YEAB - BACSU - GREMLIN Contacts

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YEAB - Uncharacterized transporter YeaB

UniProt:	P46348	Sequences: MERYDELKKGESGALVSIAAYLVLSAIKLIIGYLFHSEALTADGLNNTTDIIASVAVLIGLRISQKPPDEDHPYGHFRAETIASLIASFIMMVVGLQVLFSAGESIFSAKQETPDMIAAWTAAGGAVLMLIVYRYNKRLAKKVKSQALLAAAADNKSDAFVSIGTFIGIVAAQFHLAWIDTVTAFVIGLLICKTAWDIFKESSHSLTDGFDIKDISAYKQTIEKISGVSRLKDIKARYLGSTVHVDVVVEVSADLNITESHDIANEIERRMKEEHAIDYSHVHMEPLEQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	290 (275)
Sequences:	10379 (7263)
Seq/√Len:	438.0

ECOLI - FIEF ZITB
BACSU - YEAB YDBO CZCD YDFM
HALSA - Q9HP06
SULSO - Q97WH2 Q97WI8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
178_W	182_V	3.364	1.00
193_K	197_D	3.167	1.00
247_V	282_V	2.876	1.00
232_K	248_V	2.829	1.00
222_I	247_V	2.808	1.00
219_K	223_E	2.682	1.00
31_I	121_T	2.488	1.00
221_T	274_E	2.399	1.00
221_T	275_H	2.375	1.00
100_F	104_E	2.365	1.00
29_L	44_G	2.309	1.00
99_L	185_F	2.252	1.00
225_I	270_R	2.216	1.00
222_I	267_I	2.203	1.00
69_D	76_H	2.188	1.00
171_A	179_I	2.130	1.00
88_S	199_F	2.124	1.00
140_A	149_L	2.069	1.00
200_K	204_H	2.030	1.00
216_S	220_Q	2.002	1.00
79_A	207_T	1.999	1.00
211_D	214_D	1.997	1.00
120_W	124_G	1.992	1.00
229_S	252_S	1.970	1.00
32_G	41_T	1.950	1.00
269_R	273_E	1.944	1.00
99_L	188_G	1.917	1.00
170_V	174_F	1.915	1.00
256_N	259_E	1.890	1.00
253_A	258_T	1.886	1.00
11_E	65_Q	1.864	1.00
225_I	267_I	1.862	1.00
72_H	76_H	1.788	1.00
78_R	208_D	1.779	1.00
119_A	166_F	1.767	1.00
104_E	108_S	1.746	1.00
221_T	270_R	1.740	1.00
249_V	267_I	1.720	1.00
204_H	209_G	1.711	1.00
217_A	274_E	1.702	1.00
261_H	283_H	1.698	1.00
30_I	34_L	1.692	1.00
196_W	200_K	1.690	1.00
215_I	236_A	1.672	1.00
15_L	19_A	1.661	1.00
225_I	266_E	1.651	1.00
96_L	100_F	1.639	1.00
259_E	262_D	1.630	1.00
230_R	250_E	1.620	1.00
257_I	260_S	1.612	1.00
262_D	266_E	1.580	1.00
98_V	184_A	1.568	1.00
138_R	142_K	1.564	1.00
168_G	183_T	1.561	1.00
137_K	141_K	1.559	1.00
119_A	173_Q	1.538	1.00
103_G	107_F	1.522	1.00
11_E	62_R	1.515	1.00
189_L	193_K	1.511	1.00
185_F	189_L	1.507	1.00
55_V	59_I	1.502	1.00
29_L	33_Y	1.491	1.00
260_S	284_M	1.484	1.00
15_L	58_L	1.451	1.00
102_A	184_A	1.444	1.00
116_M	120_W	1.439	1.00
270_R	274_E	1.428	1.00
46_N	154_D	1.423	1.00
149_L	201_E	1.403	1.00
130_L	134_R	1.401	1.00
170_V	173_Q	1.400	1.00
74_Y	246_D	1.388	1.00
22_L	51_I	1.388	1.00
266_E	270_R	1.379	1.00
119_A	170_V	1.375	1.00
164_G	183_T	1.372	1.00
236_A	245_V	1.372	1.00
217_A	221_T	1.367	1.00
137_K	152_A	1.363	1.00
232_K	285_E	1.361	1.00
123_A	127_V	1.354	1.00
197_D	200_K	1.351	1.00
20_A	128_L	1.344	1.00
220_Q	224_K	1.338	1.00
178_W	181_T	1.272	1.00
