NLPD - ECOLI - GREMLIN Contacts

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NLPD - Murein hydrolase activator NlpD

UniProt:	P0ADA3	Sequences: MSAGSPKFTVRRIAALSLVSLWLAGCSDTSNPPAPVSSVNGNAPANTNSGMLITPPPKMGTTSTAQQPQIQPVQQPQIQATQQPQIQPVQPVAQQPVQMENGRIVYNRQYGNIPKGSYSGSTYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYALNVGQTLQVGNASGTPITGGNAITQADAAEQGVVIKPAQNSTVAVASQPTITYSESSGEQSANKMLPNNKPTATTVTAPVTVPTASTTEPTVSSTSTSTPISTWRWPTEGKVIETFGASEGGNKGIDIAGSKGQAIIATADGRVVYAGNALRGYGNLIIIKHNDDYLSAYAHNDTMLVREQQEVKAGQKIATMGSTGTSSTRLHFEIRYKGKSVNPLRYLPQR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12111
Length:	379 (351)
Sequences:	3433 (3186)
Seq/√Len:	170.1

ECOLI - NLPD ENVC MEPM YGER
BACSU - LYTH SP4FA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
329_N	347_A	3.865	1.00
303_A	332_M	3.649	1.00
269_I	285_A	3.179	1.00
292_I	329_N	3.164	1.00
286_G	349_M	3.101	1.00
318_H	324_S	3.081	1.00
351_S	355_S	3.050	1.00
333_L	348_T	2.974	1.00
262_W	284_I	2.890	1.00
291_A	345_K	2.736	1.00
218_A	222_L	2.701	1.00
297_D	341_K	2.674	1.00
271_T	373_L	2.664	1.00
261_R	342_A	2.664	1.00
272_F	369_S	2.394	1.00
224_N	228_T	2.256	1.00
316_I	346_I	2.214	1.00
310_Y	327_A	2.199	1.00
232_V	236_V	2.192	1.00
295_T	324_S	2.185	1.00
288_K	357_T	2.172	1.00
334_V	338_Q	1.982	1.00
228_T	231_T	1.980	1.00
156_A	160_G	1.980	1.00
324_S	363_I	1.966	1.00
221_M	224_N	1.940	1.00
231_T	235_P	1.925	1.00
226_K	230_T	1.923	1.00
299_R	339_E	1.917	1.00
222_L	226_K	1.882	1.00
230_T	234_A	1.876	1.00
294_A	316_I	1.866	1.00
225_N	229_A	1.850	1.00
190_V	193_P	1.843	1.00
197_S	201_V	1.822	1.00
345_K	348_T	1.821	1.00
218_A	221_M	1.815	1.00
220_K	224_N	1.788	1.00
236_V	239_P	1.778	1.00
227_P	231_T	1.769	1.00
283_D	360_H	1.751	1.00
234_A	238_V	1.701	1.00
215_E	219_N	1.689	1.00
295_T	361_F	1.681	1.00
233_T	236_V	1.677	1.00
270_E	275_S	1.675	1.00
170_G	174_T	1.661	1.00
322_Y	365_Y	1.643	1.00
329_N	332_M	1.640	1.00
204_Q	207_I	1.633	1.00
315_I	325_A	1.630	1.00
228_T	232_V	1.618	1.00
229_A	233_T	1.617	1.00
226_K	229_A	1.612	1.00
280_K	362_E	1.598	1.00
180_T	184_A	1.597	1.00
172_P	176_G	1.596	1.00
144_D	147_Q	1.567	1.00
341_K	344_Q	1.562	1.00
235_P	238_V	1.560	1.00
292_I	349_M	1.553	1.00
235_P	239_P	1.547	1.00
