182_E	1.523	1.00
47_K	51_K	1.518	1.00
364_S	367_T	1.518	1.00
343_L	357_V	1.516	1.00
328_S	347_S	1.511	1.00
334_A	378_F	1.500	1.00
74_V	242_F	1.500	1.00
86_Y	244_F	1.488	1.00
153_L	156_D	1.480	1.00
106_F	130_I	1.477	1.00
73_A	76_L	1.469	1.00
78_M	244_F	1.467	1.00
127_E	131_N	1.465	1.00
243_L	253_I	1.437	1.00
318_F	346_G	1.432	1.00
188_A	192_G	1.426	1.00
69_E	277_T	1.426	1.00
181_E	184_K	1.419	1.00
296_Y	365_M	1.417	1.00
190_L	195_V	1.415	1.00
265_S	268_S	1.408	1.00
339_A	374_R	1.398	1.00
284_L	288_E	1.397	1.00
330_D	334_A	1.394	1.00
89_E	247_K	1.392	1.00
298_Y	317_I	1.384	1.00
158_L	189_L	1.373	1.00
224_I	245_A	1.371	1.00
303_S	376_E	1.363	1.00
120_G	141_D	1.358	1.00
155_E	193_R	1.356	1.00
159_T	162_T	1.350	1.00
297_V	372_L	1.348	1.00
189_L	193_R	1.347	1.00
151_A	189_L	1.334	1.00
229_L	272_A	1.333	1.00
93_I	250_A	1.320	1.00
74_V	94_I	1.306	1.00
151_A	185_S	1.300	1.00
141_D	153_L	1.298	1.00
73_A	273_L	1.298	1.00
373_D	377_L	1.283	1.00
48_A	51_K	1.281	1.00
304_M	376_E	1.274	1.00
298_Y	308_V	1.258	1.00
289_Q	292_K	1.255	1.00
180_E	218_Y	1.253	1.00
180_E	213_Y	1.251	1.00
369_R	373_D	1.246	1.00
327_T	354_E	1.244	1.00
288_E	291_K	1.234	1.00
289_Q	365_M	1.234	1.00
117_I	162_T	1.232	1.00
47_K	55_D	1.230	1.00
330_D	333_M	1.230	1.00
100_Q	257_H	1.229	1.00
76_L	80_K	1.225	1.00
50_A	271_A	1.224	1.00
284_L	287_R	1.222	1.00
319_P	359_L	1.221	1.00
214_S	217_T	1.220	1.00
189_L	195_V	1.218	1.00
182_E	185_S	1.213	1.00
50_A	54_I	1.212	1.00
49_A	274_E	1.211	1.00
65_A	254_L	1.209	1.00
320_S	356_Y	1.207	1.00
67_Y	270_K	1.202	1.00
117_I	140_V	1.195	1.00
118_M	137_P	1.194	1.00
78_M	242_F	1.191	1.00
188_A	191_K	1.186	1.00
302_V	310_K	1.182	1.00
28_E	340_G	1.169	1.00
294_L	298_Y	1.163	1.00
74_V	92_I	1.162	1.00
106_F	110_L	1.161	1.00
65_A	71_R	1.157	1.00
127_E	139_I	1.156	1.00
106_F	166_V	1.152	1.00
110_L	116_V	1.142	1.00
227_N	242_F	1.137	1.00
332_S	343_L	1.136	1.00
71_R	75_Q	1.136	1.00
320_S	355_G	1.135	1.00
155_E	159_T	1.134	1.00
96_T	100_Q	1.130	1.00
257_H	261_V	1.128	1.00
252_H	255_K	1.127	1.00
187_A	219_L	1.124	1.00
52_K	56_E	1.115	1.00
156_D	160_P	1.106	1.00
69_E	270_K	1.102	1.00
289_Q	293_R	1.101	1.00
288_E	292_K	1.100	1.00
181_E	185_S	1.097	1.00
108_T	256_V	1.095	1.00
365_M	369_R	1.093	1.00
221_D	246_P	1.091	1.00
273_L	277_T	1.090	1.00
300_R	369_R	1.085	1.00
224_I	243_L	1.081	1.00
107_R	133_C	1.079	1.00
87_D	91_E	1.074	1.00
130_I	137_P	1.073	1.00
274_E	277_T	1.066	1.00
251_K	255_K	1.063	1.00
335_L	375_L	1.058	1.00
44_H	47_K	1.056	1.00
322_K	355_G	1.055	1.00
87_D	247_K	1.052	1.00
68_L	88_A	1.051	1.00
112_P	134_G	1.046	1.00
180_E	217_T	1.045	1.00
359_L	371_G	1.037	1.00
109_I	164_C	1.036	1.00
329_F	347_S	1.035	1.00
45_H	278_N	1.033	1.00
69_E	72_Q	1.032	1.00
