RFAG - ECOLI - GREMLIN Contacts

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RFAG - Lipopolysaccharide core biosynthesis protein RfaG

UniProt:	P25740	Sequences: MIVAFCLYKYFPFGGLQRDFMRIASTVAARGHHVRVYTQSWEGDCPKAFELIQVPVKSHTNHGRNAEYYAWVQNHLKEHPADRVVGFNKMPGLDVYFAADVCYAEKVAQEKGFLYRLTSRYRHYAAFERATFEQGKSTKLMMLTDKQIADFQKHYQTEPERFQILPPGIYPDRKYSEQIPNSREIYRQKNGIKEQQNLLLQVGSDFGRKGVDRSIEALASLPESLRHNTLLFVVGQDKPRKFEALAEKLGVRSNVHFFSGRNDVSELMAAADLLLHPAYQEAAGIVLLEAITAGLPVLTTAVCGYAHYIADANCGTVIAEPFSQEQLNEVLRKALTQSPLRMAWAENARHYADTQDLYSLPEKAADIITGGLDG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11339
Length:	374 (341)
Sequences:	57125 (48461)
Seq/√Len:	2624.3

ECOLI - RFAG WCAL GLGA RFAB WCAI WBBK WCAC
BACSU - YPJH EPSD EPSF GLGA YTCC COTSA YQGM TUAC TUAH YKVP CGEB TAGE
HALSA - Q9HQQ0 Q9HSW1 Q9HS45 Q9HRP8 Q9HSV4 Q9HSV2 Q9HQT2 Q9HRP9
SULSO - Q97ZD3 Q97V61 Q97UM0 Q980C8 Q97XT7 Q97VL4 Q97V80 Q97XT8 Q7LXI2 Q97XT9 Q97XU2 Q97UU3 Q97XF6 Q97XT5 Q7LXM9 Q7LXF8 Q97XT1 Q97XT6 Q7LXF5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
200_L	271_A	4.876	1.00
230_L	256_H	3.802	1.00
139_K	163_Q	3.297	1.00
274_L	290_A	3.287	1.00
198_L	232_F	3.155	1.00
85_V	368_I	2.941	1.00
220_S	328_N	2.884	1.00
232_F	258_F	2.864	1.00
201_Q	211_V	2.757	1.00
196_Q	230_L	2.730	1.00
216_E	245_L	2.657	1.00
222_P	254_N	2.488	1.00
216_E	324_Q	2.287	1.00
210_G	213_R	2.250	1.00
35_R	81_A	2.239	1.00
148_I	152_Q	2.234	1.00
197_N	335_L	2.212	1.00
245_L	249_L	2.167	1.00
35_R	79_H	2.155	1.00
301_A	306_A	2.122	1.00
198_L	230_L	2.115	1.00
330_V	333_K	2.086	1.00
232_F	256_H	2.069	1.00
234_V	267_L	2.063	1.00
32_H	365_A	2.045	1.00
351_Y	354_T	2.039	1.00
218_L	231_L	2.017	1.00
198_L	270_A	2.012	1.00
337_Q	340_L	2.004	1.00
197_N	272_D	1.990	1.00
199_L	273_L	1.979	1.00
220_S	325_E	1.968	1.00
333_K	340_L	1.929	1.00
310_A	313_N	1.902	1.00
341_R	345_A	1.894	1.00
294_G	349_R	1.888	1.00
219_A	249_L	1.863	1.00
210_G	279_Y	1.860	1.00
314_C	351_Y	1.843	1.00
309_I	315_G	1.831	1.00
316_T	330_V	1.807	1.00
359_S	363_K	1.789	1.00
85_V	109_Q	1.780	1.00
214_S	231_L	1.760	1.00
333_K	337_Q	1.759	1.00
274_L	295_L	1.753	1.00
145_D	148_I	1.752	1.00
35_R	52_I	1.741	1.00
168_G	357_L	1.739	1.00
310_A	351_Y	1.721	1.00
139_K	367_I	1.709	1.00
