YEDA - ECOLI - GREMLIN Contacts

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YEDA - Uncharacterized inner membrane transporter YedA

UniProt:	P0AA70	Sequences: MRFRQLLPLFGALFALYIIWGSTYFVIRIGVESWPPLMMAGVRFLAAGILLLAFLLLRGHKLPPLRPLLNAALIGLLLLAVGNGMVTVAEHQNVPSGIAAVVVATVPLFTLCFSRLFGIKTRKLEWVGIAIGLAGIIMLNSGGNLSGNPWGAILILIGSISWAFGSVYGSRITLPVGMMAGAIEMLAAGVVLMIASMIAGEKLTALPSLSGFLAVGYLALFGSIIAINAYMYLIRNVSPALATSYAYVNPVVAVLLGTGLGGETLSKIEWLALGVIVFAVVLVTLGKYLFPAKPVVAPVIQDASSE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11141
Length:	306 (275)
Sequences:	38874 (28649)
Seq/√Len:	1727.6

ECOLI - YEDA YHBE YICL YIJE RHTA RARD YTFF EAMA YDDG YIGM
BACSU - YDED YVBV YRDR YDFC YBFH YCXC YXXF YETK YWFM YOJE YDEK YCBK YYAM YOAV
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
89_A	155_I	3.340	1.00
98_I	152_A	2.894	1.00
12_A	232_Y	2.860	1.00
232_Y	236_N	2.705	1.00
257_G	263_E	2.683	1.00
88_V	154_L	2.474	1.00
128_G	279_A	2.350	1.00
85_M	157_I	2.313	1.00
41_G	193_M	2.303	1.00
48_G	186_L	2.299	1.00
232_Y	235_R	2.281	1.00
26_V	217_Y	2.280	1.00
119_I	170_S	2.278	1.00
64_P	67_P	2.195	1.00
109_F	159_S	2.177	1.00
113_F	167_V	2.136	1.00
28_R	263_E	2.127	1.00
85_M	154_L	2.110	1.00
100_A	253_A	2.093	1.00
27_I	87_T	2.023	1.00
46_A	219_A	2.004	1.00
115_R	121_T	1.997	1.00
209_L	213_L	1.980	1.00
13_L	233_L	1.961	1.00
21_G	252_V	1.959	1.00
114_S	119_I	1.930	1.00
81_V	161_S	1.891	1.00
111_L	129_I	1.882	1.00
45_L	189_G	1.856	1.00
94_V	152_A	1.804	1.00
67_P	175_P	1.774	1.00
105_T	109_F	1.762	1.00
53_A	56_L	1.730	1.00
122_R	125_E	1.729	1.00
110_T	243_T	1.714	1.00
219_A	224_I	1.714	1.00
94_V	151_G	1.697	1.00
93_N	150_W	1.693	1.00
21_G	256_L	1.693	1.00
190_V	194_I	1.692	1.00
153_I	157_I	1.689	1.00
52_L	182_A	1.687	1.00
238_S	241_L	1.649	1.00
132_G	247_Y	1.621	1.00
208_S	211_G	1.618	1.00
85_M	161_S	1.606	1.00
22_S	217_Y	1.593	1.00
281_V	285_L	1.540	1.00
109_F	163_A	1.539	1.00
128_G	283_V	1.539	1.00
266_S	269_E	1.534	1.00
18_I	252_V	1.511	1.00
194_I	197_M	1.472	1.00
54_F	58_R	1.465	1.00
99_A	155_I	1.461	1.00
48_G	189_G	1.405	1.00
66_R	70_N	1.400	1.00
52_L	56_L	1.396	1.00
30_G	39_M	1.388	1.00
169_G	231_M	1.388	1.00
135_G	272_A	1.386	1.00
113_F	117_F	1.382	1.00
20_W	226_A	1.375	1.00
267_K	271_L	1.364	1.00
16_L	233_L	1.355	1.00
34_W	211_G	1.350	1.00
65_L	69_L	1.349	1.00
109_F	160_I	1.341	1.00
70_N	168_Y	1.339	1.00
132_G	279_A	1.323	1.00
29_I	214_A	1.316	1.00
88_V	93_N	1.316	1.00
53_A	57_L	1.315	1.00
128_G	282_L	1.308	1.00
33_S	211_G	1.308	1.00
50_L	224_I	1.301	1.00
94_V	98_I	1.300	1.00
97_G	254_V	1.292	1.00
66_R	69_L	1.290	1.00
96_S	257_G	1.285	1.00
41_G	189_G	1.284	1.00
88_V	92_Q	1.284	1.00
93_N	151_G	1.283	1.00