301_V	323_L	1.537	1.00
214_G	217_S	1.514	1.00
177_N	181_Q	1.506	1.00
267_K	285_A	1.503	1.00
223_P	226_K	1.498	1.00
327_A	362_E	1.498	1.00
223_P	227_P	1.490	1.00
286_G	290_Q	1.487	1.00
120_G	123_Y	1.486	1.00
236_V	240_T	1.474	1.00
233_T	237_T	1.462	1.00
190_V	194_A	1.455	1.00
144_D	148_R	1.453	1.00
125_V	128_G	1.441	1.00
32_P	36_V	1.434	1.00
333_L	347_A	1.426	1.00
219_N	223_P	1.414	1.00
110_Y	114_P	1.408	1.00
296_A	342_A	1.402	1.00
214_G	218_A	1.401	1.00
279_N	358_R	1.396	1.00
166_G	170_G	1.394	1.00
120_G	124_T	1.390	1.00
186_E	189_V	1.375	1.00
36_V	40_N	1.375	1.00
148_R	152_Q	1.371	1.00
238_V	241_A	1.370	1.00
229_A	232_V	1.364	1.00
221_M	225_N	1.363	1.00
204_Q	208_T	1.357	1.00
184_A	188_G	1.354	1.00
309_G	327_A	1.353	1.00
147_Q	151_I	1.344	1.00
149_N	153_A	1.336	1.00
315_I	323_L	1.335	1.00
279_N	283_D	1.328	1.00
334_V	344_Q	1.325	1.00
283_D	358_R	1.324	1.00
301_V	317_K	1.323	1.00
266_G	284_I	1.319	1.00
293_I	345_K	1.317	1.00
210_S	214_G	1.316	1.00
174_T	178_A	1.306	1.00
349_M	359_L	1.304	1.00
215_E	218_A	1.298	1.00
80_A	84_P	1.290	1.00
216_Q	220_K	1.285	1.00
167_N	171_T	1.277	1.00
270_E	279_N	1.276	1.00
103_R	107_N	1.256	1.00
371_N	374_R	1.244	1.00
31_N	35_P	1.219	1.00
177_N	180_T	1.216	1.00
72_P	76_P	1.210	1.00
148_R	151_I	1.209	1.00
137_I	141_D	1.207	1.00
234_A	237_T	1.200	1.00
37_S	40_N	1.197	1.00
302_Y	315_I	1.197	1.00
310_Y	362_E	1.195	1.00
169_S	172_P	1.182	1.00
314_I	346_I	1.180	1.00
225_N	228_T	1.176	1.00
335_R	338_Q	1.173	1.00
159_V	163_L	1.171	1.00
364_R	369_S	1.170	1.00
224_N	227_P	1.161	1.00
129_D	132_F	1.158	1.00
237_T	241_A	1.158	1.00
96_P	100_E	1.152	1.00
227_P	230_T	1.151	1.00
152_Q	156_A	1.150	1.00
275_S	278_G	1.148	1.00
349_M	357_T	1.146	1.00
126_K	133_Y	1.145	1.00
230_T	233_T	1.143	1.00
205_P	209_Y	1.143	1.00
160_G	164_Q	1.141	1.00
126_K	135_A	1.139	1.00
260_W	322_Y	1.136	1.00
212_S	215_E	1.135	1.00
44_P	47_T	1.134	1.00
119_S	123_Y	1.134	1.00
146_A	149_N	1.131	1.00
370_V	375_Y	1.129	1.00
173_I	177_N	1.125	1.00
143_R	147_Q	1.122	1.00
283_D	328_H	1.119	1.00
231_T	234_A	1.114	1.00
322_Y	363_I	1.112	1.00
101_N	105_V	1.104	1.00
187_Q	191_I	1.103	1.00
313_L	327_A	1.096	1.00
102_G	105_V	1.093	1.00
36_V	39_V	1.089	1.00
173_I	176_G	1.081	1.00
106_Y	113_I	1.080	1.00
