YBBN - ECOLI - GREMLIN Contacts

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YBBN - Uncharacterized protein YbbN

UniProt:	P77395	Sequences: MSVENIVNINESNLQQVLEQSMTTPVLFYFWSERSQHCLQLTPILESLAAQYNGQFILAKLDCDAEQMIAAQFGLRAIPTVYLFQNGQPVDGFQGPQPEEAIRALLDKVLPREEELKAQQAMQLMQESNYTDALPLLKDAWQLSNQNGEIGLLLAETLIALNRSEDAEAVLKTIPLQDQDTRYQGLVAQIELLKQAADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLRKDLTAADGQTRKTFQEILAALGTGDALASKYRRQLYALLY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13261
Length:	284 (276)
Sequences:	1132 (836)
Seq/√Len:	50.3

ECOLI - YBBN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_D	65_A	7.369	1.00
129_N	132_D	5.568	1.00
231_R	234_E	5.234	1.00
212_N	215_D	3.809	1.00
163_R	166_D	3.306	1.00
168_E	172_K	3.243	1.00
217_A	221_Q	3.226	1.00
9_I	59_A	3.100	1.00
51_Q	103_R	2.904	1.00
33_E	62_D	2.671	1.00
187_V	190_I	2.647	1.00
188_A	191_E	2.388	1.00
241_G	245_K	2.386	1.00
101_A	104_A	2.324	1.00
187_V	191_E	2.309	1.00
206_Q	210_A	2.260	1.00
35_S	38_C	2.157	1.00
17_V	20_Q	2.148	1.00
195_Q	200_P	2.137	1.00
29_Y	35_S	2.122	1.00
34_R	37_H	2.091	1.00
208_Q	215_D	2.077	1.00
47_S	99_E	2.070	1.00
185_G	188_A	1.952	0.99
29_Y	34_R	1.939	0.99
130_Y	157_T	1.934	0.99
81_V	93_F	1.901	0.99
16_Q	20_Q	1.865	0.99
32_S	35_S	1.855	0.99
274_K	278_Q	1.806	0.99
181_T	184_Q	1.793	0.99
223_A	239_L	1.778	0.99
44_I	102_I	1.771	0.99
120_Q	124_L	1.744	0.99
248_T	252_G	1.735	0.99
47_S	51_Q	1.734	0.99
250_A	253_Q	1.719	0.99
119_Q	123_Q	1.686	0.98
32_S	37_H	1.681	0.98
137_L	153_L	1.643	0.98
196_A	199_T	1.641	0.98
16_Q	19_E	1.607	0.98
33_E	65_A	1.598	0.98
179_Q	188_A	1.596	0.98
29_Y	37_H	1.596	0.98
195_Q	199_T	1.566	0.97
104_A	107_D	1.552	0.97
63_C	78_I	1.550	0.97
37_H	43_P	1.549	0.97
29_Y	60_K	1.527	0.97
99_E	103_R	1.502	0.97
24_T	57_I	1.494	0.97
11_E	68_M	1.494	0.97
144_S	147_N	1.493	0.97
184_Q	188_A	1.492	0.97
123_Q	127_E	1.485	0.96
198_D	201_E	1.465	0.96
83_L	109_V	1.460	0.96
35_S	43_P	1.453	0.96
82_Y	92_G	1.446	0.96
219_A	238_L	1.442	0.96
216_A	242_H	1.439	0.96
186_L	190_I	1.438	0.96
181_T	185_G	1.437	0.96
252_G	255_R	1.434	0.96
9_I	61_L	1.429	0.96
38_C	43_P	1.407	0.95
67_Q	71_A	1.406	0.95
74_G	82_Y	1.395	0.95
220_T	242_H	1.377	0.95
209_V	216_A	1.366	0.94
32_S	43_P	1.364	0.94
233_E	274_K	1.359	0.94
214_E	245_K	1.357	0.94
197_A	201_E	1.351	0.94
34_R	43_P	1.351	0.94
204_Q	208_Q	1.331	0.93
182_R	190_I	1.331	0.93
35_S	39_L	1.329	0.93
195_Q	198_D	1.294	0.92
34_R	39_L	1.292	0.92
33_E	78_I	1.281	0.92
181_T	190_I	1.263	0.92
241_G	244_R	1.251	0.91
29_Y	32_S	1.233	0.91
134_L	154_L	1.233	0.91
196_A	200_P	1.232	0.90
22_M	86_N	1.231	0.90
97_Q	101_A	1.224	0.90