256_L	260_L	1.283	1.00
69_L	73_L	1.280	1.00
95_P	98_I	1.262	1.00
138_M	275_V	1.260	1.00
123_K	127_V	1.260	1.00
12_A	229_A	1.255	1.00
252_V	256_L	1.252	1.00
171_R	175_P	1.243	1.00
149_P	152_A	1.242	1.00
56_L	60_H	1.240	1.00
25_F	256_L	1.238	1.00
47_A	185_M	1.235	1.00
209_L	212_F	1.234	1.00
10_F	245_Y	1.231	1.00
65_L	68_L	1.227	1.00
49_I	53_A	1.227	1.00
101_V	273_L	1.224	1.00
248_V	252_V	1.221	1.00
270_W	274_G	1.221	1.00
170_S	238_S	1.221	1.00
39_M	218_L	1.218	1.00
138_M	268_I	1.208	1.00
163_A	167_V	1.199	1.00
210_S	213_L	1.194	1.00
126_W	130_A	1.192	1.00
73_L	168_Y	1.178	1.00
28_R	32_E	1.177	1.00
265_L	270_W	1.167	1.00
35_P	38_M	1.166	1.00
93_N	154_L	1.165	1.00
274_G	278_F	1.163	1.00
191_V	194_I	1.148	1.00
124_L	282_L	1.142	1.00
90_E	99_A	1.141	1.00
19_I	221_F	1.132	1.00
149_P	153_I	1.127	1.00
171_R	174_L	1.114	1.00
139_L	272_A	1.114	1.00
43_R	223_S	1.109	1.00
78_L	165_G	1.108	1.00
41_G	45_L	1.108	1.00
110_T	239_P	1.108	1.00
113_F	164_F	1.101	1.00
130_A	134_A	1.100	1.00
150_W	154_L	1.088	1.00
213_L	217_Y	1.085	1.00
26_V	214_A	1.084	1.00
121_T	126_W	1.082	1.00
135_G	276_I	1.082	1.00
76_L	191_V	1.079	1.00
11_G	15_A	1.077	1.00
37_L	195_A	1.075	1.00
72_A	187_A	1.074	1.00
115_R	120_K	1.061	1.00
111_L	121_T	1.061	1.00
20_W	230_Y	1.056	1.00
210_S	214_A	1.056	1.00
170_S	174_L	1.053	1.00
80_A	191_V	1.050	1.00
94_V	155_I	1.047	1.00
9_L	233_L	1.044	1.00
170_S	239_P	1.044	1.00
110_T	166_S	1.039	1.00
40_A	87_T	1.038	1.00
16_L	229_A	1.033	1.00
234_I	242_A	1.033	1.00
16_L	20_W	1.033	1.00
124_L	286_G	1.032	1.00
123_K	126_W	1.031	1.00
113_F	163_A	1.030	1.00
15_A	229_A	1.030	1.00
150_W	153_I	1.029	1.00
93_N	148_N	1.028	1.00
22_S	256_L	1.018	1.00
41_G	196_S	1.017	1.00
216_G	219_A	1.016	1.00
27_I	90_E	1.011	1.00
48_G	182_A	1.005	1.00
19_I	229_A	1.000	1.00
86_V	90_E	0.996	1.00
194_I	198_I	0.994	1.00
56_L	59_G	0.993	1.00
102_V	159_S	0.990	1.00
113_F	116_L	0.990	1.00
119_I	125_E	0.989	1.00
70_N	172_I	0.987	1.00
80_A	192_L	0.979	1.00
30_G	211_G	0.979	1.00
124_L	285_L	0.978	1.00
96_S	261_G	0.976	1.00
213_L	216_G	0.970	1.00
159_S	163_A	0.968	1.00
105_T	136_I	0.966	1.00
137_I	141_S	0.964	1.00
267_K	270_W	0.961	1.00
195_A	199_A	0.959	1.00
77_L	164_F	0.956	1.00
238_S	242_A	0.950	1.00
36_P	40_A	0.947	1.00
30_G	214_A	0.944	1.00
151_G	155_I	0.941	1.00
67_P	176_V	0.941	1.00
113_F	160_I	0.933	1.00
37_L	84_G	0.928	1.00
146_S	149_P	0.928	1.00
96_S	263_E	0.925	1.00
122_R	126_W	0.923	1.00
102_V	152_A	0.921	1.00
234_I	238_S	0.916	1.00
9_L	236_N	0.911	1.00
75_G	187_A	0.903	1.00
181_G	184_E	0.901	1.00
45_L	193_M	0.899	1.00
17_Y	21_G	0.898	1.00
25_F	260_L	0.891	1.00
77_L	161_S	0.890	1.00
131_I	279_A	0.885	1.00
