DAPE - ECOLI - GREMLIN Contacts

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DAPE - Succinyl-diaminopimelate desuccinylase

UniProt:	P0AED7	Sequences: MSCPVIELTQQLIRRPSLSPDDAGCQALLIERLQAIGFTVERMDFADTQNFWAWRGQGETLAFAGHTDVVPPGDADRWINPPFEPTIRDGMLFGRGAADMKGSLAAMVVAAERFVAQHPNHTGRLAFLITSDEEASAHNGTVKVVEALMARNERLDYCLVGEPSSIEVVGDVVKNGRRGSLTCNLTIHGVQGHVAYPHLADNPVHRAAPFLNELVAIEWDQGNEFFPATSMQIANIQAGTGSNNVIPGELFVQFNFRFSTELTDEMIKAQVLALLEKHQLRYTVDWWLSGQPFLTARGKLVDAVVNAVEHYNEIKPQLLTTGGTSDGRFIARMGAQVVELGPVNATIHKINECVNAADLQLLARMYQRIMEQLVA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10208
Length:	375 (344)
Sequences:	29424 (20645)
Seq/√Len:	1113.1

ECOLI - DAPE YGEY ARGE PEPT ABGA PEPD ALLC ABGB
BACSU - YODQ FAPD YQJE PEPT YHAA YTNL YXEP DAPEL AMHX PEPVL ALLC YQJN ROCB
HALSA - Q9HS25
SULSO - Q97Y12 Q97V97 Q97ZB7 LYSK CBPX1 CBPX2 Q97VB6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_W	126_A	3.383	1.00
186_T	249_E	3.152	1.00
186_T	251_F	2.968	1.00
30_I	34_Q	2.912	1.00
11_Q	28_L	2.888	1.00
91_M	353_C	2.743	1.00
30_I	42_R	2.636	1.00
206_R	280_L	2.535	1.00
184_N	251_F	2.501	1.00
192_G	200_A	2.481	1.00
113_R	367_Q	2.457	1.00
187_I	210_F	2.443	1.00
60_T	124_R	2.443	1.00
268_K	272_L	2.429	1.00
272_L	276_E	2.373	1.00
188_H	281_R	2.350	1.00
36_I	112_E	2.343	1.00
188_H	249_E	2.334	1.00
28_L	32_R	2.263	1.00
237_Q	251_F	2.258	1.00
32_R	35_A	2.258	1.00
60_T	126_A	2.253	1.00
186_T	283_T	2.242	1.00
54_W	124_R	2.226	1.00
33_L	53_A	2.198	1.00
184_N	253_Q	2.197	1.00
207_A	236_I	2.175	1.00
188_H	283_T	2.167	1.00
310_H	368_R	2.150	1.00
207_A	250_L	2.147	1.00
113_R	117_Q	2.093	1.00
184_N	285_D	2.060	1.00
235_N	253_Q	2.060	1.00
207_A	252_V	2.055	1.00
269_A	273_A	2.032	1.00
209_P	212_N	1.973	1.00
305_V	309_E	1.945	1.00
15_R	28_L	1.943	1.00
208_A	211_L	1.865	1.00
311_Y	368_R	1.858	1.00
80_N	88_R	1.848	1.00
186_T	285_D	1.845	1.00
32_R	36_I	1.780	1.00
142_V	146_E	1.776	1.00
201_D	206_R	1.767	1.00
81_P	84_E	1.757	1.00
31_E	35_A	1.720	1.00
304_V	369_I	1.708	1.00
28_L	31_E	1.705	1.00
79_I	351_N	1.685	1.00
8_L	32_R	1.680	1.00
208_A	212_N	1.678	1.00
210_F	275_L	1.678	1.00
10_Q	14_R	1.663	1.00
24_G	27_A	1.658	1.00
190_V	201_D	1.658	1.00
27_A	31_E	1.651	1.00
38_F	55_R	1.641	1.00
205_H	215_V	1.641	1.00
270_Q	273_A	1.630	1.00
30_I	51_F	1.608	1.00
143_K	146_E	1.592	1.00
191_Q	248_G	1.579	1.00
112_E	116_A	1.578	1.00
203_P	250_L	1.564	1.00
11_Q	24_G	1.545	1.00
5_V	363_A	1.541	1.00
265_E	269_A	1.534	1.00
263_T	266_M	1.531	1.00
368_R	371_E	1.526	1.00
238_A	250_L	1.513	1.00
302_D	305_V	1.506	1.00
26_Q	67_T	1.505	1.00
213_E	274_L	1.503	1.00
11_Q	15_R	1.499	1.00
27_A	42_R	1.494	1.00