208_T	212_S	1.080	1.00
198_T	202_A	1.079	1.00
213_S	217_S	1.070	1.00
287_S	290_Q	1.070	1.00
265_E	293_I	1.068	1.00
295_T	326_Y	1.067	1.00
351_S	356_S	1.062	1.00
26_C	29_T	1.059	1.00
88_P	92_V	1.058	0.99
310_Y	325_A	1.057	0.99
196_N	200_A	1.057	0.99
194_A	198_T	1.055	0.99
241_A	245_E	1.042	0.99
262_W	376_L	1.040	0.99
142_F	148_R	1.037	0.99
219_N	222_L	1.036	0.99
159_V	162_T	1.027	0.99
282_I	373_L	1.026	0.99
288_K	330_D	1.026	0.99
73_V	76_P	1.026	0.99
331_T	348_T	1.024	0.99
94_Q	98_Q	1.023	0.99
123_Y	126_K	1.021	0.99
178_A	181_Q	1.021	0.99
237_T	240_T	1.019	0.99
197_S	200_A	1.018	0.99
44_P	48_N	1.016	0.99
299_R	317_K	1.014	0.99
118_Y	122_T	1.014	0.99
264_T	286_G	1.012	0.99
164_Q	168_A	1.012	0.99
32_P	35_P	1.008	0.99
69_Q	73_V	1.004	0.99
175_G	178_A	1.002	0.99
162_T	166_G	0.999	0.99
138_T	141_D	0.999	0.99
201_V	207_I	0.997	0.99
314_I	329_N	0.997	0.99
56_P	60_G	0.995	0.99
63_S	67_Q	0.993	0.99
271_T	371_N	0.989	0.99
106_Y	109_Q	0.988	0.99
46_N	49_S	0.983	0.99
39_V	43_A	0.982	0.99
277_G	280_K	0.979	0.99
130_T	133_Y	0.978	0.99
183_D	187_Q	0.976	0.99
140_N	144_D	0.973	0.99
207_I	210_S	0.962	0.99
126_K	130_T	0.960	0.99
216_Q	219_N	0.959	0.99
313_L	325_A	0.959	0.99
55_P	58_K	0.959	0.99
30_S	33_P	0.957	0.99
329_N	349_M	0.957	0.99
69_Q	72_P	0.956	0.99
187_Q	190_V	0.954	0.99
330_D	348_T	0.952	0.99
155_Y	159_V	0.952	0.99
157_L	161_Q	0.949	0.99
62_T	66_Q	0.948	0.99
111_G	114_P	0.940	0.99
178_A	182_A	0.940	0.99
362_E	369_S	0.939	0.99
108_R	112_N	0.937	0.99
176_G	179_I	0.936	0.99
183_D	186_E	0.934	0.99
207_I	211_E	0.934	0.99
253_T	257_I	0.933	0.99
23_L	26_C	0.933	0.99
142_F	146_A	0.932	0.99
98_Q	101_N	0.931	0.99
95_Q	99_M	0.928	0.99
282_I	376_L	0.928	0.99
317_K	321_D	0.925	0.99
264_T	284_I	0.923	0.99
73_V	77_Q	0.921	0.99
217_S	221_M	0.921	0.99
168_A	172_P	0.919	0.99
282_I	372_P	0.914	0.99
179_I	183_D	0.913	0.99
302_Y	313_L	0.912	0.98
130_T	135_A	0.912	0.98
176_G	180_T	0.907	0.98
318_H	326_Y	0.906	0.98
141_D	151_I	0.903	0.98
203_S	206_T	0.902	0.98
84_P	88_P	0.901	0.98
205_P	208_T	0.898	0.98
194_A	197_S	0.896	0.98
50_G	53_I	0.889	0.98
82_Q	86_I	0.888	0.98
314_I	334_V	0.887	0.98
43_A	47_T	0.885	0.98
60_G	63_S	0.882	0.98
311_G	350_G	0.881	0.98
169_S	173_I	0.880	0.98
