YDED - BACSU - GREMLIN Contacts

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YDED - Uncharacterized transporter YdeD

UniProt:	P96661	Sequences: MNTSNRRMGLFYVITGATCWGIGGTVAKKLFQEYQIDVNWLVTTRLLTAGMLLLMLQLFRKDRSQVIEVWKHKASAGQLLIFGLLGMLAVQYTYMASIQHGNAAVATLLQYLSPVIVIIYTLLRKQTVLTKQDIITVVLALVGCFFLLTNGSMSQLSVPAAAVVWGVLSGFAAAFYTLYAVGLLNKFDSLVVVGWAMIIGGFALGFIHPPWQLDFQRLTAEAYAYILFVILFGTMIAFWFFIKSLESLSPKETSLLGSLEPLSAVVTTVVWLKAPFGSFQWIGAICIIGITLILALHKEPSMESEKSILKIRNHANRDI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	319 (277)
Sequences:	39270 (28479)
Seq/√Len:	1711.2

ECOLI - YEDA YHBE YICL YIJE YTFF RARD EAMA RHTA YDDG YIGM
BACSU - YDED YVBV YDFC YCXC YBFH YRDR YXXF YETK YCBK YWFM YYAM YOAV YOJE YDEK
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
97_S	166_G	3.205	1.00
12_Y	243_K	2.851	1.00
105_V	163_V	2.808	1.00
243_K	247_S	2.720	1.00
268_T	274_A	2.640	1.00
96_A	165_W	2.489	1.00
50_G	198_I	2.428	1.00
43_T	205_G	2.346	1.00
93_T	168_L	2.312	1.00
136_T	290_I	2.306	1.00
26_V	228_F	2.286	1.00
243_K	246_E	2.252	1.00
72_H	75_S	2.243	1.00
127_T	181_V	2.180	1.00
116_I	170_G	2.178	1.00
28_K	274_A	2.092	1.00
107_T	264_A	2.051	1.00
120_Y	178_L	2.045	1.00
93_T	165_W	2.037	1.00
13_V	244_S	2.026	1.00
220_A	224_A	2.004	1.00
48_T	230_I	2.003	1.00
27_A	95_M	1.967	1.00
21_G	263_S	1.931	1.00
122_L	129_L	1.878	1.00
47_L	201_G	1.865	1.00
89_A	172_A	1.863	1.00
118_I	137_V	1.824	1.00
121_T	127_T	1.801	1.00
101_G	163_V	1.771	1.00
54_L	194_G	1.768	1.00
112_L	116_I	1.762	1.00
117_V	254_S	1.754	1.00
130_T	133_D	1.746	1.00
75_S	186_K	1.740	1.00
164_V	168_L	1.734	1.00
101_G	162_A	1.703	1.00
100_H	161_A	1.663	1.00
21_G	267_T	1.659	1.00
292_L	296_L	1.658	1.00
55_M	58_L	1.648	1.00
202_F	206_F	1.636	1.00
230_I	235_M	1.610	1.00
219_T	222_A	1.608	1.00
249_S	252_E	1.578	1.00
50_G	201_G	1.570	1.00
22_I	228_F	1.566	1.00
188_D	191_V	1.559	1.00
140_A	258_S	1.552	1.00
206_F	209_P	1.539	1.00
93_T	172_A	1.534	1.00
116_I	174_A	1.524	1.00
18_T	263_S	1.517	1.00
277_G	280_Q	1.506	1.00
215_F	218_L	1.488	1.00
136_T	294_L	1.478	1.00
56_L	60_R	1.471	1.00
96_A	100_H	1.449	1.00
106_A	166_G	1.434	1.00
54_L	58_L	1.416	1.00
120_Y	124_R	1.409	1.00
36_I	222_A	1.404	1.00
74_A	78_Q	1.389	1.00
116_I	171_F	1.389	1.00
78_Q	179_Y	1.388	1.00
43_T	201_G	1.382	1.00
160_A	163_V	1.375	1.00
30_L	41_L	1.364	1.00
180_A	242_I	1.364	1.00
16_G	244_S	1.356	1.00
136_T	293_I	1.354	1.00
55_M	59_F	1.351	1.00
32_Q	35_Q	1.342	1.00
29_K	225_Y	1.329	1.00
51_M	55_M	1.328	1.00
220_A	223_Y	1.316	1.00
20_W	237_A	1.312	1.00
73_K	77_G	1.308	1.00
96_A	99_Q	1.304	1.00
160_A	164_V	1.303	1.00
140_A	290_I	1.302	1.00
278_S	282_I	1.291	1.00
131_K	135_I	1.285	1.00
49_A	197_M	1.279	1.00
