DAPEL - BACSU - GREMLIN Contacts

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DAPEL - N-acetyldiaminopimelate deacetylase

UniProt:	O34916	Sequences: MKIEELIAIRRDLHRIPELGFQEFKTQQYLLNVLEQYPQDRIEIEKWRTGLFVKVNGTAPEKMLAYRADIDALSIEEQTGLPFASEHHGNMHACGHDLHMTIALGIIDHFVHHPVKHDLLFLFQPAEEGPGGAEPMLESDVLKKWQPDFITALHIAPELPVGTIATKSGLLFANTSELVIDLEGKGGHAAYPHLAEDMVVAASTLVTQLQTIISRNTDPLDSAVITVGTITGGSAQNIIAETAHLEGTIRTLSEESMKQVKERIEDVVKGIEIGFRCKGKVTYPSVYHQVYNTSGLTEEFMSFVAEHQLATVIEAKEAMTGEDFGYMLKKYPGFMFWLGADSEHGLHHAKLNPDENAIETAVHVMTGYFSVYAN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	374 (350)
Sequences:	29192 (20857)
Seq/√Len:	1114.9

ECOLI - ABGA ARGE YGEY DAPE PEPT ABGB ALLC PEPD
BACSU - DAPEL YXEP YTNL YHAA YODQ YQJE FAPD AMHX PEPT ALLC PEPVL YQJN
HALSA - Q9HS25
SULSO - CBPX2 CBPX1 Q97Y12 Q97ZB7 Q97V97 LYSK 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_K	120_L	3.432	1.00
181_D	242_T	3.142	1.00
181_D	244_H	2.915	1.00
12_D	29_Y	2.900	1.00
31_L	35_E	2.781	1.00
56_N	118_D	2.649	1.00
179_V	244_H	2.616	1.00
187_G	195_A	2.591	1.00
90_N	352_N	2.589	1.00
63_M	118_D	2.490	1.00
201_A	277_C	2.480	1.00
182_L	205_L	2.472	1.00
261_K	265_E	2.410	1.00
183_E	242_T	2.390	1.00
265_E	269_K	2.384	1.00
33_V	36_Q	2.354	1.00
109_H	366_T	2.328	1.00
179_V	246_E	2.310	1.00
183_E	278_K	2.292	1.00
29_Y	33_V	2.248	1.00
306_E	367_G	2.247	1.00
231_T	244_H	2.233	1.00
181_D	280_K	2.220	1.00
34_L	53_V	2.212	1.00
63_M	120_L	2.203	1.00
54_K	118_D	2.183	1.00
202_A	243_A	2.165	1.00
202_A	230_I	2.160	1.00
109_H	113_H	2.151	1.00
179_V	282_T	2.110	1.00
229_T	246_E	2.081	1.00
262_E	266_D	2.057	1.00
202_A	245_L	2.056	1.00
37_Y	108_D	2.018	1.00
204_T	207_T	2.003	1.00
183_E	280_K	1.996	1.00
307_H	367_G	1.991	1.00
16_I	29_Y	1.971	1.00
301_M	305_A	1.925	1.00
203_S	206_V	1.912	1.00
83_F	87_H	1.869	1.00
33_V	37_Y	1.829	1.00
24_F	28_Q	1.818	1.00
205_L	268_V	1.808	1.00
32_N	36_Q	1.761	1.00
134_E	138_E	1.752	1.00
65_A	147_P	1.748	1.00
300_F	368_Y	1.742	1.00
29_Y	32_N	1.711	1.00
9_I	33_V	1.707	1.00
39_Q	55_V	1.696	1.00
203_S	207_T	1.686	1.00
25_K	28_Q	1.674	1.00
82_P	350_K	1.674	1.00
11_R	15_R	1.654	1.00
200_V	210_Q	1.645	1.00
269_K	273_I	1.643	1.00
198_M	243_A	1.639	1.00
196_E	201_A	1.618	1.00
