YVFS - BACSU - GREMLIN Contacts

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YVFS - Putative transport permease YvfS

UniProt:	O07017	Sequences: MNVLQKQSIAEMKRVLRNKYFVLWSLIMPIAFYYFFTNVVNTNVPDQRAWEAHYLMSMTVFSVMGSSIMTLGIRMVQERSQGWAAFIRLTPLPDHIYLSAQMIGQSVIHVLSITVIFLFGAIINDIALSPFEWMMSGLWILFGALPFLALGTLIGLMRKVETAAGISNVLYMLLALGGGMWMPFEVMPDMMQSIGQWLPSYHFGSGAWELVRGGSPTWKNILILIAYMMLFMLLSKYIRRKQEAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	245 (234)
Sequences:	20465 (14143)
Seq/√Len:	924.5

ECOLI - YADH YHHJ YBHR YBHS
BACSU - YVFS YFIM TAGG YFIN NATB
HALSA - Q9HRJ5 Q9HMU9
SULSO - Q97VH7 Q97WP5 Q97U55 Q97Z04 Q7LY08

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
139_W	206_G	5.145	1.00
9_I	13_K	4.062	1.00
153_L	234_L	3.510	1.00
143_G	203_F	3.263	1.00
114_T	137_G	3.134	1.00
7_Q	100_A	3.068	1.00
5_Q	9_I	2.910	1.00
11_E	101_Q	2.592	1.00
145_L	228_M	2.589	1.00
93_P	96_I	2.553	1.00
49_A	52_A	2.422	1.00
146_P	228_M	2.419	1.00
8_S	103_I	2.397	1.00
13_K	16_L	2.263	1.00
189_D	193_S	2.251	1.00
218_W	222_L	2.225	1.00
219_K	223_I	2.207	1.00
222_L	226_A	2.179	1.00
142_F	225_I	2.178	1.00
8_S	107_V	2.092	1.00
192_Q	196_Q	2.071	1.00
233_L	237_Y	2.042	1.00
227_Y	231_F	2.017	1.00
16_L	19_K	1.967	1.00
223_I	226_A	1.916	1.00
195_G	201_Y	1.898	1.00
118_L	122_I	1.860	1.00
189_D	192_Q	1.852	1.00
153_L	238_I	1.815	1.00
184_F	195_G	1.790	1.00
135_M	210_L	1.784	1.00
159_K	162_T	1.767	1.00
119_F	123_I	1.738	1.00
153_L	231_F	1.735	1.00
149_A	228_M	1.712	1.00
158_R	166_I	1.708	1.00
38_N	41_N	1.687	1.00
110_V	141_L	1.668	1.00
190_M	193_S	1.647	1.00
202_H	220_N	1.646	1.00
230_L	234_L	1.631	1.00
146_P	231_F	1.600	1.00
140_I	203_F	1.591	1.00
223_I	227_Y	1.586	1.00
219_K	222_L	1.585	1.00
193_S	197_W	1.569	1.00
196_Q	202_H	1.564	1.00
149_A	232_M	1.547	1.00
154_I	158_R	1.542	1.00
226_A	230_L	1.534	1.00
10_A	78_E	1.515	1.00
139_W	221_I	1.493	1.00
228_M	232_M	1.487	1.00
209_E	213_G	1.464	1.00
205_S	220_N	1.444	1.00
8_S	100_A	1.436	1.00
134_M	138_L	1.411	1.00
100_A	104_G	1.403	1.00
193_S	196_Q	1.375	1.00
142_F	221_I	1.373	1.00
196_Q	201_Y	1.351	1.00
143_G	147_F	1.334	1.00
12_M	16_L	1.332	1.00
156_L	238_I	1.328	1.00
221_I	225_I	1.324	1.00
95_H	99_S	1.311	1.00
78_E	101_Q	1.308	1.00
106_S	141_L	1.308	1.00
139_W	210_L	1.282	1.00
146_P	224_L	1.268	1.00
