YDEK - BACSU - GREMLIN Contacts

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YDEK - Uncharacterized transporter YdeK

UniProt:	P96668	Sequences: MNKTTNGWINGFIGVLIFSGSLPATRLAVSDFDPLFLTVCRAAIAGVLAGGLLLIFRQQHPAKRDLISLLVVAFGVVIGFPLLTALALQHVTSAHAIVFIGLLPLATAVFGVLRGGERPRPVFWIFSAAGSLLVAGFALIQGGGSSPLGDAYMLASIVVCGLGYAEGAKLSRRLGNWQVISWALVLSLPLMLPLSFFFTPDSWSAIGVPALLSLAYVSLFSMLIGFVFWYRGLAQGGIAAVGQLQLLQPFFGLLLASVILHEKVGWALVAVNIAVIMCVAAARRFAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	287 (272)
Sequences:	36453 (27024)
Seq/√Len:	1638.6

ECOLI - YICL YDDG YTFF YHBE YIJE YEDA EAMA RHTA RARD YIGM
BACSU - YDEK YOAV YDFC YWFM YVBV YCBK YETK YCXC YDED YBFH YYAM YRDR YXXF YOJE
HALSA - Q9HHP6 Q9HQ34 Q9HPI0
SULSO - Q97UX3 Q97X73 Q97UE8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
87_A	153_M	3.422	1.00
10_N	231_R	2.992	1.00
95_H	150_D	2.874	1.00
231_R	235_Q	2.798	1.00
256_A	262_E	2.721	1.00
86_L	152_Y	2.527	1.00
46_G	185_V	2.513	1.00
24_A	216_Y	2.452	1.00
83_L	155_A	2.404	1.00
39_V	192_L	2.366	1.00
231_R	234_A	2.346	1.00
126_F	278_C	2.315	1.00
62_A	65_D	2.198	1.00
97_I	252_G	2.195	1.00
106_A	157_I	2.183	1.00
110_F	165_A	2.156	1.00
19_S	251_F	2.135	1.00
117_E	168_A	2.122	1.00
83_L	152_Y	2.100	1.00
26_R	262_E	2.061	1.00
44_I	218_S	2.052	1.00
25_T	85_A	2.047	1.00
11_G	232_G	2.007	1.00
112_V	119_P	1.995	1.00
120_R	123_F	1.948	1.00
79_G	159_V	1.871	1.00
208_V	212_L	1.869	1.00
43_A	188_L	1.866	1.00
111_G	117_E	1.861	1.00
65_D	173_R	1.858	1.00
50_G	181_S	1.825	1.00
108_A	127_S	1.821	1.00
107_T	242_G	1.801	1.00
102_L	106_A	1.786	1.00
19_S	255_L	1.782	1.00
90_H	148_L	1.749	1.00
91_V	149_G	1.746	1.00
91_V	150_D	1.735	1.00
189_P	193_P	1.701	1.00
175_G	178_Q	1.674	1.00
207_G	210_A	1.668	1.00
151_A	155_A	1.643	1.00
130_G	246_L	1.641	1.00
218_S	223_L	1.635	1.00
16_L	251_F	1.633	1.00
46_G	188_L	1.615	1.00
51_G	54_L	1.614	1.00
237_G	240_A	1.600	1.00
83_L	159_V	1.595	1.00
193_P	196_F	1.592	1.00
20_G	216_Y	1.585	1.00
265_G	268_L	1.554	1.00
86_L	90_H	1.540	1.00
106_A	161_G	1.519	1.00
96_A	153_M	1.498	1.00
167_G	230_Y	1.459	1.00
50_G	54_L	1.445	1.00
14_G	232_G	1.438	1.00
28_A	37_L	1.428	1.00
64_R	68_S	1.421	1.00
32_F	210_A	1.415	1.00
106_A	158_V	1.411	1.00
86_L	89_Q	1.366	1.00
111_G	115_G	1.357	1.00
52_L	56_F	1.354	1.00
266_W	270_A	1.352	1.00
39_V	188_L	1.351	1.00
45_A	184_L	1.349	1.00
110_F	114_R	1.325	1.00
10_N	228_F	1.324	1.00
93_S	256_A	1.309	1.00
63_K	67_I	1.308	1.00
126_F	282_A	1.295	1.00
251_F	255_L	1.295	1.00
64_R	67_I	1.294	1.00
23_P	255_L	1.293	1.00
37_L	217_V	1.292	1.00
136_G	274_A	1.287	1.00
27_L	213_S	1.286	1.00
67_I	71_V	1.283	1.00
31_D	210_A	1.280	1.00