191_Y	194_L	1.592	1.00
31_L	51_L	1.591	1.00
186_G	241_E	1.587	1.00
185_K	196_E	1.587	1.00
28_Q	32_N	1.585	1.00
6_L	362_V	1.583	1.00
263_R	266_D	1.576	1.00
232_G	243_A	1.569	1.00
258_K	262_E	1.562	1.00
256_S	259_Q	1.562	1.00
108_D	112_H	1.561	1.00
27_Q	70_I	1.551	1.00
204_T	275_F	1.546	1.00
135_P	138_E	1.543	1.00
59_A	116_K	1.533	1.00
208_Q	267_V	1.532	1.00
62_K	148_D	1.523	1.00
12_D	15_R	1.518	1.00
367_G	370_S	1.514	1.00
298_E	301_M	1.499	1.00
24_F	49_T	1.494	1.00
8_A	12_D	1.489	1.00
135_P	139_S	1.487	1.00
12_D	25_K	1.482	1.00
12_D	16_I	1.476	1.00
181_D	282_T	1.474	1.00
65_A	122_L	1.472	1.00
30_L	70_I	1.461	1.00
221_D	253_S	1.455	1.00
259_Q	263_R	1.451	1.00
208_Q	270_G	1.430	1.00
40_D	56_N	1.421	1.00
305_A	311_T	1.412	1.00
328_L	333_G	1.395	1.00
182_L	202_A	1.393	1.00
65_A	150_I	1.385	1.00
360_T	363_H	1.385	1.00
39_Q	42_I	1.380	1.00
216_N	263_R	1.377	1.00
102_I	361_A	1.375	1.00
32_N	35_E	1.364	1.00
176_S	257_M	1.358	1.00
55_V	111_V	1.356	1.00
33_V	108_D	1.335	1.00
178_L	247_G	1.330	1.00
204_T	274_G	1.328	1.00
31_L	42_I	1.322	1.00
8_A	11_R	1.316	1.00
35_E	42_I	1.310	1.00
304_V	364_V	1.304	1.00
15_R	86_E	1.286	1.00
307_H	363_H	1.282	1.00
301_M	315_A	1.281	1.00
86_E	355_E	1.278	1.00
180_I	245_L	1.277	1.00
266_D	270_G	1.274	1.00
7_I	11_R	1.274	1.00
262_E	265_E	1.274	1.00
80_G	84_A	1.272	1.00
66_Y	369_F	1.268	1.00
299_E	303_F	1.261	1.00
6_L	105_G	1.258	1.00
272_E	279_G	1.256	1.00
356_N	360_T	1.247	1.00
261_K	283_Y	1.243	1.00
86_E	89_G	1.236	1.00
58_T	116_K	1.236	1.00
212_I	263_R	1.233	1.00
18_E	26_T	1.205	1.00
113_H	370_S	1.203	1.00
105_G	108_D	1.192	1.00
182_L	201_A	1.190	1.00
9_I	105_G	1.189	1.00
359_E	363_H	1.187	1.00
28_Q	31_L	1.182	1.00
98_L	353_P	1.177	1.00
113_H	366_T	1.174	1.00
199_V	232_G	1.173	1.00
268_V	279_G	1.168	1.00
66_Y	103_A	1.167	1.00
199_V	230_I	1.167	1.00
223_A	260_V	1.159	1.00
303_F	367_G	1.158	1.00
9_I	29_Y	1.156	1.00
266_D	269_K	1.141	1.00
207_T	211_T	1.140	1.00
253_S	256_S	1.135	1.00
14_H	96_H	1.125	1.00
13_L	26_T	1.121	1.00
16_I	25_K	1.121	1.00
141_V	144_K	1.115	1.00
294_S	298_E	1.113	1.00
303_F	307_H	1.112	1.00
259_Q	262_E	1.102	1.00
298_E	302_S	1.102	1.00
208_Q	211_T	1.096	1.00
267_V	270_G	1.095	1.00
227_V	247_G	1.091	1.00
