YHHJ - ECOLI - GREMLIN Contacts

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YHHJ - Inner membrane transport permease YhhJ

UniProt:	P0AGH1	Sequences: MRHLRNIFNLGIKELRSLLGDKAMLTLIVFSFTVSVYSSATVTPGSLNLAPIAIADMDQSQLSNRIVNSFYRPWFLPPEMITADEMDAGLDAGRYTFAINIPPNFQRDVLAGRQPDIQVNVDATRMSQAFTGNGYIQNIINGEVNSFVARYRDNSEPLVSLETRMRFNPNLDPAWFGGVMAIINNITMLAIVLTGSALIREREHGTVEHLLVMPITPFEIMMAKIWSMGLVVLVVSGLSLVLMVKGVLGVPIEGSIPLFMLGVALSLFATTSIGIFMGTIARSMPQLGLLVILVLLPLQMLSGGSTPRESMPQMVQDIMLTMPTTHFVSLAQAILYRGAGFEIVWPQFLTLMAIGGAFFTIALLRFRKTIGTMA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11767
Length:	374 (356)
Sequences:	11397 (9478)
Seq/√Len:	502.3

ECOLI - YHHJ YBHS YBHR
BACSU - YFIM YFIN NATB YHAP YHGE
SULSO - Q7LY08 Q97W41 Q97WP5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_A	95_Y	5.156	1.00
262_G	330_L	5.051	1.00
86_M	98_A	4.572	1.00
82_T	85_E	4.012	1.00
104_N	108_D	3.723	1.00
89_G	95_Y	3.665	1.00
108_D	113_R	3.555	1.00
10_L	223_A	3.519	1.00
12_I	16_R	3.136	1.00
7_I	226_W	3.040	1.00
88_A	92_A	2.810	1.00
11_G	226_W	2.673	1.00
83_A	87_D	2.644	1.00
90_L	98_A	2.526	1.00
14_E	224_K	2.523	1.00
11_G	230_L	2.464	1.00
263_V	327_F	2.428	1.00
313_Q	317_D	2.376	1.00
89_G	94_R	2.374	1.00
349_L	353_A	2.330	1.00
87_D	91_D	2.324	1.00
276_F	361_I	2.315	1.00
216_T	219_E	2.308	1.00
268_F	355_G	2.308	1.00
57_M	83_A	2.287	1.00
345_W	349_L	2.269	1.00
80_M	89_G	2.268	1.00
135_Y	139_I	2.234	1.00
7_I	11_G	2.195	1.00
101_I	105_F	2.161	1.00
32_F	35_S	2.132	1.00
54_I	67_V	2.129	1.00
265_L	352_M	2.108	1.00
100_N	120_N	2.090	1.00
56_D	63_S	2.077	1.00
85_E	89_G	2.060	1.00
16_R	19_L	2.060	1.00
353_A	357_A	2.053	1.00
13_K	201_E	2.036	1.00
243_M	247_V	2.023	1.00
144_V	147_F	2.022	1.00
242_L	246_G	1.978	1.00
8_F	12_I	1.974	1.00
53_A	80_M	1.934	1.00
269_A	355_G	1.908	1.00
83_A	100_N	1.840	1.00
266_S	327_F	1.822	1.00
81_I	85_E	1.818	1.00
32_F	42_V	1.818	1.00
308_R	319_M	1.815	1.00
32_F	38_S	1.793	1.00
272_S	355_G	1.768	1.00
319_M	325_T	1.754	1.00
265_L	355_G	1.736	1.00
237_G	260_M	1.732	1.00
49_L	77_P	1.716	1.00
88_A	91_D	1.716	1.00
340_G	343_I	1.712	1.00
57_M	100_N	1.694	1.00
266_S	270_T	1.667	1.00
320_L	326_H	1.666	1.00
60_S	63_S	1.662	1.00
56_D	60_S	1.649	1.00
58_D	106_Q	1.618	1.00
262_G	334_I	1.611	1.00