142_M	162_F	1.705	1.00
202_V	264_V	1.693	1.00
320_E	326_Q	1.690	1.00
148_I	164_I	1.686	1.00
30_R	362_E	1.677	1.00
247_E	252_R	1.669	1.00
145_D	307_H	1.646	1.00
332_R	336_T	1.636	1.00
218_L	229_T	1.626	1.00
214_S	275_L	1.600	1.00
313_N	347_N	1.587	1.00
316_T	333_K	1.565	1.00
365_A	369_T	1.556	1.00
145_D	164_I	1.554	1.00
340_L	343_A	1.546	1.00
26_T	358_Y	1.533	1.00
326_Q	330_V	1.529	1.00
148_I	162_F	1.529	1.00
234_V	258_F	1.513	1.00
323_S	326_Q	1.512	1.00
213_R	279_Y	1.502	1.00
26_T	29_A	1.498	1.00
21_M	25_S	1.494	1.00
310_A	314_C	1.491	1.00
343_A	347_N	1.486	1.00
26_T	361_P	1.485	1.00
208_R	280_Q	1.478	1.00
30_R	365_A	1.472	1.00
212_D	245_L	1.452	1.00
221_L	332_R	1.451	1.00
301_A	320_E	1.450	1.00
213_R	324_Q	1.448	1.00
232_F	267_L	1.430	1.00
299_T	305_Y	1.426	1.00
265_S	293_A	1.410	1.00
271_A	295_L	1.399	1.00
142_M	148_I	1.395	1.00
226_R	332_R	1.390	1.00
198_L	272_D	1.386	1.00
324_Q	328_N	1.378	1.00
232_F	271_A	1.372	1.00
211_V	233_V	1.364	1.00
261_R	267_L	1.349	1.00
318_I	330_V	1.343	1.00
220_S	324_Q	1.342	1.00
201_Q	214_S	1.339	1.00
205_D	233_V	1.336	1.00
283_A	288_L	1.326	1.00
217_A	327_L	1.319	1.00
258_F	261_R	1.316	1.00
141_M	367_I	1.309	1.00
5_F	87_F	1.302	1.00
199_L	331_L	1.287	1.00
35_R	50_E	1.285	1.00
326_Q	329_E	1.260	1.00
199_L	275_L	1.256	1.00
141_M	364_A	1.255	1.00
200_L	234_V	1.251	1.00
174_K	293_A	1.250	1.00
347_N	350_H	1.246	1.00
108_A	135_G	1.241	1.00
363_K	366_D	1.229	1.00
359_S	362_E	1.229	1.00
350_H	353_D	1.225	1.00
234_V	261_R	1.224	1.00
5_F	27_V	1.224	1.00
263_D	266_E	1.218	1.00
269_A	293_A	1.215	1.00
245_L	248_K	1.213	1.00
158_E	161_R	1.209	1.00
328_N	332_R	1.208	1.00
86_G	106_K	1.199	1.00
226_R	336_T	1.195	1.00
244_A	248_K	1.193	1.00
197_N	273_L	1.181	1.00
145_D	149_A	1.162	1.00
19_D	285_I	1.160	1.00
264_V	268_M	1.153	1.00
276_H	287_L	1.148	1.00
287_L	305_Y	1.142	1.00
357_L	360_L	1.140	1.00
345_A	348_A	1.135	1.00
356_D	359_S	1.130	1.00
342_M	346_E	1.128	1.00
212_D	216_E	1.122	1.00
303_C	306_A	1.120	1.00
173_R	265_S	1.119	1.00
198_L	271_A	1.116	1.00
213_R	216_E	1.115	1.00
197_N	229_T	1.111	1.00
294_G	346_E	1.107	1.00
268_M	293_A	1.099	1.00
213_R	300_T	1.096	1.00
149_A	152_Q	1.093	1.00
360_L	363_K	1.083	1.00
219_A	223_E	1.083	1.00