63_K	66_L	1.270	1.00
8_W	244_L	1.269	1.00
161_G	165_A	1.266	1.00
91_V	95_H	1.264	1.00
18_F	225_G	1.260	1.00
94_A	253_L	1.258	1.00
98_V	272_N	1.257	1.00
51_G	55_I	1.254	1.00
209_P	212_L	1.241	1.00
147_P	150_D	1.240	1.00
90_H	152_Y	1.236	1.00
269_V	273_I	1.236	1.00
48_L	223_L	1.234	1.00
121_P	125_I	1.232	1.00
255_L	259_I	1.225	1.00
65_D	68_S	1.223	1.00
208_V	211_L	1.217	1.00
247_L	251_F	1.215	1.00
136_G	267_A	1.213	1.00
47_V	51_G	1.209	1.00
273_I	277_M	1.197	1.00
130_G	278_C	1.193	1.00
33_D	36_F	1.192	1.00
126_F	281_A	1.180	1.00
68_S	166_E	1.175	1.00
92_T	95_H	1.169	1.00
264_V	269_V	1.159	1.00
128_A	132_L	1.154	1.00
212_L	216_Y	1.150	1.00
124_W	128_A	1.149	1.00
20_G	255_L	1.147	1.00
209_P	213_S	1.147	1.00
17_I	220_F	1.135	1.00
121_P	124_W	1.132	1.00
168_A	237_G	1.129	1.00
26_R	30_S	1.128	1.00
9_I	13_I	1.128	1.00
110_F	162_L	1.125	1.00
190_L	193_P	1.117	1.00
88_L	96_A	1.117	1.00
122_V	281_A	1.116	1.00
133_L	271_V	1.111	1.00
35_L	194_L	1.108	1.00
39_V	195_S	1.101	1.00
169_K	172_R	1.097	1.00
194_L	198_F	1.096	1.00
14_G	228_F	1.092	1.00
39_V	43_A	1.089	1.00
148_L	152_Y	1.085	1.00
110_F	161_G	1.067	1.00
133_L	275_V	1.066	1.00
90_H	146_S	1.063	1.00
91_V	153_M	1.061	1.00
84_T	88_L	1.057	1.00
90_H	149_G	1.055	1.00
24_A	213_S	1.048	1.00
18_F	229_W	1.047	1.00
70_L	73_A	1.042	1.00
112_V	118_R	1.038	1.00
115_G	165_A	1.037	1.00
233_L	241_V	1.036	1.00
14_G	18_F	1.035	1.00
137_F	271_V	1.034	1.00
70_L	186_L	1.032	1.00
74_F	190_L	1.023	1.00
212_L	215_A	1.021	1.00
169_K	173_R	1.019	1.00
68_S	72_V	1.018	1.00
119_P	124_W	1.018	1.00
54_L	58_Q	1.017	1.00
38_T	85_A	1.016	1.00
93_S	260_L	1.013	1.00
13_I	228_F	1.013	1.00
203_W	206_I	1.006	1.00
46_G	181_S	1.006	1.00
107_T	238_I	1.001	1.00
168_A	238_I	0.999	1.00
99_F	157_I	0.990	1.00
99_F	150_D	0.988	1.00
107_T	164_Y	0.985	1.00
78_I	190_L	0.982	1.00
25_T	88_L	0.981	1.00
43_A	192_L	0.980	1.00
233_L	237_G	0.979	1.00
67_I	70_L	0.976	1.00
211_L	215_A	0.974	1.00
139_L	265_G	0.970	1.00
78_I	191_M	0.969	1.00
266_W	269_V	0.964	1.00
17_I	228_F	0.956	1.00
102_L	134_V	0.950	1.00
28_A	213_S	0.940	1.00
237_G	241_V	0.935	1.00
148_L	151_A	0.934	1.00
236_G	241_V	0.932	1.00
168_A	172_R	0.928	1.00
42_A	187_S	0.928	1.00
107_T	161_G	0.927	1.00
23_P	259_I	0.925	1.00
65_D	174_L	0.925	1.00
147_P	151_A	0.924	1.00
99_F	153_M	0.921	1.00
117_E	123_F	0.920	1.00
35_L	82_L	0.918	1.00
110_F	158_V	0.917	1.00
149_G	153_M	0.917	1.00
250_F	272_N	0.916	1.00
28_A	210_A	0.916	1.00
193_P	197_F	0.914	1.00
71_V	166_E	0.914	1.00
108_A	119_P	0.912	1.00
215_A	218_S	0.910	1.00
34_P	38_T	0.909	1.00
68_S	170_L	0.905	1.00
58_Q	175_G	0.898	1.00
135_A	139_L	0.894	1.00
