YFDV - ECOLI - GREMLIN Contacts

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YFDV - Uncharacterized transporter YfdV

UniProt:	P0AA49	Sequences: MLTFFIGDLLPIIVIMLLGYFSGRRETFSEDQARAFNKLVLNYALPAALFVSITRANREMIFADTRLTLVSLVVIVGCFFFSWFGCYKFFKRTHAEAAVCALIAGSPTIGFLGFAVLDPIYGDSVSTGLVVAIISIIVNAITIPIGLYLLNPSSGADGKKNSNLSALISAAKEPVVWAPVLATILVLVGVKIPAAWDPTFNLIAKANSGVAVFAAGLTLAAHKFEFSAEIAYNTFLKLILMPLALLLVGMACHLNSEHLQMMVLAGALPPAFSGIIIASRFNVYTRTGTASLAVSVLGFVVTAPLWIYVSRLVS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14144
Length:	314 (295)
Sequences:	6529 (5090)
Seq/√Len:	296.4

ECOLI - YFDV
BACSU - YWKB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_F	185_L	5.221	1.00
168_I	172_K	4.855	1.00
249_G	259_L	4.305	1.00
21_F	25_R	3.725	1.00
44_A	206_A	3.254	1.00
96_E	284_Y	3.001	1.00
201_N	205_K	2.986	1.00
270_P	295_S	2.960	1.00
50_F	181_L	2.793	1.00
14_V	199_T	2.595	1.00
39_L	206_A	2.477	1.00
238_L	302_T	2.333	1.00
246_L	250_M	2.247	1.00
22_S	43_Y	2.167	1.00
113_G	268_L	2.111	1.00
23_G	217_L	2.095	1.00
253_H	256_S	2.090	1.00
39_L	44_A	2.050	1.00
33_A	217_L	2.037	1.00
245_L	266_G	2.032	1.00
23_G	220_A	2.003	1.00
164_L	168_I	1.967	1.00
51_V	201_N	1.955	1.00
177_W	181_L	1.952	1.00
51_V	200_F	1.942	1.00
51_V	204_A	1.939	1.00
38_K	42_N	1.939	1.00
234_T	238_L	1.937	1.00
51_V	55_R	1.935	1.00
29_S	32_Q	1.918	1.00
256_S	259_L	1.895	1.00
185_L	190_V	1.865	1.00
301_V	304_P	1.862	1.00
234_T	295_S	1.855	1.00
194_A	198_P	1.849	1.00
29_S	35_A	1.835	1.00
282_N	285_T	1.833	1.00
51_V	197_D	1.828	1.00
44_A	207_N	1.825	1.00
103_I	291_S	1.822	1.00
178_A	182_A	1.772	1.00
34_R	38_K	1.743	1.00
165_S	168_I	1.718	1.00
184_I	188_V	1.662	1.00
198_P	201_N	1.660	1.00
267_A	306_W	1.652	1.00
80_F	84_F	1.627	1.00
47_A	200_F	1.623	1.00
93_T	96_E	1.618	1.00
246_L	263_V	1.610	1.00
118_D	123_D	1.610	1.00
22_S	213_F	1.604	1.00
253_H	259_L	1.595	1.00
24_R	220_A	1.593	1.00
39_L	213_F	1.575	1.00
197_D	201_N	1.574	1.00
18_L	199_T	1.568	1.00
49_L	178_A	1.556	1.00
148_Y	152_P	1.549	1.00
257_E	261_M	1.524	1.00
38_K	280_R	1.517	1.00
235_F	239_I	1.516	1.00
169_S	172_K	1.500	1.00
256_S	260_Q	1.488	1.00
255_N	258_H	1.484	1.00
71_S	134_I	1.477	1.00
185_L	191_K	1.468	1.00
15_I	203_I	1.461	1.00
275_I	292_L	1.460	1.00
218_T	275_I	1.445	1.00