44_I	99_E	1.224	0.90
29_Y	38_C	1.218	0.90
185_G	190_I	1.210	0.90
184_Q	190_I	1.203	0.89
25_P	54_G	1.198	0.89
125_M	157_T	1.187	0.89
49_A	56_F	1.185	0.89
243_L	252_G	1.182	0.89
32_S	64_D	1.173	0.88
121_A	137_L	1.173	0.88
187_V	192_L	1.150	0.87
68_M	71_A	1.147	0.87
258_F	262_L	1.147	0.87
194_K	198_D	1.147	0.87
46_E	60_K	1.144	0.87
34_R	38_C	1.133	0.86
179_Q	191_E	1.129	0.86
185_G	191_E	1.125	0.86
227_H	261_I	1.119	0.86
205_L	222_L	1.117	0.86
193_L	197_A	1.112	0.85
215_D	218_L	1.108	0.85
75_L	82_Y	1.102	0.85
125_M	130_Y	1.097	0.85
15_Q	19_E	1.091	0.84
216_A	219_A	1.089	0.84
29_Y	39_L	1.082	0.84
186_L	192_L	1.072	0.83
96_P	102_I	1.069	0.83
188_A	192_L	1.068	0.83
236_L	275_Y	1.058	0.82
183_Y	190_I	1.057	0.82
11_E	69_I	1.056	0.82
158_L	166_D	1.047	0.82
268_G	272_A	1.046	0.82
53_N	102_I	1.043	0.81
182_R	187_V	1.039	0.81
236_L	271_L	1.039	0.81
193_L	200_P	1.038	0.81
232_N	265_L	1.032	0.81
48_L	103_R	1.022	0.80
205_L	209_V	1.007	0.79
120_Q	123_Q	1.007	0.79
52_Y	107_D	1.006	0.79
125_M	160_A	1.004	0.79
182_R	188_A	1.002	0.79
24_T	54_G	1.002	0.79
182_R	189_Q	1.000	0.79
226_L	238_L	0.999	0.78
181_T	189_Q	0.995	0.78
29_Y	43_P	0.994	0.78
181_T	188_A	0.991	0.78
179_Q	182_R	0.986	0.78
124_L	136_L	0.981	0.77
124_L	132_D	0.969	0.76
196_A	201_E	0.961	0.76
195_Q	201_E	0.956	0.75
181_T	186_L	0.955	0.75
183_Y	188_A	0.951	0.75
231_R	248_T	0.947	0.75
118_A	153_L	0.943	0.74
63_C	80_T	0.937	0.74
91_D	108_K	0.936	0.74
193_L	196_A	0.933	0.74
265_L	269_D	0.930	0.73
40_Q	44_I	0.929	0.73
252_G	256_K	0.927	0.73
8_N	60_K	0.927	0.73
181_T	191_E	0.924	0.73
197_A	200_P	0.923	0.73
243_L	282_L	0.923	0.73
82_Y	89_P	0.916	0.72
182_R	191_E	0.914	0.72
213_P	222_L	0.913	0.72
83_L	105_L	0.912	0.72
219_A	241_G	0.912	0.72
36_Q	43_P	0.911	0.72
166_D	169_A	0.909	0.72
194_K	199_T	0.908	0.72
182_R	186_L	0.904	0.71
193_L	198_D	0.904	0.71
31_W	62_D	0.901	0.71
48_L	56_F	0.897	0.71
188_A	196_A	0.894	0.70
166_D	170_V	0.889	0.70
184_Q	187_V	0.889	0.70
35_S	60_K	0.889	0.70
180_D	190_I	0.886	0.70
227_H	232_N	0.884	0.69
174_I	177_Q	0.884	0.69
9_I	13_N	0.884	0.69
75_L	109_V	0.881	0.69
48_L	106_L	0.874	0.69
184_Q	192_L	0.873	0.68
41_L	81_V	0.872	0.68
134_L	161_L	0.870	0.68
203_Q	206_Q	0.865	0.68
97_Q	105_L	0.861	0.67
181_T	192_L	0.861	0.67
32_S	39_L	0.860	0.67
207_Q	210_A	0.859	0.67
112_R	115_E	0.859	0.67
194_K	197_A	0.857	0.67
27_L	83_L	0.854	0.67
183_Y	191_E	0.854	0.67
141_W	150_I	0.854	0.67
188_A	193_L	0.849	0.66
63_C	75_L	0.842	0.66
232_N	261_I	0.841	0.66
206_Q	226_L	0.838	0.65
261_I	265_L	0.837	0.65
20_Q	23_T	0.836	0.65
268_G	271_L	0.836	0.65
32_S	46_E	0.835	0.65
189_Q	192_L	0.834	0.65
20_Q	24_T	0.831	0.65
