YDEM - ECOLI - GREMLIN Contacts

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YDEM - Anaerobic sulfatase-maturating enzyme homolog YdeM

UniProt:	P76134	Sequences: MHVTAKPSSFQCNLKCDYCFYLEKESQFTHEKWMDDSTLKEFIKQYIAASGNQVYFTWQGGEPTLAGLDFFRKVIHYQQRYAGQKRIFNALQTNGILLNNEWCAFLKEHEFLVGISIDGPQELHDRYRRSNSGNGTFAKVIAAIERLKSYQVEFNTLTVINNVNVHYPLEVYHFLKSIGSKHMQFIELLETGTPNIDFSGHSENTFRIIDFSVPPTAYGKFMSTIFMQWVKNDVGEIFIRQFESFVSRFLGNGHTSCIFQESCKDNLVVESNGDIYECDHFVYPQYKIGNINKSELKTMNSVQLTAQKKRIPAKCQQCAYKPICNGGCPKHRITKVNNETVSYFCEGYKILFSTMVPYMNAMVELAKNRVPLYHIMDVAKQMENN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13795
Length:	385 (326)
Sequences:	6360 (4995)
Seq/√Len:	276.6

ECOLI - YDEM ASLB MOAA
BACSU - ALBA SKFB MOAA YYDG
HALSA - Q9HQF5 MOAA Q9HQF7
SULSO - Q97XZ2 Q97XA7 Q97XS7 Q97WK5 Q7LXV3 Q97XA6 Q97XS8 Q97WC3 Q97Y04 MOAA Q980E0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
121_Q	138_A	5.942	1.00
14_L	96_I	3.998	1.00
100_N	146_R	3.514	1.00
38_T	292_N	3.493	1.00
104_A	150_Y	3.355	1.00
125_D	135_G	3.324	1.00
274_D	290_N	3.170	1.00
145_E	178_I	3.137	1.00
35_D	38_T	2.960	1.00
137_F	174_F	2.874	1.00
36_D	73_K	2.869	1.00
274_D	287_K	2.737	1.00
13_N	94_N	2.674	1.00
41_E	45_Q	2.586	1.00
295_E	298_T	2.565	1.00
40_K	77_Y	2.543	1.00
100_N	149_S	2.498	1.00
167_Y	170_E	2.437	1.00
120_P	123_L	2.383	1.00
278_C	328_C	2.344	1.00
95_G	115_I	2.290	1.00
72_R	105_F	2.248	1.00
66_A	70_F	2.200	1.00
120_P	167_Y	2.173	1.00
294_S	298_T	2.147	1.00
169_L	224_T	2.097	1.00
146_R	149_S	2.071	1.00
290_N	293_K	2.064	1.00
44_K	77_Y	2.044	1.00
260_Q	278_C	2.022	1.00
118_D	128_R	2.004	1.00
100_N	150_Y	1.975	1.00
11_Q	33_W	1.921	1.00
105_F	109_H	1.910	1.00
123_L	167_Y	1.900	1.00
270_E	274_D	1.894	1.00
121_Q	125_D	1.894	1.00
115_I	144_I	1.888	1.00
104_A	108_E	1.872	1.00
173_H	228_Q	1.851	1.00
173_H	177_S	1.840	1.00
162_N	217_A	1.831	1.00
126_R	163_V	1.815	1.00
79_Q	109_H	1.796	1.00
4_T	46_Y	1.791	1.00
103_C	146_R	1.791	1.00
139_K	142_A	1.785	1.00
145_E	149_S	1.780	1.00
13_N	97_L	1.757	1.00
260_Q	263_C	1.746	1.00
99_N	102_W	1.731	1.00
156_T	175_L	1.728	1.00
38_T	41_E	1.727	1.00
124_H	136_T	1.723	1.00
40_K	73_K	1.694	1.00
36_D	40_K	1.671	1.00
34_M	38_T	1.661	1.00
170_E	173_H	1.647	1.00
58_W	89_N	1.613	1.00
145_E	148_K	1.611	1.00
141_I	178_I	1.596	1.00
275_I	299_M	1.585	1.00
140_V	143_A	1.570	1.00
115_I	143_A	1.550	1.00
107_K	150_Y	1.546	1.00
73_K	76_H	1.541	1.00
39_L	74_V	1.534	1.00
44_K	85_K	1.527	1.00
98_L	103_C	1.512	1.00
121_Q	137_F	1.508	1.00
72_R	108_E	1.489	1.00