329_S	347_Q	1.579	1.00
229_G	268_F	1.564	1.00
63_S	106_Q	1.558	1.00
232_V	267_L	1.548	1.00
320_L	325_T	1.543	1.00
85_E	88_A	1.537	1.00
131_T	135_Y	1.535	1.00
56_D	59_Q	1.532	1.00
84_D	87_D	1.518	1.00
333_A	337_R	1.502	1.00
257_P	261_L	1.494	1.00
354_I	358_F	1.488	1.00
95_Y	98_A	1.485	1.00
172_D	175_W	1.474	1.00
258_L	334_I	1.465	1.00
55_A	86_M	1.461	1.00
19_L	22_K	1.455	1.00
229_G	264_A	1.437	1.00
68_N	71_Y	1.435	1.00
262_G	348_F	1.430	1.00
35_S	39_S	1.383	1.00
346_P	350_T	1.382	1.00
265_L	348_F	1.376	1.00
180_M	183_I	1.351	1.00
65_R	68_N	1.347	1.00
233_L	264_A	1.325	1.00
57_M	103_P	1.320	1.00
144_V	148_V	1.306	1.00
201_E	224_K	1.294	1.00
279_T	365_R	1.289	1.00
269_A	351_L	1.282	1.00
78_P	81_I	1.282	1.00
314_M	317_D	1.282	1.00
147_F	150_R	1.280	1.00
16_R	20_G	1.265	1.00
60_S	106_Q	1.259	1.00
84_D	88_A	1.252	1.00
15_L	234_V	1.250	1.00
255_S	258_L	1.241	1.00
199_I	202_R	1.236	1.00
35_S	38_S	1.227	1.00
308_R	311_M	1.222	1.00
350_T	354_I	1.217	1.00
62_L	109_V	1.215	1.00
199_I	287_L	1.215	1.00
90_L	95_Y	1.209	1.00
143_E	147_F	1.204	1.00
269_A	358_F	1.200	1.00
156_E	159_V	1.181	1.00
333_A	339_A	1.180	1.00
360_T	364_L	1.179	1.00
316_Q	320_L	1.178	1.00
350_T	353_A	1.172	1.00
322_M	325_T	1.168	1.00
283_S	286_Q	1.166	1.00
61_Q	64_N	1.157	1.00
273_I	294_V	1.151	1.00
53_A	89_G	1.150	1.00
81_I	89_G	1.149	1.00
201_E	206_T	1.147	1.00
58_D	104_N	1.143	1.00
106_Q	110_L	1.138	1.00
218_F	222_M	1.135	1.00
11_G	223_A	1.134	1.00
189_L	192_V	1.127	1.00
69_S	72_R	1.124	1.00
184_N	327_F	1.124	1.00
83_A	98_A	1.123	1.00
7_I	219_E	1.119	1.00
122_D	125_R	1.119	1.00
326_H	347_Q	1.112	1.00
7_I	222_M	1.111	1.00
230_L	234_V	1.098	1.00
326_H	350_T	1.093	1.00
313_Q	316_Q	1.090	1.00
51_P	77_P	1.090	1.00
276_F	362_A	1.083	1.00
104_N	107_R	1.081	1.00
317_D	321_T	1.079	1.00
314_M	318_I	1.078	1.00
142_G	146_S	1.075	1.00
100_N	118_Q	1.075	1.00
33_T	37_Y	1.069	1.00
295_L	299_Q	1.065	1.00
52_I	56_D	1.064	1.00
138_N	142_G	1.054	1.00
195_G	287_L	1.053	1.00
352_M	356_G	1.044	1.00
157_P	160_S	1.039	1.00
181_A	184_N	1.039	1.00
219_E	223_A	1.033	1.00
348_F	352_M	1.030	1.00
156_E	160_S	1.026	1.00
39_S	42_V	1.024	1.00
62_L	106_Q	1.020	1.00
119_V	122_D	1.018	1.00
179_V	183_I	1.013	1.00
312_P	316_Q	1.012	1.00
