YDEO - BACSU - GREMLIN Contacts

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YDEO - UPF0750 membrane protein YdeO

UniProt:	P96672	Sequences: MNTPKKHKKFKAKMILQIIMVIIGGIIAAYGLETVLIPNSVSDGGVTGLSIVGSQLFNLPLGILIAVINIPFVWLGYKQIGKSFALLSIIGIVSLAAGTSFFHHTPAIIEGDTLLITVVGGIILGFGMGLALRNGGALDGIDMLAVLLSRKLPFGTSDLILFLNLFVFIFVSTVFGLQGALLSVIAYYIASKVIHVVEEGLSGSKTFQIITTQPELMVETIRDQLGRSATYKEAYGGFSHEKFKEITCVINRLEETKLKEIINDIDKTAFVTVYDVAEVKGSNFRNLNHH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	290 (272)
Sequences:	3740 (2704)
Seq/√Len:	164.0

BACSU - YDEO YQFU YVJA YPJC YXKD YITT YITE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_I	90_I	5.828	1.00
213_Q	216_L	4.985	1.00
233_E	242_K	3.973	1.00
234_A	245_E	3.882	1.00
219_E	223_D	3.474	1.00
212_T	243_F	3.428	1.00
211_T	217_M	3.207	1.00
26_I	98_G	2.899	1.00
207_F	258_L	2.753	1.00
119_V	181_L	2.742	1.00
46_V	68_I	2.592	1.00
235_Y	240_H	2.563	1.00
220_T	261_I	2.389	1.00
232_K	245_E	2.347	1.00
235_Y	244_K	2.344	1.00
211_T	214_P	2.329	1.00
215_E	219_E	2.292	1.00
220_T	224_Q	2.248	1.00
205_K	275_D	2.212	1.00
233_E	244_K	2.121	1.00
229_A	237_G	2.113	1.00
53_G	57_F	2.101	1.00
18_I	90_I	2.074	1.00
33_E	102_F	2.028	1.00
17_Q	87_L	1.989	1.00
24_G	127_G	1.957	1.00
93_V	97_A	1.928	1.00
22_I	94_S	1.891	1.00
227_R	254_E	1.886	1.00
31_G	124_L	1.884	1.00
29_A	98_G	1.870	1.00
30_Y	34_T	1.866	1.00
28_A	95_L	1.865	1.00
172_S	180_A	1.859	1.00
192_K	196_V	1.823	1.00
20_M	134_N	1.808	1.00
172_S	177_L	1.770	1.00
62_G	100_S	1.765	1.00
131_A	138_L	1.747	1.00
112_D	182_L	1.725	1.00
262_I	269_A	1.725	1.00
218_V	237_G	1.713	1.00
157_S	195_H	1.703	1.00
221_I	258_L	1.681	1.00
53_G	64_L	1.678	1.00
212_T	241_E	1.659	1.00
231_Y	246_I	1.646	1.00
39_N	116_I	1.630	1.00
229_A	246_I	1.605	1.00
214_P	244_K	1.603	1.00
262_I	271_V	1.577	1.00
17_Q	134_N	1.575	1.00
235_Y	242_K	1.537	1.00
74_W	78_K	1.526	1.00
225_L	258_L	1.501	1.00
218_V	240_H	1.488	1.00
212_T	268_T	1.485	1.00
114_L	185_I	1.472	1.00
176_G	179_G	1.470	1.00
129_G	197_V	1.453	1.00
206_T	274_Y	1.441	1.00
220_T	265_I	1.437	1.00
247_T	272_T	1.422	1.00
84_F	137_A	1.414	1.00
24_G	131_A	1.402	1.00
26_I	102_F	1.391	1.00
215_E	240_H	1.391	1.00
30_Y	102_F	1.381	1.00
208_Q	247_T	1.367	1.00
21_V	91_G	1.365	1.00
166_F	170_F	1.361	1.00
218_V	231_Y	1.356	1.00
162_F	166_F	1.343	1.00
33_E	103_H	1.343	1.00
46_V	72_F	1.318	1.00
234_A	243_F	1.292	1.00
49_L	53_G	1.285	1.00
268_T	282_S	1.285	1.00
62_G	96_A	1.282	1.00
70_I	74_W	1.281	1.00
80_I	84_F	1.279	1.00
65_I	99_T	1.278	1.00
168_F	187_Y	1.274	1.00
221_I	248_C	1.273	1.00
216_L	265_I	1.272	1.00
36_L	120_G	1.260	1.00
