Q9HSW1 - HALSA - GREMLIN Contacts

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Q9HSW1 - LPS biosynthesis

UniProt:	Q9HSW1	Sequences: MHIAFIHPSFPSAEGTGATHSATQIVSGLSELDHDIDVYCASEPQQNRLSSDINLYHLDGESQHPHTNTKLNREVKARTNEFRKYDIVHSYLPSLIPSVANLGKNLDLSTVVTLNAYGGVCAKNDLLYLNEEHCEAKSNAKCLNCIARTGHQNNEQGYLYQTVSQLFSLRSINAGEDRLEYIDGFRAPSGHVRDNYTKFGFEEEKIHVIPHPLNDDFLVDHTSDFSEPINILYVGSLERHKGVDKLVPIIQGLRQREHDVELTVVGTGGLQSKMEEQSVNRNVEDYVDFAGFVSNEQLPSVYASHDVFIHPGIWEEPLARVYIEALATGTPIVTREYGSIETIIGDGGVTTDGSIDGFVQTIAELINANKLPALSEGGRSHVERYDRSQIVSQVEDLYGSVLT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	403 (348)
Sequences:	53763 (45396)
Seq/√Len:	2433.4

ECOLI - WCAL RFAG RFAB GLGA WCAI WBBK WCAC
BACSU - YPJH YQGM YTCC COTSA EPSD EPSF GLGA TUAC TUAH YKVP CGEB TAGE
HALSA - Q9HSW1 Q9HQQ0 Q9HS45 Q9HRP8 Q9HSV4 Q9HSV2 Q9HQT2 Q9HRP9
SULSO - Q980C8 Q97V61 Q97UM0 Q97XT7 Q97ZD3 Q97V80 Q97XT8 Q97VL4 Q97UU3 Q7LXM9 Q7LXI2 Q97XT6 Q97XU2 Q97XT9 Q97XT5 Q97XF6 Q7LXF8 Q97XT1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
232_L	305_H	4.766	1.00
261_E	288_D	3.742	1.00
184_G	207_H	3.242	1.00
308_F	325_A	3.182	1.00
89_H	398_Y	3.072	1.00
230_N	263_T	3.032	1.00
263_T	290_A	2.795	1.00
381_H	384_R	2.789	1.00
228_P	261_E	2.784	1.00
252_G	359_V	2.750	1.00
248_P	277_Q	2.701	1.00
271_Q	275_E	2.673	1.00
233_Y	243_V	2.629	1.00
256_R	363_A	2.420	1.00
254_R	286_Y	2.392	1.00
193_R	197_T	2.302	1.00
248_P	355_I	2.231	1.00
229_I	366_I	2.211	1.00
37_D	85_Y	2.197	1.00
242_G	245_K	2.166	1.00
37_D	83_R	2.137	1.00
336_E	341_E	2.119	1.00
277_Q	281_R	2.089	1.00
265_V	301_V	2.086	1.00
230_N	261_E	2.082	1.00
361_T	364_E	2.071	1.00
344_I	348_G	2.052	1.00
263_T	288_D	2.046	1.00
250_I	262_L	2.039	1.00
252_G	356_D	2.030	1.00
230_N	304_S	2.004	1.00
34_H	395_E	1.951	1.00
231_I	307_V	1.950	1.00
229_I	306_D	1.949	1.00
364_E	370_K	1.929	1.00
4_A	85_Y	1.904	1.00
371_L	375_S	1.887	1.00
89_H	113_T	1.864	1.00
242_G	313_I	1.842	1.00
37_D	56_Y	1.813	1.00
270_L	273_K	1.807	1.00
329_G	379_R	1.806	1.00
389_Q	393_Q	1.804	1.00
190_G	193_R	1.796	1.00
336_E	352_D	1.786	1.00
349_V	361_T	1.754	1.00
279_V	284_E	1.751	1.00
184_G	397_L	1.745	1.00
212_P	387_R	1.729	1.00
32_L	392_S	1.725	1.00
308_F	330_T	1.720	1.00
352_D	357_G	1.715	1.00
112_V	182_I	1.708	1.00