16_V	135_Y	1.270	1.00
69_D	72_H	1.251	1.00
35_F	118_A	1.231	1.00
123_A	166_F	1.228	1.00
251_V	257_I	1.225	1.00
60_G	83_A	1.224	1.00
264_A	268_E	1.223	1.00
223_E	230_R	1.222	1.00
215_I	219_K	1.218	1.00
95_G	192_C	1.207	1.00
127_V	131_I	1.207	1.00
97_Q	100_F	1.204	1.00
251_V	263_I	1.203	1.00
131_I	134_R	1.196	1.00
126_A	166_F	1.190	1.00
28_K	47_N	1.189	1.00
38_E	102_A	1.188	1.00
106_I	181_T	1.185	1.00
134_R	138_R	1.176	1.00
216_S	219_K	1.164	1.00
32_G	44_G	1.161	1.00
25_S	48_T	1.160	1.00
217_A	275_H	1.160	1.00
234_I	247_V	1.156	1.00
63_I	79_A	1.154	1.00
258_T	262_D	1.144	1.00
264_A	283_H	1.142	1.00
92_M	195_A	1.140	1.00
248_V	285_E	1.137	1.00
227_G	259_E	1.134	1.00
119_A	169_I	1.124	1.00
77_F	242_T	1.123	1.00
268_E	272_K	1.121	1.00
208_D	244_H	1.110	1.00
20_A	132_V	1.102	1.00
225_I	263_I	1.098	1.00
257_I	284_M	1.085	1.00
19_A	23_V	1.084	1.00
176_L	179_I	1.083	1.00
71_D	76_H	1.078	1.00
235_K	279_Y	1.076	1.00
106_I	178_W	1.075	1.00
224_K	270_R	1.069	1.00
72_H	204_H	1.068	1.00
261_H	264_A	1.065	1.00
139_L	142_K	1.064	1.00
264_A	284_M	1.061	1.00
56_A	83_A	1.057	1.00
62_R	65_Q	1.050	1.00
24_L	28_K	1.048	1.00
217_A	220_Q	1.045	1.00
232_K	250_E	1.040	1.00
120_W	123_A	1.040	1.00
245_V	280_S	1.038	1.00
151_A	154_D	1.038	1.00
18_I	51_I	1.038	1.00
63_I	66_K	1.037	1.00
118_A	169_I	1.035	1.00
140_A	143_V	1.030	1.00
92_M	96_L	1.029	1.00
99_L	103_G	1.025	1.00
25_S	29_L	1.024	1.00
25_S	44_G	1.024	1.00
245_V	277_I	1.022	1.00
131_I	135_Y	1.021	1.00
268_E	283_H	1.021	1.00
101_S	104_E	1.015	1.00
29_L	41_T	1.012	1.00
81_T	205_S	1.009	1.00
88_S	198_I	1.006	1.00
12_S	16_V	1.005	1.00
221_T	225_I	1.004	1.00
221_T	224_K	1.000	1.00
92_M	196_W	0.991	1.00
115_D	173_Q	0.988	1.00
254_D	258_T	0.988	1.00
152_A	156_K	0.987	1.00
260_S	264_A	0.984	1.00
92_M	192_C	0.983	1.00
122_A	166_F	0.971	1.00
24_L	128_L	0.971	1.00
134_R	137_K	0.968	1.00
261_H	286_P	0.965	1.00
17_S	132_V	0.959	1.00
218_Y	271_M	0.950	1.00
163_I	167_I	0.947	1.00
139_L	143_V	0.946	1.00
43_D	162_S	0.946	1.00
271_M	277_I	0.945	1.00
38_E	105_S	0.941	1.00
106_I	185_F	0.939	1.00
38_E	184_A	0.937	1.00
218_Y	236_A	0.935	1.00
102_A	185_F	0.925	1.00
18_I	58_L	0.925	1.00
33_Y	41_T	0.923	1.00
57_V	147_A	0.919	1.00
133_Y	152_A	0.913	1.00
18_I	55_V	0.911	1.00
223_E	231_L	0.910	1.00
43_D	46_N	0.908	1.00
265_N	269_R	0.907	1.00
133_Y	137_K	0.906	1.00
101_S	105_S	0.904	1.00
112_E	115_D	0.902	1.00
82_I	207_T	0.896	1.00
89_F	93_V	0.895	1.00
231_L	234_I	0.894	1.00
26_A	30_I	0.894	1.00
208_D	239_L	0.890	1.00
57_V	150_A	0.887	1.00
227_G	263_I	0.883	1.00
251_V	260_S	0.882	1.00
251_V	284_M	0.872	1.00
59_I	63_I	0.871	1.00
103_G	185_F	0.869	1.00
233_D	279_Y	0.859	1.00
