YEJE - ECOLI - GREMLIN Contacts

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YEJE - Inner membrane ABC transporter permease protein YejE

UniProt:	P33915	Sequences: MSRLSPVNQARWARFRHNRRGYWSLWIFLVLFGLSLCSELIANDKPLLVRYDGSWYFPLLKNYSESDFGGPLASQADYQDPWLKQRLENNGWVLWAPIRFGATSINFATNKPFPSPPSRQNWLGTDANGGDVLARILYGTRISVLFGLMLTLCSSVMGVLAGALQGYYGGKVDLWGQRFIEVWSGMPTLFLIILLSSVVQPNFWWLLAITVLFGWMSLVGVVRAEFLRTRNFDYIRAAQALGVSDRSIILRHMLPNAMVATLTFLPFILCSSITTLTSLDFLGFGLPLGSPSLGELLLQGKNNLQAPWLGITAFLSVAILLSLLIFIGEAVRDAFDPNKAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12040
Length:	341 (327)
Sequences:	2514 (1649)
Seq/√Len:	91.2

ECOLI - YEJE YEJB DPPC SAPC DDPC GSID OPPC NIKC DPPB GSIC NIKB DDPB OPPB SAPB
BACSU - DPPC APPC OPPC OPPB APPB DPPB
HALSA - Q9HMW2 Q9HMX1 Q9HMI1 Q9HMX0 Q9HMW3 Q9HMI2
SULSO - Q97YP9 Q97YP2 Q97VK7 Q97UH2 Q97UG3 Q97VF8 Q97VF6 Q97VK6 Q97UH1 Q97YQ0 Q97YP1 Q97UG4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_G	330_A	4.995	1.00
161_A	176_G	4.251	1.00
12_W	16_R	4.005	1.00
243_V	247_S	3.997	1.00
35_S	140_T	3.320	1.00
229_T	253_M	3.122	1.00
126_D	130_G	2.849	1.00
168_Y	245_D	2.799	1.00
293_L	320_L	2.768	1.00
175_W	179_F	2.698	1.00
133_L	137_L	2.657	1.00
25_L	29_L	2.569	1.00
123_L	136_I	2.542	1.00
15_F	327_I	2.452	1.00
132_V	296_L	2.366	1.00
167_Y	245_D	2.349	1.00
110_N	113_F	2.292	1.00
311_I	315_L	2.239	1.00
19_R	22_Y	2.231	1.00
226_F	253_M	2.229	1.00
171_K	175_W	2.113	1.00
233_D	236_R	2.098	1.00
123_L	133_L	2.077	1.00
81_P	84_K	2.064	1.00
165_Q	177_Q	2.054	1.00
276_L	292_S	2.050	1.00
28_F	327_I	2.049	1.00
33_G	37_C	2.037	1.00
79_Q	82_W	2.006	1.00
109_T	113_F	2.000	1.00
168_Y	172_V	1.988	1.00
132_V	309_L	1.947	1.00
293_L	316_S	1.946	1.00
13_A	16_R	1.910	1.00
195_L	199_V	1.905	1.00
123_L	312_T	1.898	1.00
50_R	53_G	1.894	1.00
235_I	253_M	1.873	1.00
39_E	141_R	1.862	1.00
114_P	117_P	1.836	1.00
27_I	319_I	1.827	1.00
244_S	247_S	1.799	1.00
45_K	48_L	1.797	1.00
247_S	250_L	1.787	1.00
83_L	87_L	1.735	1.00
184_S	216_M	1.714	1.00
37_C	40_L	1.669	1.00
23_W	26_W	1.667	1.00
229_T	234_Y	1.659	1.00
9_Q	13_A	1.655	1.00
79_Q	84_K	1.642	1.00
330_A	334_A	1.620	1.00
30_V	34_L	1.608	1.00
202_N	205_W	1.606	1.00
277_T	298_L	1.604	1.00
24_S	323_L	1.576	1.00
130_G	135_R	1.573	1.00
329_E	336_D	1.569	1.00
16_R	26_W	1.566	1.00
246_R	250_L	1.564	1.00
131_D	134_A	1.552	1.00
173_D	223_R	1.535	1.00
111_K	114_P	1.533	1.00
111_K	115_S	1.524	1.00
157_M	161_A	1.507	1.00
106_N	121_N	1.504	1.00
16_R	22_Y	1.491	1.00
140_T	293_L	1.491	1.00