135_P	139_D	0.830	0.65
233_E	237_E	0.829	0.64
206_Q	238_L	0.827	0.64
217_A	250_A	0.824	0.64
138_K	158_L	0.822	0.64
183_Y	187_V	0.813	0.63
236_L	265_L	0.812	0.63
41_L	93_F	0.808	0.62
145_N	170_V	0.805	0.62
77_A	92_G	0.799	0.62
27_L	74_G	0.793	0.61
9_I	16_Q	0.789	0.61
34_R	64_D	0.786	0.60
117_K	139_D	0.781	0.60
148_G	151_G	0.776	0.59
48_L	51_Q	0.775	0.59
273_S	281_A	0.771	0.59
266_G	272_A	0.766	0.58
122_M	137_L	0.765	0.58
198_D	202_I	0.764	0.58
269_D	273_S	0.760	0.58
249_A	254_T	0.758	0.58
185_G	189_Q	0.758	0.58
62_D	75_L	0.756	0.57
114_E	140_A	0.747	0.56
37_H	60_K	0.742	0.56
116_L	119_Q	0.741	0.56
91_D	105_L	0.737	0.55
243_L	255_R	0.733	0.55
9_I	66_E	0.729	0.55
182_R	192_L	0.726	0.54
55_Q	107_D	0.723	0.54
181_T	187_V	0.722	0.54
175_P	179_Q	0.722	0.54
10_N	66_E	0.721	0.54
261_I	272_A	0.720	0.54
36_Q	39_L	0.720	0.54
55_Q	110_L	0.719	0.54
265_L	271_L	0.715	0.53
243_L	247_L	0.712	0.53
243_L	279_L	0.712	0.53
179_Q	185_G	0.711	0.53
128_S	133_A	0.711	0.53
93_F	97_Q	0.704	0.52
38_C	64_D	0.703	0.52
121_A	128_S	0.702	0.52
159_I	171_L	0.701	0.52
52_Y	106_L	0.701	0.52
261_I	271_L	0.700	0.52
174_I	178_D	0.698	0.51
206_Q	222_L	0.695	0.51
180_D	183_Y	0.688	0.50
39_L	43_P	0.687	0.50
101_A	108_K	0.687	0.50
266_G	269_D	0.684	0.50
226_L	234_E	0.683	0.50
19_E	22_M	0.682	0.50
25_P	83_L	0.682	0.50
131_T	135_P	0.682	0.50
183_Y	186_L	0.681	0.50
155_A	171_L	0.680	0.50
31_W	35_S	0.680	0.50
28_F	31_W	0.680	0.50
56_F	106_L	0.677	0.49
75_L	92_G	0.677	0.49
42_T	78_I	0.676	0.49
186_L	189_Q	0.674	0.49
271_L	275_Y	0.673	0.49
192_L	200_P	0.672	0.49
248_T	255_R	0.668	0.48
131_T	158_L	0.668	0.48
61_L	66_E	0.668	0.48
141_W	151_G	0.664	0.48
176_L	179_Q	0.662	0.48
30_F	61_L	0.659	0.47
84_F	89_P	0.656	0.47
159_I	212_N	0.655	0.47
47_S	103_R	0.655	0.47
181_T	193_L	0.654	0.47
202_I	206_Q	0.653	0.47
168_E	193_L	0.651	0.47
42_T	58_L	0.647	0.46
242_H	252_G	0.646	0.46
189_Q	193_L	0.645	0.46
120_Q	139_D	0.645	0.46
180_D	188_A	0.641	0.46
62_D	128_S	0.639	0.45
187_V	193_L	0.639	0.45
29_Y	96_P	0.636	0.45
243_L	266_G	0.636	0.45
48_L	52_Y	0.634	0.45
89_P	92_G	0.632	0.45
118_A	140_A	0.630	0.44
184_Q	191_E	0.629	0.44
151_G	173_T	0.626	0.44
193_L	201_E	0.625	0.44
44_I	48_L	0.622	0.44
151_G	174_I	0.620	0.43
21_S	26_V	0.620	0.43
192_L	195_Q	0.615	0.43
68_M	72_Q	0.614	0.43
209_V	219_A	0.609	0.42
140_A	150_I	0.609	0.42
14_L	34_R	0.607	0.42
180_D	184_Q	0.605	0.42
13_N	16_Q	0.605	0.42
277_R	281_A	0.604	0.42
206_Q	231_R	0.604	0.42
41_L	102_I	0.603	0.42
37_H	77_A	0.602	0.42
52_Y	56_F	0.602	0.42
29_Y	42_T	0.602	0.42
35_S	96_P	0.601	0.42
102_I	108_K	0.601	0.42
182_R	185_G	0.596	0.41
39_L	46_E	0.595	0.41