220_Q	223_E	0.853	1.00
228_V	249_V	0.850	1.00
239_L	244_H	0.848	1.00
168_G	179_I	0.843	1.00
214_D	243_V	0.842	1.00
104_E	107_F	0.842	1.00
210_F	214_D	0.841	1.00
117_I	120_W	0.829	1.00
13_G	135_Y	0.828	1.00
141_K	144_K	0.828	1.00
116_M	173_Q	0.828	1.00
233_D	248_V	0.827	1.00
182_V	186_V	0.826	1.00
125_G	129_M	0.822	1.00
227_G	266_E	0.817	1.00
260_S	263_I	0.817	1.00
222_I	231_L	0.815	1.00
109_A	112_E	0.815	1.00
272_K	278_D	0.812	1.00
205_S	238_Y	0.809	1.00
132_V	155_N	0.808	1.00
271_M	280_S	0.808	1.00
270_R	273_E	0.804	1.00
140_A	152_A	0.802	1.00
130_L	156_K	0.801	1.00
27_I	124_G	0.799	1.00
208_D	237_R	0.792	1.00
264_A	282_V	0.788	1.00
46_N	50_D	0.788	1.00
80_E	145_S	0.786	1.00
93_V	97_Q	0.785	1.00
231_L	247_V	0.782	1.00
38_E	101_S	0.778	1.00
22_L	26_A	0.776	1.00
104_E	110_K	0.776	1.00
212_I	216_S	0.773	1.00
21_Y	47_N	0.765	1.00
266_E	269_R	0.764	1.00
97_Q	101_S	0.760	1.00
228_V	231_L	0.760	1.00
218_Y	245_V	0.759	1.00
49_T	94_V	0.759	1.00
219_K	231_L	0.757	1.00
210_F	243_V	0.753	1.00
179_I	183_T	0.753	1.00
74_Y	237_R	0.747	1.00
29_L	48_T	0.741	1.00
238_Y	243_V	0.740	1.00
61_L	147_A	0.739	1.00
78_R	237_R	0.738	1.00
129_M	132_V	0.736	1.00
119_A	123_A	0.735	1.00
85_L	89_F	0.733	1.00
265_N	268_E	0.732	1.00
126_A	163_I	0.732	1.00
85_L	202_S	0.730	1.00
85_L	199_F	0.728	1.00
261_H	285_E	0.727	1.00
28_K	44_G	0.726	1.00
11_E	58_L	0.725	1.00
268_E	280_S	0.719	1.00
154_D	158_D	0.719	1.00
157_S	194_T	0.719	1.00
59_I	62_R	0.717	1.00
110_K	113_T	0.717	1.00
27_I	121_T	0.715	1.00
13_G	139_L	0.715	1.00
133_Y	156_K	0.713	1.00
235_K	246_D	0.711	1.00
190_L	194_T	0.710	1.00
260_S	286_P	0.706	1.00
146_Q	205_S	0.705	1.00
13_G	138_R	0.700	1.00
25_S	47_N	0.700	1.00
82_I	203_S	0.698	1.00
263_I	267_I	0.694	1.00
135_Y	139_L	0.694	1.00
33_Y	44_G	0.692	1.00
183_T	187_I	0.692	1.00
37_S	180_D	0.690	1.00
25_S	51_I	0.686	1.00
272_K	280_S	0.685	1.00
11_E	15_L	0.685	1.00
210_F	236_A	0.685	1.00
93_V	100_F	0.685	1.00
82_I	86_I	0.676	1.00
277_I	280_S	0.673	1.00
238_Y	241_S	0.672	1.00
15_L	18_I	0.671	1.00
39_A	183_T	0.670	1.00
64_S	80_E	0.667	1.00
153_A	156_K	0.665	1.00
150_A	198_I	0.661	1.00
84_S	147_A	0.661	1.00
96_L	192_C	0.660	1.00
102_A	188_G	0.657	1.00
53_A	90_I	0.654	1.00
53_A	57_V	0.653	0.99
222_I	249_V	0.653	0.99
71_D	204_H	0.652	0.99
227_G	252_S	0.648	0.99
141_K	149_L	0.647	0.99
136_N	151_A	0.646	0.99
267_I	270_R	0.646	0.99
138_R	141_K	0.646	0.99
30_I	33_Y	0.644	0.99
146_Q	201_E	0.641	0.99
48_T	52_I	0.640	0.99
95_G	195_A	0.640	0.99
267_I	282_V	0.639	0.99
149_L	153_A	0.638	0.99
21_Y	50_D	0.637	0.99
17_S	136_N	0.635	0.99
132_V	136_N	0.635	0.99
28_K	43_D	0.634	0.99
58_L	62_R	0.630	0.99
129_M	136_N	0.629	0.99