125_G	129_G	1.257	1.00
250_I	258_L	1.253	1.00
161_L	191_S	1.236	1.00
206_T	272_T	1.220	1.00
86_L	90_I	1.198	1.00
31_G	127_G	1.182	1.00
60_P	100_S	1.177	1.00
77_Y	82_K	1.170	1.00
76_G	85_A	1.169	1.00
21_V	136_G	1.168	1.00
40_S	179_G	1.167	1.00
18_I	87_L	1.153	1.00
145_A	160_I	1.150	1.00
73_V	92_I	1.149	1.00
188_Y	192_K	1.147	1.00
206_T	276_V	1.146	1.00
259_K	278_E	1.145	1.00
255_E	273_V	1.141	1.00
25_G	94_S	1.140	1.00
66_A	96_A	1.133	1.00
208_Q	274_Y	1.131	1.00
148_L	152_L	1.129	1.00
220_T	264_D	1.120	1.00
266_D	269_A	1.119	1.00
31_G	123_I	1.111	1.00
222_R	237_G	1.109	1.00
37_I	61_L	1.108	1.00
231_Y	244_K	1.103	1.00
115_L	119_V	1.098	1.00
15_I	19_I	1.096	1.00
122_I	193_V	1.095	1.00
207_F	255_E	1.086	1.00
165_L	169_I	1.085	1.00
209_I	262_I	1.084	1.00
59_L	64_L	1.077	0.99
62_G	66_A	1.076	0.99
230_T	234_A	1.069	0.99
77_Y	85_A	1.064	0.99
19_I	23_I	1.060	0.99
117_T	121_G	1.051	0.99
236_G	239_S	1.049	0.99
94_S	98_G	1.047	0.99
113_T	179_G	1.038	0.99
90_I	94_S	1.036	0.99
16_L	20_M	1.035	0.99
261_I	264_D	1.023	0.99
49_L	170_F	1.022	0.99
218_V	229_A	1.021	0.99
231_Y	237_G	1.020	0.99
42_S	171_V	1.013	0.99
18_I	22_I	1.011	0.99
80_I	146_V	1.007	0.99
91_G	136_G	1.001	0.99
221_I	227_R	0.999	0.99
51_I	54_S	0.992	0.99
112_D	178_Q	0.988	0.99
35_V	119_V	0.988	0.99
79_Q	151_K	0.985	0.99
258_L	262_I	0.972	0.99
63_I	100_S	0.963	0.99
20_M	130_L	0.962	0.99
208_Q	232_K	0.952	0.99
42_S	164_N	0.952	0.99
25_G	91_G	0.936	0.99
217_M	261_I	0.935	0.99
47_T	99_T	0.933	0.99
14_M	17_Q	0.932	0.99
122_I	188_Y	0.929	0.98
206_T	249_V	0.926	0.98
64_L	68_I	0.926	0.98
157_S	194_I	0.918	0.98
206_T	247_T	0.915	0.98
272_T	276_V	0.911	0.98
195_H	252_R	0.907	0.98
205_K	278_E	0.907	0.98
117_T	185_I	0.906	0.98
157_S	191_S	0.898	0.98
208_Q	272_T	0.894	0.98
222_R	229_A	0.889	0.98
113_T	117_T	0.886	0.98
256_T	260_E	0.884	0.98
71_P	74_W	0.883	0.98
36_L	186_A	0.871	0.98
40_S	55_Q	0.870	0.98
121_G	125_G	0.864	0.98
79_Q	147_L	0.859	0.97
160_I	164_N	0.854	0.97
75_L	79_Q	0.850	0.97
222_R	228_S	0.850	0.97
211_T	266_D	0.847	0.97
128_M	132_L	0.846	0.97
80_I	137_A	0.844	0.97
128_M	194_I	0.841	0.97
83_S	87_L	0.839	0.97
204_S	248_C	0.835	0.97
100_S	103_H	0.833	0.97
126_F	197_V	0.827	0.97
207_F	262_I	0.824	0.97
52_V	56_L	0.823	0.97
42_S	183_S	0.821	0.97
232_K	247_T	0.818	0.97
25_G	131_A	0.818	0.97
41_V	117_T	0.814	0.97
137_A	146_V	0.814	0.97
207_F	250_I	0.812	0.96
190_A	194_I	0.810	0.96
52_V	175_F	0.808	0.96
231_Y	235_Y	0.805	0.96
251_N	254_E	0.805	0.96
115_L	181_L	0.803	0.96
132_L	146_V	0.798	0.96
261_I	265_I	0.797	0.96
154_F	159_L	0.794	0.96
63_I	67_V	0.790	0.96
249_V	272_T	0.787	0.96