142_A	146_R	1.484	1.00
33_W	66_A	1.469	1.00
17_D	126_R	1.458	1.00
113_V	147_L	1.458	1.00
138_A	142_A	1.450	1.00
64_T	91_L	1.438	1.00
142_A	145_E	1.431	1.00
174_F	178_I	1.421	1.00
40_K	44_K	1.405	1.00
270_E	276_Y	1.391	1.00
127_Y	161_N	1.385	1.00
223_S	227_M	1.378	1.00
101_E	104_A	1.358	1.00
45_Q	295_E	1.355	1.00
158_T	171_V	1.338	1.00
260_Q	328_C	1.331	1.00
100_N	104_A	1.317	1.00
64_T	97_L	1.312	1.00
158_T	183_M	1.309	1.00
66_A	69_D	1.306	1.00
73_K	77_Y	1.303	1.00
92_Q	114_G	1.285	1.00
141_I	174_F	1.273	1.00
10_F	271_S	1.272	1.00
34_M	39_L	1.269	1.00
44_K	81_Y	1.264	1.00
148_K	179_G	1.264	1.00
214_P	217_A	1.255	1.00
120_P	170_E	1.248	1.00
220_K	224_T	1.234	1.00
13_N	96_I	1.233	1.00
125_D	136_T	1.231	1.00
172_Y	176_K	1.231	1.00
103_C	107_K	1.219	1.00
103_C	150_Y	1.218	1.00
13_N	62_E	1.215	1.00
102_W	106_L	1.210	1.00
41_E	44_K	1.203	1.00
105_F	108_E	1.199	1.00
124_H	135_G	1.195	1.00
117_I	156_T	1.189	1.00
144_I	154_F	1.179	1.00
32_K	272_N	1.178	1.00
156_T	180_S	1.178	1.00
107_K	151_Q	1.163	1.00
146_R	150_Y	1.162	1.00
36_D	70_F	1.160	1.00
91_L	106_L	1.146	1.00
17_D	127_Y	1.146	1.00
8_S	58_W	1.145	1.00
275_I	296_L	1.141	1.00
103_C	143_A	1.140	1.00
55_Y	88_F	1.139	1.00
74_V	78_Q	1.134	1.00
75_I	105_F	1.126	1.00
281_F	330_K	1.118	1.00
276_Y	287_K	1.117	1.00
66_A	73_K	1.115	1.00
175_L	180_S	1.114	1.00
6_K	39_L	1.114	1.00
64_T	102_W	1.113	1.00
20_F	59_Q	1.110	1.00
224_T	228_Q	1.105	1.00
18_Y	118_D	1.102	1.00
119_G	137_F	1.101	1.00
14_L	136_T	1.100	1.00
43_I	85_K	1.098	1.00
119_G	123_L	1.098	1.00
137_F	141_I	1.094	1.00
139_K	143_A	1.089	1.00
312_P	338_N	1.086	1.00
42_F	269_V	1.083	1.00
76_H	80_R	1.082	1.00
217_A	220_K	1.081	1.00
9_S	33_W	1.075	1.00
219_G	223_S	1.066	1.00
78_Q	89_N	1.066	1.00
43_I	56_F	1.059	1.00
64_T	143_A	1.054	1.00
313_A	316_Q	1.045	1.00
115_I	147_L	1.043	1.00
41_E	292_N	1.042	1.00
238_F	241_Q	1.037	1.00
224_T	227_M	1.032	1.00
169_L	228_Q	1.023	1.00
294_S	299_M	1.023	1.00
114_G	157_L	1.023	1.00
228_Q	231_K	1.020	1.00
18_Y	127_Y	1.019	1.00
245_F	248_R	1.016	1.00
119_G	128_R	1.016	1.00
6_K	42_F	1.012	1.00
216_T	220_K	1.007	1.00
45_Q	49_A	1.005	1.00
43_I	78_Q	1.000	1.00
300_N	304_L	0.999	1.00
81_Y	84_Q	0.994	1.00
124_H	137_F	0.993	1.00
315_C	318_C	0.986	1.00
133_G	136_T	0.985	1.00
116_S	159_V	0.978	1.00
267_L	296_L	0.978	1.00
143_A	146_R	0.975	1.00
141_I	145_E	0.974	1.00
124_H	140_V	0.974	1.00
329_P	332_R	0.973	1.00
220_K	223_S	0.972	1.00
315_C	324_C	0.970	1.00
70_F	73_K	0.965	1.00
76_H	109_H	0.964	1.00
