YKOY - BACSU - GREMLIN Contacts

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YKOY - Uncharacterized membrane protein YkoY

UniProt:	O34997	Sequences: MYSGNKVVISWIVSIGFVGMPEFMSSKTFALCRQRSFLHGPAGIRSDEEKENNFFGRVSFMDAALLLEYGWVLLVLIGLEGILAADNALVMAVMVKHLPEEKRKKALFYGLAGAFVLRFGSLFAISFLVNVWQVQAIGAIYLLYISASHLLKRYVFKKEDTHKETKQSGFWPTVLKVELADIAFAVDSILAAVALAVTLPGTSLPKIGGLDGGQFLVILAGGIIGLVIMRFAASMFVKLLKERPSLETAAFVIVGWVGVKLALYTLAHRDIAVVSEHFIHSGTWKLIFWGVLAAIAVCGWFMSGGKKQPEGAQNEQKNSTRERA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	324 (276)
Sequences:	2036 (1029)
Seq/√Len:	61.9

ECOLI - ALX
BACSU - YKOY YCEF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_V	74_L	4.981	1.00
55_F	74_L	4.394	1.00
36_S	42_A	4.161	1.00
68_E	72_V	4.007	1.00
117_L	182_I	3.588	1.00
47_D	81_G	3.551	1.00
249_A	296_A	3.445	1.00
146_S	255_G	3.358	1.00
45_R	49_E	3.188	1.00
76_L	192_A	3.127	1.00
119_F	123_F	2.917	1.00
60_F	64_A	2.701	1.00
128_L	134_V	2.666	1.00
106_A	177_V	2.547	1.00
55_F	59_S	2.456	1.00
41_P	45_R	2.359	1.00
40_G	238_K	2.330	1.00
113_G	117_L	2.317	1.00
79_L	195_L	2.309	1.00
252_V	292_L	2.301	1.00
37_F	101_E	2.209	1.00
277_H	280_H	2.201	1.00
252_V	295_I	2.196	1.00
59_S	63_A	2.105	1.00
284_W	288_F	2.100	1.00
26_S	30_A	2.069	1.00
44_I	48_E	2.051	1.00
58_V	73_L	2.024	1.00
303_S	307_K	2.012	1.00
11_W	15_I	1.942	1.00
115_F	223_I	1.917	1.00
253_I	294_A	1.913	1.00
75_V	195_L	1.884	1.00
113_G	178_E	1.877	1.00
98_L	173_T	1.876	1.00
167_Q	171_W	1.875	1.00
69_Y	214_Q	1.861	1.00
54_F	73_L	1.860	1.00
134_V	137_I	1.839	1.00
148_S	151_L	1.821	1.00
56_G	60_F	1.805	1.00
245_S	303_S	1.802	1.00
253_I	292_L	1.801	1.00
14_S	18_V	1.770	0.99
52_N	56_G	1.766	0.99
161_T	166_K	1.754	0.99
22_E	26_S	1.748	0.99
37_F	100_E	1.634	0.99
11_W	14_S	1.628	0.99
253_I	293_A	1.619	0.99
132_W	136_A	1.593	0.99
277_H	281_S	1.585	0.99
147_A	151_L	1.581	0.99
58_V	70_G	1.572	0.99
263_L	266_L	1.560	0.99
65_L	214_Q	1.556	0.99
71_W	75_V	1.546	0.99
61_M	217_V	1.531	0.99
17_F	219_L	1.515	0.98
15_I	19_G	1.503	0.98
288_F	292_L	1.495	0.98
259_V	263_L	1.472	0.98
244_P	303_S	1.438	0.98
126_S	193_V	1.428	0.98
104_K	108_F	1.426	0.98
62_D	70_G	1.408	0.97
242_E	304_G	1.407	0.97
98_L	174_V	1.403	0.97
245_S	299_G	1.402	0.97
152_K	155_V	1.382	0.97
109_Y	113_G	1.381	0.97
119_F	219_L	1.363	0.97
143_L	147_A	1.361	0.97
17_F	21_P	1.356	0.97
298_C	302_M	1.340	0.97
193_V	196_A	1.334	0.96
51_E	81_G	1.327	0.96
25_S	29_F	1.327	0.96
59_S	62_D	1.292	0.96
278_F	281_S	1.280	0.95
48_E	52_N	1.277	0.95
139_A	262_A	1.274	0.95
196_A	217_V	1.263	0.95
120_G	124_A	1.253	0.95
79_L	194_A	1.248	0.95
66_L	70_G	1.243	0.95
100_E	103_R	1.240	0.95