251_Q	281_R	1.705	1.00
246_L	262_L	1.681	1.00
363_A	367_N	1.670	1.00
187_A	206_I	1.666	1.00
345_G	381_H	1.662	1.00
193_R	208_V	1.644	1.00
250_I	260_V	1.638	1.00
190_G	342_T	1.637	1.00
234_V	298_L	1.624	1.00
28_G	388_S	1.555	1.00
349_V	364_E	1.551	1.00
28_G	391_V	1.551	1.00
4_A	39_Y	1.530	1.00
246_L	309_I	1.528	1.00
193_R	206_I	1.523	1.00
354_S	357_G	1.523	1.00
395_E	399_G	1.520	1.00
357_G	361_T	1.507	1.00
28_G	31_E	1.505	1.00
32_L	395_E	1.500	1.00
294_S	297_Q	1.484	1.00
265_V	290_A	1.478	1.00
240_H	314_W	1.467	1.00
23_T	27_S	1.467	1.00
297_Q	300_S	1.461	1.00
257_E	363_A	1.455	1.00
253_L	363_A	1.454	1.00
370_K	373_A	1.452	1.00
190_G	208_V	1.442	1.00
380_S	383_E	1.441	1.00
334_T	340_I	1.429	1.00
245_K	355_I	1.424	1.00
263_T	301_V	1.423	1.00
245_K	313_I	1.419	1.00
244_D	277_Q	1.419	1.00
37_D	54_N	1.410	1.00
373_A	377_G	1.407	1.00
305_H	330_T	1.394	1.00
230_N	306_D	1.391	1.00
351_T	361_T	1.347	1.00
293_V	297_Q	1.346	1.00
90_S	110_T	1.333	1.00
231_I	362_I	1.333	1.00
197_T	203_E	1.325	1.00
249_I	358_F	1.322	1.00
243_V	264_V	1.318	1.00
5_F	29_L	1.315	1.00
355_I	359_V	1.315	1.00
299_P	328_T	1.315	1.00
252_G	355_I	1.305	1.00
263_T	305_H	1.303	1.00
231_I	309_I	1.303	1.00
186_R	394_V	1.300	1.00
276_E	280_N	1.298	1.00
186_R	397_L	1.296	1.00
187_A	193_R	1.291	1.00
377_G	380_S	1.290	1.00
277_Q	280_N	1.284	1.00
232_L	265_V	1.283	1.00
237_L	264_V	1.281	1.00
233_Y	246_L	1.272	1.00
5_F	91_Y	1.271	1.00
393_Q	396_D	1.254	1.00
357_G	360_Q	1.252	1.00
318_L	323_I	1.244	1.00
202_E	205_K	1.240	1.00
190_G	194_D	1.236	1.00
218_L	328_T	1.234	1.00
389_Q	392_S	1.228	1.00
229_I	307_V	1.220	1.00
375_S	378_G	1.207	1.00
295_N	298_L	1.194	1.00
30_S	33_D	1.191	1.00
275_E	279_V	1.173	1.00
322_Y	340_I	1.166	1.00
313_I	353_G	1.166	1.00
267_T	271_Q	1.157	1.00
245_K	353_G	1.157	1.00
21_S	320_R	1.155	1.00
257_E	367_N	1.154	1.00
359_V	363_A	1.153	1.00
310_H	322_Y	1.151	1.00
303_A	328_T	1.146	1.00
272_S	275_E	1.144	1.00
298_L	302_Y	1.143	1.00
338_G	341_E	1.137	1.00
349_V	374_L	1.131	1.00
387_R	390_I	1.126	1.00
272_S	276_E	1.117	1.00
330_T	375_S	1.113	1.00
28_G	32_L	1.099	1.00
188_P	192_V	1.098	1.00
194_D	197_T	1.096	1.00
386_D	389_Q	1.096	1.00
115_N	320_R	1.095	1.00
372_P	376_E	1.095	1.00
368_A	371_L	1.092	1.00
5_F	26_V	1.091	1.00