35_S	43_T	1.010	1.00
134_G	138_N	1.008	1.00
179_V	182_I	1.008	1.00
357_A	361_I	1.008	1.00
87_D	120_N	1.006	1.00
7_I	223_A	1.001	1.00
187_T	191_I	1.000	1.00
311_M	316_Q	0.999	1.00
221_M	363_L	0.998	1.00
39_S	43_T	0.996	1.00
146_S	150_R	0.994	1.00
15_L	227_S	0.994	1.00
269_A	354_I	0.992	1.00
276_F	365_R	0.990	1.00
59_Q	103_P	0.988	1.00
267_L	271_T	0.986	1.00
130_F	133_N	0.986	1.00
244_V	247_V	0.984	1.00
325_T	329_S	0.981	1.00
218_F	363_L	0.979	1.00
182_I	185_N	0.971	1.00
344_V	348_F	0.970	1.00
276_F	358_F	0.969	1.00
133_N	136_I	0.967	1.00
188_M	191_I	0.964	1.00
132_G	135_Y	0.963	1.00
37_Y	41_T	0.962	1.00
317_D	320_L	0.960	1.00
56_D	67_V	0.959	1.00
133_N	137_Q	0.957	1.00
36_V	39_S	0.952	1.00
32_F	39_S	0.949	1.00
206_T	209_H	0.945	1.00
272_S	359_F	0.940	1.00
118_Q	121_V	0.940	1.00
139_I	143_E	0.934	1.00
223_A	227_S	0.932	1.00
38_S	42_V	0.928	1.00
51_P	96_T	0.924	1.00
78_P	89_G	0.924	1.00
243_M	248_L	0.922	1.00
80_M	95_Y	0.918	1.00
180_M	184_N	0.918	1.00
15_L	230_L	0.914	1.00
279_T	362_A	0.913	1.00
32_F	37_Y	0.913	1.00
53_A	57_M	0.910	1.00
258_L	261_L	0.909	1.00
296_L	299_Q	0.908	1.00
35_S	42_V	0.902	1.00
241_V	245_K	0.898	1.00
145_N	148_V	0.897	1.00
275_I	362_A	0.893	1.00
52_I	99_I	0.892	1.00
311_M	314_M	0.891	1.00
240_L	244_V	0.889	1.00
272_S	362_A	0.888	1.00
259_F	331_A	0.888	1.00
33_T	38_S	0.883	1.00
132_G	139_I	0.882	1.00
274_G	278_G	0.877	1.00
242_L	245_K	0.874	1.00
339_A	343_I	0.873	1.00
140_I	144_V	0.873	1.00
53_A	98_A	0.864	1.00
13_K	17_S	0.863	1.00
10_L	215_I	0.863	1.00
83_A	86_M	0.858	1.00
183_I	191_I	0.855	1.00
299_Q	302_S	0.853	1.00
122_D	126_M	0.848	1.00
80_M	86_M	0.847	1.00
211_L	220_I	0.847	1.00
329_S	333_A	0.847	1.00
210_L	220_I	0.846	1.00
319_M	322_M	0.845	1.00
323_P	327_F	0.840	1.00
272_S	358_F	0.839	1.00
32_F	41_T	0.838	1.00
67_V	71_Y	0.835	1.00
55_A	98_A	0.834	1.00
26_T	30_F	0.833	1.00
66_I	101_I	0.832	1.00
119_V	124_T	0.832	1.00
148_V	151_Y	0.832	1.00
15_L	19_L	0.831	1.00
326_H	354_I	0.830	1.00
64_N	68_N	0.830	1.00
55_A	58_D	0.830	1.00
342_E	346_P	0.829	1.00
226_W	230_L	0.828	1.00
147_F	151_Y	0.826	1.00
193_L	196_S	0.826	1.00
132_G	136_I	0.823	1.00
13_K	16_R	0.822	1.00
355_G	359_F	0.822	1.00
289_L	292_I	0.822	1.00
8_F	11_G	0.818	1.00
69_S	146_S	0.817	1.00