28_T	112_A	1.238	0.95
85_A	88_A	1.234	0.94
294_A	298_C	1.232	0.94
28_T	108_F	1.230	0.94
10_S	14_S	1.230	0.94
76_L	196_A	1.225	0.94
161_T	164_E	1.221	0.94
143_L	258_G	1.212	0.94
121_S	249_A	1.205	0.94
88_A	91_M	1.202	0.94
244_P	304_G	1.201	0.94
124_A	128_L	1.195	0.93
103_R	237_V	1.194	0.93
255_G	259_V	1.181	0.93
103_R	233_A	1.177	0.93
55_F	58_V	1.174	0.93
62_D	67_L	1.172	0.93
70_G	74_L	1.171	0.93
84_A	232_A	1.168	0.93
161_T	165_T	1.167	0.93
281_S	287_I	1.166	0.93
256_W	288_F	1.166	0.93
16_G	220_A	1.141	0.92
92_A	240_L	1.137	0.92
38_L	100_E	1.113	0.91
38_L	43_G	1.108	0.91
56_G	59_S	1.108	0.91
155_V	158_K	1.106	0.90
109_Y	174_V	1.102	0.90
76_L	218_I	1.091	0.90
214_Q	217_V	1.087	0.90
9_I	15_I	1.084	0.90
129_V	134_V	1.083	0.90
72_V	217_V	1.075	0.89
81_G	227_V	1.075	0.89
293_A	296_A	1.062	0.89
52_N	59_S	1.042	0.88
163_K	168_S	1.030	0.87
26_S	50_K	1.025	0.87
35_R	42_A	1.018	0.86
106_A	112_A	1.015	0.86
288_F	291_V	1.010	0.86
171_W	175_L	1.003	0.86
81_G	231_F	1.002	0.86
40_G	44_I	1.000	0.85
28_T	104_K	0.999	0.85
67_L	71_W	0.994	0.85
264_Y	268_H	0.991	0.85
183_A	186_V	0.986	0.85
267_A	277_H	0.985	0.85
46_S	50_K	0.984	0.84
148_S	152_K	0.979	0.84
144_Y	148_S	0.973	0.84
217_V	220_A	0.973	0.84
21_P	158_K	0.968	0.83
101_E	105_K	0.962	0.83
268_H	277_H	0.959	0.83
26_S	31_L	0.956	0.83
108_F	178_E	0.955	0.83
144_Y	147_A	0.954	0.83
141_Y	145_I	0.947	0.82
59_S	74_L	0.943	0.82
78_G	290_G	0.942	0.82
132_W	268_H	0.940	0.82
135_Q	257_V	0.938	0.81
295_I	299_G	0.930	0.81
129_V	135_Q	0.930	0.81
253_I	288_F	0.919	0.80
44_I	235_M	0.918	0.80
82_I	245_S	0.917	0.80
14_S	17_F	0.914	0.80
77_I	81_G	0.912	0.80
298_C	301_F	0.906	0.79
66_L	232_A	0.900	0.79
14_S	25_S	0.896	0.78
15_I	18_V	0.893	0.78
53_N	91_M	0.890	0.78
162_H	166_K	0.879	0.77
173_T	180_A	0.876	0.77
284_W	287_I	0.875	0.77
299_G	302_M	0.874	0.77
60_F	65_L	0.873	0.77
248_T	251_F	0.872	0.77
61_M	70_G	0.863	0.76
141_Y	144_Y	0.862	0.76
51_E	55_F	0.861	0.76
40_G	47_D	0.854	0.75
281_S	284_W	0.851	0.75
93_V	186_V	0.849	0.75
32_C	104_K	0.845	0.74
43_G	46_S	0.845	0.74
28_T	31_L	0.842	0.74
55_F	73_L	0.841	0.74
12_I	60_F	0.839	0.74
17_F	22_E	0.829	0.73
81_G	232_A	0.827	0.73
140_I	144_Y	0.825	0.72
46_S	49_E	0.825	0.72
149_H	251_F	0.820	0.72
61_M	69_Y	0.818	0.72
19_G	60_F	0.814	0.71
178_E	226_L	0.811	0.71
291_V	294_A	0.810	0.71
189_I	192_A	0.806	0.71
104_K	178_E	0.804	0.70
20_M	253_I	0.799	0.70
43_G	47_D	0.795	0.70
192_A	195_L	0.790	0.69
61_M	66_L	0.784	0.69
19_G	53_N	0.781	0.68
216_L	220_A	0.781	0.68
222_G	225_G	0.781	0.68
179_L	183_A	0.780	0.68
157_K	160_D	0.777	0.68
292_L	295_I	0.776	0.68
85_A	224_I	0.774	0.68
145_I	149_H	0.774	0.68