145_L	149_N	0.877	0.98
185_A	188_G	0.875	0.98
326_Y	361_F	0.872	0.98
180_T	183_D	0.868	0.98
310_Y	364_R	0.867	0.98
333_L	345_K	0.867	0.98
166_G	169_S	0.865	0.98
312_N	352_T	0.864	0.98
324_S	361_F	0.862	0.98
295_T	363_I	0.859	0.98
100_E	103_R	0.853	0.98
37_S	41_G	0.853	0.98
351_S	357_T	0.853	0.98
128_G	132_F	0.852	0.98
144_D	151_I	0.851	0.98
136_W	139_G	0.850	0.98
279_N	360_H	0.847	0.98
191_I	194_A	0.845	0.98
203_S	207_I	0.838	0.97
257_I	296_A	0.836	0.97
151_I	156_A	0.833	0.97
81_T	84_P	0.829	0.97
65_A	69_Q	0.829	0.97
243_T	247_T	0.828	0.97
87_Q	91_P	0.827	0.97
170_G	173_I	0.826	0.97
157_L	160_G	0.823	0.97
118_Y	123_Y	0.820	0.97
188_G	192_K	0.820	0.97
269_I	358_R	0.817	0.97
307_L	313_L	0.816	0.97
305_N	312_N	0.816	0.97
242_S	245_E	0.815	0.97
286_G	289_G	0.815	0.97
92_V	99_M	0.815	0.97
291_A	348_T	0.814	0.97
86_I	89_V	0.814	0.97
88_P	91_P	0.812	0.97
274_A	277_G	0.811	0.97
62_T	65_A	0.810	0.97
318_H	361_F	0.809	0.97
136_W	140_N	0.809	0.97
322_Y	375_Y	0.808	0.97
297_D	342_A	0.807	0.97
238_V	242_S	0.805	0.97
290_Q	349_M	0.797	0.96
244_T	247_T	0.797	0.96
147_Q	150_N	0.796	0.96
268_V	282_I	0.795	0.96
107_N	110_Y	0.794	0.96
155_Y	158_N	0.790	0.96
315_I	364_R	0.789	0.96
305_N	309_G	0.789	0.96
144_D	152_Q	0.787	0.96
269_I	279_N	0.785	0.96
211_E	214_G	0.785	0.96
143_R	146_A	0.784	0.96
232_V	235_P	0.783	0.96
253_T	256_P	0.782	0.96
42_N	46_N	0.780	0.96
202_A	205_P	0.776	0.96
240_T	244_T	0.775	0.96
64_T	67_Q	0.774	0.96
327_A	364_R	0.771	0.96
34_A	37_S	0.768	0.96
243_T	246_P	0.763	0.96
58_K	62_T	0.760	0.95
302_Y	307_L	0.759	0.95
119_S	126_K	0.758	0.95
137_I	140_N	0.749	0.95
298_G	316_I	0.747	0.95
200_A	203_S	0.747	0.95
28_D	32_P	0.746	0.95
328_H	355_S	0.737	0.95
305_N	352_T	0.735	0.95
329_N	333_L	0.735	0.95
121_S	124_T	0.734	0.94
328_H	358_R	0.734	0.94
156_A	170_G	0.731	0.94
156_A	159_V	0.731	0.94
261_R	295_T	0.731	0.94
195_Q	198_T	0.731	0.94
146_A	150_N	0.730	0.94
328_H	353_G	0.730	0.94
165_V	169_S	0.729	0.94
85_Q	88_P	0.728	0.94
38_S	42_N	0.728	0.94
29_T	33_P	0.726	0.94
257_I	375_Y	0.725	0.94
313_L	329_N	0.725	0.94
284_I	376_L	0.715	0.94
121_S	125_V	0.713	0.94
188_G	191_I	0.711	0.93
97_V	101_N	0.708	0.93
104_I	107_N	0.704	0.93
280_K	369_S	0.702	0.93
31_N	34_A	0.701	0.93
270_E	283_D	0.700	0.93
