YPBB - BACSU - GREMLIN Contacts

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YPBB - Uncharacterized protein YpbB

UniProt:	P50728	Sequences: MSLNYFDIMVLDCLCKINGERSGSAVFHLFKGKRSSQTIQDAGLFQTAKYFGMAAKCSRSDISASLDKLEKHSYLAPMSESDTYKVTASGAAVLRHALSERPWPVHCHGAHYQQAAGVLWKRLSLLVQVLSHKQQGSRQYIPVTKDHKTLHWVKKYLSRHTDHIEMAKSLFAMLEAHLKKIENKAAQIFVYSLTSHHRIGYTSRQLADTLKEDEWYVYIMFWASVHYFIHSLPECEDALLKDLLSDVHLDNALTESTRKTWQMVKQGFPIQRIAEIRKLKTATIEDHIVEISLHEPAFMINDYVSAEDQLQIAEFAKRMRTNKIKQIRDGLEQRFSYFQIRLALTKQVQQYD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	352 (328)
Sequences:	394 (324)
Seq/√Len:	17.9

BACSU - YPBB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
129_V	140_Y	7.684	1.00
87_T	90_G	4.310	1.00
327_I	340_I	3.789	1.00
312_I	340_I	3.602	1.00
308_D	339_Q	3.346	1.00
121_K	146_D	3.139	0.99
268_F	272_R	3.007	0.99
312_I	327_I	3.001	0.99
304_V	343_A	2.965	0.99
340_I	343_A	2.855	0.98
324_I	337_Y	2.670	0.97
12_D	16_K	2.577	0.97
277_R	287_H	2.413	0.95
86_V	90_G	2.412	0.95
131_S	202_T	2.347	0.95
270_I	288_I	2.256	0.93
324_I	328_R	2.243	0.93
286_D	337_Y	2.185	0.92
340_I	344_L	2.182	0.92
324_I	340_I	2.156	0.92
226_H	229_I	2.107	0.91
260_T	287_H	2.036	0.89
316_A	344_L	1.987	0.88
283_T	324_I	1.962	0.87
300_I	304_V	1.948	0.87
23_G	66_L	1.932	0.86
289_V	324_I	1.921	0.86
150_L	202_T	1.921	0.86
133_K	157_L	1.913	0.86
132_H	286_D	1.882	0.85
45_F	157_L	1.879	0.85
69_L	74_Y	1.865	0.84
299_M	343_A	1.859	0.84
224_S	229_I	1.830	0.83
119_L	124_S	1.824	0.83
200_G	205_Q	1.808	0.82
131_S	142_P	1.802	0.82
125_L	283_T	1.779	0.81
128_Q	205_Q	1.774	0.81
240_L	243_L	1.735	0.79
279_L	287_H	1.713	0.79
301_N	309_Q	1.698	0.78
33_K	36_S	1.697	0.78
131_S	140_Y	1.690	0.78
37_Q	40_Q	1.680	0.77
286_D	289_V	1.674	0.77
122_R	152_W	1.669	0.77
283_T	337_Y	1.668	0.77
140_Y	292_S	1.663	0.76
127_V	193_L	1.629	0.75
108_H	111_H	1.627	0.75
128_Q	154_K	1.625	0.75
142_P	173_M	1.621	0.75
123_L	192_S	1.621	0.75
22_S	37_Q	1.607	0.74
293_L	345_T	1.591	0.73
34_R	319_M	1.590	0.73
254_T	282_A	1.582	0.73
69_L	228_F	1.579	0.73
22_S	345_T	1.577	0.72
264_V	288_I	1.558	0.72
40_Q	286_D	1.546	0.71
29_L	185_A	1.529	0.70
10_V	14_L	1.514	0.69
75_L	89_S	1.496	0.68
22_S	293_L	1.494	0.68
205_Q	286_D	1.481	0.68
280_K	290_E	1.475	0.67
256_S	277_R	1.473	0.67
178_L	189_F	1.461	0.66
328_R	340_I	1.455	0.66
299_M	302_D	1.442	0.65
163_H	288_I	1.435	0.65
332_E	335_F	1.433	0.65
324_I	345_T	1.430	0.65
260_T	273_I	1.425	0.64
39_I	44_L	1.418	0.64
150_L	347_Q	1.415	0.64
325_K	337_Y	1.411	0.64