54_T	185_L	1.432	1.00
233_N	291_S	1.416	1.00
120_I	307_I	1.416	1.00
39_L	210_V	1.404	1.00
130_V	258_H	1.386	1.00
182_A	186_V	1.384	1.00
247_L	250_M	1.378	1.00
32_Q	35_A	1.378	1.00
99_V	288_G	1.370	1.00
103_I	270_P	1.368	1.00
86_C	97_A	1.366	1.00
122_G	125_V	1.357	1.00
116_V	268_L	1.354	1.00
76_V	80_F	1.349	1.00
65_T	69_L	1.347	1.00
10_L	14_V	1.345	1.00
10_L	195_A	1.343	1.00
17_L	21_F	1.340	1.00
18_L	43_Y	1.333	1.00
57_N	60_M	1.332	1.00
305_L	308_Y	1.330	1.00
180_V	184_I	1.324	1.00
53_I	182_A	1.309	1.00
259_L	263_V	1.297	1.00
131_V	265_A	1.296	1.00
55_R	197_D	1.289	1.00
278_A	283_V	1.282	1.00
47_A	178_A	1.282	1.00
297_L	301_V	1.260	1.00
107_P	268_L	1.260	1.00
15_I	213_F	1.257	1.00
257_E	260_Q	1.257	1.00
248_V	251_A	1.239	1.00
104_A	236_L	1.232	1.00
31_D	35_A	1.220	1.00
82_S	104_A	1.206	1.00
215_A	272_F	1.206	1.00
243_L	247_L	1.203	1.00
47_A	203_I	1.200	1.00
54_T	197_D	1.178	1.00
237_K	241_M	1.175	1.00
250_M	259_L	1.160	1.00
170_A	176_V	1.156	1.00
143_I	147_L	1.156	1.00
231_A	235_F	1.156	1.00
40_V	211_A	1.149	1.00
71_S	75_I	1.147	1.00
15_I	202_L	1.142	1.00
236_L	240_L	1.140	1.00
100_C	233_N	1.132	1.00
196_W	199_T	1.126	1.00
36_F	210_V	1.123	1.00
124_S	257_E	1.122	1.00
106_S	145_I	1.121	1.00
102_L	106_S	1.119	1.00
263_V	306_W	1.119	1.00
121_Y	261_M	1.119	1.00
249_G	254_L	1.115	1.00
87_Y	91_K	1.114	1.00
117_L	131_V	1.111	1.00
279_S	285_T	1.106	1.00
58_R	186_V	1.103	1.00
206_A	210_V	1.102	1.00
44_A	210_V	1.101	1.00
143_I	146_G	1.101	1.00
185_L	192_I	1.100	1.00
247_L	251_A	1.099	1.00
234_T	294_V	1.097	1.00
139_N	143_I	1.094	1.00
14_V	18_L	1.093	1.00
267_A	303_A	1.092	1.00
18_L	203_I	1.081	1.00
200_F	204_A	1.068	1.00
121_Y	260_Q	1.067	1.00
270_P	291_S	1.061	1.00
230_I	294_V	1.053	1.00
299_F	303_A	1.047	1.00
92_R	96_E	1.046	1.00
65_T	68_T	1.043	1.00
42_N	280_R	1.041	1.00
117_L	121_Y	1.039	1.00
243_L	306_W	1.037	1.00
128_G	132_A	1.034	1.00
250_M	255_N	1.029	1.00
172_K	177_W	1.016	1.00
255_N	259_L	1.015	1.00
83_W	87_Y	1.010	1.00
31_D	34_R	1.009	1.00
195_A	199_T	1.005	1.00
40_V	44_A	0.991	1.00
70_V	74_V	0.985	1.00
43_Y	213_F	0.985	1.00
32_Q	36_F	0.981	1.00
74_V	245_L	0.980	1.00
87_Y	97_A	0.979	1.00
20_Y	24_R	0.979	1.00
270_P	274_G	0.977	1.00
20_Y	220_A	0.977	1.00
234_T	298_G	0.972	1.00
85_G	89_F	0.971	1.00