34_Q	77_I	0.771	0.67
248_T	252_V	0.768	0.67
38_L	104_K	0.765	0.67
106_A	174_V	0.765	0.67
91_M	177_V	0.765	0.67
38_L	92_A	0.761	0.66
88_A	261_L	0.759	0.66
297_V	301_F	0.757	0.66
134_V	141_Y	0.756	0.66
31_L	38_L	0.750	0.65
84_A	265_T	0.749	0.65
263_L	278_F	0.740	0.64
195_L	248_T	0.739	0.64
109_Y	178_E	0.739	0.64
47_D	51_E	0.738	0.64
23_F	50_K	0.738	0.64
303_S	306_K	0.735	0.64
291_V	295_I	0.732	0.63
162_H	165_T	0.732	0.63
193_V	215_F	0.732	0.63
136_A	265_T	0.727	0.63
139_A	267_A	0.727	0.63
143_L	255_G	0.726	0.63
36_S	39_H	0.726	0.63
66_L	69_Y	0.725	0.62
99_P	106_A	0.721	0.62
9_I	12_I	0.721	0.62
279_I	284_W	0.720	0.62
128_L	131_V	0.719	0.62
73_L	224_I	0.717	0.62
175_L	179_L	0.716	0.62
56_G	73_L	0.714	0.61
13_V	33_R	0.712	0.61
121_S	296_A	0.712	0.61
137_I	140_I	0.710	0.61
54_F	77_I	0.707	0.61
151_L	164_E	0.706	0.60
32_C	38_L	0.698	0.60
12_I	16_G	0.698	0.60
34_Q	37_F	0.697	0.59
299_G	303_S	0.695	0.59
178_E	230_R	0.692	0.59
23_F	49_E	0.691	0.59
233_A	236_F	0.689	0.59
19_G	22_E	0.687	0.58
16_G	216_L	0.687	0.58
114_A	181_D	0.685	0.58
235_M	242_E	0.684	0.58
197_V	215_F	0.683	0.58
79_L	129_V	0.681	0.58
75_V	79_L	0.678	0.57
225_G	237_V	0.678	0.57
133_Q	140_I	0.675	0.57
21_P	25_S	0.671	0.57
92_A	174_V	0.668	0.56
150_L	255_G	0.668	0.56
20_M	65_L	0.666	0.56
180_A	186_V	0.666	0.56
23_F	34_Q	0.666	0.56
31_L	105_K	0.665	0.56
302_M	306_K	0.665	0.56
43_G	173_T	0.664	0.56
296_A	299_G	0.663	0.56
47_D	227_V	0.661	0.55
139_A	249_A	0.660	0.55
143_L	262_A	0.657	0.55
59_S	70_G	0.656	0.55
197_V	217_V	0.654	0.55
10_S	56_G	0.654	0.55
174_V	178_E	0.654	0.55
71_W	288_F	0.650	0.54
88_A	250_A	0.648	0.54
135_Q	264_Y	0.647	0.54
92_A	236_F	0.647	0.54
135_Q	261_L	0.644	0.54
50_K	70_G	0.644	0.54
138_G	289_W	0.643	0.53
41_P	137_I	0.636	0.53
124_A	127_F	0.632	0.52
47_D	50_K	0.629	0.52
141_Y	186_V	0.628	0.52
38_L	42_A	0.625	0.51
79_L	265_T	0.625	0.51
99_P	168_S	0.622	0.51
133_Q	136_A	0.619	0.51
148_S	175_L	0.618	0.51
292_L	296_A	0.617	0.50
252_V	288_F	0.616	0.50
176_K	240_L	0.615	0.50
69_Y	217_V	0.614	0.50
9_I	22_E	0.613	0.50
301_F	305_G	0.611	0.50
245_S	300_W	0.611	0.50
19_G	23_F	0.610	0.50
68_E	147_A	0.609	0.50
285_K	289_W	0.609	0.50
90_V	246_L	0.607	0.49
153_R	160_D	0.607	0.49
53_N	60_F	0.606	0.49
10_S	15_I	0.605	0.49
93_V	149_H	0.601	0.49
12_I	19_G	0.600	0.49
98_L	171_W	0.599	0.48
136_A	231_F	0.599	0.48
301_F	304_G	0.598	0.48
192_A	218_I	0.597	0.48
147_A	263_L	0.596	0.48
98_L	224_I	0.594	0.48
121_S	289_W	0.594	0.48
43_G	261_L	0.593	0.48
54_F	104_K	0.591	0.47
153_R	248_T	0.590	0.47
117_L	178_E	0.590	0.47
114_A	117_L	0.590	0.47
84_A	176_K	0.588	0.47
136_A	192_A	0.587	0.47
150_L	153_R	0.587	0.47