112_P	116_P	1.489	1.00
332_R	336_D	1.486	1.00
79_Q	83_L	1.478	1.00
178_R	181_E	1.467	1.00
145_L	149_M	1.459	1.00
83_L	88_E	1.456	1.00
110_N	114_P	1.450	0.99
25_L	327_I	1.438	0.99
150_L	272_S	1.426	0.99
82_W	86_R	1.420	0.99
315_L	319_I	1.414	0.99
83_L	86_R	1.410	0.99
163_A	226_F	1.398	0.99
84_K	87_L	1.386	0.99
84_K	88_E	1.376	0.99
26_W	30_V	1.371	0.99
158_G	162_G	1.368	0.99
96_A	100_F	1.357	0.99
38_S	42_A	1.356	0.99
80_D	83_L	1.341	0.99
104_S	107_F	1.338	0.99
97_P	100_F	1.337	0.99
76_A	80_D	1.333	0.99
56_Y	67_D	1.322	0.99
70_G	73_A	1.313	0.99
63_Y	68_F	1.309	0.99
78_Y	83_L	1.302	0.99
166_G	230_R	1.299	0.99
140_T	320_L	1.295	0.99
207_L	211_V	1.294	0.99
143_S	147_G	1.293	0.99
97_P	102_A	1.290	0.99
75_Q	79_Q	1.286	0.99
229_T	232_F	1.276	0.99
147_G	272_S	1.276	0.99
150_L	211_V	1.272	0.99
145_L	207_L	1.269	0.99
101_G	104_S	1.266	0.99
82_W	87_L	1.260	0.99
79_Q	87_L	1.256	0.99
110_N	116_P	1.254	0.98
234_Y	256_N	1.250	0.98
177_Q	219_V	1.244	0.98
29_L	33_G	1.243	0.98
34_L	137_L	1.237	0.98
239_Q	248_I	1.232	0.98
243_V	251_R	1.220	0.98
167_Y	248_I	1.217	0.98
165_Q	176_G	1.214	0.98
157_M	160_L	1.213	0.98
155_S	265_L	1.211	0.98
310_G	314_F	1.204	0.98
162_G	166_G	1.202	0.98
163_A	249_I	1.201	0.98
18_N	21_G	1.198	0.98
100_F	104_S	1.194	0.98
102_A	106_N	1.186	0.98
82_W	85_Q	1.184	0.98
74_S	80_D	1.181	0.98
138_Y	141_R	1.180	0.98
168_Y	249_I	1.179	0.98
31_L	319_I	1.177	0.98
103_T	106_N	1.160	0.97
20_R	24_S	1.159	0.97
136_I	316_S	1.152	0.97
98_I	101_G	1.151	0.97
333_D	336_D	1.150	0.97
67_D	70_G	1.149	0.97
46_P	51_Y	1.131	0.97
12_W	25_L	1.129	0.97
42_A	134_A	1.125	0.97
28_F	323_L	1.119	0.97
195_L	209_I	1.113	0.97
158_G	218_L	1.113	0.97
50_R	55_W	1.109	0.97
115_S	118_S	1.094	0.96
9_Q	12_W	1.093	0.96
96_A	99_R	1.090	0.96
239_Q	245_D	1.086	0.96
87_L	90_N	1.085	0.96
77_D	83_L	1.075	0.96
75_Q	82_W	1.069	0.96
164_L	168_Y	1.067	0.96
109_T	112_P	1.065	0.96
221_V	260_A	1.063	0.96
68_F	71_P	1.060	0.96
108_A	113_F	1.058	0.96
156_V	160_L	1.057	0.96
136_I	312_T	1.055	0.96
155_S	218_L	1.047	0.95
74_S	77_D	1.042	0.95
77_D	82_W	1.025	0.95
258_M	261_T	1.024	0.95
58_P	61_K	1.021	0.95
238_A	243_V	1.017	0.95
183_W	216_M	1.010	0.94
76_A	79_Q	1.010	0.94
33_G	41_I	1.002	0.94
74_S	83_L	1.001	0.94
199_V	284_F	1.001	0.94
257_A	260_A	1.000	0.94
36_L	141_R	0.999	0.94
172_V	176_G	0.998	0.94
71_P	74_S	0.994	0.94
80_D	88_E	0.990	0.94
27_I	31_L	0.990	0.94
60_L	64_S	0.988	0.94
245_D	249_I	0.987	0.94
110_N	115_S	0.985	0.94
185_G	188_T	0.984	0.94
117_P	120_Q	0.983	0.94
81_P	86_R	0.978	0.93