295_L	298_L	0.814	1.00
99_I	119_V	0.813	1.00
141_N	145_N	0.811	1.00
187_T	190_A	0.810	1.00
159_V	163_T	0.810	1.00
70_F	136_I	0.805	1.00
327_F	330_L	0.804	1.00
97_F	132_G	0.803	1.00
195_G	199_I	0.803	1.00
303_G	307_P	0.799	1.00
281_A	286_Q	0.787	1.00
137_Q	141_N	0.785	1.00
256_I	260_M	0.784	1.00
260_M	263_V	0.782	1.00
136_I	144_V	0.780	1.00
359_F	363_L	0.780	1.00
304_G	328_V	0.780	1.00
64_N	67_V	0.779	1.00
178_G	182_I	0.778	1.00
63_S	101_I	0.778	1.00
229_G	271_T	0.777	1.00
333_A	347_Q	0.775	1.00
244_V	248_L	0.774	1.00
37_Y	40_A	0.772	1.00
203_E	284_M	0.771	1.00
145_N	149_A	0.770	1.00
257_P	260_M	0.770	1.00
199_I	203_E	0.764	1.00
86_M	89_G	0.763	1.00
22_K	25_L	0.762	1.00
139_I	144_V	0.758	1.00
18_L	28_I	0.757	1.00
146_S	149_A	0.757	1.00
34_V	38_S	0.753	1.00
56_D	64_N	0.751	1.00
224_K	228_M	0.750	1.00
358_F	361_I	0.747	1.00
186_I	190_A	0.747	1.00
172_D	176_F	0.747	1.00
130_F	137_Q	0.746	1.00
152_R	156_E	0.745	1.00
300_M	306_T	0.744	1.00
330_L	344_V	0.742	1.00
155_S	159_V	0.741	1.00
21_D	24_M	0.739	1.00
263_V	331_A	0.736	1.00
38_S	41_T	0.734	1.00
276_F	280_I	0.734	1.00
143_E	148_V	0.733	1.00
115_P	119_V	0.732	1.00
98_A	120_N	0.729	1.00
215_I	220_I	0.726	1.00
56_D	101_I	0.725	1.00
243_M	246_G	0.724	1.00
138_N	141_N	0.724	1.00
225_I	271_T	0.724	1.00
345_W	348_F	0.721	1.00
194_T	198_L	0.720	1.00
312_P	315_V	0.718	1.00
42_V	45_G	0.718	1.00
225_I	272_S	0.717	1.00
249_G	252_I	0.716	1.00
141_N	144_V	0.705	1.00
112_G	115_P	0.703	1.00
186_I	191_I	0.700	1.00
286_Q	289_L	0.700	1.00
134_G	139_I	0.695	1.00
11_G	15_L	0.693	1.00
80_M	83_A	0.692	1.00
292_I	296_L	0.691	1.00
276_F	279_T	0.690	1.00
180_M	187_T	0.684	1.00
33_T	36_V	0.684	1.00
308_R	316_Q	0.684	1.00
185_N	188_M	0.681	1.00
65_R	69_S	0.679	1.00
32_F	45_G	0.679	1.00
161_L	164_R	0.677	1.00
330_L	347_Q	0.677	1.00
339_A	344_V	0.676	1.00
262_G	344_V	0.676	1.00
31_S	35_S	0.674	1.00
54_I	57_M	0.673	1.00
30_F	35_S	0.669	1.00
210_L	224_K	0.669	1.00
361_I	365_R	0.668	1.00
135_Y	138_N	0.668	1.00
155_S	158_L	0.666	1.00
54_I	58_D	0.665	1.00
241_V	263_V	0.664	1.00
58_D	101_I	0.663	1.00
358_F	362_A	0.663	1.00
139_I	142_G	0.661	1.00
139_I	147_F	0.659	1.00
131_T	139_I	0.656	1.00
281_A	290_L	0.656	1.00
72_R	75_F	0.655	1.00
356_G	360_T	0.653	1.00