157_I	161_G	0.894	1.00
120_R	124_W	0.889	1.00
98_V	135_A	0.880	1.00
41_R	222_M	0.878	1.00
15_V	19_S	0.872	1.00
110_F	113_L	0.871	1.00
118_R	122_V	0.869	1.00
129_A	278_C	0.867	1.00
69_L	73_A	0.867	1.00
31_D	207_G	0.866	1.00
113_L	116_G	0.863	1.00
66_L	186_L	0.859	1.00
36_F	195_S	0.859	1.00
54_L	59_Q	0.858	1.00
236_G	240_A	0.858	1.00
71_V	74_F	0.852	1.00
50_G	185_V	0.852	1.00
205_A	208_V	0.851	1.00
82_L	86_L	0.850	1.00
93_S	262_E	0.845	1.00
185_V	189_P	0.843	1.00
54_L	57_R	0.842	1.00
48_L	219_L	0.837	1.00
15_V	247_L	0.826	1.00
15_V	251_F	0.826	1.00
253_L	264_V	0.824	1.00
134_V	138_A	0.822	1.00
66_L	70_L	0.820	1.00
232_G	241_V	0.819	1.00
12_F	251_F	0.811	1.00
197_F	200_P	0.801	1.00
118_R	121_P	0.800	1.00
132_L	136_G	0.796	1.00
257_S	264_V	0.794	1.00
23_P	256_A	0.794	1.00
68_S	169_K	0.792	1.00
78_I	82_L	0.789	1.00
174_L	179_V	0.785	1.00
136_G	270_A	0.782	1.00
194_L	197_F	0.782	1.00
21_S	221_S	0.782	1.00
144_G	147_P	0.780	1.00
75_G	159_V	0.780	1.00
73_A	186_L	0.776	1.00
55_I	58_Q	0.775	1.00
80_F	159_V	0.775	1.00
38_T	191_M	0.771	1.00
186_L	189_P	0.770	1.00
267_A	270_A	0.762	1.00
182_W	186_L	0.761	1.00
132_L	274_A	0.757	1.00
40_C	44_I	0.756	1.00
48_L	51_G	0.756	1.00
224_I	228_F	0.750	1.00
105_L	130_G	0.748	1.00
109_V	113_L	0.745	1.00
11_G	244_L	0.744	1.00
49_A	223_L	0.743	1.00
108_A	123_F	0.742	1.00
215_A	219_L	0.740	1.00
107_T	165_A	0.727	1.00
70_L	74_F	0.725	1.00
77_V	163_G	0.725	1.00
22_L	84_T	0.722	1.00
53_L	181_S	0.718	1.00
253_L	272_N	0.718	1.00
153_M	157_I	0.717	1.00
46_G	50_G	0.710	1.00
162_L	166_E	0.709	1.00
69_L	174_L	0.709	1.00
270_A	274_A	0.707	1.00
213_S	216_Y	0.707	1.00
66_L	69_L	0.705	1.00
180_I	183_A	0.705	1.00
143_G	146_S	0.704	1.00
91_V	96_A	0.704	1.00
257_S	263_K	0.703	1.00
181_S	185_V	0.703	1.00
125_I	129_A	0.701	1.00
160_C	164_Y	0.697	1.00
188_L	192_L	0.697	1.00
207_G	211_L	0.691	1.00
8_W	240_A	0.691	1.00
196_F	199_T	0.686	1.00
272_N	276_I	0.685	1.00
23_P	93_S	0.685	1.00
214_L	218_S	0.683	1.00
68_S	71_V	0.679	1.00
87_A	149_G	0.679	1.00
11_G	236_G	0.675	1.00
186_L	190_L	0.673	1.00
69_L	72_V	0.670	1.00
43_A	47_V	0.669	1.00
146_S	150_D	0.668	1.00
247_L	250_F	0.667	1.00
62_A	66_L	0.667	1.00
99_F	154_L	0.664	1.00
256_A	260_L	0.663	1.00
32_F	36_F	0.663	1.00
57_R	60_H	0.662	1.00
56_F	175_G	0.660	1.00
279_V	282_A	0.659	1.00
112_V	116_G	0.657	1.00
36_F	40_C	0.654	1.00
264_V	268_L	0.654	1.00
119_P	123_F	0.651	1.00
75_G	162_L	0.651	1.00
102_L	105_L	0.650	1.00
106_A	154_L	0.649	1.00
160_C	229_W	0.647	1.00
139_L	142_G	0.647	1.00
22_L	97_I	0.647	1.00
87_A	96_A	0.647	1.00
52_L	177_W	0.646	1.00
117_E	239_A	0.639	1.00
182_W	185_V	0.639	1.00
80_F	163_G	0.638	1.00