318_I	327_L	1.082	1.00
311_D	330_V	1.082	1.00
143_L	147_Q	1.076	1.00
340_L	344_W	1.075	1.00
316_T	344_W	1.073	1.00
276_H	286_V	1.071	1.00
295_L	345_A	1.070	1.00
240_R	244_A	1.070	1.00
143_L	167_P	1.063	1.00
26_T	30_R	1.062	1.00
334_A	344_W	1.061	1.00
28_A	31_G	1.061	1.00
243_E	247_E	1.059	1.00
236_Q	260_G	1.058	1.00
111_K	285_I	1.052	1.00
279_Y	322_F	1.049	1.00
213_R	322_F	1.049	1.00
300_T	318_I	1.042	1.00
338_S	341_R	1.041	1.00
142_M	151_F	1.028	1.00
346_E	350_H	1.027	1.00
265_S	269_A	1.026	1.00
199_L	218_L	1.025	1.00
299_T	317_V	1.024	1.00
258_F	267_L	1.024	1.00
277_P	327_L	1.023	1.00
274_L	286_V	1.022	1.00
193_K	196_Q	1.022	1.00
196_Q	228_N	1.017	1.00
200_L	267_L	1.014	1.00
202_V	234_V	1.014	1.00
197_N	228_N	1.010	1.00
304_G	307_H	1.010	1.00
232_F	270_A	1.004	1.00
284_G	305_Y	1.004	1.00
287_L	299_T	1.001	1.00
278_A	281_E	0.999	1.00
142_M	147_Q	0.994	1.00
86_G	108_A	0.993	1.00
329_E	333_K	0.992	1.00
22_R	25_S	0.990	1.00
212_D	279_Y	0.990	1.00
222_P	226_R	0.990	1.00
240_R	243_E	0.990	1.00
360_L	364_A	0.983	1.00
216_E	249_L	0.982	1.00
5_F	24_A	0.982	1.00
22_R	357_L	0.976	1.00
291_I	297_V	0.974	1.00
167_P	285_I	0.969	1.00
204_S	208_R	0.968	1.00
174_K	265_S	0.964	1.00
70_A	74_N	0.961	1.00
206_F	238_K	0.961	1.00
215_I	246_A	0.961	1.00
202_V	268_M	0.956	1.00
212_D	241_K	0.956	1.00
246_A	257_F	0.954	1.00
316_T	334_A	0.945	1.00
338_S	342_M	0.939	1.00
171_P	356_D	0.937	1.00
87_F	111_K	0.935	1.00
14_G	17_Q	0.933	1.00
168_G	360_L	0.932	1.00
362_E	366_D	0.931	1.00
221_L	331_L	0.930	1.00
218_L	254_N	0.928	1.00
201_Q	233_V	0.925	1.00
291_I	348_A	0.923	1.00
143_L	282_A	0.921	1.00
24_A	36_V	0.919	1.00
345_A	349_R	0.918	1.00
299_T	309_I	0.917	1.00
349_R	353_D	0.916	1.00
150_D	153_K	0.914	1.00
163_Q	367_I	0.913	1.00
214_S	277_P	0.909	1.00
221_L	229_T	0.908	1.00
150_D	154_H	0.900	1.00
73_Q	101_V	0.900	1.00
287_L	297_V	0.900	1.00
290_A	295_L	0.899	1.00
281_E	284_G	0.898	1.00
149_A	153_K	0.893	1.00
342_M	345_A	0.889	1.00
246_A	251_V	0.888	1.00
24_A	28_A	0.887	1.00
230_L	254_N	0.885	1.00
213_R	327_L	0.882	1.00
316_T	340_L	0.879	1.00
344_W	347_N	0.878	1.00
320_E	323_S	0.871	1.00
220_S	223_E	0.871	1.00
217_A	328_N	0.867	1.00
73_Q	77_K	0.866	1.00
209_K	281_E	0.866	1.00