142_F	228_M	1.268	1.00
80_S	160_V	1.253	1.00
138_L	221_I	1.238	1.00
37_T	123_I	1.231	1.00
205_S	209_E	1.230	1.00
42_T	45_P	1.219	1.00
5_Q	8_S	1.215	1.00
109_H	144_A	1.213	1.00
41_N	44_V	1.207	1.00
129_S	132_E	1.207	1.00
32_F	36_F	1.202	1.00
117_F	136_S	1.190	1.00
40_V	43_N	1.180	1.00
146_P	227_Y	1.178	1.00
101_Q	105_Q	1.172	1.00
158_R	162_T	1.166	1.00
135_M	138_L	1.166	1.00
205_S	216_P	1.164	1.00
12_M	104_G	1.159	1.00
28_M	32_F	1.148	1.00
23_L	27_I	1.144	1.00
174_L	198_L	1.136	1.00
225_I	229_M	1.131	1.00
106_S	145_L	1.123	1.00
13_K	17_R	1.122	1.00
30_I	119_F	1.122	1.00
234_L	237_Y	1.114	1.00
180_M	204_G	1.111	1.00
52_A	55_L	1.107	1.00
157_M	238_I	1.107	1.00
55_L	58_M	1.102	1.00
164_A	168_N	1.101	1.00
234_L	238_I	1.097	1.00
127_A	132_E	1.096	1.00
50_W	53_H	1.090	1.00
72_G	163_A	1.085	1.00
202_H	206_G	1.085	1.00
169_V	173_L	1.081	1.00
187_M	192_Q	1.075	1.00
153_L	235_S	1.074	1.00
192_Q	195_G	1.074	1.00
135_M	217_T	1.069	1.00
134_M	137_G	1.066	1.00
230_L	233_L	1.065	1.00
149_A	231_F	1.063	1.00
201_Y	205_S	1.059	1.00
220_N	224_L	1.036	1.00
202_H	223_I	1.035	1.00
118_L	121_A	1.028	1.00
33_Y	116_I	1.023	1.00
184_F	192_Q	1.023	1.00
150_L	170_L	1.011	1.00
204_G	208_W	1.004	1.00
171_Y	175_A	1.004	1.00
184_F	201_Y	0.990	1.00
199_P	203_F	0.984	1.00
76_V	80_S	0.976	1.00
8_S	12_M	0.974	1.00
39_V	43_N	0.974	1.00
98_L	236_K	0.970	1.00
77_Q	80_S	0.967	1.00
8_S	104_G	0.965	1.00
6_K	9_I	0.961	1.00
92_L	97_Y	0.957	1.00
49_A	53_H	0.953	1.00
40_V	44_V	0.946	1.00
78_E	83_W	0.938	1.00
184_F	196_Q	0.937	1.00
218_W	221_I	0.925	1.00
131_F	134_M	0.923	1.00
11_E	104_G	0.921	1.00
222_L	225_I	0.921	1.00
168_N	172_M	0.920	1.00
225_I	228_M	0.917	1.00
98_L	235_S	0.916	1.00
198_L	201_Y	0.914	1.00
138_L	142_F	0.912	1.00
55_L	120_G	0.910	1.00
202_H	205_S	0.910	1.00
140_I	207_A	0.909	1.00
173_L	176_L	0.902	1.00
56_M	61_F	0.897	1.00
114_T	118_L	0.896	1.00
133_W	137_G	0.895	1.00
19_K	22_V	0.885	1.00
216_P	219_K	0.883	1.00
102_M	232_M	0.865	1.00
15_V	25_S	0.865	1.00
162_T	165_G	0.862	1.00
83_W	86_F	0.861	1.00
50_W	54_Y	0.855	1.00
11_E	14_R	0.855	1.00
220_N	223_I	0.851	1.00
150_L	231_F	0.849	1.00
227_Y	230_L	0.843	1.00
231_F	235_S	0.840	1.00
215_S	219_K	0.836	1.00
48_R	52_A	0.832	1.00
41_N	123_I	0.830	1.00
161_E	165_G	0.828	1.00
236_K	239_R	0.827	1.00