41_L	229_V	1.276	1.00
81_I	179_Y	1.275	1.00
77_G	81_I	1.272	1.00
102_N	105_V	1.272	1.00
121_T	125_K	1.268	1.00
143_G	283_G	1.266	1.00
104_A	265_V	1.265	1.00
103_A	268_T	1.258	1.00
35_Q	222_A	1.258	1.00
74_A	77_G	1.250	1.00
101_G	105_V	1.243	1.00
263_S	267_T	1.236	1.00
221_E	224_A	1.234	1.00
174_A	178_L	1.229	1.00
25_T	267_T	1.228	1.00
146_F	286_C	1.226	1.00
100_H	165_W	1.225	1.00
267_T	271_W	1.224	1.00
285_I	289_G	1.222	1.00
12_Y	240_F	1.222	1.00
52_L	235_M	1.221	1.00
281_W	285_I	1.216	1.00
221_E	225_Y	1.203	1.00
182_G	186_K	1.200	1.00
73_K	76_A	1.198	1.00
80_L	199_I	1.195	1.00
146_F	279_F	1.191	1.00
132_Q	293_I	1.191	1.00
259_L	263_S	1.189	1.00
134_I	138_V	1.184	1.00
203_A	206_F	1.180	1.00
37_D	40_W	1.178	1.00
10_L	256_L	1.173	1.00
276_F	281_W	1.159	1.00
147_L	283_G	1.146	1.00
161_A	165_W	1.133	1.00
108_L	284_A	1.128	1.00
138_V	142_V	1.117	1.00
181_V	249_S	1.114	1.00
83_G	199_I	1.111	1.00
224_A	228_F	1.111	1.00
98_I	106_A	1.105	1.00
181_V	185_N	1.102	1.00
39_N	207_I	1.099	1.00
182_G	185_N	1.098	1.00
245_L	253_T	1.091	1.00
43_T	47_L	1.086	1.00
143_G	287_I	1.082	1.00
58_L	62_D	1.080	1.00
50_G	194_G	1.078	1.00
78_Q	183_L	1.076	1.00
100_H	159_P	1.075	1.00
20_W	241_F	1.069	1.00
117_V	250_P	1.068	1.00
43_T	208_H	1.065	1.00
19_C	232_F	1.065	1.00
85_L	175_F	1.064	1.00
100_H	162_A	1.064	1.00
125_K	178_L	1.061	1.00
16_G	20_W	1.061	1.00
88_L	203_A	1.054	1.00
131_K	134_I	1.051	1.00
16_G	240_F	1.050	1.00
101_G	166_G	1.050	1.00
84_L	203_A	1.049	1.00
117_V	177_T	1.048	1.00
120_Y	175_F	1.048	1.00
28_K	32_Q	1.044	1.00
11_F	15_T	1.042	1.00
120_Y	174_A	1.039	1.00
122_L	128_V	1.038	1.00
127_T	133_D	1.030	1.00
181_V	250_P	1.029	1.00
9_G	244_S	1.018	1.00
19_C	240_F	1.014	1.00
22_I	267_T	1.009	1.00
88_L	204_L	1.008	1.00
27_A	98_I	1.005	1.00
103_A	272_L	1.005	1.00
30_L	222_A	1.001	1.00
132_Q	297_H	1.001	1.00
38_V	42_V	1.000	1.00
15_T	240_F	0.996	1.00
75_S	187_F	0.994	1.00
118_I	129_L	0.988	1.00
94_Y	98_I	0.987	1.00
26_V	225_Y	0.986	1.00
85_L	172_A	0.977	1.00
129_L	134_I	0.975	1.00
109_L	170_G	0.971	1.00
112_L	144_C	0.970	1.00
161_A	164_V	0.969	1.00
30_L	225_Y	0.967	1.00
47_L	205_G	0.967	1.00
278_S	281_W	0.963	1.00
149_T	277_G	0.960	1.00
58_L	61_K	0.960	1.00
207_I	211_W	0.958	1.00
132_Q	296_L	0.955	1.00
42_V	95_M	0.949	1.00
139_L	290_I	0.948	1.00
224_A	227_L	0.947	1.00
62_D	188_D	0.944	1.00
249_S	253_T	0.941	1.00
120_Y	123_L	0.939	1.00
78_Q	182_G	0.938	1.00
77_G	80_L	0.930	1.00
123_L	126_Q	0.926	1.00
170_G	174_A	0.926	1.00
76_A	199_I	0.925	1.00
117_V	174_A	0.924	1.00
227_L	230_I	0.922	1.00
145_F	149_T	0.921	1.00
109_L	163_V	0.916	1.00
39_N	92_Y	0.916	1.00
9_G	247_S	0.913	1.00
223_Y	227_L	0.912	1.00
130_T	134_I	0.911	1.00