94_H	97_A	0.969	1.00
103_I	274_G	0.968	1.00
132_A	135_S	0.964	1.00
74_V	78_C	0.964	1.00
98_A	150_L	0.958	1.00
136_I	140_A	0.956	1.00
37_N	214_A	0.954	1.00
79_F	105_G	0.951	1.00
13_I	16_M	0.948	1.00
121_Y	125_V	0.948	1.00
206_A	209_G	0.944	1.00
85_G	90_F	0.943	1.00
97_A	101_A	0.942	1.00
238_L	298_G	0.942	1.00
208_S	211_A	0.940	1.00
185_L	188_V	0.939	1.00
150_L	278_A	0.936	1.00
103_I	288_G	0.924	1.00
23_G	221_A	0.923	1.00
140_A	143_I	0.921	1.00
299_F	302_T	0.920	1.00
125_V	129_L	0.915	1.00
254_L	259_L	0.901	1.00
181_L	185_L	0.900	1.00
230_I	234_T	0.891	1.00
54_T	182_A	0.889	1.00
147_L	281_F	0.888	1.00
102_L	146_G	0.885	1.00
40_V	207_N	0.884	1.00
263_V	310_S	0.876	1.00
114_F	128_G	0.871	1.00
188_V	191_K	0.869	1.00
107_P	237_K	0.866	1.00
284_Y	287_T	0.866	1.00
260_Q	310_S	0.855	1.00
184_I	187_L	0.842	1.00
23_G	30_E	0.839	1.00
249_G	263_V	0.836	1.00
102_L	150_L	0.833	1.00
82_S	236_L	0.832	1.00
23_G	26_E	0.829	1.00
22_S	27_T	0.828	1.00
64_D	67_L	0.825	1.00
228_A	231_A	0.825	1.00
8_D	11_P	0.823	1.00
92_R	229_E	0.820	1.00
26_E	29_S	0.818	1.00
48_A	207_N	0.817	1.00
231_A	234_T	0.806	1.00
201_N	204_A	0.804	1.00
183_T	187_L	0.804	1.00
96_E	229_E	0.799	1.00
130_V	133_I	0.795	0.99
112_L	116_V	0.792	0.99
109_I	134_I	0.790	0.99
72_L	75_I	0.787	0.99
114_F	135_S	0.783	0.99
41_L	111_F	0.782	0.99
118_D	125_V	0.777	0.99
267_A	302_T	0.776	0.99
137_I	148_Y	0.774	0.99
85_G	232_Y	0.773	0.99
214_A	275_I	0.773	0.99
244_A	247_L	0.771	0.99
66_R	69_L	0.767	0.99
116_V	264_L	0.763	0.99
54_T	186_V	0.760	0.99
13_I	17_L	0.759	0.99
78_C	82_S	0.757	0.99
177_W	180_V	0.756	0.99
144_P	147_L	0.754	0.99
43_Y	203_I	0.753	0.99
239_I	242_P	0.751	0.99
194_A	197_D	0.750	0.99
128_G	131_V	0.749	0.99
167_L	170_A	0.749	0.99
138_V	141_I	0.748	0.99
190_V	193_P	0.745	0.99
54_T	192_I	0.736	0.99
163_N	167_L	0.736	0.99
96_E	287_T	0.734	0.99
64_D	68_T	0.729	0.99
202_L	205_K	0.728	0.99
235_F	240_L	0.727	0.99
270_P	292_L	0.726	0.99
242_P	267_A	0.724	0.99
161_N	164_L	0.722	0.99
301_V	305_L	0.721	0.99
34_R	282_N	0.719	0.99
298_G	301_V	0.718	0.99
7_G	195_A	0.718	0.99
82_S	86_C	0.718	0.99
150_L	283_V	0.717	0.99
250_M	253_H	0.713	0.99
86_C	90_F	0.711	0.99
72_L	137_I	0.711	0.99
19_G	217_L	0.708	0.99
77_G	244_A	0.708	0.99
80_F	83_W	0.705	0.99
175_V	178_A	0.704	0.99