147_L	152_V	0.964	1.00
46_Y	56_F	0.963	1.00
44_K	48_A	0.962	1.00
125_D	128_R	0.962	1.00
113_V	152_V	0.959	1.00
173_H	176_K	0.952	1.00
314_K	341_V	0.948	1.00
47_I	85_K	0.946	1.00
75_I	111_F	0.945	1.00
228_Q	232_N	0.934	1.00
13_N	65_L	0.933	1.00
96_I	143_A	0.932	1.00
166_H	217_A	0.926	1.00
91_L	113_V	0.920	1.00
241_Q	244_S	0.919	1.00
66_A	74_V	0.916	1.00
120_P	174_F	0.916	1.00
76_H	105_F	0.914	1.00
171_V	175_L	0.909	1.00
70_F	74_V	0.908	1.00
45_Q	48_A	0.901	1.00
75_I	109_H	0.900	1.00
72_R	76_H	0.899	1.00
72_R	102_W	0.896	1.00
79_Q	108_E	0.895	1.00
168_P	224_T	0.894	1.00
98_L	143_A	0.891	1.00
8_S	66_A	0.889	1.00
226_F	230_V	0.888	1.00
240_R	243_E	0.887	1.00
55_Y	90_A	0.885	1.00
165_V	217_A	0.883	1.00
144_I	156_T	0.881	1.00
314_K	342_S	0.880	1.00
77_Y	81_Y	0.874	1.00
94_N	97_L	0.869	1.00
101_E	105_F	0.869	1.00
7_P	59_Q	0.868	1.00
156_T	183_M	0.860	1.00
301_S	304_L	0.853	1.00
34_M	42_F	0.851	1.00
72_R	101_E	0.844	1.00
56_F	89_N	0.842	1.00
286_Y	333_I	0.841	1.00
313_A	317_Q	0.837	1.00
215_P	219_G	0.835	1.00
98_L	106_L	0.830	1.00
4_T	267_L	0.826	0.99
79_Q	89_N	0.823	0.99
92_Q	157_L	0.823	0.99
102_W	105_F	0.822	0.99
59_Q	92_Q	0.821	0.99
9_S	66_A	0.819	0.99
92_Q	279_D	0.816	0.99
59_Q	279_D	0.815	0.99
39_L	42_F	0.814	0.99
240_R	244_S	0.812	0.99
124_H	128_R	0.810	0.99
56_F	78_Q	0.804	0.99
69_D	72_R	0.797	0.99
158_T	175_L	0.795	0.99
36_D	66_A	0.786	0.99
305_T	308_K	0.782	0.99
289_G	294_S	0.781	0.99
117_I	137_F	0.778	0.99
98_L	147_L	0.777	0.99
138_A	141_I	0.774	0.99
324_C	345_C	0.773	0.99
121_Q	135_G	0.769	0.99
122_E	126_R	0.769	0.99
300_N	303_Q	0.766	0.99
128_R	133_G	0.760	0.99
58_W	78_Q	0.756	0.99
53_Q	88_F	0.750	0.99
148_K	180_S	0.746	0.99
62_E	94_N	0.745	0.99
7_P	271_S	0.743	0.99
239_I	243_E	0.742	0.99
229_W	232_N	0.742	0.99
237_I	242_F	0.742	0.99
244_S	247_S	0.741	0.99
5_A	266_N	0.741	0.99
40_K	81_Y	0.740	0.99
269_V	275_I	0.739	0.99
21_Y	59_Q	0.738	0.99
103_C	113_V	0.738	0.99
311_I	321_K	0.733	0.99
66_A	71_F	0.731	0.99
62_E	93_T	0.731	0.99
57_T	90_A	0.730	0.99
7_P	268_V	0.726	0.99
161_N	164_N	0.726	0.99
257_C	260_Q	0.724	0.99
166_H	220_K	0.724	0.99
238_F	243_E	0.723	0.99
227_M	231_K	0.723	0.99
284_P	287_K	0.719	0.99
157_L	186_I	0.718	0.99
176_K	232_N	0.717	0.99
12_C	19_C	0.717	0.99
259_F	263_C	0.715	0.99
223_S	350_I	0.715	0.99
289_G	299_M	0.715	0.99
18_Y	128_R	0.714	0.99
327_G	342_S	0.714	0.99
227_M	230_V	0.712	0.99
287_K	290_N	0.711	0.98
226_F	229_W	0.710	0.98
225_I	229_W	0.709	0.98
168_P	185_F	0.708	0.98
71_F	75_I	0.707	0.98