193_K	196_W	0.626	0.99
249_V	284_M	0.624	0.99
186_V	190_L	0.622	0.99
259_E	266_E	0.621	0.99
261_H	265_N	0.621	0.99
114_P	117_I	0.621	0.99
46_N	91_M	0.621	0.99
222_I	225_I	0.619	0.99
19_A	22_L	0.619	0.99
73_P	235_K	0.617	0.99
234_I	245_V	0.615	0.99
108_S	111_Q	0.615	0.99
17_S	155_N	0.610	0.99
35_F	117_I	0.610	0.99
84_S	198_I	0.609	0.99
246_D	279_Y	0.604	0.99
128_L	132_V	0.604	0.99
32_G	35_F	0.602	0.99
88_S	202_S	0.597	0.99
132_V	135_Y	0.593	0.99
130_L	159_A	0.593	0.99
105_S	110_K	0.592	0.99
14_A	57_V	0.592	0.99
85_L	206_L	0.589	0.99
160_F	163_I	0.586	0.99
171_A	174_F	0.586	0.99
154_D	157_S	0.584	0.99
156_K	160_F	0.581	0.99
271_M	282_V	0.580	0.99
66_K	76_H	0.579	0.99
31_I	117_I	0.577	0.99
133_Y	155_N	0.575	0.99
269_R	272_K	0.575	0.99
183_T	186_V	0.575	0.99
124_G	128_L	0.572	0.99
264_A	267_I	0.572	0.99
94_V	97_Q	0.572	0.99
222_I	228_V	0.569	0.99
17_S	54_S	0.565	0.99
137_K	156_K	0.564	0.99
84_S	202_S	0.562	0.98
137_K	140_A	0.561	0.98
209_G	212_I	0.560	0.98
54_S	151_A	0.559	0.98
139_L	148_L	0.556	0.98
16_V	19_A	0.552	0.98
21_Y	51_I	0.551	0.98
111_Q	177_A	0.551	0.98
52_I	55_V	0.548	0.98
122_A	125_G	0.547	0.98
53_A	154_D	0.546	0.98
203_S	207_T	0.546	0.98
165_T	168_G	0.545	0.98
161_V	164_G	0.545	0.98
74_Y	235_K	0.545	0.98
85_L	203_S	0.545	0.98
283_H	286_P	0.545	0.98
79_A	83_A	0.544	0.98
214_D	217_A	0.539	0.98
126_A	130_L	0.539	0.98
175_H	178_W	0.538	0.98
161_V	165_T	0.536	0.98
190_L	193_K	0.536	0.98
164_G	187_I	0.535	0.98
14_A	18_I	0.534	0.98
118_A	172_A	0.534	0.98
38_E	41_T	0.534	0.98
149_L	152_A	0.533	0.98
272_K	279_Y	0.529	0.98
101_S	185_F	0.529	0.98
24_L	27_I	0.528	0.98
129_M	155_N	0.526	0.98
120_W	127_V	0.524	0.98
245_V	278_D	0.524	0.98
16_V	20_A	0.522	0.98
218_Y	275_H	0.521	0.98
62_R	66_K	0.520	0.98
102_A	181_T	0.518	0.97
56_A	86_I	0.517	0.97
67_P	76_H	0.516	0.97
136_N	155_N	0.515	0.97
157_S	198_I	0.515	0.97
25_S	45_L	0.513	0.97
254_D	259_E	0.511	0.97
229_S	251_V	0.511	0.97
17_S	151_A	0.509	0.97
83_A	147_A	0.509	0.97
40_L	122_A	0.508	0.97
201_E	204_H	0.505	0.97
226_S	266_E	0.505	0.97
18_I	54_S	0.504	0.97
262_D	265_N	0.502	0.97
225_I	282_V	0.500	0.97

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
3j1zP	8	1	100	0.108	Contact Map
3h90A	3	0.9724	100	0.119	Contact Map
2zztA	2	0.2724	99.5	0.758	Contact Map
3bypA	2	0.2724	99.5	0.761	Contact Map
3w61A	2	0.2724	99.4	0.772	Contact Map
3cq1A	2	0.2621	29	0.949	Contact Map
3lnoA	1	0.2828	27.4	0.95	Contact Map
3ne5A	3	0.431	24.5	0.951	Contact Map
3w9iA	3	0.3897	22.2	0.952	Contact Map
4mt1A	3	0.3862	21.3	0.952	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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