29_L	67_T	1.490	1.00
11_Q	14_R	1.485	1.00
309_E	315_K	1.462	1.00
62_A	128_L	1.461	1.00
266_M	270_Q	1.458	1.00
106_A	362_L	1.449	1.00
143_K	147_A	1.448	1.00
31_E	34_Q	1.440	1.00
34_Q	40_V	1.429	1.00
7_E	11_Q	1.428	1.00
187_I	207_A	1.410	1.00
30_I	40_V	1.408	1.00
62_A	155_L	1.395	1.00
268_K	286_W	1.393	1.00
34_Q	42_R	1.381	1.00
32_R	112_E	1.362	1.00
14_R	87_I	1.358	1.00
361_L	364_R	1.347	1.00
5_V	109_V	1.339	1.00
229_T	267_I	1.337	1.00
305_V	318_L	1.335	1.00
63_F	107_M	1.322	1.00
55_R	115_V	1.314	1.00
87_I	356_A	1.313	1.00
213_E	277_K	1.310	1.00
181_L	264_D	1.298	1.00
27_A	30_I	1.295	1.00
197_P	200_A	1.288	1.00
269_A	272_L	1.283	1.00
102_G	359_L	1.282	1.00
185_L	252_V	1.264	1.00
90_G	357_A	1.264	1.00
183_C	254_F	1.262	1.00
80_N	84_E	1.257	1.00
209_P	278_H	1.256	1.00
184_N	287_W	1.254	1.00
115_V	118_H	1.246	1.00
308_V	365_M	1.244	1.00
7_E	10_Q	1.242	1.00
8_L	109_V	1.234	1.00
204_V	238_A	1.231	1.00
102_G	354_V	1.230	1.00
360_Q	364_R	1.229	1.00
6_I	10_Q	1.229	1.00
65_G	100_M	1.224	1.00
23_A	49_Q	1.221	1.00
63_F	370_M	1.217	1.00
19_S	135_A	1.216	1.00
357_A	361_L	1.210	1.00
117_Q	367_Q	1.207	1.00
273_A	277_K	1.200	1.00
227_P	260_T	1.200	1.00
307_A	368_R	1.196	1.00
303_A	307_A	1.195	1.00
331_A	337_V	1.192	1.00
17_S	25_C	1.190	1.00
204_V	236_I	1.181	1.00
187_I	206_R	1.179	1.00
41_E	54_W	1.179	1.00
272_L	284_V	1.175	1.00
311_Y	364_R	1.173	1.00
221_Q	270_Q	1.165	1.00
23_A	27_A	1.164	1.00
8_L	28_L	1.153	1.00
12_L	25_C	1.141	1.00
217_I	270_Q	1.137	1.00
91_M	355_N	1.133	1.00
355_N	358_D	1.133	1.00
307_A	311_Y	1.131	1.00
117_Q	371_E	1.126	1.00
10_Q	87_I	1.125	1.00
78_W	81_P	1.124	1.00
275_L	282_Y	1.123	1.00
201_D	280_L	1.122	1.00
13_I	94_G	1.120	1.00
111_A	127_F	1.120	1.00
260_T	263_T	1.119	1.00
80_N	86_T	1.119	1.00
298_G	302_D	1.119	1.00
212_N	216_A	1.118	1.00
24_G	28_L	1.118	1.00
59_E	123_G	1.115	1.00
15_R	24_G	1.111	1.00
266_M	269_A	1.106	1.00
59_E	156_D	1.091	1.00
213_E	216_A	1.085	1.00
334_G	337_V	1.069	1.00
302_D	306_N	1.068	1.00
11_Q	32_R	1.057	1.00
273_A	276_E	1.052	1.00
211_L	252_V	1.043	1.00
142_V	329_F	1.042	1.00
367_Q	371_E	1.038	1.00
29_L	104_L	1.036	1.00
13_I	97_A	1.036	1.00
173_V	302_D	1.028	1.00
270_Q	274_L	1.028	1.00
306_N	309_E	1.015	1.00
12_L	28_L	1.015	1.00
14_R	84_E	1.014	1.00
5_V	105_A	1.006	1.00
10_Q	356_A	0.996	1.00
205_H	211_L	0.995	1.00
243_N	253_Q	0.992	1.00
183_C	268_K	0.989	1.00
107_M	127_F	0.988	1.00
33_L	108_V	0.987	1.00
268_K	288_L	0.986	1.00
20_P	132_D	0.983	1.00
73_G	89_D	0.977	1.00
80_N	83_F	0.977	1.00
26_Q	51_F	0.975	1.00
209_P	216_A	0.969	1.00
307_A	310_H	0.969	1.00
304_V	338_V	0.968	1.00
274_L	277_K	0.965	1.00