50_L	220_L	0.884	1.00
67_P	70_N	0.884	1.00
141_S	266_S	0.882	1.00
101_V	137_I	0.881	1.00
64_P	68_L	0.877	1.00
212_F	216_G	0.877	1.00
195_A	198_I	0.874	1.00
110_T	163_A	0.874	1.00
102_V	155_I	0.873	1.00
237_V	242_A	0.868	1.00
74_I	78_L	0.868	1.00
187_A	190_V	0.861	1.00
69_L	72_A	0.861	1.00
70_N	171_R	0.854	1.00
17_Y	252_V	0.848	1.00
55_L	59_G	0.840	1.00
120_K	124_L	0.839	1.00
50_L	53_A	0.837	1.00
182_A	186_L	0.836	1.00
33_S	208_S	0.835	1.00
155_I	159_S	0.825	1.00
233_L	242_A	0.821	1.00
186_L	190_V	0.813	1.00
38_M	196_S	0.812	1.00
237_V	241_L	0.812	1.00
134_A	138_M	0.811	1.00
84_G	88_V	0.810	1.00
162_W	166_S	0.807	1.00
216_G	220_L	0.799	1.00
115_R	118_G	0.798	1.00
48_G	52_L	0.796	1.00
208_S	212_F	0.795	1.00
25_F	257_G	0.794	1.00
206_L	209_L	0.794	1.00
44_F	188_A	0.793	1.00
136_I	140_N	0.792	1.00
57_L	60_H	0.791	1.00
68_L	187_A	0.790	1.00
254_V	265_L	0.790	1.00
197_M	200_G	0.787	1.00
120_K	123_K	0.782	1.00
70_N	74_I	0.776	1.00
254_V	273_L	0.775	1.00
183_I	187_A	0.772	1.00
273_L	277_V	0.772	1.00
251_V	273_L	0.770	1.00
27_I	31_V	0.768	1.00
179_M	183_I	0.765	1.00
207_P	211_G	0.765	1.00
148_N	152_A	0.763	1.00
268_I	271_L	0.763	1.00
77_L	168_Y	0.760	1.00
164_F	168_Y	0.760	1.00
258_T	265_L	0.759	1.00
134_A	275_V	0.756	1.00
138_M	271_L	0.755	1.00
75_G	80_A	0.754	1.00
271_L	275_V	0.751	1.00
111_L	125_E	0.749	1.00
14_F	252_V	0.746	1.00
258_T	264_T	0.744	1.00
108_L	132_G	0.744	1.00
127_V	131_I	0.741	1.00
73_L	76_L	0.740	1.00
248_V	251_V	0.734	1.00
215_V	219_A	0.732	1.00
207_P	212_F	0.732	1.00
51_L	224_I	0.729	1.00
80_A	84_G	0.728	1.00
68_L	72_A	0.725	1.00
82_G	161_S	0.725	1.00
75_G	78_L	0.721	1.00
181_G	185_M	0.721	1.00
214_A	217_Y	0.716	1.00
198_I	201_E	0.714	1.00
81_V	85_M	0.714	1.00
13_L	245_Y	0.713	1.00
105_T	108_L	0.712	1.00
199_A	202_K	0.710	1.00
54_F	178_M	0.709	1.00
38_M	42_V	0.705	1.00
244_S	283_V	0.705	1.00
42_V	46_A	0.705	1.00
187_A	191_V	0.701	1.00
135_G	279_A	0.700	1.00
279_A	283_V	0.696	1.00
10_F	241_L	0.695	1.00
225_I	229_A	0.694	1.00
40_A	192_L	0.694	1.00
70_N	73_L	0.692	1.00
190_V	193_M	0.690	1.00
17_Y	248_V	0.689	1.00
189_G	193_M	0.688	1.00
89_A	99_A	0.686	1.00
265_L	269_E	0.686	1.00
110_T	167_V	0.686	1.00
211_G	214_A	0.686	1.00
109_F	156_L	0.685	1.00
121_T	125_E	0.682	1.00
112_C	116_L	0.681	1.00
183_I	186_L	0.679	1.00
24_Y	86_V	0.673	1.00
52_L	186_L	0.672	1.00
25_F	96_S	0.668	1.00
34_W	39_M	0.666	1.00
72_A	76_L	0.663	1.00
45_L	49_I	0.663	1.00
82_G	165_G	0.660	1.00
94_V	99_A	0.660	1.00
19_I	226_A	0.658	1.00
104_A	136_I	0.657	1.00
257_G	261_G	0.651	1.00
54_F	57_L	0.649	1.00
102_V	156_L	0.647	1.00
119_I	240_A	0.647	1.00
278_F	282_L	0.644	1.00
89_A	151_G	0.643	1.00
71_A	180_A	0.643	1.00