230_N	305_H	1.088	1.00
245_K	335_R	1.086	1.00
252_G	256_R	1.085	1.00
187_A	196_Y	1.085	1.00
390_I	393_Q	1.080	1.00
244_D	248_P	1.080	1.00
329_G	376_E	1.076	1.00
229_I	260_V	1.072	1.00
245_K	248_P	1.069	1.00
319_A	340_I	1.062	1.00
302_Y	328_T	1.059	1.00
217_F	299_P	1.058	1.00
346_D	361_T	1.047	1.00
308_F	321_V	1.044	1.00
370_K	374_L	1.043	1.00
365_L	374_L	1.042	1.00
351_T	358_F	1.040	1.00
335_R	351_T	1.038	1.00
24_Q	27_S	1.025	1.00
334_T	350_T	1.025	1.00
263_T	304_S	1.024	1.00
299_P	303_A	1.024	1.00
232_L	301_V	1.018	1.00
278_S	289_F	1.016	1.00
310_H	321_V	1.014	1.00
360_Q	364_E	1.009	1.00
188_P	211_H	1.007	1.00
339_S	342_T	1.006	1.00
229_I	259_D	1.006	1.00
311_P	358_F	1.001	1.00
244_D	273_K	1.001	1.00
390_I	394_V	0.999	1.00
290_A	301_V	0.998	1.00
24_Q	387_R	0.998	1.00
228_P	259_D	0.993	1.00
374_L	377_G	0.989	1.00
326_L	332_I	0.988	1.00
234_V	265_V	0.988	1.00
236_S	240_H	0.985	1.00
265_V	293_V	0.982	1.00
231_I	250_I	0.981	1.00
376_E	380_S	0.981	1.00
248_P	281_R	0.980	1.00
234_V	302_Y	0.978	1.00
188_P	317_P	0.978	1.00
90_S	112_V	0.975	1.00
247_V	278_S	0.972	1.00
246_L	311_P	0.970	1.00
244_D	313_I	0.968	1.00
253_L	362_I	0.968	1.00
110_T	182_I	0.967	1.00
253_L	260_V	0.967	1.00
325_A	330_T	0.960	1.00
91_Y	115_N	0.960	1.00
375_S	379_R	0.958	1.00
392_S	396_D	0.957	1.00
21_S	115_N	0.952	1.00
293_V	301_V	0.951	1.00
250_I	286_Y	0.947	1.00
187_A	192_V	0.943	1.00
16_T	19_T	0.933	1.00
349_V	365_L	0.930	1.00
211_H	320_R	0.930	1.00
278_S	283_V	0.924	1.00
111_V	186_R	0.921	1.00
334_T	344_I	0.920	1.00
368_A	372_P	0.910	1.00
326_L	381_H	0.909	1.00
212_P	390_I	0.909	1.00
245_K	358_F	0.906	1.00
26_V	38_V	0.906	1.00
218_L	299_P	0.904	1.00
22_A	91_Y	0.902	1.00
26_V	30_S	0.902	1.00
290_A	293_V	0.902	1.00
322_Y	332_I	0.901	1.00
261_E	286_Y	0.897	1.00
21_S	113_T	0.896	1.00
326_L	378_G	0.894	1.00
260_V	366_I	0.890	1.00
253_L	366_I	0.888	1.00
249_I	359_V	0.885	1.00
76_K	105_N	0.883	1.00
20_H	24_Q	0.883	1.00
333_V	351_T	0.880	1.00
349_V	370_K	0.879	1.00
254_R	257_E	0.878	1.00
182_I	185_F	0.878	1.00
372_P	375_S	0.878	1.00
344_I	350_T	0.877	1.00
307_V	365_L	0.875	1.00
374_L	378_G	0.873	1.00
207_H	397_L	0.873	1.00
273_K	276_E	0.872	1.00
103_G	110_T	0.871	1.00
302_Y	330_T	0.870	1.00
322_Y	334_T	0.870	1.00
337_Y	340_I	0.866	1.00
