YDBO - BACSU - GREMLIN Contacts

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YDBO - Uncharacterized transporter YdbO

UniProt:	P96610	Sequences: MERTENLKKGEKGALLNIFAYVILAVVKLVIGILYHSEALRADGLNNGTDIVASVAVLIGLRISQRPADSDHPYGHYRAETISSLVASFIMMAVGIEVLIGGGKAIAGGTTETPNLIAAWTALGSAVFMYGIYLYNKRLAASIKSSALMAAAKDSRSDAFVSAGAFIGVFSSQLKLPWVDPVTAFIIGIIICKTAWDIFKDASHSLTDGFHLKDLEPYKQTVGRIENVHRLKDVKARYLGSTVHIEMVITVDPKLTVEEGHGVADEVEDKIKHEHDVTHVHVHVEPDDIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	290 (273)
Sequences:	10472 (7330)
Seq/√Len:	443.7

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

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	3.482	1.00
193_K	197_D	3.075	1.00
204_H	209_G	2.916	1.00
247_M	282_V	2.904	1.00
232_K	248_V	2.847	1.00
222_V	247_M	2.759	1.00
219_K	223_G	2.578	1.00
31_I	121_T	2.443	1.00
221_T	275_H	2.406	1.00
99_L	185_F	2.319	1.00
100_I	104_K	2.308	1.00
29_L	44_G	2.305	1.00
221_T	274_E	2.298	1.00
69_D	76_H	2.219	1.00
222_V	267_V	2.155	1.00
88_S	199_F	2.121	1.00
171_S	179_V	2.116	1.00
200_K	204_H	2.072	1.00
32_G	41_R	2.015	1.00
79_A	207_T	1.989	1.00
229_H	252_D	1.981	1.00
120_W	124_G	1.948	1.00
256_T	259_E	1.938	1.00
216_E	220_Q	1.884	1.00
253_P	258_E	1.867	1.00
170_F	174_L	1.863	1.00
99_L	188_G	1.860	1.00
225_I	267_V	1.854	1.00
211_H	214_D	1.848	1.00
11_E	65_Q	1.847	1.00
72_H	76_H	1.822	1.00
269_D	273_H	1.812	1.00
119_A	166_F	1.769	1.00
225_I	270_K	1.758	1.00
78_R	208_D	1.725	1.00
217_P	274_E	1.724	1.00
221_T	270_K	1.723	1.00
261_H	283_H	1.704	1.00
11_E	62_R	1.698	1.00
104_K	108_G	1.694	1.00
249_I	267_V	1.681	1.00
30_V	34_L	1.665	1.00
259_E	262_G	1.663	1.00
215_L	236_A	1.652	1.00
138_R	142_S	1.636	1.00
230_R	250_T	1.624	1.00
262_G	266_E	1.616	1.00
137_K	141_A	1.613	1.00
15_L	19_F	1.613	1.00
96_I	100_I	1.612	1.00
185_F	189_I	1.601	1.00
225_I	266_E	1.585	1.00
98_V	184_A	1.583	1.00
196_W	200_K	1.573	1.00
257_V	260_G	1.546	1.00
189_I	193_K	1.538	1.00
55_V	59_I	1.524	1.00
119_A	173_Q	1.517	1.00
168_G	183_T	1.514	1.00
46_N	154_D	1.513	1.00
29_L	33_I	1.500	1.00
103_G	107_A	1.488	1.00
20_A	128_F	1.468	1.00
102_G	184_A	1.462	1.00
260_G	284_V	1.456	1.00
270_K	274_E	1.455	1.00
149_M	201_D	1.448	1.00
236_A	245_I	1.437	1.00
15_L	58_L	1.410	1.00
170_F	173_Q	1.402	1.00
130_Y	134_L	1.396	1.00
164_G	183_T	1.391	1.00
119_A	170_F	1.381	1.00
137_K	152_A	1.375	1.00
22_V	51_I	1.371	1.00
197_D	200_K	1.371	1.00
232_K	285_E	1.359	1.00
266_E	270_K	1.356	1.00
74_Y	246_E	1.346	1.00
35_Y	118_A	1.323	1.00
217_P	221_T	1.312	1.00
123_L	127_V	1.295	1.00
264_A	283_H	1.286	1.00
178_W	181_P	1.282	1.00
28_K	47_N	1.281	1.00
123_L	166_F	1.267	1.00