228_N	232_Y	0.641	1.00
162_W	230_Y	0.639	1.00
13_L	237_V	0.639	1.00
71_A	176_V	0.637	1.00
86_V	99_A	0.633	1.00
264_T	268_I	0.633	1.00
29_I	261_G	0.628	1.00
196_S	200_G	0.628	1.00
107_P	247_Y	0.627	1.00
105_T	159_S	0.625	1.00
50_L	219_A	0.621	1.00
208_S	213_L	0.620	1.00
104_A	107_P	0.616	1.00
19_I	222_G	0.615	1.00
47_A	224_I	0.615	1.00
269_E	273_L	0.613	1.00
24_Y	100_A	0.612	1.00
254_V	258_T	0.611	1.00
34_W	38_M	0.611	1.00
86_V	158_G	0.611	1.00
111_L	115_R	0.611	1.00
64_P	69_L	0.610	1.00
180_A	183_I	0.606	1.00
55_L	182_A	0.604	1.00
180_A	184_E	0.604	1.00
188_A	192_L	0.602	1.00
186_L	189_G	0.599	1.00
82_G	86_V	0.596	1.00
46_A	50_L	0.595	1.00
17_Y	249_N	0.595	1.00
23_T	222_G	0.594	1.00
165_G	231_M	0.594	1.00
181_G	231_M	0.593	1.00
24_Y	28_R	0.592	1.00
131_I	282_L	0.586	1.00
256_L	259_G	0.582	1.00
154_L	157_I	0.574	1.00
144_N	147_G	0.573	1.00
166_S	243_T	0.570	1.00
166_S	230_Y	0.566	1.00
25_F	253_A	0.564	1.00
140_N	152_A	0.561	1.00
80_A	195_A	0.560	1.00
53_A	58_R	0.559	1.00
217_Y	221_F	0.557	1.00
68_L	183_I	0.556	1.00
9_L	237_V	0.556	1.00
247_Y	280_V	0.555	1.00
15_A	19_I	0.549	1.00
101_V	140_N	0.548	1.00
42_V	215_V	0.547	1.00
104_A	159_S	0.547	1.00
35_P	200_G	0.546	1.00
246_A	249_N	0.546	1.00
125_E	238_S	0.546	1.00
31_V	90_E	0.544	1.00
185_M	189_G	0.543	1.00
259_G	262_G	0.541	1.00
117_F	164_F	0.539	1.00
184_E	187_A	0.539	1.00
101_V	139_L	0.538	1.00
221_F	225_I	0.535	1.00
68_L	71_A	0.532	1.00
266_S	270_W	0.531	1.00
114_S	240_A	0.530	1.00
142_G	268_I	0.528	1.00
105_T	132_G	0.527	1.00
125_E	287_K	0.525	1.00
21_G	249_N	0.523	1.00
23_T	87_T	0.523	1.00
178_M	181_G	0.521	1.00
22_S	222_G	0.520	1.00
14_F	17_Y	0.520	1.00
70_N	175_P	0.519	1.00
145_L	148_N	0.519	1.00
165_G	169_G	0.517	1.00
280_V	283_V	0.517	1.00
205_A	209_L	0.516	1.00
255_L	259_G	0.516	1.00
13_L	230_Y	0.515	1.00
49_I	52_L	0.515	1.00
146_S	150_W	0.514	1.00
60_H	177_G	0.514	1.00
233_L	237_V	0.514	1.00
85_M	158_G	0.512	1.00
127_V	134_A	0.510	1.00
193_M	197_M	0.509	1.00
255_L	258_T	0.508	1.00
82_G	162_W	0.507	1.00
55_L	58_R	0.507	1.00
264_T	269_E	0.506	1.00
258_T	270_W	0.500	1.00
147_G	150_W	0.500	1.00
106_V	159_S	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	0.2516	98.9	0.755	Contact Map
3b5dA	2	0.3301	98	0.813	Contact Map
2cfqA	1	0.6078	75	0.909	Contact Map
4j05A	3	0.9248	73.3	0.91	Contact Map
4pypA	1	0.7843	72.2	0.911	Contact Map
3l1lA	2	0.8595	66.5	0.914	Contact Map
1pw4A	1	0.8137	60.8	0.917	Contact Map
4he8J	1	0.5131	60.7	0.917	Contact Map
3zuxA	1	0.8987	56.7	0.919	Contact Map
4czbA	2	0.9346	52.9	0.921	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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