14_H	93_A	1.091	1.00
62_K	117_H	1.088	1.00
354_D	357_A	1.086	1.00
20_G	129_G	1.081	1.00
153_L	365_M	1.078	1.00
196_E	277_C	1.072	1.00
87_H	90_N	1.069	1.00
12_D	33_V	1.067	1.00
178_L	261_K	1.065	1.00
89_G	356_N	1.055	1.00
206_V	245_L	1.055	1.00
25_K	29_Y	1.054	1.00
90_N	354_D	1.048	1.00
157_P	346_L	1.047	1.00
31_L	45_E	1.047	1.00
98_L	155_I	1.044	1.00
76_E	88_H	1.035	1.00
204_T	211_T	1.026	1.00
39_Q	53_V	1.016	1.00
37_Y	111_V	1.015	1.00
30_L	100_M	1.015	1.00
107_I	121_F	1.014	1.00
43_E	54_K	1.012	1.00
11_R	86_E	1.010	1.00
265_E	281_V	1.010	1.00
50_G	125_P	1.007	1.00
134_E	326_Y	1.004	1.00
27_Q	51_L	0.997	1.00
63_M	148_D	0.997	1.00
235_A	238_I	0.993	1.00
269_K	272_E	0.990	1.00
200_V	206_V	0.990	1.00
263_R	267_V	0.988	1.00
363_H	367_G	0.987	1.00
366_T	370_S	0.983	1.00
336_F	340_A	0.979	1.00
57_G	118_D	0.978	1.00
81_L	84_A	0.977	1.00
302_S	305_A	0.974	1.00
106_I	366_T	0.971	1.00
55_V	115_V	0.971	1.00
202_A	206_V	0.971	1.00
206_V	227_V	0.968	1.00
98_L	358_I	0.967	1.00
6_L	358_I	0.961	1.00
11_R	355_E	0.961	1.00
64_L	149_F	0.960	1.00
267_V	271_I	0.955	1.00
204_T	208_Q	0.949	1.00
303_F	306_E	0.947	1.00
149_F	296_L	0.945	1.00
70_I	123_F	0.941	1.00
13_L	29_Y	0.940	1.00
209_L	264_I	0.939	1.00
17_P	22_Q	0.938	1.00
40_D	54_K	0.937	1.00
180_I	268_V	0.936	1.00
68_A	98_L	0.936	1.00
305_A	310_A	0.936	1.00
362_V	366_T	0.935	1.00
42_I	45_E	0.934	1.00
261_K	285_S	0.931	1.00
27_Q	31_L	0.930	1.00
230_I	243_A	0.928	1.00
353_P	358_I	0.924	1.00
236_Q	246_E	0.922	1.00
108_D	111_V	0.922	1.00
208_Q	271_I	0.921	1.00
21_F	126_A	0.921	1.00
179_V	236_Q	0.917	1.00
338_L	341_D	0.917	1.00
6_L	101_T	0.916	1.00
357_A	360_T	0.914	1.00
9_I	108_D	0.912	1.00
107_I	111_V	0.912	1.00
299_E	368_Y	0.909	1.00
270_G	273_I	0.907	1.00
270_G	274_G	0.906	1.00
34_L	104_L	0.903	1.00
297_T	334_F	0.900	1.00
302_S	306_E	0.894	1.00
299_E	302_S	0.883	1.00
297_T	301_M	0.883	1.00
300_F	334_F	0.881	1.00
174_N	251_T	0.881	1.00
120_L	147_P	0.878	1.00
308_Q	311_T	0.876	1.00
271_I	274_G	0.876	1.00
43_E	144_K	0.874	1.00
180_I	205_L	0.873	1.00
200_V	203_S	0.865	1.00
168_S	298_E	0.865	1.00
340_A	353_P	0.862	1.00
109_H	363_H	0.861	1.00
143_K	330_K	0.858	1.00
52_F	120_L	0.858	1.00
176_S	261_K	0.853	1.00
344_H	350_K	0.853	1.00