116_L	120_W	1.259	1.00
264_A	268_E	1.256	1.00
220_Q	224_R	1.256	1.00
16_L	135_Y	1.254	1.00
251_V	257_V	1.253	1.00
119_A	169_V	1.232	1.00
60_G	83_S	1.222	1.00
131_G	134_L	1.216	1.00
251_V	263_V	1.215	1.00
97_E	100_I	1.209	1.00
127_V	131_G	1.202	1.00
106_I	181_P	1.198	1.00
69_D	72_H	1.194	1.00
215_L	219_K	1.190	1.00
63_I	79_A	1.189	1.00
32_G	44_G	1.185	1.00
224_R	270_K	1.179	1.00
208_D	244_H	1.179	1.00
151_A	154_D	1.175	1.00
248_V	285_E	1.173	1.00
92_M	195_A	1.171	1.00
38_E	102_G	1.169	1.00
134_L	138_R	1.163	1.00
216_E	219_K	1.161	1.00
234_V	247_M	1.159	1.00
95_G	192_C	1.146	1.00
223_G	230_R	1.146	1.00
258_E	262_G	1.144	1.00
261_H	264_A	1.128	1.00
72_H	204_H	1.127	1.00
235_K	279_H	1.124	1.00
24_L	28_K	1.120	1.00
25_A	48_G	1.119	1.00
20_A	132_I	1.112	1.00
257_V	284_V	1.097	1.00
19_F	23_I	1.094	1.00
106_I	178_W	1.092	1.00
217_P	275_H	1.091	1.00
225_I	263_V	1.080	1.00
227_N	259_E	1.077	1.00
131_G	135_Y	1.077	1.00
77_Y	242_T	1.069	1.00
268_E	283_H	1.069	1.00
264_A	284_V	1.068	1.00
217_P	220_Q	1.068	1.00
268_E	272_K	1.067	1.00
25_A	44_G	1.065	1.00
126_A	166_F	1.062	1.00
134_L	137_K	1.059	1.00
18_I	51_I	1.056	1.00
56_A	83_S	1.056	1.00
245_I	277_V	1.054	1.00
71_D	76_H	1.053	1.00
176_L	179_V	1.049	1.00
24_L	128_F	1.044	1.00
120_W	123_L	1.044	1.00
245_I	280_V	1.034	1.00
133_Y	137_K	1.033	1.00
25_A	29_L	1.030	1.00
92_M	96_I	1.029	1.00
232_K	250_T	1.027	1.00
88_S	198_I	1.025	1.00
99_L	103_G	1.018	1.00
81_T	205_S	1.017	1.00
254_K	258_E	1.014	1.00
62_R	65_Q	1.013	1.00
218_Y	236_A	1.013	1.00
92_M	196_W	1.011	1.00
101_G	104_K	0.999	1.00
152_A	156_R	0.998	1.00
163_A	167_I	0.997	1.00
12_K	16_L	0.991	1.00
138_R	141_A	0.987	1.00
109_G	112_E	0.984	1.00
63_I	66_R	0.980	1.00
43_D	46_N	0.980	1.00
260_G	264_A	0.979	1.00
92_M	192_C	0.978	1.00
218_Y	271_I	0.978	1.00
38_E	184_A	0.970	1.00
43_D	162_S	0.970	1.00
118_A	169_V	0.970	1.00
17_N	132_I	0.970	1.00
261_H	286_P	0.968	1.00
208_D	239_L	0.966	1.00
29_L	41_R	0.964	1.00
18_I	58_L	0.962	1.00
122_A	166_F	0.956	1.00
38_E	105_A	0.951	1.00
102_G	185_F	0.946	1.00
117_I	120_W	0.941	1.00
116_L	173_Q	0.935	1.00
18_I	55_V	0.934	1.00
57_V	150_A	0.930	1.00
57_V	147_A	0.927	1.00
271_I	277_V	0.911	1.00
141_A	144_K	0.904	1.00
80_E	145_S	0.904	1.00
265_D	269_D	0.903	1.00
71_D	209_G	0.902	1.00
103_G	185_F	0.900	1.00
133_Y	152_A	0.894	1.00
26_V	30_V	0.891	1.00
114_P	117_I	0.890	1.00
208_D	237_R	0.889	1.00
33_I	41_R	0.885	1.00
210_F	214_D	0.880	1.00
205_S	238_Y	0.879	1.00
106_I	185_F	0.879	1.00
251_V	284_V	0.876	1.00
82_I	207_T	0.871	1.00
214_D	243_V	0.870	1.00
101_G	105_A	0.869	1.00
59_I	63_I	0.867	1.00
239_L	244_H	0.866	1.00