109_V	112_E	0.965	1.00
26_Q	30_I	0.963	1.00
55_R	121_H	0.961	1.00
67_T	129_I	0.959	1.00
233_I	254_F	0.952	1.00
38_F	53_A	0.951	1.00
339_E	342_P	0.950	1.00
297_R	300_L	0.950	1.00
87_I	90_G	0.947	1.00
50_N	131_S	0.943	1.00
113_R	364_R	0.943	1.00
188_H	248_G	0.943	1.00
110_A	367_Q	0.943	1.00
303_A	306_N	0.940	1.00
36_I	115_V	0.940	1.00
155_L	158_C	0.938	1.00
358_D	361_L	0.935	1.00
78_W	82_P	0.935	1.00
161_G	366_Y	0.934	1.00
179_G	258_F	0.933	1.00
113_R	363_A	0.931	1.00
209_P	213_E	0.929	1.00
211_L	233_I	0.928	1.00
364_R	368_R	0.926	1.00
207_A	211_L	0.922	1.00
65_G	104_L	0.921	1.00
363_A	367_Q	0.916	1.00
237_Q	240_T	0.913	1.00
32_R	108_V	0.912	1.00
184_N	243_N	0.908	1.00
299_K	303_A	0.908	1.00
55_R	111_A	0.905	1.00
90_G	355_N	0.905	1.00
40_V	43_M	0.904	1.00
354_V	359_L	0.903	1.00
241_G	245_V	0.902	1.00
111_A	115_V	0.901	1.00
306_N	310_H	0.900	1.00
309_E	314_I	0.900	1.00
67_T	104_L	0.892	1.00
303_A	369_I	0.891	1.00
214_L	271_V	0.890	1.00
39_T	54_W	0.890	1.00
40_V	53_A	0.884	1.00
261_E	265_E	0.879	1.00
301_V	305_V	0.877	1.00
5_V	359_L	0.877	1.00
110_A	366_Y	0.876	1.00
38_F	111_A	0.872	1.00
176_G	320_T	0.869	1.00
60_T	156_D	0.868	1.00
181_L	268_K	0.865	1.00
258_F	264_D	0.859	1.00
56_G	124_R	0.855	1.00
185_L	210_F	0.855	1.00
117_Q	120_N	0.854	1.00
291_Q	332_R	0.851	1.00
205_H	208_A	0.851	1.00
52_W	126_A	0.851	1.00
204_V	250_L	0.850	1.00
26_Q	42_R	0.845	1.00
211_L	236_I	0.845	1.00
156_D	160_V	0.845	1.00
196_Y	199_L	0.840	1.00
209_P	215_V	0.836	1.00
25_C	67_T	0.834	1.00
212_N	215_V	0.831	1.00
299_K	302_D	0.824	1.00
156_D	162_E	0.824	1.00
236_I	250_L	0.822	1.00
339_E	343_V	0.818	1.00
185_L	275_L	0.817	1.00
86_T	89_D	0.817	1.00
44_D	49_Q	0.816	1.00
265_E	268_K	0.816	1.00
88_R	91_M	0.815	1.00
63_F	110_A	0.815	1.00
182_T	255_N	0.815	1.00
11_Q	31_E	0.813	1.00
264_D	268_K	0.806	1.00
79_I	88_R	0.802	1.00
8_L	112_E	0.800	1.00
20_P	135_A	0.800	1.00
113_R	116_A	0.794	1.00
357_A	360_Q	0.794	1.00
340_L	365_M	0.790	1.00
41_E	148_L	0.784	1.00
6_I	87_I	0.784	1.00
205_H	216_A	0.783	1.00
337_V	341_G	0.783	1.00
301_V	338_V	0.782	1.00
106_A	363_A	0.776	1.00
38_F	115_V	0.773	1.00
327_G	337_V	0.773	1.00
160_V	163_P	0.773	1.00
329_F	332_R	0.772	1.00
88_R	93_F	0.770	1.00
256_F	267_I	0.769	1.00
110_A	363_A	0.768	1.00
304_V	365_M	0.766	1.00
233_I	252_V	0.764	1.00
9_T	92_L	0.763	1.00
167_E	317_Q	0.761	1.00
359_L	363_A	0.760	1.00
214_L	231_M	0.760	1.00
41_E	52_W	0.760	1.00
158_C	335_A	0.759	1.00
335_A	338_V	0.756	1.00
8_L	105_A	0.750	1.00
60_T	123_G	0.750	1.00
106_A	366_Y	0.743	1.00
190_V	349_K	0.741	1.00
201_D	279_Q	0.741	1.00
17_S	101_K	0.739	1.00
8_L	11_Q	0.738	1.00