28_A	127_G	0.786	0.96
49_L	52_V	0.786	0.96
27_I	126_F	0.783	0.96
31_G	35_V	0.780	0.96
26_I	94_S	0.780	0.96
67_V	71_P	0.778	0.96
220_T	223_D	0.778	0.96
147_L	151_K	0.770	0.95
113_T	116_I	0.769	0.95
73_V	88_S	0.768	0.95
155_G	195_H	0.766	0.95
72_F	144_L	0.766	0.95
66_A	93_V	0.765	0.95
219_E	240_H	0.764	0.95
129_G	133_R	0.762	0.95
138_L	142_D	0.753	0.95
218_V	222_R	0.751	0.95
54_S	61_L	0.745	0.94
14_M	87_L	0.743	0.94
214_P	217_M	0.741	0.94
148_L	159_L	0.740	0.94
192_K	195_H	0.740	0.94
16_L	134_N	0.738	0.94
260_E	264_D	0.737	0.94
118_V	189_I	0.737	0.94
162_F	165_L	0.736	0.94
259_K	280_K	0.735	0.94
161_L	188_Y	0.735	0.94
52_V	170_F	0.729	0.94
32_L	95_L	0.728	0.94
73_V	89_I	0.726	0.94
66_A	70_I	0.724	0.93
187_Y	191_S	0.724	0.93
71_P	75_L	0.722	0.93
213_Q	265_I	0.717	0.93
86_L	89_I	0.716	0.93
227_R	251_N	0.712	0.93
144_L	148_L	0.712	0.93
72_F	88_S	0.712	0.93
73_V	76_G	0.709	0.93
57_F	64_L	0.708	0.93
76_G	84_F	0.708	0.93
25_G	95_L	0.705	0.93
224_Q	261_I	0.702	0.92
116_I	178_Q	0.702	0.92
49_L	68_I	0.700	0.92
98_G	101_F	0.700	0.92
230_T	236_G	0.699	0.92
155_G	158_D	0.698	0.92
141_I	163_L	0.698	0.92
229_A	248_C	0.698	0.92
166_F	169_I	0.695	0.92
202_S	285_R	0.690	0.92
205_K	273_V	0.690	0.92
141_I	175_F	0.689	0.92
207_F	273_V	0.689	0.92
141_I	164_N	0.689	0.92
117_T	189_I	0.687	0.92
213_Q	266_D	0.680	0.91
131_A	136_G	0.679	0.91
102_F	105_T	0.677	0.91
228_S	238_F	0.675	0.91
146_V	156_T	0.674	0.91
92_I	96_A	0.673	0.91
84_F	146_V	0.673	0.91
34_T	102_F	0.672	0.91
217_M	265_I	0.671	0.91
28_A	124_L	0.671	0.91
224_Q	257_K	0.671	0.91
53_G	68_I	0.670	0.91
48_G	182_L	0.670	0.91
227_R	284_F	0.669	0.90
111_G	178_Q	0.668	0.90
50_S	65_I	0.667	0.90
20_M	23_I	0.667	0.90
236_G	243_F	0.666	0.90
139_D	142_D	0.664	0.90
15_I	18_I	0.662	0.90
87_L	135_G	0.662	0.90
128_M	138_L	0.662	0.90
110_E	178_Q	0.660	0.90
124_L	190_A	0.660	0.90
227_R	283_N	0.659	0.90
32_L	50_S	0.657	0.90
118_V	185_I	0.657	0.90
143_M	157_S	0.657	0.90
130_L	134_N	0.655	0.90
170_F	173_T	0.653	0.89
158_D	195_H	0.651	0.89
32_L	37_I	0.650	0.89
146_V	150_R	0.649	0.89
209_I	248_C	0.648	0.89
27_I	123_I	0.645	0.89
23_I	27_I	0.643	0.89
168_F	171_V	0.643	0.89
132_L	142_D	0.643	0.89
112_D	117_T	0.640	0.88
210_I	247_T	0.640	0.88
74_W	77_Y	0.638	0.88
201_L	204_S	0.636	0.88
171_V	180_A	0.634	0.88
78_K	96_A	0.633	0.88
215_E	244_K	0.630	0.88
47_T	95_L	0.629	0.88
119_V	184_V	0.626	0.87
37_I	54_S	0.624	0.87
164_N	183_S	0.624	0.87
160_I	194_I	0.623	0.87
263_N	280_K	0.623	0.87
199_E	277_A	0.622	0.87
43_D	142_D	0.621	0.87
29_A	95_L	0.620	0.87
37_I	51_I	0.619	0.87
97_A	101_F	0.619	0.87
273_V	278_E	0.615	0.86