248_L	253_T	0.911	1.00
87_M	176_Y	0.910	1.00
120_Y	171_F	0.909	1.00
162_A	166_G	0.906	1.00
35_Q	219_T	0.905	1.00
245_L	249_S	0.904	1.00
25_T	271_W	0.897	1.00
40_W	208_H	0.896	1.00
109_L	166_G	0.892	1.00
207_I	210_P	0.890	1.00
206_F	210_P	0.887	1.00
23_G	233_G	0.885	1.00
103_A	274_A	0.883	1.00
17_A	21_G	0.866	1.00
108_L	145_F	0.860	1.00
157_S	160_A	0.859	1.00
46_L	200_G	0.858	1.00
52_L	55_M	0.857	1.00
92_Y	96_A	0.843	1.00
248_L	252_E	0.835	1.00
17_A	263_S	0.834	1.00
45_R	234_T	0.833	1.00
85_L	179_Y	0.829	1.00
128_V	132_Q	0.825	1.00
27_A	31_F	0.821	1.00
219_T	223_Y	0.818	1.00
72_H	76_A	0.815	1.00
265_V	276_F	0.812	1.00
52_L	231_L	0.810	1.00
142_V	146_F	0.802	1.00
54_L	198_I	0.800	1.00
198_I	202_F	0.800	1.00
159_P	163_V	0.799	1.00
279_F	282_I	0.798	1.00
166_G	170_G	0.795	1.00
244_S	253_T	0.795	1.00
262_L	284_A	0.785	1.00
226_I	230_I	0.784	1.00
128_V	131_K	0.777	1.00
199_I	202_F	0.773	1.00
13_V	256_L	0.771	1.00
144_C	148_L	0.770	1.00
269_V	276_F	0.769	1.00
25_T	268_T	0.767	1.00
75_S	78_Q	0.766	1.00
284_A	288_I	0.766	1.00
175_F	179_Y	0.764	1.00
142_V	286_C	0.759	1.00
57_Q	61_K	0.756	1.00
88_L	92_Y	0.756	1.00
194_G	198_I	0.756	1.00
265_V	284_A	0.751	1.00
44_T	48_T	0.748	1.00
146_F	282_I	0.747	1.00
201_G	205_G	0.745	1.00
115_V	140_A	0.742	1.00
50_G	54_L	0.733	1.00
83_G	88_L	0.733	1.00
282_I	286_C	0.727	1.00
259_L	262_L	0.726	1.00
87_M	238_F	0.726	1.00
42_V	204_L	0.724	1.00
53_L	235_M	0.720	1.00
14_I	263_S	0.718	1.00
156_L	159_P	0.717	1.00
276_F	280_Q	0.714	1.00
135_I	139_L	0.714	1.00
59_F	62_D	0.713	1.00
187_F	192_V	0.712	1.00
236_I	240_F	0.712	1.00
90_V	172_A	0.711	1.00
189_S	193_V	0.710	1.00
227_L	231_L	0.708	1.00
195_W	199_I	0.705	1.00
202_F	205_G	0.705	1.00
193_V	196_A	0.703	1.00
56_L	190_L	0.703	1.00
97_S	162_A	0.703	1.00
119_I	123_L	0.702	1.00
79_L	187_F	0.700	1.00
289_G	293_I	0.698	1.00
60_R	188_D	0.698	1.00
118_I	133_D	0.695	1.00
173_A	177_T	0.692	1.00
143_G	290_I	0.692	1.00
89_A	93_T	0.689	1.00
57_Q	194_G	0.688	1.00
109_L	167_V	0.688	1.00
269_V	275_P	0.687	1.00
209_P	212_Q	0.686	1.00
78_Q	82_F	0.685	1.00
25_T	103_A	0.685	1.00
112_L	115_V	0.680	1.00
17_A	259_L	0.680	1.00
76_A	80_L	0.679	1.00
29_K	272_L	0.679	1.00
228_F	232_F	0.677	1.00
117_V	178_L	0.677	1.00
10_L	252_E	0.675	1.00
219_T	224_A	0.673	1.00
122_L	126_Q	0.673	1.00
173_A	241_F	0.671	1.00
199_I	203_A	0.670	1.00
47_L	51_M	0.669	1.00
24_G	94_Y	0.666	1.00
90_V	176_Y	0.665	1.00
81_I	84_L	0.665	1.00
79_L	192_V	0.661	1.00
56_L	59_F	0.661	1.00
127_T	251_K	0.658	1.00
13_V	248_L	0.654	1.00
268_T	272_L	0.651	1.00
101_G	106_A	0.649	1.00
129_L	133_D	0.648	1.00
40_W	44_T	0.647	1.00
255_L	294_L	0.646	1.00
290_I	294_L	0.641	1.00
76_A	195_W	0.636	1.00