253_Q	257_T	0.593	0.41
220_T	254_T	0.591	0.41
61_L	70_A	0.590	0.40
155_A	170_V	0.589	0.40
189_Q	195_Q	0.587	0.40
23_T	82_Y	0.587	0.40
169_A	173_T	0.586	0.40
188_A	194_K	0.585	0.40
267_T	272_A	0.583	0.40
223_A	235_A	0.583	0.40
180_D	191_E	0.583	0.40
61_L	82_Y	0.582	0.40
159_I	164_S	0.581	0.40
10_N	13_N	0.575	0.39
43_P	60_K	0.571	0.39
201_E	204_Q	0.571	0.39
93_F	102_I	0.570	0.38
93_F	105_L	0.570	0.38
216_A	245_K	0.569	0.38
270_A	278_Q	0.569	0.38
31_W	37_H	0.568	0.38
147_N	235_A	0.567	0.38
182_R	193_L	0.567	0.38
39_L	60_K	0.566	0.38
247_L	255_R	0.564	0.38
115_E	147_N	0.564	0.38
138_K	166_D	0.562	0.38
121_A	136_L	0.561	0.38
14_L	43_P	0.560	0.37
191_E	196_A	0.558	0.37
242_H	249_A	0.558	0.37
61_L	260_E	0.556	0.37
32_S	36_Q	0.551	0.37
14_L	32_S	0.551	0.37
78_I	156_E	0.547	0.36
28_F	32_S	0.547	0.36
54_G	93_F	0.546	0.36
216_A	241_G	0.545	0.36
191_E	195_Q	0.544	0.36
222_L	238_L	0.544	0.36
76_R	103_R	0.544	0.36
114_E	147_N	0.543	0.36
41_L	77_A	0.542	0.36
120_Q	136_L	0.540	0.36
146_Q	194_K	0.539	0.35
34_R	60_K	0.538	0.35
232_N	269_D	0.537	0.35
69_I	77_A	0.537	0.35
184_Q	197_A	0.536	0.35
118_A	137_L	0.536	0.35
176_L	182_R	0.535	0.35
80_T	94_Q	0.533	0.35
179_Q	184_Q	0.533	0.35
193_L	199_T	0.532	0.35
195_Q	203_Q	0.531	0.35
259_Q	278_Q	0.530	0.35
38_C	81_V	0.528	0.34
29_Y	77_A	0.527	0.34
139_D	143_L	0.527	0.34
63_C	272_A	0.526	0.34
262_L	272_A	0.526	0.34
33_E	39_L	0.525	0.34
180_D	185_G	0.523	0.34
27_L	106_L	0.523	0.34
204_Q	209_V	0.523	0.34
29_Y	41_L	0.520	0.34
232_N	236_L	0.519	0.34
206_Q	224_L	0.519	0.34
44_I	47_S	0.519	0.34
22_M	88_Q	0.518	0.34
43_P	77_A	0.518	0.34
233_E	236_L	0.517	0.33
31_W	43_P	0.516	0.33
38_C	76_R	0.516	0.33
240_F	258_F	0.515	0.33
179_Q	186_L	0.512	0.33
33_E	80_T	0.512	0.33
208_Q	218_L	0.511	0.33
44_I	113_E	0.510	0.33
199_T	202_I	0.509	0.33
117_K	143_L	0.509	0.33
12_S	23_T	0.509	0.33
61_L	80_T	0.508	0.33
37_H	96_P	0.508	0.33
14_L	19_E	0.507	0.33
179_Q	190_I	0.505	0.32
55_Q	112_R	0.504	0.32
18_L	101_A	0.504	0.32
191_E	198_D	0.503	0.32
63_C	94_Q	0.502	0.32
222_L	226_L	0.502	0.32
247_L	262_L	0.501	0.32
184_Q	189_Q	0.500	0.32

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
3qouA	1	0.9648	100	0.323	Contact Map
2qc7A	2	0.6866	99.9	0.657	Contact Map
2c0gA	1	0.6831	99.9	0.669	Contact Map
3bj5A	1	0.4261	99.9	0.669	Contact Map
3apqA	1	0.4049	99.9	0.672	Contact Map
3apoA	1	0.3908	99.9	0.676	Contact Map
2yzuA	1	0.3662	99.9	0.676	Contact Map
2qgvA	2	0.3838	99.9	0.677	Contact Map
4xhmA	1	0.3803	99.9	0.681	Contact Map
1thxA	1	0.3803	99.9	0.682	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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