89_F	93_A	0.863	1.00
251_V	260_G	0.861	1.00
233_D	279_H	0.855	1.00
130_Y	156_R	0.852	1.00
46_N	50_D	0.850	1.00
220_Q	223_G	0.842	1.00
22_V	26_V	0.838	1.00
227_N	263_V	0.833	1.00
233_D	248_V	0.832	1.00
265_D	268_E	0.830	1.00
27_V	124_G	0.829	1.00
231_L	234_V	0.826	1.00
78_R	237_R	0.825	1.00
228_V	249_I	0.822	1.00
93_A	97_E	0.820	1.00
182_V	186_I	0.820	1.00
21_Y	47_N	0.819	1.00
154_D	158_D	0.818	1.00
210_F	243_V	0.816	1.00
221_T	225_I	0.814	1.00
126_A	163_A	0.808	1.00
221_T	224_R	0.807	1.00
264_A	282_V	0.806	1.00
270_K	273_H	0.802	1.00
104_K	107_A	0.798	1.00
125_S	129_M	0.798	1.00
38_E	101_G	0.798	1.00
168_G	179_V	0.794	1.00
271_I	280_V	0.793	1.00
13_G	135_Y	0.792	1.00
61_L	147_A	0.787	1.00
132_I	135_Y	0.782	1.00
227_N	266_E	0.780	1.00
218_Y	245_I	0.778	1.00
132_I	155_S	0.777	1.00
263_V	267_V	0.777	1.00
129_M	132_I	0.777	1.00
35_Y	117_I	0.775	1.00
179_V	183_T	0.767	1.00
115_N	173_Q	0.759	1.00
29_L	48_G	0.754	1.00
223_G	231_L	0.745	1.00
85_L	199_F	0.745	1.00
97_E	101_G	0.743	1.00
261_H	285_E	0.738	1.00
27_V	121_T	0.738	1.00
74_Y	237_R	0.738	1.00
25_A	47_N	0.736	1.00
37_S	180_D	0.734	1.00
153_K	156_R	0.733	1.00
222_V	231_L	0.731	1.00
39_A	183_T	0.730	1.00
260_G	263_V	0.729	1.00
93_A	100_I	0.729	1.00
33_I	44_G	0.719	1.00
25_A	51_I	0.719	1.00
11_E	58_L	0.718	1.00
219_K	231_L	0.717	1.00
271_I	282_V	0.717	1.00
266_E	269_D	0.716	1.00
157_S	194_T	0.715	1.00
235_K	246_E	0.713	1.00
136_N	151_A	0.711	1.00
183_T	187_I	0.711	1.00
49_T	94_V	0.709	1.00
228_V	231_L	0.708	1.00
238_Y	243_V	0.708	1.00
210_F	236_A	0.707	1.00
130_Y	159_A	0.704	1.00
150_A	198_I	0.703	1.00
28_K	44_G	0.701	1.00
133_Y	156_R	0.700	1.00
132_I	136_N	0.697	1.00
82_I	86_V	0.694	1.00
231_L	247_M	0.692	1.00
64_S	80_E	0.691	1.00
59_I	62_R	0.691	1.00
268_E	280_V	0.690	1.00
17_N	155_S	0.686	1.00
17_N	136_N	0.684	1.00
85_L	89_F	0.684	1.00
119_A	123_L	0.678	1.00
190_I	194_T	0.676	1.00
212_L	216_E	0.676	1.00
222_V	249_I	0.672	1.00
149_M	153_K	0.671	1.00
96_I	192_C	0.670	1.00
46_N	91_M	0.669	1.00
267_V	282_V	0.667	1.00
30_V	33_I	0.667	1.00
277_V	280_V	0.667	1.00
95_G	195_A	0.667	1.00
104_K	110_T	0.664	1.00
85_L	202_A	0.661	1.00
146_S	205_S	0.661	1.00
102_G	188_G	0.659	1.00
249_I	284_V	0.654	1.00
19_F	22_V	0.653	1.00
53_A	57_V	0.648	0.99
272_K	278_T	0.647	0.99
54_S	151_A	0.645	0.99
267_V	270_K	0.644	0.99
186_I	190_I	0.644	0.99
272_K	280_V	0.643	0.99
193_K	196_W	0.642	0.99
53_A	90_I	0.640	0.99
11_E	15_L	0.638	0.99
71_D	204_H	0.637	0.99
227_N	252_D	0.637	0.99
165_A	168_G	0.637	0.99
128_F	132_I	0.636	0.99
141_A	149_M	0.635	0.99
48_G	52_V	0.635	0.99
116_L	119_A	0.634	0.99
21_Y	50_D	0.634	0.99
15_L	18_I	0.631	0.99