239_W	243_K	0.636	1.00
116_I	167_V	0.634	1.00
48_T	52_L	0.633	1.00
217_R	220_A	0.630	1.00
265_V	269_V	0.629	1.00
24_G	107_T	0.628	1.00
195_W	198_I	0.627	1.00
111_Y	170_G	0.622	1.00
232_F	236_I	0.622	1.00
158_V	161_A	0.620	1.00
36_I	41_L	0.620	1.00
139_L	293_I	0.615	1.00
111_Y	114_P	0.615	1.00
19_C	237_A	0.612	1.00
222_A	225_Y	0.611	1.00
176_Y	242_I	0.610	1.00
210_P	213_L	0.610	1.00
78_Q	81_I	0.609	1.00
97_S	106_A	0.609	1.00
94_Y	169_S	0.605	1.00
275_P	279_F	0.604	1.00
114_P	258_S	0.602	1.00
45_R	233_G	0.602	1.00
267_T	270_V	0.601	1.00
60_R	190_L	0.600	1.00
72_H	77_G	0.596	1.00
165_W	168_L	0.595	1.00
225_Y	228_F	0.594	1.00
133_D	249_S	0.594	1.00
125_K	182_G	0.594	1.00
198_I	201_G	0.593	1.00
112_L	170_G	0.591	1.00
36_I	40_W	0.589	1.00
193_V	242_I	0.586	1.00
280_Q	284_A	0.584	1.00
118_I	122_L	0.582	1.00
17_A	260_E	0.579	1.00
15_T	19_C	0.579	1.00
9_G	248_L	0.576	1.00
44_T	226_I	0.576	1.00
124_R	175_F	0.574	1.00
211_W	214_D	0.574	1.00
155_Q	158_V	0.571	1.00
49_A	235_M	0.571	1.00
111_Y	144_C	0.568	1.00
95_M	99_Q	0.566	1.00
82_F	179_Y	0.566	1.00
87_M	196_A	0.566	1.00
258_S	291_T	0.564	1.00
191_V	195_W	0.563	1.00
277_G	281_W	0.562	1.00
94_Y	106_A	0.561	1.00
52_L	230_I	0.555	1.00
90_V	94_Y	0.555	1.00
266_V	270_V	0.553	1.00
88_L	207_I	0.553	1.00
78_Q	186_K	0.551	1.00
10_L	14_I	0.550	1.00
148_L	163_V	0.550	1.00
130_T	297_H	0.549	1.00
157_S	161_A	0.549	1.00
270_V	273_K	0.547	1.00
31_F	98_I	0.547	1.00
93_T	169_S	0.545	1.00
51_M	54_L	0.543	1.00
257_G	260_E	0.536	1.00
42_V	92_Y	0.532	1.00
87_M	91_Q	0.531	1.00
291_T	294_L	0.531	1.00
82_F	180_A	0.529	1.00
37_D	212_Q	0.526	1.00
244_S	248_L	0.524	1.00
177_T	241_F	0.524	1.00
25_T	264_A	0.522	1.00
125_K	181_V	0.521	1.00
87_M	200_G	0.518	1.00
80_L	84_L	0.518	1.00
193_V	197_M	0.516	1.00
150_N	279_F	0.514	1.00
48_T	51_M	0.514	1.00
97_S	101_G	0.513	1.00
75_S	79_L	0.513	1.00
13_V	241_F	0.512	1.00
74_A	186_K	0.511	1.00
228_F	231_L	0.511	1.00
281_W	284_A	0.509	1.00
143_G	286_C	0.507	1.00
266_V	269_V	0.507	1.00
108_L	147_L	0.506	1.00
112_L	140_A	0.505	1.00
177_T	254_S	0.505	1.00
39_N	211_W	0.504	1.00
62_D	68_E	0.503	1.00
180_A	245_L	0.501	1.00
19_C	236_I	0.501	1.00
76_A	79_L	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	0.2414	99	0.755	Contact Map
3b5dA	2	0.3166	98.1	0.816	Contact Map
4j05A	3	0.9342	92.5	0.887	Contact Map
3wdoA	1	0.9342	88.1	0.898	Contact Map
1pw4A	1	0.9498	85	0.903	Contact Map
4pypA	1	0.906	84.7	0.903	Contact Map
2cfqA	1	0.5987	81	0.907	Contact Map
4tphA	2	0.8558	80.9	0.907	Contact Map
4zw9A	1	0.9373	80.5	0.907	Contact Map
4he8J	1	0.4859	69.3	0.916	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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