106_S	110_G	0.703	0.99
117_L	261_M	0.703	0.99
278_A	288_G	0.701	0.99
274_G	288_G	0.700	0.99
181_L	184_I	0.690	0.99
84_F	87_Y	0.690	0.99
28_F	217_L	0.685	0.98
238_L	295_S	0.684	0.98
117_L	125_V	0.680	0.98
264_L	310_S	0.679	0.98
150_L	277_I	0.674	0.98
244_A	248_V	0.672	0.98
129_L	132_A	0.671	0.98
47_A	204_A	0.669	0.98
198_P	202_L	0.669	0.98
173_E	177_W	0.669	0.98
83_W	101_A	0.667	0.98
73_V	77_G	0.665	0.98
12_I	40_V	0.665	0.98
113_G	265_A	0.664	0.98
263_V	267_A	0.664	0.98
50_F	200_F	0.663	0.98
86_C	101_A	0.662	0.98
164_L	167_L	0.660	0.98
110_G	132_A	0.659	0.98
30_E	221_A	0.658	0.98
305_L	309_V	0.658	0.98
131_V	135_S	0.658	0.98
78_C	241_M	0.656	0.98
28_F	32_Q	0.655	0.98
22_S	25_R	0.651	0.98
64_D	79_F	0.651	0.98
240_L	282_N	0.649	0.98
229_E	287_T	0.649	0.98
79_F	83_W	0.646	0.98
192_I	197_D	0.645	0.98
196_W	200_F	0.644	0.98
5_F	9_L	0.643	0.98
131_V	134_I	0.642	0.98
167_L	171_A	0.642	0.98
50_F	178_A	0.641	0.98
18_L	213_F	0.637	0.98
268_L	274_G	0.637	0.98
50_F	54_T	0.632	0.97
85_G	236_L	0.629	0.97
74_V	79_F	0.628	0.97
146_G	150_L	0.627	0.97
53_I	184_I	0.625	0.97
40_V	210_V	0.624	0.97
109_I	138_V	0.622	0.97
67_L	262_M	0.620	0.97
27_T	42_N	0.619	0.97
163_N	166_A	0.616	0.97
45_L	211_A	0.615	0.97
140_A	144_P	0.613	0.97
33_A	214_A	0.611	0.97
202_L	206_A	0.611	0.97
279_S	282_N	0.611	0.97
242_P	302_T	0.609	0.97
22_S	26_E	0.608	0.97
191_K	194_A	0.607	0.97
138_V	142_T	0.605	0.97
101_A	105_G	0.605	0.97
140_A	146_G	0.604	0.97
64_D	258_H	0.603	0.97
69_L	73_V	0.603	0.97
41_L	273_S	0.603	0.97
14_V	17_L	0.601	0.97
106_S	141_I	0.601	0.97
98_A	101_A	0.599	0.96
83_W	97_A	0.599	0.96
25_R	28_F	0.598	0.96
298_G	302_T	0.597	0.96
75_I	86_C	0.597	0.96
278_A	285_T	0.595	0.96
77_G	81_F	0.595	0.96
41_L	173_E	0.592	0.96
131_V	142_T	0.591	0.96
141_I	144_P	0.590	0.96
42_N	111_F	0.589	0.96
139_N	142_T	0.588	0.96
73_V	248_V	0.588	0.96
28_F	35_A	0.588	0.96
199_T	202_L	0.587	0.96
110_G	139_N	0.586	0.96
6_I	9_L	0.583	0.96
110_G	271_A	0.582	0.96
13_I	297_L	0.581	0.96
45_L	175_V	0.578	0.96
99_V	150_L	0.578	0.96
70_V	248_V	0.578	0.96
94_H	152_P	0.578	0.96
67_L	71_S	0.577	0.96
135_S	139_N	0.574	0.96
19_G	213_F	0.574	0.96
107_P	113_G	0.572	0.95
111_F	208_S	0.571	0.95
82_S	105_G	0.567	0.95
215_A	275_I	0.566	0.95
162_S	165_S	0.565	0.95
