YBGF - ECOLI - GREMLIN Contacts

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YBGF - Uncharacterized protein YbgF

UniProt:	P45955	Sequences: MSSNFRHQLLSLSLLVGIAAPWAAFAQAPISSVGSGSVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQIDSLSSGGAAAQSTSGDQSGAAASTTPTADAGTANAGAPVKSGNANTDYNAAIALVQDKSRQDDAMVAFQNFIKNYPDSTYLPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGVIMQDKGDTAKAKAVYQQVISKYPGTDGAKQAQKRLNAM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12854
Length:	263 (222)
Sequences:	1959 (1661)
Seq/√Len:	111.5

ECOLI - YBGF
BACSU - YSOA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
158_R	161_D	6.998	1.00
195_K	198_D	5.009	1.00
232_D	235_K	4.831	1.00
41_R	46_E	2.961	1.00
224_G	240_Y	2.871	1.00
83_Q	88_V	2.594	1.00
183_N	202_Y	2.583	1.00
200_A	223_V	2.490	1.00
190_N	198_D	2.473	1.00
227_M	239_V	2.398	1.00
242_Q	246_K	2.302	1.00
200_A	226_I	2.282	1.00
223_V	239_V	2.261	1.00
69_D	74_R	2.241	1.00
187_G	203_F	2.203	1.00
62_Q	67_Q	2.153	1.00
218_D	252_G	2.111	1.00
188_Q	222_K	2.097	1.00
160_D	193_K	2.047	1.00
143_N	147_N	2.027	1.00
152_L	165_A	1.928	1.00
167_Q	186_L	1.890	1.00
228_Q	240_Y	1.884	1.00
205_S	209_N	1.845	1.00
166_F	185_W	1.844	1.00
186_L	223_V	1.833	1.00
203_F	222_K	1.807	1.00
227_M	235_K	1.793	1.00
206_V	219_A	1.738	1.00
184_Y	203_F	1.724	1.00
142_A	176_S	1.723	1.00
186_L	202_Y	1.701	1.00
27_Q	30_I	1.700	1.00
146_Y	150_I	1.691	1.00
204_A	223_V	1.683	1.00
66_N	70_I	1.664	1.00
163_M	193_K	1.659	1.00
156_K	159_Q	1.659	1.00
146_Y	181_N	1.651	1.00
190_N	202_Y	1.647	1.00
168_N	172_N	1.574	1.00
163_M	186_L	1.571	1.00
226_I	230_K	1.563	1.00
38_V	42_V	1.557	1.00
191_Y	196_K	1.547	1.00
163_M	189_L	1.530	1.00
146_Y	149_A	1.530	1.00
204_A	208_K	1.482	1.00
197_D	230_K	1.481	1.00
170_I	182_A	1.463	1.00
170_I	183_N	1.462	1.00
150_I	154_Q	1.424	1.00
187_G	202_Y	1.422	1.00
237_K	241_Q	1.390	1.00
68_S	71_D	1.377	1.00
250_T	256_A	1.328	1.00
152_L	161_D	1.290	0.99
200_A	227_M	1.289	0.99
90_R	94_I	1.288	0.99
29_P	32_S	1.287	0.99
207_V	220_M	1.283	0.99
223_V	227_M	1.281	0.99
181_N	185_W	1.277	0.99
35_S	38_V	1.276	0.99
184_Y	222_K	1.247	0.99
152_L	158_R	1.245	0.99
148_A	152_L	1.237	0.99
227_M	232_D	1.229	0.99
168_N	171_K	1.223	0.99
146_Y	185_W	1.209	0.99
38_V	41_R	1.200	0.99
244_I	253_A	1.190	0.99
146_Y	166_F	1.188	0.99
222_K	225_V	1.185	0.99
150_I	166_F	1.173	0.99
161_D	165_A	1.168	0.99
169_F	176_S	1.161	0.99
196_K	226_I	1.147	0.99
97_Q	101_L	1.141	0.99
191_Y	203_F	1.137	0.99
186_L	190_N	1.123	0.98
89_E	93_Q	1.119	0.98
95_L	99_D	1.119	0.98
147_N	151_A	1.111	0.98
129_G	132_N	1.110	0.98
42_V	46_E	1.101	0.98
181_N	215_K	1.100	0.98
170_I	179_L	1.097	0.98
43_T	47_R	1.090	0.98
145_D	148_A	1.085	0.98
185_W	188_Q	1.083	0.98
241_Q	245_S	1.079	0.98
254_K	257_Q	1.076	0.98
183_N	205_S	1.075	0.98
107_A	111_T	1.067	0.98
27_Q	32_S	1.058	0.98
49_S	52_H	1.057	0.98
155_D	158_R	1.051	0.98
112_S	115_Q	1.046	0.97
58_Q	61_Q	1.043	0.97