183_E	241_E	0.848	1.00
144_K	147_P	0.845	1.00
293_T	296_L	0.842	1.00
40_D	43_E	0.839	1.00
199_V	243_A	0.839	1.00
345_G	348_H	0.836	1.00
39_Q	107_I	0.835	1.00
106_I	365_M	0.831	1.00
204_T	210_Q	0.830	1.00
82_P	87_H	0.829	1.00
251_T	257_M	0.829	1.00
42_I	53_V	0.829	1.00
103_A	121_F	0.828	1.00
206_V	230_I	0.824	1.00
295_G	298_E	0.821	1.00
258_K	261_K	0.820	1.00
150_I	331_Y	0.818	1.00
214_S	217_T	0.818	1.00
26_T	70_I	0.815	1.00
207_T	210_Q	0.815	1.00
109_H	362_V	0.815	1.00
18_E	99_H	0.808	1.00
254_E	258_K	0.807	1.00
68_A	100_M	0.806	1.00
285_S	288_H	0.805	1.00
33_V	104_L	0.800	1.00
12_D	32_N	0.798	1.00
57_G	60_P	0.798	1.00
231_T	234_S	0.796	1.00
295_G	299_E	0.793	1.00
266_D	273_I	0.792	1.00
162_G	167_K	0.787	1.00
55_V	107_I	0.785	1.00
21_F	129_G	0.784	1.00
89_G	354_D	0.783	1.00
209_L	225_I	0.782	1.00
200_V	211_T	0.780	1.00
102_I	106_I	0.779	1.00
151_T	368_Y	0.779	1.00
152_A	335_M	0.777	1.00
177_E	248_T	0.776	1.00
326_Y	330_K	0.776	1.00
109_H	112_H	0.774	1.00
358_I	362_V	0.772	1.00
140_D	143_K	0.769	1.00
117_H	148_D	0.768	1.00
324_F	333_G	0.767	1.00
37_Y	104_L	0.766	1.00
255_E	259_Q	0.766	1.00
227_V	245_L	0.763	1.00
27_Q	49_T	0.762	1.00
9_I	101_T	0.761	1.00
102_I	362_V	0.760	1.00
9_I	12_D	0.758	1.00
178_L	264_I	0.758	1.00
162_G	314_E	0.754	1.00
356_N	359_E	0.754	1.00
340_A	357_A	0.752	1.00
196_E	276_R	0.752	1.00
70_I	100_M	0.751	1.00
133_A	137_L	0.750	1.00
300_F	336_F	0.749	1.00
185_K	348_H	0.746	1.00
46_K	49_T	0.744	1.00
10_R	91_M	0.743	1.00
163_T	314_E	0.742	1.00
225_I	249_I	0.737	1.00
164_I	167_K	0.736	1.00
217_T	223_A	0.732	1.00
168_S	294_S	0.732	1.00
326_Y	329_K	0.730	1.00
182_L	245_L	0.729	1.00
66_Y	106_I	0.726	1.00
64_L	369_F	0.720	1.00
63_M	117_H	0.720	1.00
271_I	275_F	0.719	1.00
7_I	86_E	0.718	1.00
249_I	260_V	0.718	1.00
257_M	261_K	0.717	1.00
30_L	123_F	0.711	1.00
304_V	307_H	0.705	1.00
13_L	100_M	0.705	1.00
193_H	196_E	0.703	1.00
167_K	317_E	0.703	1.00
106_I	362_V	0.701	1.00
101_T	105_G	0.701	1.00
58_T	114_P	0.701	1.00
60_P	118_D	0.700	1.00
162_G	168_S	0.700	1.00
179_V	284_P	0.699	1.00
151_T	296_L	0.699	1.00
43_E	52_F	0.698	1.00
229_T	244_H	0.696	1.00
105_G	109_H	0.693	1.00
187_G	239_I	0.693	1.00
344_H	348_H	0.693	1.00
102_I	365_M	0.688	1.00