47_K	54_I	1.031	1.00
75_Q	87_D	1.025	1.00
111_S	114_D	1.020	1.00
209_D	312_S	1.018	1.00
184_K	218_Y	1.016	1.00
101_A	243_L	1.014	1.00
104_A	257_H	1.013	1.00
75_Q	92_I	1.012	1.00
328_S	355_G	1.011	1.00
155_E	189_L	1.008	1.00
196_F	224_I	1.007	1.00
143_T	150_T	1.005	1.00
101_A	226_I	1.003	1.00
294_L	361_F	0.999	1.00
68_L	71_R	0.999	1.00
122_I	168_P	0.989	1.00
49_A	52_K	0.987	1.00
335_L	343_L	0.985	1.00
187_A	223_T	0.985	1.00
187_A	197_V	0.984	1.00
331_F	357_V	0.984	1.00
70_L	94_I	0.980	1.00
367_T	370_E	0.980	1.00
91_E	250_A	0.980	1.00
165_V	195_V	0.977	1.00
293_R	296_Y	0.976	1.00
191_K	221_D	0.972	1.00
295_D	310_K	0.964	1.00
109_I	196_F	0.961	1.00
304_M	373_D	0.959	1.00
191_K	220_R	0.957	1.00
184_K	219_L	0.947	1.00
108_T	253_I	0.943	1.00
203_Y	316_Y	0.940	1.00
196_F	222_Q	0.940	1.00
96_T	265_S	0.931	1.00
38_P	290_Y	0.917	1.00
80_K	280_F	0.917	1.00
299_D	369_R	0.917	1.00
93_I	253_I	0.913	1.00
92_I	244_F	0.911	1.00
29_D	340_G	0.901	1.00
274_E	278_N	0.894	1.00
226_I	243_L	0.892	1.00
116_V	164_C	0.892	1.00
140_V	157_A	0.891	1.00
98_A	202_I	0.891	1.00
296_Y	299_D	0.890	1.00
33_L	368_L	0.888	1.00
158_L	195_V	0.885	1.00
91_E	220_R	0.883	1.00
77_Y	205_E	0.883	1.00
306_L	321_I	0.882	1.00
196_F	249_I	0.880	1.00
216_A	225_V	0.878	1.00
299_D	302_V	0.878	1.00
40_F	289_Q	0.878	1.00
197_V	215_I	0.875	1.00
152_R	156_D	0.871	1.00
247_K	251_K	0.871	1.00
297_V	300_R	0.868	1.00
105_A	253_I	0.865	1.00
52_K	55_D	0.864	1.00
297_V	368_L	0.864	1.00
334_A	339_A	0.862	1.00
215_I	218_Y	0.861	1.00
341_V	375_L	0.860	1.00
131_N	137_P	0.860	1.00
158_L	162_T	0.859	1.00
152_R	155_E	0.854	1.00
207_T	210_R	0.854	1.00
149_L	182_E	0.849	1.00
99_S	125_G	0.845	1.00
215_I	223_T	0.844	1.00
285_I	288_E	0.843	1.00
98_A	228_G	0.843	1.00
285_I	289_Q	0.840	1.00
296_Y	372_L	0.839	1.00
159_T	193_R	0.835	1.00
117_I	165_V	0.830	1.00
201_E	225_V	0.826	1.00
49_A	53_A	0.825	1.00
304_M	372_L	0.822	1.00
250_A	254_L	0.819	1.00
67_Y	273_L	0.814	1.00
329_F	333_M	0.814	1.00
294_L	311_P	0.812	1.00
207_T	212_H	0.811	1.00
117_I	157_A	0.809	1.00
180_E	211_P	0.807	1.00
29_D	370_E	0.804	1.00
143_T	153_L	0.803	1.00
306_L	319_P	0.802	1.00
281_D	285_I	0.801	1.00
77_Y	233_H	0.798	1.00
48_A	55_D	0.798	1.00
307_D	322_K	0.794	1.00
100_Q	261_V	0.789	1.00
343_L	359_L	0.788	1.00
162_T	195_V	0.788	1.00
45_H	48_A	0.786	1.00
333_M	338_D	0.785	1.00
119_P	140_V	0.783	1.00
208_Y	291_K	0.782	1.00
229_L	242_F	0.781	1.00
95_T	243_L	0.780	1.00
77_Y	82_A	0.779	1.00
270_K	273_L	0.778	1.00
162_T	165_V	0.778	1.00
99_S	123_Y	0.775	1.00
97_G	239_R	0.770	1.00
341_V	374_R	0.768	1.00
151_A	186_I	0.767	1.00
321_I	357_V	0.766	1.00
116_V	135_A	0.765	1.00
257_H	264_A	0.765	1.00
205_E	232_S	0.764	1.00
292_K	295_D	0.761	1.00
138_V	159_T	0.759	1.00