132_V	299_Q	0.974	0.93
102_A	105_I	0.974	0.93
226_F	257_A	0.972	0.93
76_A	81_P	0.971	0.93
114_P	118_S	0.971	0.93
108_A	111_K	0.968	0.93
38_S	138_Y	0.966	0.93
180_I	216_M	0.962	0.93
236_R	240_A	0.961	0.93
19_R	251_R	0.959	0.93
82_W	90_N	0.958	0.93
297_L	313_A	0.956	0.93
329_E	332_R	0.955	0.93
64_S	70_G	0.951	0.92
238_A	248_I	0.948	0.92
10_A	14_R	0.946	0.92
74_S	81_P	0.946	0.92
285_G	329_E	0.943	0.92
225_E	228_R	0.941	0.92
69_G	72_L	0.937	0.92
75_Q	83_L	0.933	0.92
12_W	22_Y	0.928	0.91
126_D	135_R	0.927	0.91
63_Y	67_D	0.924	0.91
102_A	107_F	0.923	0.91
85_Q	89_N	0.921	0.91
52_D	90_N	0.914	0.91
140_T	144_V	0.914	0.91
278_S	282_L	0.910	0.91
48_L	57_F	0.909	0.91
289_G	336_D	0.908	0.91
50_R	54_S	0.905	0.90
79_Q	86_R	0.904	0.90
75_Q	80_D	0.895	0.90
108_A	112_P	0.882	0.89
97_P	103_T	0.873	0.89
32_F	144_V	0.872	0.89
149_M	203_F	0.872	0.89
26_W	37_C	0.866	0.88
80_D	84_K	0.865	0.88
144_V	331_V	0.865	0.88
154_S	214_G	0.859	0.88
76_A	83_L	0.856	0.88
291_P	295_E	0.854	0.88
266_P	325_I	0.854	0.88
99_R	103_T	0.852	0.88
82_W	89_N	0.852	0.88
42_A	138_Y	0.851	0.88
112_P	115_S	0.848	0.87
111_K	118_S	0.847	0.87
62_N	65_E	0.847	0.87
80_D	87_L	0.846	0.87
82_W	88_E	0.843	0.87
80_D	85_Q	0.840	0.87
64_S	67_D	0.840	0.87
160_L	250_L	0.838	0.87
286_L	289_G	0.838	0.87
81_P	85_Q	0.837	0.87
58_P	64_S	0.835	0.87
53_G	60_L	0.834	0.86
150_L	276_L	0.824	0.86
270_C	297_L	0.820	0.86
32_F	145_L	0.819	0.85
10_A	15_F	0.817	0.85
79_Q	89_N	0.817	0.85
238_A	252_H	0.817	0.85
56_Y	60_L	0.817	0.85
22_Y	25_L	0.812	0.85
189_L	211_V	0.811	0.85
77_D	81_P	0.811	0.85
172_V	175_W	0.807	0.85
63_Y	69_G	0.807	0.85
29_L	32_F	0.806	0.85
171_K	174_L	0.802	0.84
220_G	224_A	0.799	0.84
153_C	211_V	0.796	0.84
216_M	317_V	0.795	0.84
78_Y	81_P	0.794	0.84
22_Y	26_W	0.794	0.84
85_Q	88_E	0.791	0.83
212_L	302_N	0.788	0.83
267_F	325_I	0.788	0.83
16_R	19_R	0.787	0.83
270_C	325_I	0.786	0.83
79_Q	90_N	0.785	0.83
18_N	333_D	0.784	0.83
196_S	284_F	0.781	0.83
177_Q	180_I	0.777	0.82
109_T	114_P	0.776	0.82
214_G	275_T	0.774	0.82
33_G	88_E	0.772	0.82
56_Y	59_L	0.771	0.82
185_G	301_K	0.771	0.82
123_L	132_V	0.763	0.81
65_E	69_G	0.762	0.81
221_V	265_L	0.756	0.81
169_G	230_R	0.754	0.80
164_L	176_G	0.752	0.80
276_L	280_D	0.751	0.80
38_S	137_L	0.751	0.80
192_I	284_F	0.750	0.80
117_P	121_N	0.749	0.80
74_S	78_Y	0.747	0.80
201_P	205_W	0.744	0.79
24_S	27_I	0.742	0.79
71_P	80_D	0.740	0.79
199_V	202_N	0.739	0.79
57_F	61_K	0.738	0.79
32_F	36_L	0.736	0.79
191_L	213_F	0.735	0.79
154_S	268_I	0.731	0.78
16_R	23_W	0.729	0.78