315_E	319_A	0.865	1.00
253_L	359_V	0.863	1.00
3_I	34_H	0.862	1.00
233_Y	264_V	0.861	1.00
238_E	269_G	0.859	1.00
232_L	302_Y	0.856	1.00
333_V	361_T	0.855	1.00
273_K	277_Q	0.851	1.00
215_D	386_D	0.850	1.00
195_N	198_K	0.847	1.00
186_R	209_I	0.847	1.00
392_S	395_E	0.843	1.00
295_N	299_P	0.840	1.00
322_Y	343_I	0.837	1.00
360_Q	363_A	0.831	1.00
214_N	217_F	0.830	1.00
241_K	321_V	0.829	1.00
276_E	279_V	0.828	1.00
386_D	390_I	0.828	1.00
197_T	206_I	0.828	1.00
209_I	397_L	0.827	1.00
331_P	375_S	0.826	1.00
233_Y	311_P	0.825	1.00
356_D	360_Q	0.823	1.00
300_S	304_S	0.823	1.00
381_H	385_Y	0.818	1.00
251_Q	254_R	0.812	1.00
309_I	362_I	0.809	1.00
16_T	236_S	0.808	1.00
207_H	393_Q	0.804	1.00
249_I	355_I	0.803	1.00
254_R	258_H	0.802	1.00
251_Q	283_V	0.801	1.00
73_R	77_A	0.799	1.00
331_P	365_L	0.799	1.00
310_H	340_I	0.798	1.00
300_S	303_A	0.796	1.00
306_D	371_L	0.792	1.00
109_S	183_D	0.788	1.00
235_G	243_V	0.787	1.00
35_D	54_N	0.786	1.00
312_G	315_E	0.784	1.00
20_H	295_N	0.781	1.00
301_V	304_S	0.781	1.00
233_Y	308_F	0.780	1.00
307_V	362_I	0.778	1.00
387_R	391_V	0.771	1.00
256_R	360_Q	0.771	1.00
21_S	211_H	0.770	1.00
188_P	320_R	0.770	1.00
239_R	244_D	0.769	1.00
248_P	251_Q	0.769	1.00
177_D	181_Y	0.768	1.00
388_S	392_S	0.767	1.00
278_S	287_V	0.765	1.00
394_V	398_Y	0.764	1.00
278_S	281_R	0.764	1.00
32_L	388_S	0.762	1.00
257_E	260_V	0.759	1.00
24_Q	28_G	0.756	1.00
248_P	252_G	0.754	1.00
191_H	194_D	0.752	1.00
210_P	393_Q	0.752	1.00
173_N	177_D	0.749	1.00
244_D	270_L	0.740	1.00
256_R	359_V	0.732	1.00
24_Q	214_N	0.732	1.00
30_S	52_D	0.731	1.00
241_K	312_G	0.729	1.00
69_T	73_R	0.728	1.00
78_R	83_R	0.727	1.00
210_P	342_T	0.727	1.00
234_V	308_F	0.724	1.00
364_E	367_N	0.722	1.00
319_A	322_Y	0.722	1.00
333_V	365_L	0.721	1.00
191_H	195_N	0.719	1.00
336_E	350_T	0.719	1.00
173_N	176_E	0.719	1.00
111_V	184_G	0.716	1.00
254_R	259_D	0.714	1.00
233_Y	262_L	0.713	1.00
231_I	260_V	0.710	1.00
21_S	394_V	0.710	1.00
37_D	41_A	0.710	1.00
116_A	240_H	0.709	1.00
87_I	398_Y	0.709	1.00
7_H	18_A	0.708	1.00
91_Y	113_T	0.707	1.00
365_L	371_L	0.706	1.00
5_F	36_I	0.705	1.00
30_S	36_I	0.702	1.00
115_N	188_P	0.701	1.00
101_N	105_N	0.697	1.00
102_L	106_L	0.697	1.00
335_R	358_F	0.690	1.00
32_L	391_V	0.690	1.00
209_I	394_V	0.688	1.00