35_S	40_Q	1.410	0.64
309_Q	312_I	1.408	0.63
267_G	273_I	1.404	0.63
140_Y	324_I	1.401	0.63
128_Q	286_D	1.395	0.63
53_M	202_T	1.383	0.62
28_H	33_K	1.364	0.61
133_K	163_H	1.361	0.61
125_L	142_P	1.344	0.60
202_T	253_L	1.326	0.59
283_T	286_D	1.320	0.58
125_L	128_Q	1.315	0.58
86_V	261_W	1.315	0.58
127_V	131_S	1.312	0.58
237_D	240_L	1.309	0.58
292_S	298_F	1.308	0.58
286_D	324_I	1.299	0.57
69_L	87_T	1.298	0.57
21_R	37_Q	1.295	0.57
109_G	273_I	1.294	0.57
220_M	263_M	1.291	0.57
206_L	217_V	1.286	0.56
17_I	25_A	1.285	0.56
238_A	241_K	1.284	0.56
156_Y	159_R	1.282	0.56
36_S	51_F	1.282	0.56
328_R	339_Q	1.280	0.56
286_D	298_F	1.276	0.56
142_P	290_E	1.259	0.55
128_Q	200_G	1.255	0.54
40_Q	327_I	1.247	0.54
256_S	260_T	1.242	0.54
150_L	157_L	1.239	0.53
122_R	338_F	1.235	0.53
260_T	277_R	1.234	0.53
34_R	290_E	1.231	0.53
31_K	210_L	1.228	0.53
21_R	38_T	1.226	0.53
35_S	338_F	1.225	0.53
109_G	192_S	1.219	0.52
192_S	303_Y	1.213	0.52
51_F	193_L	1.208	0.52
61_D	64_A	1.205	0.51
205_Q	292_S	1.190	0.50
202_T	206_L	1.189	0.50
316_A	326_Q	1.188	0.50
35_S	279_L	1.186	0.50
25_A	341_R	1.185	0.50
216_Y	284_I	1.181	0.50
241_K	249_L	1.175	0.50
195_S	200_G	1.167	0.49
142_P	205_Q	1.163	0.49
142_P	286_D	1.160	0.49
36_S	59_R	1.156	0.48
44_L	303_Y	1.154	0.48
194_T	200_G	1.154	0.48
128_Q	142_P	1.152	0.48
192_S	290_E	1.147	0.48
57_C	342_L	1.146	0.48
37_Q	337_Y	1.133	0.47
26_V	133_K	1.132	0.47
325_K	328_R	1.128	0.47
304_V	309_Q	1.126	0.47
178_L	182_E	1.125	0.46
36_S	120_W	1.125	0.46
337_Y	344_L	1.114	0.46
152_W	243_L	1.113	0.46
205_Q	287_H	1.110	0.46
186_A	189_F	1.109	0.45
303_Y	309_Q	1.109	0.45
327_I	343_A	1.107	0.45
128_Q	140_Y	1.107	0.45
244_L	247_V	1.106	0.45
133_K	140_Y	1.105	0.45
10_V	65_S	1.104	0.45
283_T	328_R	1.103	0.45
312_I	343_A	1.101	0.45
30_F	263_M	1.091	0.44
89_S	327_I	1.088	0.44
305_S	336_S	1.082	0.44
301_N	306_A	1.077	0.44
280_K	292_S	1.073	0.43
92_A	305_S	1.069	0.43
72_H	89_S	1.066	0.43
337_Y	341_R	1.056	0.42
28_H	35_S	1.052	0.42
96_H	271_Q	1.042	0.41
63_S	66_L	1.042	0.41
112_Y	226_H	1.042	0.41
35_S	321_T	1.040	0.41
57_C	195_S	1.039	0.41
248_H	273_I	1.038	0.41
195_S	205_Q	1.036	0.41
122_R	125_L	1.031	0.41
197_H	312_I	1.031	0.41
266_Q	314_E	1.026	0.40
157_L	325_K	1.026	0.40
62_I	75_L	1.026	0.40
293_L	296_P	1.023	0.40
97_A	332_E	1.023	0.40
66_L	88_A	1.020	0.40
132_H	137_S	1.017	0.40
21_R	28_H	1.016	0.40
299_M	304_V	1.016	0.40
37_Q	324_I	1.008	0.39
285_E	336_S	1.007	0.39
125_L	140_Y	0.992	0.38
109_G	254_T	0.991	0.38
28_H	36_S	0.989	0.38