315_C	345_C	0.707	0.98
237_I	241_Q	0.707	0.98
47_I	87_I	0.707	0.98
188_L	194_P	0.706	0.98
12_C	16_C	0.706	0.98
106_L	111_F	0.704	0.98
97_L	143_A	0.699	0.98
16_C	19_C	0.699	0.98
80_R	84_Q	0.698	0.98
5_A	57_T	0.697	0.98
168_P	172_Y	0.696	0.98
125_D	133_G	0.696	0.98
39_L	43_I	0.694	0.98
62_E	65_L	0.694	0.98
38_T	42_F	0.692	0.98
5_A	279_D	0.692	0.98
84_Q	87_I	0.691	0.98
296_L	299_M	0.688	0.98
157_L	279_D	0.688	0.98
114_G	155_N	0.684	0.98
98_L	102_W	0.683	0.98
116_S	128_R	0.682	0.98
239_I	242_F	0.681	0.98
154_F	180_S	0.680	0.98
297_K	300_N	0.680	0.98
57_T	92_Q	0.679	0.98
125_D	137_F	0.678	0.98
148_K	181_K	0.678	0.98
39_L	77_Y	0.677	0.98
144_I	178_I	0.676	0.98
112_L	155_N	0.675	0.98
148_K	154_F	0.673	0.98
244_S	248_R	0.672	0.98
295_E	299_M	0.671	0.98
43_I	58_W	0.668	0.98
136_T	140_V	0.668	0.98
117_I	141_I	0.666	0.98
159_V	188_L	0.662	0.98
174_F	177_S	0.662	0.98
321_K	325_N	0.661	0.98
72_R	77_Y	0.660	0.98
237_I	240_R	0.658	0.98
238_F	242_F	0.657	0.97
37_S	41_E	0.656	0.97
147_L	154_F	0.654	0.97
45_Q	297_K	0.653	0.97
64_T	71_F	0.653	0.97
77_Y	84_Q	0.651	0.97
103_C	152_V	0.649	0.97
218_Y	222_M	0.649	0.97
123_L	126_R	0.648	0.97
235_G	239_I	0.648	0.97
103_C	147_L	0.646	0.97
99_N	143_A	0.646	0.97
119_G	167_Y	0.646	0.97
246_V	250_L	0.645	0.97
100_N	103_C	0.644	0.97
235_G	238_F	0.642	0.97
18_Y	159_V	0.640	0.97
115_I	140_V	0.639	0.97
312_P	340_T	0.639	0.97
40_K	80_R	0.638	0.97
18_Y	21_Y	0.637	0.97
107_K	152_V	0.635	0.97
273_G	291_I	0.634	0.97
128_R	136_T	0.634	0.97
162_N	214_P	0.633	0.97
79_Q	110_E	0.632	0.97
42_F	46_Y	0.632	0.97
269_V	291_I	0.629	0.97
342_S	348_Y	0.629	0.97
117_I	140_V	0.628	0.97
236_E	240_R	0.628	0.97
119_G	124_H	0.628	0.97
23_E	193_T	0.628	0.97
62_E	95_G	0.626	0.97
277_E	286_Y	0.625	0.97
332_R	343_Y	0.622	0.97
48_A	297_K	0.622	0.97
118_D	124_H	0.618	0.96
7_P	157_L	0.618	0.96
319_A	349_K	0.617	0.96
81_Y	85_K	0.615	0.96
153_E	181_K	0.615	0.96
96_I	139_K	0.614	0.96
119_G	125_D	0.612	0.96
259_F	262_S	0.611	0.96
277_E	281_F	0.609	0.96
69_D	73_K	0.609	0.96
7_P	21_Y	0.606	0.96
15_K	133_G	0.606	0.96
324_C	328_C	0.603	0.96
11_Q	31_E	0.603	0.96
277_E	280_H	0.602	0.96
213_V	217_A	0.602	0.96
144_I	180_S	0.602	0.96
59_Q	114_G	0.600	0.96
306_A	309_K	0.599	0.96
220_K	350_I	0.599	0.96
56_F	87_I	0.598	0.96
21_Y	279_D	0.598	0.96
92_Q	280_H	0.597	0.96
253_G	256_S	0.597	0.96
246_V	249_F	0.595	0.96
268_V	279_D	0.594	0.95
312_P	341_V	0.590	0.95
8_S	39_L	0.584	0.95
318_C	345_C	0.582	0.95
18_Y	59_Q	0.581	0.95
175_L	183_M	0.580	0.95
148_K	178_I	0.580	0.95