60_V	200_S	0.822	1.00
15_V	108_I	0.819	1.00
149_A	235_S	0.819	1.00
86_F	89_L	0.818	1.00
63_V	68_I	0.818	1.00
144_A	148_L	0.817	1.00
190_M	194_I	0.816	1.00
110_V	114_T	0.816	1.00
18_N	21_F	0.816	1.00
208_W	212_R	0.811	1.00
12_M	107_V	0.802	1.00
58_M	61_F	0.792	1.00
78_E	85_A	0.792	1.00
57_S	63_V	0.787	1.00
58_M	63_V	0.776	1.00
145_L	149_A	0.771	1.00
96_I	100_A	0.758	1.00
115_V	118_L	0.753	1.00
118_L	133_W	0.751	1.00
62_S	65_G	0.750	1.00
210_L	217_T	0.750	1.00
103_I	107_V	0.747	1.00
11_E	105_Q	0.744	1.00
236_K	240_R	0.744	1.00
203_F	206_G	0.743	1.00
95_H	236_K	0.742	1.00
137_G	141_L	0.742	1.00
50_W	55_L	0.738	1.00
59_T	62_S	0.735	1.00
216_P	220_N	0.725	1.00
7_Q	96_I	0.724	1.00
86_F	90_T	0.723	1.00
131_F	135_M	0.721	1.00
113_I	141_L	0.718	1.00
120_G	136_S	0.708	1.00
132_E	135_M	0.708	1.00
188_P	192_Q	0.707	1.00
224_L	227_Y	0.706	1.00
60_V	68_I	0.699	1.00
232_M	236_K	0.698	1.00
86_F	91_P	0.697	1.00
136_S	207_A	0.697	1.00
229_M	233_L	0.695	1.00
105_Q	109_H	0.688	1.00
83_W	87_I	0.687	1.00
73_I	76_V	0.684	1.00
57_S	60_V	0.682	1.00
125_D	129_S	0.681	1.00
76_V	163_A	0.681	1.00
224_L	228_M	0.680	1.00
152_T	155_G	0.680	1.00
125_D	128_L	0.679	1.00
61_F	65_G	0.679	1.00
151_G	155_G	0.677	1.00
223_I	231_F	0.677	1.00
154_I	170_L	0.671	1.00
51_E	55_L	0.669	1.00
41_N	45_P	0.668	1.00
20_Y	24_W	0.667	1.00
34_Y	38_N	0.667	1.00
167_S	171_Y	0.659	1.00
152_T	156_L	0.659	1.00
122_I	128_L	0.659	1.00
179_G	183_P	0.656	1.00
142_F	224_L	0.655	1.00
58_M	62_S	0.654	1.00
113_I	140_I	0.650	1.00
107_V	110_V	0.650	1.00
29_P	33_Y	0.649	1.00
177_G	191_M	0.647	1.00
168_N	173_L	0.641	1.00
60_V	63_V	0.640	1.00
182_M	186_V	0.635	1.00
165_G	168_N	0.634	1.00
102_M	148_L	0.632	1.00
55_L	66_S	0.632	1.00
46_D	49_A	0.629	1.00
57_S	208_W	0.629	1.00
121_A	125_D	0.627	1.00
99_S	103_I	0.624	1.00
188_P	191_M	0.622	1.00
34_Y	119_F	0.622	1.00
184_F	187_M	0.621	1.00
203_F	224_L	0.620	1.00
228_M	231_F	0.619	1.00
88_R	94_D	0.619	1.00
30_I	34_Y	0.618	1.00
154_I	167_S	0.618	1.00
207_A	211_V	0.614	1.00
233_L	236_K	0.614	1.00
139_W	203_F	0.614	1.00
117_F	137_G	0.611	1.00
10_A	14_R	0.611	1.00
178_G	201_Y	0.610	1.00
62_S	66_S	0.610	1.00
86_F	112_S	0.609	1.00
72_G	75_M	0.609	1.00
97_Y	239_R	0.604	1.00
84_A	88_R	0.603	1.00
34_Y	123_I	0.601	1.00
55_L	63_V	0.600	1.00