59_L	63_L	1.040	0.97
145_D	149_A	1.038	0.97
185_W	215_K	1.024	0.97
33_V	36_G	1.024	0.97
207_V	216_A	1.023	0.97
167_Q	190_N	1.022	0.97
34_G	39_E	1.020	0.97
252_G	256_A	1.019	0.97
101_L	106_A	1.012	0.97
187_G	224_G	1.008	0.97
126_A	129_G	1.005	0.97
141_N	144_T	1.004	0.97
149_A	152_L	1.001	0.97
142_A	149_A	0.994	0.97
220_M	242_Q	0.992	0.97
205_S	208_K	0.983	0.96
166_F	170_I	0.978	0.96
39_E	42_V	0.972	0.96
82_Y	86_Q	0.970	0.96
180_P	206_V	0.966	0.96
36_G	40_D	0.963	0.96
221_F	243_V	0.959	0.96
45_L	50_N	0.953	0.96
116_S	124_P	0.953	0.96
127_D	131_A	0.951	0.96
35_S	46_E	0.951	0.96
128_A	131_A	0.947	0.95
199_A	203_F	0.947	0.95
37_S	41_R	0.941	0.95
149_A	166_F	0.939	0.95
80_N	84_L	0.935	0.95
77_I	80_N	0.935	0.95
163_M	190_N	0.932	0.95
63_L	66_N	0.932	0.95
200_A	230_K	0.926	0.95
224_G	243_V	0.923	0.95
76_Q	79_E	0.922	0.95
97_Q	100_S	0.921	0.95
45_L	49_S	0.906	0.94
250_T	253_A	0.899	0.94
85_N	88_V	0.898	0.94
35_S	39_E	0.897	0.94
198_D	201_Y	0.897	0.94
84_L	87_V	0.894	0.94
91_Q	94_I	0.886	0.94
221_F	225_V	0.879	0.93
41_R	45_L	0.875	0.93
30_I	33_V	0.866	0.93
183_N	220_M	0.864	0.93
194_G	229_D	0.862	0.93
247_Y	250_T	0.856	0.92
200_A	204_A	0.853	0.92
221_F	240_Y	0.841	0.92
103_S	109_Q	0.839	0.92
181_N	184_Y	0.839	0.92
142_A	169_F	0.836	0.91
29_P	33_V	0.831	0.91
76_Q	81_Q	0.828	0.91
61_Q	64_S	0.823	0.91
220_M	239_V	0.822	0.91
189_L	226_I	0.817	0.90
207_V	219_A	0.815	0.90
66_N	69_D	0.811	0.90
58_Q	78_Q	0.811	0.90
42_V	45_L	0.810	0.90
217_A	247_Y	0.808	0.90
57_T	61_Q	0.802	0.90
235_K	238_A	0.800	0.90
170_I	202_Y	0.799	0.90
93_Q	96_L	0.799	0.90
153_V	166_F	0.794	0.89
34_G	38_V	0.792	0.89
28_A	33_V	0.788	0.89
215_K	222_K	0.787	0.89
113_G	116_S	0.785	0.89
210_Y	213_S	0.781	0.88
249_G	257_Q	0.781	0.88
217_A	248_P	0.780	0.88
167_Q	171_K	0.780	0.88
162_A	166_F	0.777	0.88
188_Q	191_Y	0.776	0.88
44_Q	47_R	0.773	0.88
128_A	132_N	0.772	0.88
204_A	235_K	0.767	0.88
107_A	110_S	0.764	0.87
167_Q	198_D	0.763	0.87
180_P	185_W	0.760	0.87
184_Y	188_Q	0.759	0.87
197_D	200_A	0.756	0.87
69_D	72_S	0.748	0.86
180_P	213_S	0.746	0.86
153_V	189_L	0.746	0.86
220_M	243_V	0.744	0.86
149_A	169_F	0.744	0.86
136_P	139_S	0.741	0.86
103_S	106_A	0.733	0.85
58_Q	62_Q	0.732	0.85
190_N	194_G	0.732	0.85
93_Q	100_S	0.732	0.85
191_Y	226_I	0.729	0.85
151_A	155_D	0.724	0.84
146_Y	182_A	0.721	0.84
209_N	214_P	0.720	0.84
244_I	257_Q	0.719	0.84
34_G	37_S	0.717	0.84
79_E	82_Y	0.714	0.84
126_A	131_A	0.713	0.83
103_S	107_A	0.712	0.83
81_Q	84_L	0.708	0.83
222_K	243_V	0.705	0.83
47_R	51_A	0.705	0.83
215_K	218_D	0.701	0.82
221_F	256_A	0.700	0.82
148_A	165_A	0.689	0.81
173_Y	182_A	0.683	0.81
170_I	186_L	0.683	0.81
44_Q	48_I	0.680	0.80
184_Y	218_D	0.678	0.80
150_I	153_V	0.677	0.80
185_W	218_D	0.667	0.79
64_S	68_S	0.665	0.79
94_I	97_Q	0.665	0.79
109_Q	113_G	0.664	0.79
196_K	229_D	0.662	0.79
144_T	234_A	0.660	0.78
40_D	44_Q	0.658	0.78
196_K	230_K	0.657	0.78
227_M	230_K	0.656	0.78