298_L	318_I	0.866	1.00
314_C	348_A	0.865	1.00
291_I	351_Y	0.863	1.00
273_L	334_A	0.861	1.00
221_L	335_L	0.859	1.00
221_L	328_N	0.855	1.00
170_Y	173_R	0.854	1.00
18_R	22_R	0.853	1.00
302_V	305_Y	0.848	1.00
241_K	244_A	0.847	1.00
201_Q	277_P	0.844	1.00
241_K	245_L	0.842	1.00
229_T	335_L	0.840	1.00
19_D	111_K	0.840	1.00
276_H	305_Y	0.840	1.00
152_Q	162_F	0.837	1.00
291_I	314_C	0.837	1.00
268_M	295_L	0.834	1.00
146_K	149_A	0.834	1.00
209_K	286_V	0.831	1.00
267_L	270_A	0.828	1.00
287_L	308_Y	0.827	1.00
126_A	129_R	0.826	1.00
362_E	365_A	0.825	1.00
107_V	141_M	0.823	1.00
219_A	222_P	0.822	1.00
296_P	345_A	0.819	1.00
298_L	330_V	0.814	1.00
217_A	324_Q	0.810	1.00
165_L	367_I	0.810	1.00
129_R	133_E	0.809	1.00
275_L	331_L	0.806	1.00
20_F	87_F	0.796	1.00
216_E	220_S	0.794	1.00
222_P	227_H	0.794	1.00
105_E	138_T	0.792	1.00
19_D	109_Q	0.788	1.00
309_I	317_V	0.787	1.00
351_Y	355_Q	0.786	1.00
200_L	268_M	0.786	1.00
75_H	79_H	0.785	1.00
22_R	170_Y	0.785	1.00
107_V	139_K	0.783	1.00
244_A	247_E	0.783	1.00
301_A	317_V	0.783	1.00
216_E	219_A	0.782	1.00
311_D	314_C	0.780	1.00
356_D	360_L	0.779	1.00
130_A	134_Q	0.778	1.00
33_H	50_E	0.778	1.00
273_L	331_L	0.774	1.00
141_M	165_L	0.774	1.00
266_E	270_A	0.768	1.00
246_A	249_L	0.768	1.00
201_Q	231_L	0.762	1.00
219_A	251_V	0.758	1.00
207_G	212_D	0.757	1.00
357_L	361_P	0.756	1.00
261_R	264_V	0.754	1.00
30_R	358_Y	0.753	1.00
272_D	341_R	0.750	1.00
166_P	363_K	0.749	1.00
266_E	269_A	0.745	1.00
111_K	143_L	0.744	1.00
296_P	334_A	0.744	1.00
201_Q	274_L	0.743	1.00
325_E	329_E	0.743	1.00
112_G	208_R	0.741	1.00
209_K	278_A	0.740	1.00
163_Q	363_K	0.740	1.00
146_K	150_D	0.737	1.00
329_E	332_R	0.737	1.00
246_A	255_V	0.736	1.00
177_E	269_A	0.734	1.00
19_D	167_P	0.733	1.00
312_A	333_K	0.729	1.00
22_R	26_T	0.727	1.00
170_Y	174_K	0.726	1.00
207_G	279_Y	0.725	1.00
344_W	348_A	0.722	1.00
349_R	352_A	0.722	1.00
35_R	39_Q	0.721	1.00
202_V	274_L	0.720	1.00
358_Y	362_E	0.720	1.00
69_Y	73_Q	0.716	1.00
74_N	78_E	0.716	1.00
99_A	106_K	0.715	1.00
276_H	284_G	0.715	1.00
343_A	346_E	0.713	1.00
364_A	368_I	0.712	1.00
226_R	229_T	0.707	1.00
333_K	336_T	0.701	1.00
203_G	211_V	0.699	1.00
143_L	285_I	0.696	1.00
166_P	307_H	0.692	1.00
284_G	287_L	0.692	1.00
194_E	197_N	0.688	1.00