175_N	318_L	0.737	1.00
36_I	108_V	0.735	1.00
141_T	145_V	0.734	1.00
40_V	51_F	0.733	1.00
72_P	83_F	0.732	1.00
153_E	160_V	0.728	1.00
61_L	370_M	0.727	1.00
231_M	256_F	0.726	1.00
109_V	363_A	0.725	1.00
182_T	243_N	0.724	1.00
262_L	266_M	0.723	1.00
62_A	158_C	0.723	1.00
29_L	129_I	0.722	1.00
57_Q	122_T	0.719	1.00
183_C	271_V	0.718	1.00
84_E	95_R	0.718	1.00
187_I	252_V	0.718	1.00
173_V	298_G	0.713	1.00
311_Y	314_I	0.713	1.00
218_E	231_M	0.711	1.00
364_R	367_Q	0.710	1.00
308_V	311_Y	0.709	1.00
153_E	162_E	0.709	1.00
163_P	347_I	0.708	1.00
185_L	284_V	0.708	1.00
265_E	288_L	0.705	1.00
157_Y	300_L	0.705	1.00
12_L	104_L	0.697	1.00
179_G	292_P	0.697	1.00
183_C	286_W	0.696	1.00
346_T	349_K	0.692	1.00
128_L	144_V	0.691	1.00
61_L	157_Y	0.691	1.00
153_E	156_D	0.691	1.00
173_V	305_V	0.690	1.00
132_D	135_A	0.689	1.00
104_L	129_I	0.689	1.00
286_W	289_S	0.688	1.00
192_G	246_I	0.687	1.00
237_Q	253_Q	0.686	1.00
336_Q	342_P	0.686	1.00
79_I	83_F	0.686	1.00
69_V	83_F	0.686	1.00
18_L	71_P	0.680	1.00
29_L	51_F	0.679	1.00
177_R	325_S	0.677	1.00
79_I	84_E	0.676	1.00
29_L	108_V	0.675	1.00
205_H	209_P	0.675	1.00
100_M	103_S	0.672	1.00
78_W	351_N	0.671	1.00
107_M	161_G	0.670	1.00
307_A	369_I	0.670	1.00
10_Q	92_L	0.666	1.00
343_V	354_V	0.666	1.00
8_L	108_V	0.664	1.00
57_Q	124_R	0.659	1.00
18_L	21_D	0.659	1.00
342_P	362_L	0.659	1.00
112_E	115_V	0.659	1.00
50_N	55_R	0.657	1.00
346_T	353_C	0.657	1.00
26_Q	49_Q	0.656	1.00
35_A	112_E	0.656	1.00
235_N	251_F	0.652	1.00
51_F	129_I	0.652	1.00
290_G	293_F	0.652	1.00
272_L	286_W	0.651	1.00
24_G	31_E	0.650	1.00
210_F	252_V	0.649	1.00
93_F	353_C	0.647	1.00
203_P	247_P	0.646	1.00
33_L	38_F	0.646	1.00
8_L	12_L	0.645	1.00
10_Q	13_I	0.642	1.00
6_I	360_Q	0.640	1.00
261_E	291_Q	0.639	1.00
12_L	105_A	0.638	1.00
202_N	247_P	0.638	1.00
298_G	336_Q	0.636	1.00
158_C	162_E	0.636	1.00
183_C	284_V	0.635	1.00
18_L	91_M	0.631	1.00
337_V	342_P	0.630	1.00
163_P	166_I	0.629	1.00
84_E	87_I	0.629	1.00
307_A	365_M	0.628	1.00
65_G	107_M	0.627	1.00
55_R	127_F	0.627	1.00
106_A	110_A	0.626	1.00
158_C	161_G	0.624	1.00
174_K	319_L	0.624	1.00
114_F	119_P	0.624	1.00
206_R	278_H	0.623	1.00
220_D	270_Q	0.622	1.00
261_E	332_R	0.621	1.00
187_I	203_P	0.620	1.00
335_A	341_G	0.620	1.00
239_G	249_E	0.619	1.00
365_M	369_I	0.618	1.00
38_F	127_F	0.617	1.00
43_M	147_A	0.617	1.00
126_A	155_L	0.616	1.00
41_E	44_D	0.616	1.00
92_L	356_A	0.615	1.00
275_L	284_V	0.615	1.00
64_A	128_L	0.613	1.00
237_Q	249_E	0.611	1.00
346_T	351_N	0.608	1.00
210_F	274_L	0.607	1.00
37_G	40_V	0.607	1.00
344_N	358_D	0.606	1.00
194_V	232_Q	0.606	1.00
144_V	148_L	0.605	1.00
292_P	295_T	0.602	1.00
338_V	341_G	0.598	1.00