117_S	121_S	0.699	0.93
117_S	123_Y	0.698	0.93
100_E	104_I	0.698	0.93
122_T	125_V	0.696	0.93
35_P	38_S	0.694	0.93
160_G	170_G	0.693	0.93
268_V	271_T	0.690	0.92
33_P	36_V	0.690	0.92
279_N	328_H	0.686	0.92
260_W	375_Y	0.685	0.92
129_D	133_Y	0.683	0.92
26_C	31_N	0.678	0.92
142_F	147_Q	0.677	0.92
342_A	363_I	0.671	0.91
279_N	355_S	0.669	0.91
253_T	258_S	0.668	0.91
64_T	68_P	0.668	0.91
86_I	90_Q	0.667	0.91
109_Q	112_N	0.667	0.91
173_I	180_T	0.664	0.91
163_L	167_N	0.663	0.91
209_Y	213_S	0.661	0.91
25_G	28_D	0.661	0.91
279_N	356_S	0.661	0.91
106_Y	110_Y	0.660	0.91
42_N	45_A	0.658	0.91
328_H	360_H	0.658	0.91
102_G	106_Y	0.657	0.91
305_N	332_M	0.657	0.91
256_P	296_A	0.656	0.90
45_A	49_S	0.656	0.90
142_F	149_N	0.652	0.90
260_W	296_A	0.651	0.90
310_Y	313_L	0.650	0.90
211_E	215_E	0.649	0.90
43_A	63_S	0.647	0.90
161_Q	164_Q	0.646	0.90
78_I	82_Q	0.646	0.90
89_V	93_A	0.645	0.90
307_L	315_I	0.642	0.89
147_Q	152_Q	0.639	0.89
92_V	96_P	0.638	0.89
95_Q	98_Q	0.638	0.89
155_Y	169_S	0.636	0.89
310_Y	315_I	0.636	0.89
210_S	213_S	0.632	0.89
225_N	232_V	0.628	0.88
297_D	339_E	0.627	0.88
24_A	31_N	0.619	0.88
143_R	151_I	0.618	0.88
317_K	366_K	0.618	0.88
91_P	94_Q	0.617	0.88
197_S	214_G	0.615	0.87
172_P	175_G	0.614	0.87
174_T	177_N	0.614	0.87
209_Y	212_S	0.612	0.87
242_S	246_P	0.612	0.87
167_N	170_G	0.612	0.87
158_N	162_T	0.612	0.87
325_A	364_R	0.612	0.87
152_Q	155_Y	0.610	0.87
168_A	171_T	0.610	0.87
117_S	120_G	0.610	0.87
29_T	32_P	0.606	0.87
352_T	355_S	0.606	0.87
278_G	356_S	0.604	0.86
40_N	44_P	0.604	0.86
74_Q	78_I	0.604	0.86
160_G	163_L	0.603	0.86
123_Y	129_D	0.603	0.86
39_V	46_N	0.601	0.86
127_K	130_T	0.600	0.86
274_A	278_G	0.600	0.86
244_T	248_V	0.600	0.86
39_V	42_N	0.600	0.86
220_K	223_P	0.599	0.86
185_A	189_V	0.598	0.86
202_A	206_T	0.597	0.86
41_G	44_P	0.595	0.86
138_T	142_F	0.593	0.85
239_P	243_T	0.591	0.85
268_V	373_L	0.591	0.85
93_A	97_V	0.590	0.85
126_K	132_F	0.590	0.85
301_V	316_I	0.589	0.85
328_H	350_G	0.586	0.85
132_F	137_I	0.586	0.85
148_R	155_Y	0.586	0.85
99_M	102_G	0.585	0.85
171_T	174_T	0.583	0.84
338_Q	344_Q	0.583	0.84
347_A	359_L	0.582	0.84
197_S	211_E	0.581	0.84
182_A	186_E	0.577	0.84
28_D	31_N	0.576	0.84
200_A	204_Q	0.576	0.84
170_G	184_A	0.574	0.84