197_V	214_Q	0.586	0.47
93_V	247_E	0.585	0.47
26_S	29_F	0.583	0.47
38_L	231_F	0.583	0.47
23_F	31_L	0.582	0.46
290_G	294_A	0.582	0.46
129_V	218_I	0.577	0.46
69_Y	72_V	0.576	0.46
29_F	32_C	0.576	0.46
20_M	73_L	0.574	0.46
75_V	128_L	0.573	0.45
18_V	22_E	0.568	0.45
88_A	233_A	0.567	0.45
216_L	253_I	0.566	0.45
30_A	214_Q	0.565	0.45
29_F	111_L	0.564	0.44
174_V	177_V	0.563	0.44
287_I	291_V	0.563	0.44
16_G	19_G	0.562	0.44
219_L	223_I	0.562	0.44
133_Q	137_I	0.559	0.44
125_I	228_I	0.558	0.44
119_F	225_G	0.558	0.44
54_F	227_V	0.556	0.44
151_L	155_V	0.555	0.43
93_V	250_A	0.555	0.43
49_E	52_N	0.555	0.43
68_E	175_L	0.554	0.43
89_L	189_I	0.554	0.43
76_L	239_L	0.553	0.43
197_V	291_V	0.553	0.43
231_F	289_W	0.552	0.43
243_R	296_A	0.552	0.43
122_L	222_G	0.551	0.43
24_M	108_F	0.548	0.43
164_E	167_Q	0.548	0.43
247_E	251_F	0.544	0.42
158_K	294_A	0.544	0.42
12_I	22_E	0.543	0.42
253_I	295_I	0.543	0.42
50_K	289_W	0.540	0.42
24_M	88_A	0.540	0.42
63_A	284_W	0.538	0.42
147_A	255_G	0.534	0.41
108_F	250_A	0.534	0.41
249_A	292_L	0.534	0.41
91_M	249_A	0.533	0.41
95_V	178_E	0.533	0.41
29_F	34_Q	0.532	0.41
152_K	159_E	0.531	0.41
12_I	65_L	0.530	0.41
302_M	305_G	0.530	0.41
74_L	78_G	0.529	0.41
121_S	223_I	0.528	0.40
85_A	293_A	0.528	0.40
99_P	102_K	0.528	0.40
122_L	142_L	0.527	0.40
20_M	227_V	0.526	0.40
50_K	111_L	0.524	0.40
144_Y	159_E	0.523	0.40
306_K	310_E	0.521	0.40
93_V	143_L	0.521	0.40
132_W	265_T	0.521	0.40
111_L	173_T	0.519	0.39
111_L	245_S	0.519	0.39
170_F	174_V	0.519	0.39
197_V	264_Y	0.517	0.39
41_P	63_A	0.517	0.39
192_A	196_A	0.517	0.39
129_V	189_I	0.517	0.39
9_I	48_E	0.516	0.39
194_A	257_V	0.516	0.39
67_L	70_G	0.515	0.39
92_A	96_K	0.515	0.39
9_I	139_A	0.515	0.39
93_V	240_L	0.515	0.39
192_A	231_F	0.514	0.39
116_V	120_G	0.513	0.39
22_E	25_S	0.512	0.39
77_I	230_R	0.511	0.39
100_E	171_W	0.511	0.39
107_L	230_R	0.508	0.38
106_A	178_E	0.507	0.38
194_A	256_W	0.506	0.38
45_R	48_E	0.505	0.38
84_A	182_I	0.504	0.38
17_F	223_I	0.504	0.38
156_F	160_D	0.503	0.38
98_L	170_F	0.502	0.38
29_F	109_Y	0.502	0.38
106_A	170_F	0.501	0.37
48_E	295_I	0.500	0.37
268_H	278_F	0.500	0.37

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
4uisB	1	0.1389	37.5	0.967	Contact Map
4he8J	1	0.4537	35.2	0.967	Contact Map
2cfqA	1	0.4815	29.7	0.969	Contact Map
2gfpA	2	0.8827	27.7	0.969	Contact Map
2kncA	1	0.1512	26.6	0.969	Contact Map
4xnjA	1	0.466	25.1	0.97	Contact Map
4uvmA	1	0.4815	18.2	0.971	Contact Map
4tphA	2	0.4012	15.6	0.972	Contact Map
4w6vA	1	0.4321	13.7	0.973	Contact Map
3giaA	1	0.8395	13.6	0.973	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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