14_E	227_S	0.653	1.00
298_L	322_M	0.651	1.00
188_M	192_V	0.650	1.00
160_S	163_T	0.649	1.00
52_I	97_F	0.648	1.00
273_I	358_F	0.647	1.00
154_N	160_S	0.646	1.00
27_L	32_F	0.645	1.00
9_N	12_I	0.644	1.00
245_K	252_I	0.641	1.00
207_V	220_I	0.638	1.00
221_M	275_I	0.637	1.00
53_A	78_P	0.635	1.00
86_M	90_L	0.633	1.00
136_I	140_I	0.631	1.00
184_N	324_T	0.631	1.00
53_A	56_D	0.629	1.00
152_R	155_S	0.629	1.00
129_A	133_N	0.628	1.00
135_Y	143_E	0.627	1.00
245_K	248_L	0.627	1.00
333_A	343_I	0.627	1.00
196_S	278_G	0.627	1.00
132_G	140_I	0.626	1.00
129_A	139_I	0.625	1.00
265_L	351_L	0.623	1.00
82_T	86_M	0.622	1.00
135_Y	141_N	0.622	1.00
201_E	205_G	0.622	1.00
323_P	326_H	0.620	1.00
32_F	287_L	0.620	1.00
62_L	67_V	0.617	1.00
89_G	92_A	0.617	1.00
326_H	329_S	0.616	1.00
47_L	51_P	0.614	1.00
164_R	167_F	0.613	1.00
137_Q	145_N	0.613	1.00
36_V	42_V	0.612	1.00
99_I	117_I	0.611	1.00
248_L	252_I	0.610	1.00
36_V	40_A	0.610	1.00
58_D	63_S	0.609	0.99
14_E	18_L	0.608	0.99
167_F	170_N	0.608	0.99
298_L	324_T	0.606	0.99
194_T	271_T	0.605	0.99
202_R	207_V	0.605	0.99
245_K	249_G	0.604	0.99
123_A	128_Q	0.602	0.99
355_G	358_F	0.600	0.99
209_H	213_M	0.599	0.99
351_L	354_I	0.598	0.99
62_L	65_R	0.598	0.99
34_V	37_Y	0.598	0.99
170_N	173_P	0.598	0.99
185_N	189_L	0.596	0.99
341_F	345_W	0.596	0.99
28_I	31_S	0.595	0.99
32_F	36_V	0.594	0.99
123_A	126_M	0.594	0.99
252_I	256_I	0.593	0.99
71_Y	74_W	0.592	0.99
347_Q	351_L	0.592	0.99
47_L	50_A	0.592	0.99
258_L	344_V	0.591	0.99
346_P	349_L	0.591	0.99
324_T	328_V	0.591	0.99
61_Q	65_R	0.591	0.99
344_V	347_Q	0.590	0.99
11_G	227_S	0.590	0.99
295_L	300_M	0.589	0.99
55_A	80_M	0.588	0.99
229_G	233_L	0.587	0.99
125_R	128_Q	0.586	0.99
225_I	268_F	0.586	0.99
40_A	43_T	0.585	0.99
52_I	57_M	0.583	0.99
117_I	121_V	0.582	0.99
133_N	148_V	0.580	0.99
121_V	128_Q	0.578	0.99
347_Q	350_T	0.578	0.99
187_T	192_V	0.577	0.99
123_A	127_S	0.577	0.99
97_F	102_P	0.574	0.99
220_I	223_A	0.574	0.99
27_L	31_S	0.573	0.99
10_L	220_I	0.572	0.99
143_E	146_S	0.572	0.99
248_L	251_P	0.571	0.99
280_I	365_R	0.571	0.99
38_S	45_G	0.570	0.99
178_G	181_A	0.570	0.99
64_N	103_P	0.569	0.99
14_E	228_M	0.568	0.99
129_A	135_Y	0.567	0.99
56_D	106_Q	0.565	0.99
7_I	10_L	0.564	0.99
117_I	120_N	0.564	0.99
297_P	300_M	0.564	0.99