25_T	29_V	0.633	1.00
33_D	199_T	0.632	1.00
178_Q	182_W	0.627	1.00
108_A	112_V	0.626	1.00
187_S	191_M	0.623	1.00
176_N	180_I	0.622	1.00
278_C	282_A	0.622	1.00
48_L	218_S	0.621	1.00
204_S	207_G	0.621	1.00
227_V	231_R	0.620	1.00
220_F	224_I	0.619	1.00
253_L	257_S	0.615	1.00
27_L	260_L	0.612	1.00
68_S	73_A	0.609	1.00
268_L	272_N	0.606	1.00
101_G	134_V	0.600	1.00
255_L	258_V	0.599	1.00
180_I	184_L	0.597	1.00
85_A	89_Q	0.597	1.00
152_Y	155_A	0.597	1.00
79_G	83_L	0.595	1.00
32_F	37_L	0.594	1.00
277_M	281_A	0.594	1.00
189_P	192_L	0.591	1.00
210_A	213_S	0.590	1.00
84_T	96_A	0.587	1.00
62_A	67_I	0.586	1.00
29_V	88_L	0.585	1.00
138_A	150_D	0.583	1.00
206_I	211_L	0.577	1.00
185_V	188_L	0.576	1.00
163_G	230_Y	0.575	1.00
265_G	269_V	0.575	1.00
78_I	194_L	0.573	1.00
216_Y	220_F	0.572	1.00
29_V	89_Q	0.571	1.00
263_K	267_A	0.565	1.00
56_F	60_H	0.565	1.00
77_V	226_F	0.565	1.00
104_P	246_L	0.562	1.00
52_L	55_I	0.561	1.00
216_Y	219_L	0.560	1.00
83_L	156_S	0.558	1.00
180_I	230_Y	0.557	1.00
115_G	169_K	0.551	1.00
114_R	162_L	0.551	1.00
254_L	257_S	0.549	1.00
245_Q	248_Q	0.548	1.00
109_V	127_S	0.547	1.00
56_F	177_W	0.547	1.00
101_G	157_I	0.546	1.00
40_C	214_L	0.545	1.00
12_F	15_V	0.541	1.00
98_V	138_A	0.539	1.00
44_I	48_L	0.539	1.00
55_I	59_Q	0.539	1.00
41_R	221_S	0.538	1.00
35_L	198_F	0.538	1.00
163_G	183_A	0.538	1.00
102_L	157_I	0.537	1.00
21_S	217_V	0.531	1.00
129_A	281_A	0.531	1.00
258_V	261_H	0.530	1.00
158_V	162_L	0.529	1.00
73_A	78_I	0.529	1.00
246_L	279_V	0.529	1.00
232_G	236_G	0.528	1.00
97_I	101_G	0.528	1.00
254_L	258_V	0.527	1.00
27_L	30_S	0.525	1.00
77_V	183_A	0.524	1.00
8_W	12_F	0.524	1.00
45_A	223_L	0.524	1.00
174_L	178_Q	0.524	1.00
75_G	166_E	0.524	1.00
196_F	200_P	0.523	1.00
131_S	246_L	0.522	1.00
163_G	167_G	0.522	1.00
164_Y	229_W	0.521	1.00
263_K	268_L	0.520	1.00
23_P	252_G	0.518	1.00
19_S	248_Q	0.518	1.00
70_L	190_L	0.518	1.00
123_F	237_G	0.516	1.00
87_A	91_V	0.514	1.00
115_G	168_A	0.514	1.00
65_D	69_L	0.511	1.00
164_Y	242_G	0.511	1.00
17_I	225_G	0.510	1.00
15_V	248_Q	0.509	1.00
21_S	85_A	0.506	1.00
228_F	231_R	0.505	1.00
98_V	137_F	0.501	1.00
206_I	210_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
2i68A	2	0.2683	98.7	0.768	Contact Map
3b5dA	2	0.3519	98.5	0.782	Contact Map
1u7gA	3	0.8223	26.1	0.932	Contact Map
4pgrA	1	0.676	6.9	0.948	Contact Map
4uc1A	3	0.5192	5.9	0.949	Contact Map
3o7qA	1	0.7875	5.8	0.949	Contact Map
4j05A	3	0.9443	5.2	0.95	Contact Map
2gfpA	2	0.7875	5	0.951	Contact Map
4o9uB	2	0.2544	4.8	0.952	Contact Map
2cfqA	1	0.5819	4.5	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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