313_A	317_V	0.724	0.78
60_L	63_Y	0.723	0.78
23_W	27_I	0.723	0.78
56_Y	125_T	0.721	0.77
135_R	296_L	0.718	0.77
217_S	271_S	0.717	0.77
215_W	282_L	0.713	0.77
278_S	288_L	0.712	0.76
218_L	222_V	0.711	0.76
97_P	101_G	0.710	0.76
55_W	309_L	0.706	0.76
108_A	115_S	0.704	0.76
78_Y	89_N	0.701	0.75
225_E	260_A	0.700	0.75
24_S	330_A	0.700	0.75
44_D	49_V	0.699	0.75
108_A	114_P	0.696	0.75
135_R	289_G	0.695	0.75
99_R	102_A	0.694	0.75
79_Q	88_E	0.693	0.75
63_Y	66_S	0.693	0.75
81_P	88_E	0.688	0.74
266_P	328_G	0.687	0.74
41_I	133_L	0.686	0.74
160_L	246_R	0.685	0.74
53_G	121_N	0.684	0.74
19_R	23_W	0.681	0.73
233_D	237_A	0.675	0.73
78_Y	82_W	0.673	0.72
199_V	205_W	0.670	0.72
99_R	106_N	0.669	0.72
98_I	106_N	0.669	0.72
210_T	275_T	0.666	0.72
37_C	41_I	0.663	0.71
46_P	134_A	0.661	0.71
62_N	75_Q	0.659	0.71
280_D	285_G	0.658	0.71
274_T	307_P	0.654	0.70
60_L	65_E	0.653	0.70
244_S	250_L	0.651	0.70
263_T	332_R	0.651	0.70
81_P	89_N	0.650	0.70
221_V	264_F	0.647	0.69
181_E	233_D	0.646	0.69
83_L	89_N	0.644	0.69
98_I	105_I	0.644	0.69
76_A	90_N	0.643	0.69
236_R	239_Q	0.642	0.69
86_R	90_N	0.641	0.69
205_W	209_I	0.639	0.68
78_Y	86_R	0.638	0.68
83_L	90_N	0.636	0.68
181_E	255_P	0.635	0.68
125_T	131_D	0.635	0.68
227_L	284_F	0.633	0.68
234_Y	238_A	0.632	0.68
139_G	282_L	0.631	0.67
98_I	104_S	0.631	0.67
20_R	23_W	0.630	0.67
228_R	232_F	0.629	0.67
77_D	80_D	0.627	0.67
66_S	73_A	0.626	0.67
11_R	14_R	0.626	0.67
220_G	223_R	0.625	0.67
307_P	311_I	0.624	0.67
60_L	67_D	0.623	0.66
147_G	196_S	0.622	0.66
75_Q	78_Y	0.622	0.66
257_A	263_T	0.621	0.66
286_L	295_E	0.620	0.66
270_C	313_A	0.620	0.66
80_D	89_N	0.620	0.66
15_F	18_N	0.617	0.66
97_P	106_N	0.615	0.65
209_I	222_V	0.615	0.65
33_G	86_R	0.614	0.65
269_L	273_I	0.614	0.65
85_Q	90_N	0.614	0.65
304_L	307_P	0.614	0.65
198_V	232_F	0.610	0.65
72_L	78_Y	0.610	0.65
188_T	192_I	0.608	0.65
61_K	64_S	0.608	0.65
186_M	191_L	0.606	0.64
254_L	258_M	0.606	0.64
96_A	102_A	0.602	0.64
232_F	256_N	0.601	0.64
21_G	25_L	0.601	0.64
121_N	125_T	0.601	0.64
159_V	336_D	0.600	0.64
229_T	257_A	0.600	0.64
112_P	117_P	0.598	0.63
72_L	84_K	0.598	0.63
155_S	269_L	0.598	0.63
111_K	116_P	0.597	0.63
215_W	219_V	0.593	0.63
106_N	120_Q	0.591	0.62
317_V	325_I	0.590	0.62
263_T	321_L	0.590	0.62
325_I	329_E	0.589	0.62
28_F	36_L	0.588	0.62
195_L	200_Q	0.587	0.62
68_F	72_L	0.587	0.62
12_W	234_Y	0.586	0.62
99_R	104_S	0.584	0.62
196_S	201_P	0.584	0.62
100_F	105_I	0.583	0.61
75_Q	87_L	0.581	0.61
77_D	87_L	0.580	0.61
172_V	227_L	0.579	0.61
262_L	335_F	0.578	0.61