205_L	245_L	0.685	1.00
364_V	368_Y	0.681	1.00
165_A	168_S	0.679	1.00
336_F	364_V	0.678	1.00
66_Y	151_T	0.675	1.00
177_E	236_Q	0.672	1.00
300_F	364_V	0.671	1.00
39_Q	111_V	0.670	1.00
303_F	368_Y	0.669	1.00
19_L	74_S	0.669	1.00
79_T	84_A	0.666	1.00
9_I	13_L	0.666	1.00
105_G	362_V	0.665	1.00
30_L	51_L	0.664	1.00
51_L	123_F	0.663	1.00
19_L	22_Q	0.662	1.00
217_T	220_L	0.661	1.00
201_A	275_F	0.660	1.00
82_P	85_S	0.660	1.00
126_A	129_G	0.660	1.00
231_T	246_E	0.659	1.00
322_E	335_M	0.658	1.00
36_Q	108_D	0.657	1.00
11_R	14_H	0.652	1.00
283_Y	286_V	0.649	1.00
100_M	103_A	0.648	1.00
286_V	289_Q	0.647	1.00
43_E	46_K	0.647	1.00
67_R	122_L	0.643	1.00
231_T	242_T	0.637	1.00
180_I	281_V	0.636	1.00
258_K	285_S	0.635	1.00
204_T	271_I	0.635	1.00
310_A	313_I	0.627	1.00
92_H	352_N	0.627	1.00
254_E	329_K	0.626	1.00
30_L	104_L	0.626	1.00
55_V	121_F	0.626	1.00
182_L	198_M	0.625	1.00
334_F	337_W	0.625	1.00
7_I	359_E	0.624	1.00
56_N	60_P	0.622	1.00
106_I	110_F	0.622	1.00
142_L	331_Y	0.621	1.00
355_E	359_E	0.621	1.00
87_H	92_H	0.618	1.00
34_L	39_Q	0.618	1.00
100_M	123_F	0.615	1.00
39_Q	121_F	0.614	1.00
197_D	240_A	0.612	1.00
296_L	334_F	0.612	1.00
91_M	94_C	0.611	1.00
81_L	85_S	0.611	1.00
48_R	135_P	0.608	1.00
156_A	337_W	0.608	1.00
200_V	204_T	0.608	1.00
77_E	80_G	0.608	1.00
200_V	207_T	0.603	1.00
72_A	94_C	0.602	1.00
363_H	366_T	0.602	1.00
101_T	104_L	0.602	1.00
338_L	361_A	0.600	1.00
126_A	131_G	0.599	1.00
81_L	352_N	0.590	1.00
189_A	226_T	0.590	1.00
102_I	153_L	0.589	1.00
189_A	228_G	0.588	1.00
103_A	153_L	0.588	1.00
16_I	26_T	0.587	1.00
303_F	364_V	0.587	1.00
42_I	51_L	0.586	1.00
150_I	333_G	0.585	1.00
233_G	242_T	0.584	1.00
272_E	277_C	0.582	1.00
61_E	118_D	0.582	1.00
152_A	324_F	0.580	1.00
337_W	340_A	0.577	1.00
150_I	327_M	0.576	1.00
293_T	298_E	0.575	1.00
7_I	355_E	0.574	1.00
162_G	165_A	0.574	1.00
218_D	221_D	0.574	1.00
91_M	355_E	0.573	1.00
25_K	32_N	0.571	1.00
210_Q	275_F	0.571	1.00
251_T	260_V	0.571	1.00
120_L	144_K	0.571	1.00
136_M	141_V	0.570	1.00
180_I	247_G	0.569	1.00
359_E	362_V	0.569	1.00
173_A	224_V	0.568	1.00
61_E	117_H	0.568	1.00
138_E	330_K	0.567	1.00
9_I	104_L	0.567	1.00
164_I	168_S	0.567	1.00
122_L	136_M	0.566	1.00
291_Y	294_S	0.565	1.00
205_L	271_I	0.565	1.00