219_L	223_T	0.759	1.00
328_S	354_E	0.757	1.00
119_P	149_L	0.756	1.00
191_K	222_Q	0.756	1.00
45_H	274_E	0.754	1.00
329_F	345_P	0.754	1.00
297_V	361_F	0.753	1.00
224_I	249_I	0.753	1.00
76_L	79_K	0.750	1.00
70_L	74_V	0.750	1.00
245_A	253_I	0.749	1.00
240_I	264_A	0.747	1.00
110_L	164_C	0.747	1.00
282_D	286_M	0.738	1.00
191_K	219_L	0.734	1.00
106_F	164_C	0.733	1.00
67_Y	269_Q	0.732	1.00
142_T	171_S	0.731	1.00
331_F	378_F	0.731	1.00
145_H	182_E	0.730	1.00
339_A	378_F	0.729	1.00
151_A	182_E	0.726	1.00
201_E	214_S	0.726	1.00
281_D	284_L	0.726	1.00
50_A	267_I	0.726	1.00
213_Y	217_T	0.725	1.00
66_G	71_R	0.724	1.00
332_S	345_P	0.722	1.00
240_I	268_S	0.721	1.00
118_M	130_I	0.721	1.00
93_I	243_L	0.721	1.00
341_V	371_G	0.721	1.00
110_L	114_D	0.721	1.00
119_P	171_S	0.721	1.00
151_A	155_E	0.719	1.00
366_D	369_R	0.717	1.00
32_S	37_Q	0.715	1.00
53_A	271_A	0.714	1.00
27_H	340_G	0.714	1.00
43_P	46_V	0.711	1.00
209_D	294_L	0.708	1.00
117_I	154_I	0.702	1.00
328_S	345_P	0.698	1.00
219_L	222_Q	0.697	1.00
172_N	203_Y	0.696	1.00
100_Q	104_A	0.694	1.00
41_F	47_K	0.693	1.00
126_Y	130_I	0.690	1.00
295_D	298_Y	0.686	1.00
293_R	364_S	0.678	1.00
29_D	367_T	0.676	1.00
27_H	30_V	0.676	1.00
221_D	248_D	0.676	1.00
84_F	216_A	0.672	1.00
220_R	223_T	0.672	1.00
171_S	174_T	0.671	1.00
113_G	136_K	0.670	1.00
286_M	290_Y	0.667	1.00
75_Q	86_Y	0.665	1.00
120_G	350_S	0.665	1.00
138_V	162_T	0.664	1.00
128_P	131_N	0.662	1.00
58_V	270_K	0.662	1.00
71_R	88_A	0.660	1.00
346_G	356_Y	0.659	1.00
143_T	146_G	0.658	1.00
115_E	163_K	0.656	1.00
158_L	193_R	0.653	1.00
292_K	296_Y	0.651	1.00
282_D	285_I	0.651	1.00
167_L	183_L	0.647	1.00
36_G	203_Y	0.644	1.00
42_T	45_H	0.642	1.00
296_Y	368_L	0.642	1.00
73_A	276_V	0.642	1.00
232_S	283_A	0.641	1.00
165_V	190_L	0.640	1.00
94_I	240_I	0.640	1.00
104_A	253_I	0.640	1.00
105_A	226_I	0.636	1.00
213_Y	218_Y	0.635	1.00
102_I	129_I	0.633	1.00
319_P	356_Y	0.630	1.00
166_V	198_L	0.630	1.00
154_I	189_L	0.630	1.00
42_T	282_D	0.630	1.00
140_V	153_L	0.628	1.00
46_V	275_A	0.628	1.00
305_G	322_K	0.626	1.00
332_S	357_V	0.625	1.00
39_D	293_R	0.625	1.00
106_F	135_A	0.625	1.00
283_A	287_R	0.624	1.00
245_A	249_I	0.623	1.00
326_M	331_F	0.623	1.00
177_T	313_G	0.622	1.00
82_A	204_S	0.621	1.00
154_I	165_V	0.620	1.00
199_S	225_V	0.620	1.00
318_F	356_Y	0.617	1.00
209_D	291_K	0.615	1.00
104_A	256_V	0.615	1.00
45_H	282_D	0.613	1.00
197_V	219_L	0.609	1.00
51_K	54_I	0.609	1.00
328_S	332_S	0.607	1.00
211_P	217_T	0.607	1.00
208_Y	313_G	0.605	1.00
212_H	217_T	0.605	1.00
118_M	127_E	0.604	1.00
297_V	359_L	0.602	1.00
294_L	310_K	0.601	1.00
363_C	367_T	0.601	1.00
206_L	287_R	0.599	1.00
331_F	335_L	0.599	1.00
31_I	370_E	0.598	1.00
373_D	376_E	0.598	1.00
49_A	271_A	0.595	1.00
99_S	262_S	0.595	1.00