154_I	157_M	0.599	1.00
56_M	60_V	0.598	1.00
160_V	167_S	0.598	1.00
46_D	53_H	0.598	1.00
155_G	174_L	0.597	1.00
231_F	234_L	0.595	1.00
135_M	206_G	0.593	1.00
56_M	59_T	0.592	1.00
158_R	163_A	0.591	1.00
183_P	187_M	0.589	1.00
135_M	139_W	0.587	1.00
107_V	111_L	0.586	1.00
86_F	92_L	0.584	1.00
63_V	66_S	0.582	1.00
37_T	41_N	0.582	1.00
155_G	163_A	0.575	1.00
162_T	166_I	0.575	1.00
10_A	86_F	0.574	1.00
102_M	149_A	0.571	1.00
9_I	12_M	0.570	1.00
106_S	148_L	0.569	1.00
31_A	36_F	0.569	1.00
119_F	122_I	0.569	1.00
117_F	121_A	0.566	1.00
196_Q	205_S	0.564	1.00
79_R	84_A	0.561	1.00
11_E	79_R	0.560	1.00
206_G	220_N	0.560	1.00
229_M	232_M	0.559	1.00
40_V	45_P	0.557	1.00
87_I	90_T	0.557	1.00
57_S	61_F	0.555	1.00
76_V	79_R	0.554	1.00
105_Q	152_T	0.554	1.00
57_S	211_V	0.549	1.00
202_H	227_Y	0.544	1.00
28_M	173_L	0.543	1.00
186_V	189_D	0.541	1.00
58_M	65_G	0.540	1.00
151_G	177_G	0.540	1.00
27_I	31_A	0.540	1.00
105_Q	148_L	0.540	1.00
114_T	117_F	0.539	1.00
231_F	236_K	0.537	1.00
237_Y	240_R	0.534	1.00
10_A	83_W	0.534	1.00
80_S	83_W	0.533	1.00
82_G	85_A	0.532	1.00
86_F	151_G	0.529	1.00
156_L	235_S	0.527	1.00
105_Q	156_L	0.526	1.00
111_L	114_T	0.522	1.00
161_E	164_A	0.521	1.00
29_P	35_F	0.519	1.00
187_M	195_G	0.517	1.00
217_T	220_N	0.516	1.00
108_I	112_S	0.515	1.00
15_V	104_G	0.515	1.00
153_L	157_M	0.513	1.00
177_G	182_M	0.513	1.00
151_G	179_G	0.511	1.00
210_L	213_G	0.509	1.00
197_W	202_H	0.509	1.00
141_L	145_L	0.508	1.00
140_I	144_A	0.508	1.00
38_N	123_I	0.508	1.00
38_N	44_V	0.507	1.00
219_K	226_A	0.505	1.00
153_L	156_L	0.503	1.00
38_N	42_T	0.503	1.00
66_S	70_T	0.502	1.00
150_L	153_L	0.502	1.00
63_V	67_S	0.502	1.00
195_G	198_L	0.501	1.00
7_Q	92_L	0.501	1.00
168_N	171_Y	0.501	1.00
58_M	66_S	0.501	1.00
226_A	233_L	0.500	1.00
30_I	115_V	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
2a65A	2	0.3469	13.4	0.927	Contact Map
2rddB	1	0.1224	6	0.937	Contact Map
2wswA	3	0.6653	4.3	0.941	Contact Map
2ks1B	1	0.1673	4.3	0.942	Contact Map
3qbgA	3	0.2	3.4	0.944	Contact Map
2gsmB	1	0.2367	2.8	0.947	Contact Map
4lz6A	1	0.849	2.7	0.947	Contact Map
2m20A	2	0.1306	2.7	0.947	Contact Map
2ksdA	1	0.2571	2.6	0.947	Contact Map
2jwaA	2	0.1592	2.6	0.948	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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