212_S	218_Y	0.578	0.95
332_R	342_S	0.576	0.95
243_E	248_R	0.575	0.95
242_F	246_V	0.575	0.95
21_Y	268_V	0.574	0.95
70_F	77_Y	0.574	0.95
122_E	170_E	0.572	0.94
185_F	225_I	0.572	0.94
318_C	324_C	0.572	0.94
163_V	211_F	0.571	0.94
93_T	115_I	0.570	0.94
143_A	147_L	0.569	0.94
169_L	173_H	0.569	0.94
40_K	76_H	0.569	0.94
104_A	107_K	0.568	0.94
239_I	244_S	0.568	0.94
159_V	186_I	0.567	0.94
314_K	349_K	0.565	0.94
298_T	301_S	0.565	0.94
231_K	234_V	0.564	0.94
70_F	76_H	0.564	0.94
327_G	332_R	0.564	0.94
242_F	245_F	0.560	0.94
236_E	243_E	0.559	0.94
258_I	261_E	0.558	0.94
42_F	291_I	0.556	0.94
158_T	185_F	0.553	0.93
333_I	338_N	0.553	0.93
292_N	295_E	0.553	0.93
305_T	309_K	0.552	0.93
139_K	146_R	0.551	0.93
276_Y	288_I	0.550	0.93
235_G	242_F	0.550	0.93
43_I	87_I	0.548	0.93
333_I	337_N	0.546	0.93
89_N	111_F	0.544	0.93
8_S	71_F	0.540	0.93
191_T	194_P	0.537	0.92
8_S	74_V	0.536	0.92
121_Q	174_F	0.535	0.92
65_L	139_K	0.533	0.92
168_P	221_F	0.532	0.92
285_Q	333_I	0.530	0.92
241_Q	245_F	0.528	0.92
342_S	346_E	0.528	0.92
236_E	239_I	0.527	0.92
333_I	336_V	0.527	0.92
176_K	228_Q	0.526	0.92
210_D	214_P	0.526	0.92
214_P	222_M	0.524	0.92
39_L	66_A	0.524	0.92
250_L	254_H	0.522	0.91
120_P	137_F	0.522	0.91
165_V	220_K	0.521	0.91
120_P	171_V	0.520	0.91
336_V	341_V	0.519	0.91
208_I	211_F	0.516	0.91
75_I	78_Q	0.515	0.91
11_Q	65_L	0.514	0.91
327_G	331_H	0.512	0.91
288_I	304_L	0.512	0.91
344_F	347_G	0.512	0.91
21_Y	159_V	0.512	0.91
41_E	295_E	0.510	0.90
266_N	279_D	0.510	0.90
232_N	236_E	0.510	0.90
218_Y	221_F	0.510	0.90
59_Q	157_L	0.509	0.90
117_I	124_H	0.509	0.90
213_V	221_F	0.508	0.90
7_P	10_F	0.508	0.90
186_I	279_D	0.506	0.90
7_P	279_D	0.506	0.90
216_T	219_G	0.506	0.90
34_M	70_F	0.506	0.90
183_M	187_E	0.506	0.90
222_M	225_I	0.504	0.90
46_Y	53_Q	0.504	0.90
336_V	340_T	0.502	0.90
20_F	186_I	0.502	0.90
77_Y	80_R	0.501	0.90
172_Y	225_I	0.501	0.90
172_Y	232_N	0.500	0.90
60_G	63_P	0.500	0.90
106_L	152_V	0.500	0.90
106_L	110_E	0.500	0.90

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
4k36A	1	0.9377	100	0.271	Contact Map
1tv8A	2	0.7766	100	0.509	Contact Map
4m7tA	1	0.5948	100	0.544	Contact Map
4rtbA	2	0.8312	100	0.595	Contact Map
4wcxA	1	0.9065	100	0.625	Contact Map
3c8fA	1	0.5662	100	0.631	Contact Map
2yx0A	1	0.6234	99.9	0.657	Contact Map
2z2uA	1	0.5325	99.9	0.668	Contact Map
2qgqA	1	0.6494	99.9	0.674	Contact Map
2a5hA	4	0.7325	99.9	0.679	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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