110_A	202_T	0.989	0.38
289_V	337_Y	0.985	0.38
178_L	200_G	0.983	0.38
31_K	59_R	0.982	0.38
59_R	63_S	0.979	0.38
154_K	261_W	0.977	0.38
142_P	283_T	0.976	0.38
157_L	253_L	0.973	0.37
40_Q	337_Y	0.970	0.37
186_A	217_V	0.962	0.37
186_A	190_V	0.953	0.36
109_G	125_L	0.952	0.36
128_Q	283_T	0.949	0.36
22_S	35_S	0.943	0.36
51_F	300_I	0.943	0.36
305_S	308_D	0.935	0.35
27_F	143_V	0.930	0.35
140_Y	286_D	0.921	0.34
340_I	345_T	0.919	0.34
261_W	347_Q	0.915	0.34
337_Y	340_I	0.912	0.34
21_R	25_A	0.912	0.34
205_Q	290_E	0.906	0.34
286_D	290_E	0.899	0.33
37_Q	344_L	0.898	0.33
124_S	144_T	0.893	0.33
229_I	244_L	0.889	0.33
19_G	30_F	0.888	0.33
143_V	194_T	0.888	0.33
37_Q	286_D	0.887	0.33
172_A	270_I	0.887	0.33
128_Q	131_S	0.885	0.32
38_T	122_R	0.885	0.32
112_Y	194_T	0.885	0.32
254_T	329_D	0.881	0.32
28_H	338_F	0.864	0.31
162_D	228_F	0.861	0.31
68_K	73_S	0.858	0.31
59_R	129_V	0.858	0.31
242_D	334_R	0.848	0.31
11_L	181_I	0.845	0.30
20_E	40_Q	0.838	0.30
285_E	338_F	0.835	0.30
17_I	288_I	0.835	0.30
287_H	341_R	0.833	0.30
187_Q	190_V	0.831	0.30
84_Y	134_Q	0.828	0.29
337_Y	345_T	0.828	0.29
11_L	76_A	0.826	0.29
204_R	225_V	0.825	0.29
126_L	156_Y	0.824	0.29
236_E	281_T	0.824	0.29
58_S	209_T	0.821	0.29
36_S	264_V	0.817	0.29
143_V	303_Y	0.815	0.29
22_S	126_L	0.806	0.28
52_G	289_V	0.806	0.28
280_K	283_T	0.804	0.28
324_I	344_L	0.802	0.28
140_Y	345_T	0.802	0.28
328_R	337_Y	0.798	0.28
25_A	37_Q	0.797	0.28
109_G	122_R	0.794	0.28
119_L	125_L	0.789	0.28
238_A	245_S	0.783	0.27
84_Y	223_A	0.781	0.27
128_Q	132_H	0.781	0.27
206_L	308_D	0.780	0.27
164_I	317_K	0.773	0.27
131_S	195_S	0.771	0.27
171_F	340_I	0.771	0.27
69_L	300_I	0.768	0.27
183_N	267_G	0.765	0.26
132_H	337_Y	0.763	0.26
279_L	284_I	0.761	0.26
28_H	39_I	0.760	0.26
338_F	341_R	0.760	0.26
157_L	202_T	0.752	0.26
110_A	124_S	0.752	0.26
153_V	336_S	0.746	0.25
69_L	206_L	0.744	0.25
156_Y	312_I	0.743	0.25
130_L	270_I	0.743	0.25
142_P	154_K	0.739	0.25
120_W	133_K	0.737	0.25
256_S	265_K	0.736	0.25
39_I	283_T	0.736	0.25
191_Y	206_L	0.734	0.25
224_S	252_A	0.731	0.25
140_Y	205_Q	0.731	0.25
192_S	200_G	0.729	0.25
34_R	37_Q	0.729	0.25
242_D	248_H	0.721	0.24
256_S	287_H	0.719	0.24
100_E	170_L	0.718	0.24
70_E	79_S	0.718	0.24
80_E	93_V	0.711	0.24
171_F	311_Q	0.710	0.24
23_G	175_E	0.709	0.24
54_A	65_S	0.709	0.24
194_T	199_I	0.707	0.24
33_K	298_F	0.706	0.24
85_K	269_P	0.706	0.24
25_A	47_T	0.706	0.24
264_V	304_V	0.700	0.23
37_Q	340_I	0.700	0.23
120_W	157_L	0.698	0.23
243_L	336_S	0.697	0.23
170_L	261_W	0.697	0.23