374_R	377_L	0.594	1.00
303_S	369_R	0.592	1.00
183_L	215_I	0.592	1.00
56_E	274_E	0.591	1.00
103_D	133_C	0.590	1.00
169_Y	201_E	0.590	1.00
45_H	280_F	0.590	1.00
208_Y	361_F	0.590	1.00
138_V	157_A	0.587	1.00
77_Y	204_S	0.585	1.00
214_S	225_V	0.585	1.00
103_D	129_I	0.585	1.00
106_F	133_C	0.582	1.00
78_M	225_V	0.582	1.00
346_G	349_F	0.581	1.00
42_T	46_V	0.578	1.00
107_R	256_V	0.578	1.00
145_H	153_L	0.577	1.00
301_L	319_P	0.577	1.00
347_S	354_E	0.576	1.00
94_I	269_Q	0.576	1.00
208_Y	294_L	0.575	1.00
93_I	245_A	0.575	1.00
114_D	161_N	0.573	1.00
145_H	179_S	0.573	1.00
336_L	342_A	0.572	1.00
327_T	331_F	0.571	1.00
320_S	323_S	0.566	1.00
93_I	254_L	0.565	1.00
46_V	235_M	0.565	1.00
178_L	182_E	0.565	1.00
42_T	47_K	0.564	1.00
34_T	342_A	0.561	1.00
335_L	378_F	0.560	1.00
148_K	179_S	0.559	1.00
287_R	291_K	0.558	1.00
45_H	281_D	0.557	1.00
118_M	139_I	0.556	1.00
211_P	214_S	0.554	1.00
248_D	251_K	0.550	1.00
190_L	194_N	0.550	1.00
308_V	317_I	0.549	1.00
178_L	183_L	0.547	1.00
170_P	313_G	0.545	1.00
307_D	323_S	0.543	1.00
40_F	43_P	0.543	1.00
291_K	294_L	0.543	1.00
332_S	336_L	0.543	1.00
176_V	312_S	0.542	1.00
293_R	365_M	0.538	1.00
302_V	307_D	0.537	1.00
306_L	379_V	0.536	1.00
318_F	358_R	0.535	1.00
183_L	199_S	0.535	1.00
169_Y	177_T	0.535	1.00
293_R	367_T	0.533	1.00
190_L	193_R	0.532	1.00
106_F	129_I	0.532	1.00
271_A	274_E	0.531	1.00
62_T	67_Y	0.529	1.00
270_K	274_E	0.528	1.00
230_S	239_R	0.528	1.00
105_A	164_C	0.527	1.00
72_Q	277_T	0.527	1.00
326_M	334_A	0.527	1.00
96_T	264_A	0.526	1.00
328_S	331_F	0.526	1.00
31_I	374_R	0.526	1.00
254_L	257_H	0.525	1.00
204_S	227_N	0.525	1.00
364_S	369_R	0.524	1.00
199_S	215_I	0.523	1.00
266_S	270_K	0.522	1.00
370_E	377_L	0.522	1.00
229_L	276_V	0.521	1.00
214_S	218_Y	0.521	1.00
36_G	316_Y	0.521	1.00
156_D	159_T	0.521	1.00
187_A	220_R	0.520	1.00
143_T	148_K	0.519	1.00
70_L	272_A	0.518	1.00
141_D	157_A	0.515	1.00
269_Q	273_L	0.515	1.00
71_R	254_L	0.513	1.00
328_S	357_V	0.511	1.00
79_K	83_D	0.509	1.00
172_N	358_R	0.509	1.00
80_K	277_T	0.506	1.00
103_D	260_N	0.506	1.00
251_K	254_L	0.502	1.00
91_E	245_A	0.502	1.00
300_R	368_L	0.501	1.00
149_L	154_I	0.500	1.00
164_C	196_F	0.500	1.00
67_Y	266_S	0.500	1.00
246_P	249_I	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
4my5A	2	0.972	100	0.291	Contact Map
1gd9A	2	0.972	100	0.307	Contact Map
2o1bA	2	0.9389	100	0.309	Contact Map
1u08A	2	0.9542	100	0.31	Contact Map
3h14A	2	0.9237	100	0.313	Contact Map
3dydA	2	0.9338	100	0.314	Contact Map
1vp4A	2	0.9695	100	0.315	Contact Map
1xi9A	4	0.9593	100	0.315	Contact Map
1b5pA	2	0.9517	100	0.316	Contact Map
1yizA	2	0.9644	100	0.317	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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