133_A	136_M	0.562	1.00
205_L	267_V	0.558	1.00
19_L	90_N	0.557	1.00
182_L	277_C	0.556	1.00
79_T	83_F	0.555	1.00
132_G	139_S	0.554	1.00
54_K	63_M	0.554	1.00
272_E	278_K	0.554	1.00
11_R	91_M	0.554	1.00
307_H	364_V	0.554	1.00
308_Q	364_V	0.554	1.00
336_F	339_G	0.554	1.00
178_L	283_Y	0.553	1.00
203_S	210_Q	0.552	1.00
193_H	218_D	0.552	1.00
201_A	204_T	0.552	1.00
10_R	101_T	0.549	1.00
345_G	352_N	0.548	1.00
180_I	279_G	0.548	1.00
102_I	105_G	0.545	1.00
198_M	240_A	0.545	1.00
137_L	330_K	0.545	1.00
128_E	347_H	0.545	1.00
43_E	141_V	0.544	1.00
331_Y	334_F	0.543	1.00
50_G	136_M	0.541	1.00
247_G	264_I	0.540	1.00
178_L	281_V	0.537	1.00
75_I	93_A	0.536	1.00
304_V	309_L	0.536	1.00
13_L	101_T	0.535	1.00
296_L	299_E	0.535	1.00
262_E	269_K	0.535	1.00
100_M	104_L	0.535	1.00
131_G	135_P	0.534	1.00
58_T	61_E	0.533	1.00
209_L	227_V	0.533	1.00
38_P	42_I	0.532	1.00
9_I	37_Y	0.530	1.00
35_E	40_D	0.530	1.00
27_Q	45_E	0.530	1.00
174_N	289_Q	0.529	1.00
268_V	281_V	0.526	1.00
58_T	118_D	0.525	1.00
59_A	118_D	0.524	1.00
47_W	139_S	0.522	1.00
254_E	288_H	0.521	1.00
201_A	271_I	0.519	1.00
265_E	283_Y	0.516	1.00
62_K	149_F	0.514	1.00
219_P	222_S	0.514	1.00
304_V	313_I	0.514	1.00
198_M	239_I	0.514	1.00
338_L	353_P	0.513	1.00
162_G	166_T	0.513	1.00
177_E	246_E	0.512	1.00
23_E	27_Q	0.512	1.00
199_V	203_S	0.511	1.00
221_D	256_S	0.510	1.00
217_T	221_D	0.509	1.00
180_I	264_I	0.508	1.00
16_I	87_H	0.508	1.00
13_L	30_L	0.507	1.00
122_L	327_M	0.507	1.00
153_L	338_L	0.506	1.00
249_I	264_I	0.506	1.00
175_T	248_T	0.505	1.00
182_L	268_V	0.504	1.00
52_F	122_L	0.504	1.00
304_V	308_Q	0.503	1.00
132_G	136_M	0.502	1.00
214_S	218_D	0.502	1.00
24_F	27_Q	0.502	1.00
345_G	350_K	0.500	1.00
255_E	258_K	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
4ewtA	4	0.9813	100	0.232	Contact Map
1ysjA	2	0.9385	100	0.239	Contact Map
3io1A	4	0.9011	100	0.24	Contact Map
1xmbA	1	0.9385	100	0.244	Contact Map
3pfoA	2	0.9519	100	0.251	Contact Map
4pqaA	2	0.9572	100	0.269	Contact Map
3iszA	2	0.9465	100	0.279	Contact Map
3gb0A	2	0.9358	100	0.291	Contact Map
3rzaA	2	0.9305	100	0.292	Contact Map
3tx8A	2	0.9278	100	0.293	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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