7_L	20_F	0.688	1.00
165_L	364_A	0.687	1.00
83_R	107_V	0.687	1.00
18_R	21_M	0.686	1.00
135_G	138_T	0.686	1.00
98_A	102_C	0.683	1.00
203_G	209_K	0.683	1.00
28_A	34_V	0.683	1.00
163_Q	166_P	0.678	1.00
199_L	229_T	0.677	1.00
106_K	135_G	0.677	1.00
87_F	109_Q	0.676	1.00
152_Q	156_Q	0.671	1.00
166_P	355_Q	0.669	1.00
334_A	341_R	0.669	1.00
85_V	364_A	0.665	1.00
199_L	335_L	0.663	1.00
325_E	328_N	0.663	1.00
83_R	368_I	0.662	1.00
298_L	334_A	0.662	1.00
5_F	34_V	0.662	1.00
70_A	73_Q	0.660	1.00
30_R	361_P	0.659	1.00
14_G	204_S	0.656	1.00
243_E	257_F	0.653	1.00
283_A	355_Q	0.653	1.00
300_T	321_P	0.652	1.00
306_A	317_V	0.651	1.00
288_L	355_Q	0.643	1.00
107_V	368_I	0.640	1.00
314_C	347_N	0.638	1.00
192_I	232_F	0.637	1.00
300_T	327_L	0.637	1.00
311_D	316_T	0.633	1.00
97_F	101_V	0.632	1.00
337_Q	341_R	0.631	1.00
348_A	351_Y	0.631	1.00
366_D	369_T	0.631	1.00
339_P	343_A	0.626	1.00
171_P	292_T	0.625	1.00
197_N	200_L	0.622	1.00
275_L	327_L	0.621	1.00
19_D	364_A	0.621	1.00
67_E	71_W	0.618	1.00
165_L	363_K	0.617	1.00
218_L	221_L	0.617	1.00
227_H	336_T	0.617	1.00
9_K	17_Q	0.615	1.00
28_A	32_H	0.615	1.00
75_H	78_E	0.615	1.00
321_P	326_Q	0.614	1.00
101_V	104_A	0.614	1.00
126_A	130_A	0.612	1.00
197_N	338_S	0.606	1.00
24_A	34_V	0.605	1.00
205_D	211_V	0.605	1.00
274_L	297_V	0.605	1.00
264_V	267_L	0.604	1.00
5_F	85_V	0.601	1.00
29_A	358_Y	0.601	1.00
346_E	349_R	0.600	1.00
309_I	314_C	0.600	1.00
267_L	271_A	0.598	1.00
273_L	298_L	0.598	1.00
135_G	140_L	0.598	1.00
222_P	228_N	0.596	1.00
152_Q	158_E	0.594	1.00
88_N	91_P	0.593	1.00
146_K	306_A	0.593	1.00
175_Y	178_Q	0.592	1.00
214_S	218_L	0.592	1.00
109_Q	364_A	0.592	1.00
193_K	230_L	0.591	1.00
217_A	331_L	0.591	1.00
291_I	345_A	0.591	1.00
318_I	326_Q	0.590	1.00
215_I	255_V	0.590	1.00
144_T	147_Q	0.589	1.00
198_L	267_L	0.588	1.00
147_Q	150_D	0.588	1.00
48_A	51_L	0.587	1.00
7_L	16_L	0.585	1.00
142_M	164_I	0.585	1.00
86_G	95_V	0.585	1.00
213_R	217_A	0.583	1.00
99_A	102_C	0.582	1.00
347_N	351_Y	0.582	1.00
130_A	133_E	0.580	1.00
111_K	167_P	0.575	1.00
361_P	365_A	0.575	1.00
81_A	104_A	0.571	1.00
22_R	285_I	0.571	1.00
200_L	274_L	0.571	1.00
207_G	239_P	0.569	1.00
210_G	322_F	0.569	1.00
221_L	226_R	0.567	1.00
210_G	277_P	0.566	1.00