134_Q	273_I	0.696	0.23
17_I	256_S	0.692	0.23
21_R	338_F	0.691	0.23
292_S	323_K	0.691	0.23
193_L	277_R	0.689	0.23
17_I	319_M	0.688	0.23
38_T	254_T	0.687	0.23
21_R	125_L	0.686	0.23
133_K	151_H	0.683	0.23
119_L	324_I	0.680	0.23
113_Q	186_A	0.679	0.22
55_A	150_L	0.676	0.22
81_S	266_Q	0.675	0.22
27_F	50_Y	0.675	0.22
27_F	31_K	0.673	0.22
153_V	156_Y	0.672	0.22
51_F	282_A	0.672	0.22
32_G	51_F	0.670	0.22
218_Y	244_L	0.667	0.22
129_V	157_L	0.667	0.22
14_L	31_K	0.666	0.22
39_I	254_T	0.666	0.22
189_F	198_R	0.666	0.22
40_Q	285_E	0.666	0.22
20_E	321_T	0.665	0.22
148_K	252_A	0.665	0.22
205_Q	280_K	0.664	0.22
170_L	228_F	0.661	0.22
257_T	289_V	0.660	0.22
205_Q	256_S	0.656	0.22
27_F	33_K	0.655	0.21
40_Q	289_V	0.654	0.21
223_A	283_T	0.653	0.21
237_D	241_K	0.652	0.21
18_N	289_V	0.650	0.21
24_S	36_S	0.650	0.21
316_A	328_R	0.648	0.21
124_S	254_T	0.648	0.21
270_I	282_A	0.647	0.21
143_V	307_E	0.646	0.21
10_V	68_K	0.645	0.21
203_S	217_V	0.642	0.21
86_V	328_R	0.642	0.21
331_L	335_F	0.641	0.21
215_W	224_S	0.640	0.21
254_T	286_D	0.640	0.21
274_A	281_T	0.639	0.21
33_K	343_A	0.638	0.21
338_F	342_L	0.637	0.21
318_R	334_R	0.637	0.21
308_D	335_F	0.637	0.21
177_H	304_V	0.635	0.21
321_T	343_A	0.634	0.21
52_G	216_Y	0.634	0.21
135_Q	244_L	0.633	0.21
272_R	275_E	0.633	0.21
18_N	124_S	0.630	0.20
143_V	252_A	0.629	0.20
125_L	257_T	0.626	0.20
202_T	207_A	0.626	0.20
312_I	344_L	0.625	0.20
75_L	127_V	0.623	0.20
64_A	297_A	0.622	0.20
269_P	284_I	0.619	0.20
206_L	273_I	0.619	0.20
292_S	342_L	0.616	0.20
155_K	158_S	0.614	0.20
261_W	265_K	0.613	0.20
154_K	341_R	0.613	0.20
55_A	86_V	0.611	0.20
73_S	204_R	0.610	0.20
21_R	257_T	0.610	0.20
321_T	344_L	0.608	0.20
244_L	248_H	0.608	0.20
45_F	133_K	0.607	0.20
220_M	233_P	0.605	0.19
51_F	107_C	0.604	0.19
194_T	286_D	0.602	0.19
129_V	244_L	0.601	0.19
154_K	205_Q	0.599	0.19
20_E	45_F	0.598	0.19
22_S	25_A	0.597	0.19
260_T	279_L	0.597	0.19
144_T	255_E	0.596	0.19
256_S	284_I	0.595	0.19
52_G	182_E	0.595	0.19
75_L	296_P	0.595	0.19
132_H	157_L	0.594	0.19
241_K	244_L	0.594	0.19
213_D	305_S	0.593	0.19
31_K	58_S	0.593	0.19
125_L	143_V	0.591	0.19
44_L	243_L	0.591	0.19
69_L	84_Y	0.590	0.19
178_L	295_E	0.589	0.19
289_V	343_A	0.589	0.19
125_L	289_V	0.588	0.19
144_T	150_L	0.588	0.19
112_Y	320_R	0.588	0.19
125_L	254_T	0.586	0.19
173_M	286_D	0.586	0.19
280_K	286_D	0.586	0.19
25_A	144_T	0.585	0.19
320_R	330_G	0.583	0.19
205_Q	260_T	0.582	0.19
58_S	180_K	0.580	0.19
39_I	286_D	0.579	0.18
116_A	119_L	0.578	0.18
183_N	275_E	0.577	0.18