41_T	44_P	0.561	0.99
258_L	348_F	0.561	0.99
142_G	145_N	0.561	0.99
63_S	67_V	0.557	0.99
144_V	149_A	0.557	0.99
130_F	139_I	0.557	0.99
140_I	148_V	0.556	0.99
58_D	102_P	0.555	0.99
301_L	306_T	0.555	0.99
34_V	41_T	0.554	0.99
35_S	40_A	0.554	0.99
332_Q	336_Y	0.554	0.99
144_V	151_Y	0.553	0.99
260_M	264_A	0.553	0.99
266_S	324_T	0.551	0.99
277_M	281_A	0.550	0.99
210_L	213_M	0.550	0.99
183_I	187_T	0.550	0.99
268_F	272_S	0.549	0.99
131_T	134_G	0.548	0.99
349_L	352_M	0.546	0.99
207_V	221_M	0.546	0.99
285_P	289_L	0.543	0.99
302_S	305_S	0.543	0.99
22_K	26_T	0.540	0.99
59_Q	64_N	0.540	0.99
80_M	85_E	0.538	0.99
225_I	229_G	0.538	0.99
173_P	176_F	0.537	0.99
153_D	156_E	0.537	0.99
131_T	148_V	0.537	0.99
300_M	303_G	0.535	0.99
179_V	184_N	0.534	0.99
101_I	117_I	0.534	0.99
30_F	37_Y	0.534	0.99
96_T	122_D	0.533	0.99
254_G	338_G	0.533	0.99
158_L	165_M	0.533	0.99
133_N	139_I	0.532	0.99
213_M	224_K	0.531	0.99
252_I	259_F	0.530	0.99
341_F	344_V	0.528	0.99
81_I	86_M	0.528	0.99
188_M	270_T	0.527	0.99
133_N	138_N	0.526	0.99
130_F	136_I	0.524	0.98
130_F	134_G	0.523	0.98
320_L	323_P	0.522	0.98
191_I	274_G	0.521	0.98
179_V	185_N	0.520	0.98
293_L	297_P	0.520	0.98
154_N	161_L	0.520	0.98
261_L	265_L	0.519	0.98
359_F	362_A	0.518	0.98
275_I	278_G	0.517	0.98
244_V	252_I	0.516	0.98
29_V	32_F	0.515	0.98
142_G	147_F	0.515	0.98
18_L	227_S	0.514	0.98
200_R	204_H	0.514	0.98
14_E	220_I	0.514	0.98
221_M	362_A	0.514	0.98
364_L	367_R	0.513	0.98
66_I	105_F	0.513	0.98
205_G	208_E	0.512	0.98
31_S	34_V	0.506	0.98
133_N	146_S	0.506	0.98
137_Q	140_I	0.506	0.98
129_A	137_Q	0.505	0.98
79_E	85_E	0.505	0.98
294_V	298_L	0.503	0.98
17_S	20_G	0.503	0.98
116_D	119_V	0.501	0.98
347_Q	354_I	0.500	0.98
119_V	125_R	0.500	0.98

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
3cniA	2	0.369	99.5	0.734	Contact Map
2p0sA	2	0.3262	97.3	0.864	Contact Map
2z73A	2	0.5588	21	0.947	Contact Map
4ea3A	2	0.7513	13	0.951	Contact Map
4yayA	1	0.7326	10.7	0.953	Contact Map
4xesA	1	0.5401	9.6	0.954	Contact Map
4tllB	2	0.5134	8.2	0.956	Contact Map
4grvA	1	0.5241	5.9	0.959	Contact Map
4pxzA	1	0.516	5.4	0.959	Contact Map
2qv0A	2	0.2968	5.3	0.96	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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