32_G	35_Y	0.630	0.99
58_L	62_R	0.630	0.99
262_G	265_D	0.627	0.99
84_S	147_A	0.627	0.99
149_M	152_A	0.626	0.99
260_G	286_P	0.624	0.99
28_K	43_D	0.622	0.99
171_S	174_L	0.620	0.99
13_G	138_R	0.619	0.99
259_E	266_E	0.614	0.99
31_I	117_I	0.613	0.99
62_R	66_R	0.611	0.99
17_N	54_S	0.609	0.99
108_G	111_T	0.609	0.99
36_H	110_T	0.609	0.99
264_A	267_V	0.607	0.99
112_E	115_N	0.604	0.99
88_S	202_A	0.601	0.99
28_K	125_S	0.598	0.99
238_Y	241_S	0.598	0.99
146_S	201_D	0.597	0.99
234_V	245_I	0.595	0.99
122_A	125_S	0.594	0.99
133_Y	155_S	0.593	0.99
73_P	235_K	0.592	0.99
129_M	155_S	0.590	0.99
94_V	97_E	0.590	0.99
129_M	136_N	0.589	0.99
261_H	265_D	0.588	0.99
84_S	198_I	0.587	0.99
17_N	151_A	0.585	0.99
82_I	203_S	0.584	0.99
52_V	55_V	0.580	0.99
246_E	279_H	0.579	0.99
14_A	57_V	0.578	0.99
156_R	160_F	0.575	0.99
38_E	41_R	0.573	0.99
85_L	206_L	0.564	0.99
190_I	193_K	0.564	0.99
225_I	228_V	0.564	0.99
124_G	128_F	0.563	0.99
79_A	83_S	0.561	0.99
183_T	186_I	0.561	0.99
126_A	130_Y	0.557	0.98
66_R	76_H	0.557	0.98
40_L	91_M	0.557	0.98
160_F	163_A	0.557	0.98
164_G	187_I	0.555	0.98
18_I	54_S	0.555	0.98
269_D	272_K	0.554	0.98
84_S	202_A	0.553	0.98
222_V	225_I	0.553	0.98
111_T	177_P	0.552	0.98
105_A	110_T	0.550	0.98
222_V	234_V	0.549	0.98
245_I	278_T	0.549	0.98
40_L	169_V	0.545	0.98
14_A	18_I	0.544	0.98
40_L	122_A	0.539	0.98
29_L	45_L	0.539	0.98
136_N	155_S	0.538	0.98
53_A	154_D	0.537	0.98
118_A	168_G	0.536	0.98
85_L	203_S	0.535	0.98
272_K	279_H	0.535	0.98
214_D	217_P	0.533	0.98
21_Y	51_I	0.533	0.98
113_T	116_L	0.533	0.98
67_P	76_H	0.531	0.98
203_S	207_T	0.528	0.98
167_I	171_S	0.527	0.98
38_E	42_A	0.526	0.98
83_S	147_A	0.525	0.98
171_S	176_L	0.524	0.98
102_G	181_P	0.524	0.98
73_P	210_F	0.520	0.98
137_K	156_R	0.520	0.98
16_L	20_A	0.517	0.98
214_D	218_Y	0.514	0.97
70_S	215_L	0.514	0.97
129_M	154_D	0.512	0.97
118_A	172_S	0.512	0.97
225_I	282_V	0.511	0.97
222_V	228_V	0.510	0.97
16_L	19_F	0.510	0.97
161_V	165_A	0.509	0.97
249_I	282_V	0.507	0.97
101_G	185_F	0.506	0.97
259_E	263_V	0.506	0.97
21_Y	155_S	0.503	0.97
229_H	251_V	0.503	0.97
250_T	285_E	0.501	0.97
47_N	161_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	0.9966	100	0.11	Contact Map
3h90A	3	0.9724	100	0.123	Contact Map
2zztA	2	0.2724	99.4	0.766	Contact Map
3bypA	2	0.2724	99.4	0.768	Contact Map
3w61A	2	0.2724	99.3	0.78	Contact Map
3cq1A	2	0.2897	27.3	0.95	Contact Map
3lnoA	1	0.2793	26.7	0.95	Contact Map
1mhsA	2	0.7724	25	0.95	Contact Map
4k0jA	3	0.3793	24.3	0.951	Contact Map
4mt1A	3	0.4207	23.1	0.951	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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