81_P	87_L	0.578	0.61
220_G	329_E	0.575	0.60
53_G	57_F	0.574	0.60
167_Y	230_R	0.572	0.60
247_S	251_R	0.569	0.60
156_V	250_L	0.568	0.59
55_W	306_A	0.567	0.59
275_T	284_F	0.567	0.59
155_S	210_T	0.566	0.59
96_A	101_G	0.565	0.59
17_H	29_L	0.565	0.59
37_C	42_A	0.564	0.59
28_F	144_V	0.563	0.59
166_G	256_N	0.563	0.59
216_M	219_V	0.562	0.59
223_R	285_G	0.562	0.59
75_Q	86_R	0.561	0.58
289_G	329_E	0.561	0.58
292_S	332_R	0.560	0.58
192_I	207_L	0.560	0.58
164_L	172_V	0.559	0.58
102_A	175_W	0.559	0.58
79_Q	85_Q	0.559	0.58
76_A	82_W	0.558	0.58
165_Q	220_G	0.557	0.58
98_I	113_F	0.555	0.58
74_S	82_W	0.554	0.58
120_Q	133_L	0.554	0.58
129_G	261_T	0.553	0.57
316_S	320_L	0.552	0.57
276_L	285_G	0.552	0.57
155_S	159_V	0.551	0.57
217_S	264_F	0.550	0.57
84_K	90_N	0.547	0.57
111_K	117_P	0.546	0.56
165_Q	276_L	0.546	0.56
182_V	301_K	0.546	0.56
146_F	263_T	0.546	0.56
46_P	290_S	0.545	0.56
197_S	284_F	0.544	0.56
145_L	198_V	0.543	0.56
34_L	37_C	0.542	0.56
9_Q	22_Y	0.541	0.56
328_G	332_R	0.541	0.56
261_T	335_F	0.540	0.56
166_G	215_W	0.540	0.56
98_I	103_T	0.538	0.55
9_Q	16_R	0.536	0.55
237_A	252_H	0.534	0.55
15_F	22_Y	0.533	0.55
46_P	138_Y	0.533	0.55
51_Y	137_L	0.531	0.54
13_A	120_Q	0.530	0.54
126_D	222_V	0.528	0.54
77_D	85_Q	0.528	0.54
87_L	91_G	0.528	0.54
159_V	250_L	0.526	0.54
88_E	92_W	0.526	0.54
218_L	268_I	0.525	0.54
84_K	327_I	0.524	0.53
246_R	254_L	0.523	0.53
273_I	306_A	0.523	0.53
53_G	58_P	0.521	0.53
109_T	115_S	0.519	0.53
88_E	91_G	0.519	0.53
165_Q	304_L	0.519	0.53
13_A	17_H	0.518	0.53
157_M	172_V	0.517	0.52
96_A	118_S	0.516	0.52
206_L	210_T	0.515	0.52
221_V	284_F	0.515	0.52
232_F	253_M	0.514	0.52
159_V	311_I	0.513	0.52
59_L	62_N	0.512	0.52
261_T	325_I	0.510	0.51
190_F	196_S	0.509	0.51
281_F	321_L	0.508	0.51
147_G	297_L	0.507	0.51
297_L	301_K	0.506	0.51
101_G	105_I	0.506	0.51
317_V	324_L	0.504	0.51
113_F	116_P	0.503	0.51
183_W	261_T	0.503	0.51
33_G	75_Q	0.502	0.50
127_A	309_L	0.502	0.50
190_F	259_V	0.500	0.50
45_K	52_D	0.500	0.50

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
4tquM	1	0.7419	99.9	0.694	Contact Map
3tuiA	2	0.5953	99.9	0.7	Contact Map
3d31C	2	0.6804	99.9	0.724	Contact Map
2onkC	2	0.695	99.9	0.732	Contact Map
4ymuD	2	0.6129	99.8	0.743	Contact Map
3rlfF	1	0.8504	99.8	0.745	Contact Map
3rlfG	1	0.7507	99.8	0.75	Contact Map
4tquN	1	0.7683	99.8	0.755	Contact Map
4djkA	2	0.2405	12.4	0.966	Contact Map
3j9pD	4	0.6481	11.4	0.967	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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