310_H	319_A	0.680	1.00
89_H	394_V	0.680	1.00
373_A	376_E	0.679	1.00
210_P	385_Y	0.678	1.00
103_G	183_D	0.678	1.00
221_H	303_A	0.677	1.00
20_H	23_T	0.675	1.00
237_L	271_Q	0.674	1.00
356_D	359_V	0.673	1.00
341_E	350_T	0.671	1.00
379_R	382_V	0.670	1.00
323_I	385_Y	0.666	1.00
70_K	74_E	0.666	1.00
25_I	394_V	0.664	1.00
229_I	232_L	0.662	1.00
207_H	210_P	0.661	1.00
326_L	375_S	0.659	1.00
396_D	399_G	0.657	1.00
87_I	111_V	0.656	1.00
104_K	181_Y	0.656	1.00
318_L	385_Y	0.653	1.00
31_E	388_S	0.653	1.00
275_E	289_F	0.652	1.00
72_N	76_K	0.652	1.00
176_E	180_E	0.651	1.00
239_R	313_I	0.650	1.00
377_G	381_H	0.649	1.00
88_V	103_G	0.649	1.00
242_G	353_G	0.648	1.00
27_S	51_S	0.647	1.00
7_H	22_A	0.645	1.00
242_G	311_P	0.645	1.00
378_G	381_H	0.644	1.00
346_D	349_V	0.642	1.00
26_V	36_I	0.640	1.00
309_I	358_F	0.639	1.00
231_I	366_I	0.639	1.00
239_R	270_L	0.637	1.00
241_K	315_E	0.634	1.00
247_V	287_V	0.634	1.00
249_I	362_I	0.632	1.00
69_T	72_N	0.631	1.00
27_S	31_E	0.630	1.00
229_I	368_A	0.629	1.00
259_D	286_Y	0.628	1.00
266_G	291_G	0.627	1.00
209_I	393_Q	0.626	1.00
301_V	305_H	0.626	1.00
235_G	241_K	0.625	1.00
308_F	332_I	0.619	1.00
250_I	253_L	0.617	1.00
90_S	99_V	0.617	1.00
193_R	203_E	0.613	1.00
111_V	398_Y	0.613	1.00
268_G	271_Q	0.609	1.00
391_V	395_E	0.608	1.00
190_G	210_P	0.608	1.00
30_S	34_H	0.606	1.00
110_T	183_D	0.605	1.00
88_V	108_L	0.605	1.00
103_G	106_L	0.604	1.00
267_T	292_F	0.604	1.00
189_S	192_V	0.603	1.00
369_N	373_A	0.603	1.00
307_V	333_V	0.602	1.00
191_H	341_E	0.601	1.00
51_S	54_N	0.598	1.00
258_H	363_A	0.595	1.00
321_V	325_A	0.595	1.00
28_G	387_R	0.593	1.00
258_H	367_N	0.592	1.00
214_N	218_L	0.591	1.00
293_V	298_L	0.591	1.00
169_L	172_I	0.589	1.00
24_Q	320_R	0.587	1.00
21_S	91_Y	0.586	1.00
90_S	96_I	0.585	1.00
230_N	301_V	0.585	1.00
311_P	335_R	0.585	1.00
9_S	19_T	0.584	1.00
229_I	371_L	0.582	1.00
5_F	89_H	0.580	1.00
384_R	389_Q	0.580	1.00
115_N	211_H	0.580	1.00
302_Y	321_V	0.579	1.00
351_T	357_G	0.579	1.00
18_A	92_L	0.579	1.00
371_L	374_L	0.577	1.00
232_L	308_F	0.577	1.00
256_R	367_N	0.574	1.00
26_V	53_I	0.574	1.00
85_Y	108_L	0.573	1.00
245_K	249_I	0.572	1.00
113_T	186_R	0.571	1.00
274_M	289_F	0.569	1.00
113_T	394_V	0.569	1.00
34_H	399_G	0.569	1.00
306_D	368_A	0.568	1.00