75_G	82_Y	0.655	0.78
179_L	183_N	0.654	0.78
176_S	179_L	0.652	0.78
110_S	113_G	0.651	0.78
236_A	240_Y	0.651	0.78
164_V	168_N	0.651	0.78
145_D	165_A	0.648	0.77
190_N	195_K	0.647	0.77
251_D	255_Q	0.642	0.77
149_A	165_A	0.635	0.76
189_L	193_K	0.633	0.76
187_G	222_K	0.632	0.75
85_N	89_E	0.630	0.75
81_Q	87_V	0.629	0.75
94_I	103_S	0.629	0.75
130_T	133_A	0.622	0.74
91_Q	95_L	0.622	0.74
40_D	43_T	0.622	0.74
177_T	214_P	0.621	0.74
169_F	185_W	0.619	0.74
197_D	201_Y	0.615	0.73
49_S	53_S	0.614	0.73
38_V	49_S	0.614	0.73
198_D	202_Y	0.614	0.73
187_G	199_A	0.613	0.73
163_M	167_Q	0.611	0.73
240_Y	256_A	0.609	0.73
87_V	90_R	0.608	0.73
125_T	128_A	0.604	0.72
65_D	68_S	0.603	0.72
203_F	223_V	0.602	0.72
188_Q	225_V	0.601	0.72
194_G	199_A	0.601	0.72
63_L	76_Q	0.598	0.71
185_W	222_K	0.598	0.71
169_F	206_V	0.597	0.71
139_S	144_T	0.596	0.71
224_G	236_A	0.594	0.71
238_A	242_Q	0.591	0.70
79_E	83_Q	0.590	0.70
39_E	45_L	0.587	0.70
98_I	166_F	0.583	0.69
167_Q	170_I	0.579	0.69
36_G	39_E	0.578	0.69
40_D	46_E	0.578	0.69
34_G	42_V	0.577	0.69
169_F	173_Y	0.576	0.69
146_Y	153_V	0.575	0.68
148_A	151_A	0.574	0.68
200_A	237_K	0.572	0.68
93_Q	97_Q	0.571	0.68
111_T	114_D	0.566	0.67
208_K	242_Q	0.564	0.67
166_F	240_Y	0.564	0.67
169_F	172_N	0.563	0.67
199_A	223_V	0.562	0.67
39_E	46_E	0.561	0.67
110_S	115_Q	0.560	0.66
167_Q	212_K	0.558	0.66
206_V	243_V	0.557	0.66
224_G	239_V	0.556	0.66
29_P	35_S	0.555	0.66
102_S	106_A	0.553	0.65
78_Q	82_Y	0.551	0.65
191_Y	229_D	0.550	0.65
191_Y	222_K	0.548	0.65
224_G	227_M	0.546	0.64
127_D	130_T	0.546	0.64
208_K	211_P	0.546	0.64
73_L	77_I	0.545	0.64
33_V	37_S	0.544	0.64
46_E	49_S	0.543	0.64
228_Q	233_T	0.542	0.64
33_V	41_R	0.542	0.64
159_Q	193_K	0.542	0.64
83_Q	86_Q	0.540	0.64
94_I	98_I	0.538	0.63
27_Q	33_V	0.535	0.63
145_D	152_L	0.534	0.63
239_V	242_Q	0.534	0.63
99_D	102_S	0.533	0.63
243_V	254_K	0.533	0.63
220_M	247_Y	0.531	0.62
169_F	182_A	0.528	0.62
59_L	224_G	0.528	0.62
216_A	247_Y	0.527	0.62
101_L	105_G	0.524	0.61
37_S	40_D	0.524	0.61
55_L	78_Q	0.523	0.61
206_V	209_N	0.518	0.60
182_A	185_W	0.516	0.60
197_D	204_A	0.516	0.60
243_V	257_Q	0.515	0.60
97_Q	102_S	0.511	0.59
99_D	106_A	0.511	0.59
33_V	39_E	0.511	0.59
202_Y	239_V	0.509	0.59
109_Q	115_Q	0.508	0.59
82_Y	89_E	0.507	0.59
247_Y	256_A	0.507	0.59
210_Y	247_Y	0.505	0.58
96_L	102_S	0.504	0.58
46_E	50_N	0.504	0.58
90_R	162_A	0.501	0.58
88_V	92_K	0.500	0.58

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
2pziA	1	0.8897	99.8	0.514	Contact Map
1dceA	1	0.673	99.8	0.515	Contact Map
2vsyA	1	0.4449	99.8	0.518	Contact Map
4i2zA	1	0.4601	99.8	0.519	Contact Map
4ja7A	1	0.4563	99.7	0.521	Contact Map
3urzA	1	0.4449	99.7	0.522	Contact Map
3dssA	1	0.6274	99.7	0.523	Contact Map
2xevA	1	0.4601	99.7	0.526	Contact Map
3qkyA	1	0.4753	99.7	0.53	Contact Map
4gywA	2	0.5551	99.7	0.53	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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