211_E	218_A	0.574	0.84
262_W	265_E	0.574	0.84
66_Q	69_Q	0.574	0.84
34_A	38_S	0.570	0.83
161_Q	165_V	0.570	0.83
141_D	144_D	0.569	0.83
193_P	196_N	0.563	0.82
49_S	52_L	0.563	0.82
304_G	332_M	0.562	0.82
102_G	109_Q	0.562	0.82
110_Y	113_I	0.560	0.82
55_P	59_M	0.559	0.82
264_T	349_M	0.559	0.82
141_D	146_A	0.559	0.82
264_T	290_Q	0.559	0.82
317_K	323_L	0.557	0.82
329_N	359_L	0.553	0.81
40_N	43_A	0.550	0.81
208_T	214_G	0.549	0.81
279_N	350_G	0.549	0.81
198_T	201_V	0.549	0.81
95_Q	113_I	0.548	0.81
159_V	166_G	0.548	0.81
138_T	144_D	0.545	0.80
292_I	359_L	0.543	0.80
355_S	358_R	0.542	0.80
176_G	183_D	0.541	0.80
257_I	260_W	0.540	0.80
197_S	207_I	0.540	0.80
179_I	182_A	0.539	0.80
217_S	222_L	0.538	0.79
122_T	126_K	0.533	0.79
102_G	114_P	0.533	0.79
302_Y	364_R	0.533	0.79
99_M	106_Y	0.533	0.79
276_E	279_N	0.533	0.79
156_A	167_N	0.532	0.79
365_Y	370_V	0.528	0.78
134_I	138_T	0.528	0.78
56_P	59_M	0.528	0.78
184_A	190_V	0.528	0.78
123_Y	128_G	0.528	0.78
155_Y	166_G	0.527	0.78
206_T	209_Y	0.527	0.78
155_Y	170_G	0.527	0.78
201_V	205_P	0.527	0.78
105_V	108_R	0.527	0.78
245_E	248_V	0.526	0.78
81_T	85_Q	0.526	0.78
126_K	131_L	0.525	0.78
232_V	239_P	0.524	0.78
118_Y	121_S	0.523	0.78
56_P	63_S	0.523	0.78
370_V	374_R	0.522	0.77
75_Q	80_A	0.519	0.77
201_V	204_Q	0.519	0.77
142_F	151_I	0.518	0.77
67_Q	70_I	0.518	0.77
189_V	192_K	0.517	0.77
249_S	253_T	0.517	0.77
313_L	369_S	0.517	0.77
27_S	31_N	0.515	0.77
104_I	108_R	0.514	0.76
99_M	103_R	0.514	0.76
323_L	366_K	0.513	0.76
125_V	134_I	0.512	0.76
41_G	45_A	0.511	0.76
144_D	149_N	0.511	0.76
325_A	362_E	0.510	0.76
65_A	68_P	0.507	0.75
283_D	353_G	0.505	0.75
53_I	56_P	0.504	0.75
125_V	133_Y	0.502	0.75
67_Q	71_Q	0.501	0.75
207_I	212_S	0.500	0.74

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
2gu1A	1	0.6755	100	0.497	Contact Map
3sluA	1	0.6939	100	0.499	Contact Map
4bh5A	4	0.3325	100	0.5	Contact Map
4rnzA	1	0.6702	100	0.51	Contact Map
3tufB	1	0.3245	100	0.517	Contact Map
2hsiA	1	0.5831	100	0.522	Contact Map
1qwyA	1	0.5488	100	0.53	Contact Map
3nyyA	2	0.5541	100	0.553	Contact Map
4qp5A	1	0.3193	100	0.556	Contact Map
4lxcA	4	0.3298	100	0.567	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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