312_I	324_I	0.576	0.18
289_V	341_R	0.575	0.18
194_T	341_R	0.575	0.18
37_Q	289_V	0.575	0.18
286_D	340_I	0.575	0.18
38_T	338_F	0.575	0.18
210_L	327_I	0.573	0.18
180_K	329_D	0.572	0.18
33_K	37_Q	0.572	0.18
24_S	37_Q	0.572	0.18
123_L	240_L	0.572	0.18
178_L	188_I	0.571	0.18
86_V	234_E	0.570	0.18
76_A	137_S	0.569	0.18
31_K	39_I	0.568	0.18
82_D	215_W	0.566	0.18
128_Q	240_L	0.566	0.18
135_Q	346_K	0.565	0.18
108_H	128_Q	0.564	0.18
11_L	94_L	0.563	0.18
33_K	178_L	0.563	0.18
243_L	247_V	0.563	0.18
181_I	198_R	0.563	0.18
20_E	38_T	0.563	0.18
128_Q	143_V	0.562	0.18
132_H	284_I	0.561	0.18
122_R	246_D	0.561	0.18
186_A	288_I	0.560	0.18
110_A	294_H	0.558	0.18
110_A	113_Q	0.558	0.18
165_E	211_K	0.557	0.18
96_H	165_E	0.556	0.18
93_V	96_H	0.552	0.18
230_H	329_D	0.552	0.18
54_A	77_P	0.552	0.18
33_K	199_I	0.551	0.17
256_S	342_L	0.551	0.17
29_L	124_S	0.551	0.17
123_L	128_Q	0.550	0.17
29_L	51_F	0.548	0.17
15_C	79_S	0.548	0.17
277_R	283_T	0.546	0.17
154_K	188_I	0.546	0.17
213_D	253_L	0.545	0.17
58_S	210_L	0.543	0.17
66_L	255_E	0.540	0.17
140_Y	323_K	0.538	0.17
146_D	154_K	0.538	0.17
254_T	283_T	0.536	0.17
86_V	255_E	0.536	0.17
39_I	45_F	0.536	0.17
66_L	235_C	0.535	0.17
28_H	291_I	0.535	0.17
37_Q	125_L	0.534	0.17
128_Q	341_R	0.534	0.17
140_Y	256_S	0.530	0.17
24_S	28_H	0.530	0.17
191_Y	210_L	0.528	0.17
10_V	27_F	0.527	0.17
38_T	345_T	0.527	0.17
39_I	128_Q	0.523	0.17
327_I	335_F	0.523	0.17
174_L	265_K	0.520	0.16
148_K	161_T	0.517	0.16
51_F	338_F	0.516	0.16
69_L	72_H	0.516	0.16
312_I	345_T	0.515	0.16
35_S	38_T	0.515	0.16
83_T	219_I	0.512	0.16
87_T	179_K	0.512	0.16
140_Y	293_L	0.512	0.16
254_T	324_I	0.511	0.16
128_Q	287_H	0.510	0.16
37_Q	200_G	0.510	0.16
186_A	298_F	0.510	0.16
193_L	279_L	0.508	0.16
16_K	166_M	0.506	0.16
77_P	183_N	0.504	0.16
190_V	307_E	0.502	0.16
122_R	292_S	0.502	0.16
37_Q	44_L	0.502	0.16
90_G	323_K	0.501	0.16
22_S	48_A	0.501	0.16
45_F	208_D	0.501	0.16
224_S	227_Y	0.501	0.16
38_T	146_D	0.500	0.16

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
3iuoA	4	0.304	99.9	0.761	Contact Map
3aafA	1	0.2955	99.7	0.817	Contact Map
4o3mA	1	0.5028	99.7	0.819	Contact Map
4q48A	1	0.2898	99.4	0.849	Contact Map
1oywA	1	0.3011	99.4	0.852	Contact Map
2v1xA	1	0.2727	98	0.909	Contact Map
3safA	1	0.5483	96.1	0.931	Contact Map
1wudA	3	0.2017	95.1	0.936	Contact Map
2rhfA	1	0.1989	93.9	0.94	Contact Map
4wszA	2	0.1875	93.6	0.94	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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