242_G	335_R	0.567	1.00
347_G	364_E	0.564	1.00
265_V	298_L	0.563	1.00
33_D	36_I	0.562	1.00
210_P	318_L	0.562	1.00
219_V	222_T	0.562	1.00
275_E	278_S	0.562	1.00
257_E	366_I	0.562	1.00
232_L	330_T	0.561	1.00
223_S	226_S	0.561	1.00
262_L	287_V	0.559	1.00
365_L	370_K	0.559	1.00
237_L	243_V	0.559	1.00
274_M	277_Q	0.558	1.00
4_A	37_D	0.558	1.00
5_F	398_Y	0.557	1.00
333_V	362_I	0.555	1.00
96_I	99_V	0.553	1.00
337_Y	341_E	0.552	1.00
247_V	274_M	0.550	1.00
246_L	250_I	0.550	1.00
325_A	332_I	0.550	1.00
302_Y	308_F	0.550	1.00
215_D	327_A	0.549	1.00
192_V	195_N	0.548	1.00
228_P	304_S	0.548	1.00
219_V	303_A	0.547	1.00
239_R	273_K	0.545	1.00
21_S	25_I	0.545	1.00
278_S	284_E	0.544	1.00
54_N	57_H	0.543	1.00
244_D	274_M	0.543	1.00
73_R	76_K	0.543	1.00
243_V	270_L	0.543	1.00
117_Y	120_V	0.540	1.00
70_K	73_R	0.540	1.00
25_I	28_G	0.539	1.00
298_L	301_V	0.539	1.00
4_A	88_V	0.538	1.00
232_L	263_T	0.538	1.00
197_T	200_G	0.536	1.00
326_L	382_V	0.536	1.00
331_P	371_L	0.535	1.00
236_S	241_K	0.535	1.00
40_C	55_L	0.534	1.00
118_G	121_C	0.530	1.00
253_L	258_H	0.530	1.00
253_L	257_E	0.528	1.00
187_A	208_V	0.528	1.00
376_E	379_R	0.526	1.00
247_V	277_Q	0.526	1.00
15_G	292_F	0.525	1.00
237_L	266_G	0.524	1.00
319_A	323_I	0.524	1.00
312_G	319_A	0.523	1.00
249_I	253_L	0.522	1.00
384_R	393_Q	0.521	1.00
323_I	382_V	0.521	1.00
177_D	180_E	0.519	1.00
216_D	219_V	0.519	1.00
30_S	53_I	0.517	1.00
52_D	57_H	0.517	1.00
68_N	71_L	0.514	1.00
49_L	52_D	0.513	1.00
270_L	274_M	0.513	1.00
369_N	372_P	0.512	1.00
217_F	295_N	0.510	1.00
184_G	188_P	0.510	1.00
10_F	23_T	0.509	1.00
27_S	30_S	0.507	1.00
74_E	78_R	0.504	1.00
27_S	50_S	0.504	1.00
188_P	319_A	0.503	1.00
307_V	366_I	0.503	1.00
265_V	305_H	0.502	1.00
295_N	301_V	0.501	1.00
192_V	317_P	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
3c48A	2	0.8809	100	0.188	Contact Map
2r60A	1	0.928	100	0.192	Contact Map
3froA	3	0.9156	100	0.198	Contact Map
1rzuA	1	0.9231	100	0.203	Contact Map
4n9wA	1	0.8362	100	0.204	Contact Map
2qzsA	1	0.9181	100	0.218	Contact Map
3okpA	1	0.8685	100	0.232	Contact Map
2x0dA	2	0.8288	100	0.239	Contact Map
2x6qA	1	0.8511	100	0.239	Contact Map
3s28A	4	0.9206	100	0.241	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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