31_G	34_V	0.563	1.00
290_A	297_V	0.563	1.00
84_V	104_A	0.562	1.00
128_E	135_G	0.560	1.00
339_P	342_M	0.560	1.00
286_V	290_A	0.560	1.00
23_I	364_A	0.559	1.00
52_I	56_V	0.559	1.00
102_C	105_E	0.558	1.00
25_S	29_A	0.557	1.00
16_L	88_N	0.557	1.00
106_K	138_T	0.556	1.00
197_N	341_R	0.556	1.00
242_F	245_L	0.554	1.00
175_Y	269_A	0.554	1.00
268_M	286_V	0.552	1.00
122_R	125_A	0.552	1.00
71_W	74_N	0.550	1.00
288_L	308_Y	0.547	1.00
166_P	283_A	0.547	1.00
212_D	239_P	0.547	1.00
243_E	246_A	0.547	1.00
301_A	321_P	0.545	1.00
302_V	306_A	0.545	1.00
81_A	84_V	0.544	1.00
19_D	23_I	0.543	1.00
272_D	338_S	0.543	1.00
192_I	270_A	0.543	1.00
350_H	354_T	0.542	1.00
277_P	300_T	0.542	1.00
32_H	369_T	0.541	1.00
221_L	227_H	0.541	1.00
192_I	198_L	0.539	1.00
19_D	87_F	0.539	1.00
222_P	229_T	0.538	1.00
145_D	166_P	0.537	1.00
212_D	242_F	0.533	1.00
298_L	331_L	0.533	1.00
83_R	86_G	0.531	1.00
234_V	264_V	0.531	1.00
125_A	129_R	0.529	1.00
296_P	341_R	0.528	1.00
217_A	221_L	0.528	1.00
228_N	254_N	0.528	1.00
86_G	92_G	0.528	1.00
26_T	357_L	0.527	1.00
48_A	53_Q	0.527	1.00
215_I	242_F	0.527	1.00
171_P	352_A	0.527	1.00
200_L	295_L	0.526	1.00
291_I	352_A	0.526	1.00
200_L	232_F	0.526	1.00
210_G	300_T	0.524	1.00
246_A	252_R	0.523	1.00
205_D	235_G	0.523	1.00
77_K	102_C	0.522	1.00
125_A	128_E	0.521	1.00
92_G	95_V	0.521	1.00
278_A	282_A	0.520	1.00
354_T	359_S	0.519	1.00
122_R	126_A	0.518	1.00
235_G	259_S	0.516	1.00
53_Q	56_V	0.514	1.00
25_S	28_A	0.513	1.00
251_V	254_N	0.513	1.00
147_Q	282_A	0.511	1.00
127_F	130_A	0.510	1.00
109_Q	141_M	0.508	1.00
76_L	81_A	0.507	1.00
195_Q	228_N	0.507	1.00
139_K	143_L	0.504	1.00
110_E	113_F	0.502	1.00
207_G	241_K	0.502	1.00
124_Y	128_E	0.500	1.00
288_L	352_A	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
2iw1A	1	0.984	100	0.113	Contact Map
3c48A	2	0.9786	100	0.134	Contact Map
2r60A	1	0.9893	100	0.135	Contact Map
3froA	3	0.9786	100	0.151	Contact Map
1rzuA	1	0.9733	100	0.155	Contact Map
4n9wA	1	0.9118	100	0.159	Contact Map
2qzsA	1	0.9679	100	0.16	Contact Map
2jjmA	4	0.9358	100	0.167	Contact Map
2x6qA	1	0.9439	100	0.189	Contact Map
3okpA	1	0.9572	100	0.19	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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