245_L	263_V	0.562	0.95
70_V	262_M	0.562	0.95
125_V	131_V	0.561	0.95
102_L	274_G	0.561	0.95
246_L	306_W	0.561	0.95
302_T	306_W	0.561	0.95
19_G	212_V	0.559	0.95
37_N	211_A	0.558	0.95
219_L	293_A	0.554	0.95
86_C	100_C	0.554	0.95
48_A	209_G	0.552	0.94
25_R	29_S	0.552	0.94
227_S	290_A	0.548	0.94
32_Q	217_L	0.548	0.94
69_L	252_C	0.547	0.94
105_G	146_G	0.547	0.94
249_G	262_M	0.546	0.94
136_I	139_N	0.545	0.94
47_A	181_L	0.544	0.94
124_S	129_L	0.542	0.94
71_S	82_S	0.540	0.94
75_I	78_C	0.540	0.94
109_I	265_A	0.539	0.94
233_N	270_P	0.539	0.94
56_A	186_V	0.537	0.94
254_L	258_H	0.537	0.94
239_I	305_L	0.536	0.94
87_Y	90_F	0.534	0.93
265_A	293_A	0.533	0.93
232_Y	235_F	0.533	0.93
292_L	296_V	0.532	0.93
285_T	289_T	0.532	0.93
98_A	153_S	0.532	0.93
235_F	238_L	0.531	0.93
48_A	237_K	0.530	0.93
274_G	292_L	0.530	0.93
165_S	169_S	0.530	0.93
79_F	101_A	0.529	0.93
125_V	130_V	0.527	0.93
108_T	114_F	0.526	0.93
271_A	274_G	0.525	0.93
103_I	107_P	0.524	0.93
130_V	261_M	0.524	0.93
23_G	28_F	0.523	0.93
215_A	292_L	0.523	0.93
114_F	136_I	0.522	0.93
71_S	137_I	0.518	0.92
222_H	293_A	0.518	0.92
108_T	115_A	0.518	0.92
7_G	194_A	0.515	0.92
84_F	89_F	0.514	0.92
125_V	257_E	0.514	0.92
230_I	291_S	0.513	0.92
151_N	170_A	0.513	0.92
64_D	69_L	0.513	0.92
245_L	249_G	0.510	0.92
232_Y	236_L	0.507	0.92
215_A	293_A	0.506	0.92
98_A	149_L	0.506	0.92
230_I	290_A	0.506	0.92
111_F	215_A	0.506	0.92
111_F	131_V	0.506	0.92
93_T	284_Y	0.506	0.92
34_R	279_S	0.505	0.91
214_A	217_L	0.505	0.91
57_N	61_I	0.504	0.91
239_I	243_L	0.504	0.91
227_S	230_I	0.503	0.91
306_W	309_V	0.501	0.91
83_W	94_H	0.501	0.91
52_S	132_A	0.501	0.91
96_E	283_V	0.500	0.91

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
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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
3zuxA	1	0.4745	99.7	0.687	Contact Map
4n7wA	2	0.4586	99.7	0.695	Contact Map
4czbA	2	0.535	74.4	0.926	Contact Map
4cz8A	2	0.535	73.5	0.927	Contact Map
2cfqA	1	0.9554	62.9	0.932	Contact Map
4bwzA	2	0.5287	58	0.934	Contact Map
2gfpA	2	0.9268	56.1	0.935	Contact Map
4m64A	1	0.949	21.2	0.948	Contact Map
3o7qA	1	0.9395	18.1	0.95	Contact Map
1zcdA	1	0.4904	15.9	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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