128_M	190_A	0.613	0.86
88_S	143_M	0.609	0.86
64_L	67_V	0.609	0.86
164_N	283_N	0.609	0.86
75_L	147_L	0.609	0.86
249_V	276_V	0.604	0.85
60_P	63_I	0.602	0.85
257_K	260_E	0.599	0.85
42_S	51_I	0.599	0.85
270_F	279_V	0.598	0.85
41_V	110_E	0.597	0.85
121_G	189_I	0.594	0.84
224_Q	264_D	0.593	0.84
54_S	58_N	0.588	0.84
208_Q	245_E	0.587	0.84
209_I	258_L	0.587	0.84
87_L	183_S	0.585	0.84
34_T	38_P	0.580	0.83
125_G	194_I	0.579	0.83
250_I	255_E	0.579	0.83
230_T	270_F	0.577	0.83
158_D	161_L	0.576	0.83
115_L	188_Y	0.576	0.83
183_S	250_I	0.575	0.83
117_T	186_A	0.572	0.82
50_S	68_I	0.572	0.82
214_P	218_V	0.572	0.82
81_G	204_S	0.571	0.82
260_E	263_N	0.570	0.82
259_K	263_N	0.570	0.82
113_T	182_L	0.565	0.81
16_L	133_R	0.564	0.81
143_M	194_I	0.557	0.81
180_A	186_A	0.557	0.81
75_L	78_K	0.556	0.80
53_G	59_L	0.555	0.80
54_S	64_L	0.555	0.80
28_A	128_M	0.555	0.80
88_S	92_I	0.555	0.80
50_S	247_T	0.554	0.80
208_Q	276_V	0.554	0.80
59_L	67_V	0.551	0.80
169_I	173_T	0.549	0.80
91_G	138_L	0.549	0.80
60_P	104_H	0.548	0.79
132_L	156_T	0.546	0.79
132_L	198_E	0.545	0.79
32_L	47_T	0.542	0.79
56_L	71_P	0.540	0.78
227_R	236_G	0.539	0.78
175_F	179_G	0.539	0.78
82_K	85_A	0.533	0.78
126_F	193_V	0.533	0.78
26_I	105_T	0.532	0.77
146_V	164_N	0.530	0.77
163_L	167_V	0.529	0.77
113_T	178_Q	0.528	0.77
231_Y	240_H	0.525	0.77
73_V	144_L	0.525	0.77
89_I	92_I	0.524	0.76
110_E	183_S	0.523	0.76
121_G	190_A	0.521	0.76
109_I	113_T	0.520	0.76
156_T	195_H	0.520	0.76
51_I	55_Q	0.520	0.76
39_N	181_L	0.519	0.76
211_T	244_K	0.518	0.76
110_E	116_I	0.518	0.76
46_V	50_S	0.517	0.75
162_F	170_F	0.517	0.75
136_G	149_S	0.517	0.75
38_P	133_R	0.516	0.75
71_P	192_K	0.515	0.75
41_V	44_G	0.514	0.75
218_V	244_K	0.514	0.75
102_F	135_G	0.513	0.75
203_G	277_A	0.513	0.75
17_Q	83_S	0.513	0.75
62_G	65_I	0.512	0.75
51_I	61_L	0.512	0.75
51_I	115_L	0.510	0.74
114_L	124_L	0.509	0.74
216_L	219_E	0.509	0.74
61_L	65_I	0.509	0.74
212_T	217_M	0.507	0.74
16_L	264_D	0.505	0.74
22_I	98_G	0.505	0.74
239_S	268_T	0.505	0.74
197_V	248_C	0.502	0.73
26_I	30_Y	0.501	0.73
41_V	113_T	0.501	0.73
118_V	243_F	0.500	0.73

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
3hluA	2	0.2517	99.9	0.7	Contact Map
3ncqA	4	0.3069	87.9	0.938	Contact Map
2dclA	5	0.3069	82.4	0.942	Contact Map
4rwwA	3	0.2897	82.2	0.943	Contact Map
3t9zA	3	0.2862	81	0.943	Contact Map
2eg2A	5	0.2931	78.4	0.945	Contact Map
4affA	3	0.3069	78.3	0.945	Contact Map
4co3A	3	0.2966	77.3	0.945	Contact Map
4r25A	3	0.3138	75.7	0.946	Contact Map
2gw8A	3	0.3034	75.5	0.946	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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