9_T	105_A	0.597	1.00
157_Y	160_V	0.597	1.00
300_L	303_A	0.595	1.00
356_A	360_Q	0.594	1.00
206_R	209_P	0.593	1.00
325_S	339_E	0.590	1.00
109_V	113_R	0.590	1.00
18_L	83_F	0.588	1.00
87_I	92_L	0.588	1.00
177_R	341_G	0.588	1.00
205_H	212_N	0.587	1.00
336_Q	341_G	0.585	1.00
134_E	348_H	0.585	1.00
10_Q	84_E	0.585	1.00
254_F	271_V	0.584	1.00
72_P	94_G	0.582	1.00
347_I	352_E	0.582	1.00
264_D	291_Q	0.582	1.00
62_A	153_E	0.582	1.00
221_Q	266_M	0.582	1.00
283_T	286_W	0.580	1.00
360_Q	363_A	0.578	1.00
162_E	165_S	0.577	1.00
6_I	356_A	0.575	1.00
81_P	86_T	0.571	1.00
15_R	88_R	0.571	1.00
269_A	276_E	0.571	1.00
241_G	244_N	0.570	1.00
244_N	257_R	0.569	1.00
160_V	327_G	0.569	1.00
258_F	267_I	0.566	1.00
142_V	145_V	0.563	1.00
15_R	25_C	0.563	1.00
37_G	115_V	0.560	1.00
69_V	95_R	0.560	1.00
297_R	302_D	0.559	1.00
6_I	92_L	0.558	1.00
45_F	143_K	0.558	1.00
203_P	246_I	0.556	1.00
42_R	49_Q	0.554	1.00
337_V	340_L	0.553	1.00
185_L	254_F	0.551	1.00
158_C	163_P	0.551	1.00
45_F	147_A	0.549	1.00
145_V	148_L	0.546	1.00
217_I	220_D	0.544	1.00
178_R	230_S	0.544	1.00
236_I	252_V	0.543	1.00
52_W	128_L	0.542	1.00
60_T	154_R	0.541	1.00
196_Y	321_T	0.540	1.00
33_L	111_A	0.540	1.00
305_V	317_Q	0.539	1.00
8_L	36_I	0.538	1.00
336_Q	339_E	0.538	1.00
208_A	215_V	0.537	1.00
182_T	253_Q	0.535	1.00
19_S	136_S	0.532	1.00
341_G	344_N	0.532	1.00
16_P	21_D	0.530	1.00
290_G	295_T	0.529	1.00
162_E	166_I	0.529	1.00
34_Q	39_T	0.528	1.00
54_W	60_T	0.527	1.00
78_W	83_F	0.526	1.00
214_L	233_I	0.525	1.00
128_L	330_I	0.525	1.00
227_P	263_T	0.525	1.00
5_V	9_T	0.523	1.00
185_L	271_V	0.522	1.00
43_M	52_W	0.521	1.00
119_P	371_E	0.520	1.00
311_Y	365_M	0.519	1.00
194_V	234_A	0.519	1.00
194_V	255_N	0.519	1.00
345_A	353_C	0.518	1.00
50_N	144_V	0.518	1.00
215_V	278_H	0.516	1.00
159_L	163_P	0.516	1.00
210_F	214_L	0.516	1.00
49_Q	55_R	0.512	1.00
264_D	289_S	0.512	1.00
20_P	143_K	0.509	1.00
94_G	97_A	0.508	1.00
211_L	254_F	0.507	1.00
175_N	294_L	0.506	1.00
92_L	97_A	0.504	1.00
180_S	255_N	0.502	1.00
9_T	356_A	0.502	1.00
338_V	342_P	0.501	1.00
79_I	82_P	0.501	1.00
105_A	109_V	0.501	1.00
256_F	262_L	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
3iszA	2	0.9867	100	0.18	Contact Map
4pqaA	2	0.9947	100	0.181	Contact Map
3pfoA	2	0.9707	100	0.207	Contact Map
4mmoA	2	0.9893	100	0.24	Contact Map
1cg2A	4	0.9493	100	0.263	Contact Map
2pokA	2	0.9947	100	0.264	Contact Map
3gb0A	2	0.9333	100	0.264	Contact Map
2f7vA	2	0.912	100	0.266	Contact Map
3rzaA	2	0.9307	100	0.267	Contact Map
4g1pA	2	0.9947	100	0.27	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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