YYBI - BACSU - GREMLIN Contacts

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YYBI - Uncharacterized protein YybI

UniProt:	P37495	Sequences: MNVYDIRMAPYWFYEGRGLVQHPYVFRQPVSSRAIIVSTRGDVTGDGVIDEVFLTGNQMPGSPLWRNITLVIRDGRTHQEQRIQLQNNMGYNPSLFLGDMTGDKIEDVAVVMDTGGSGGAIYAYVFAYLNRQFRRIFNSDVLNDELKYSVRYQNQYKASVISHQQNETYILDLTYKGREYLNEIYNSQGVLKMPIEGWVNPLSGLYPVDFDRDGVYELLAYQRIAGRYNADSLGYVQTVLKWNGQRFMFNRQTVTIFGSDLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	262 (227)
Sequences:	176 (152)
Seq/√Len:	10.1

BACSU - YYBI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
200_N	229_N	6.535	1.00
41_G	97_L	3.426	0.97
209_D	213_D	3.254	0.95
99_D	103_D	3.187	0.95
198_W	225_A	2.914	0.92
114_T	122_Y	2.759	0.89
202_L	220_A	2.648	0.87
209_D	214_G	2.644	0.87
119_G	230_A	2.582	0.86
209_D	217_E	2.565	0.86
125_V	135_R	2.516	0.84
242_W	247_F	2.374	0.81
114_T	119_G	2.356	0.80
200_N	203_S	2.331	0.79
186_N	190_V	2.317	0.79
142_L	238_T	2.313	0.79
223_R	232_S	2.290	0.78
72_I	83_I	2.257	0.77
146_L	173_L	2.254	0.77
93_P	184_I	2.239	0.76
36_I	78_H	2.226	0.76
99_D	102_G	2.220	0.76
236_V	254_V	2.195	0.75
150_V	197_G	2.123	0.72
240_L	247_F	2.110	0.72
62_S	102_G	2.097	0.71
223_R	229_N	2.096	0.71
52_V	97_L	2.078	0.71
118_G	230_A	2.067	0.70
226_G	231_D	2.040	0.69
42_D	46_D	1.963	0.66
117_S	230_A	1.924	0.64
153_Q	159_S	1.915	0.64
200_N	225_A	1.903	0.64
181_L	240_L	1.802	0.59
116_G	230_A	1.801	0.59
131_R	158_A	1.788	0.59
202_L	205_L	1.724	0.56
107_D	118_G	1.695	0.54
52_V	154_N	1.669	0.53
50_D	161_I	1.626	0.51
43_V	50_D	1.618	0.51
102_G	214_G	1.575	0.49
102_G	209_D	1.565	0.48
42_D	45_G	1.537	0.47
156_Y	181_L	1.515	0.46
120_A	201_P	1.504	0.46
83_I	154_N	1.497	0.45
137_F	142_L	1.476	0.44
35_I	136_I	1.469	0.44
180_Y	231_D	1.468	0.44
48_V	75_G	1.464	0.44
44_T	72_I	1.463	0.44
189_G	218_L	1.438	0.43
116_G	229_N	1.436	0.42
113_D	121_I	1.414	0.41
142_L	152_Y	1.409	0.41
208_V	239_V	1.394	0.41
44_T	131_R	1.383	0.40
228_Y	232_S	1.355	0.39
144_D	159_S	1.348	0.39
148_Y	233_L	1.337	0.38
114_T	117_S	1.334	0.38
183_E	227_R	1.330	0.38
37_V	223_R	1.324	0.37
66_R	171_L	1.307	0.37
168_T	178_R	1.301	0.36
156_Y	173_L	1.298	0.36
115_G	230_A	1.277	0.35
111_V	123_A	1.231	0.34
137_F	152_Y	1.213	0.33
64_L	89_M	1.209	0.33
118_G	228_Y	1.208	0.33
50_D	174_T	1.202	0.32
142_L	181_L	1.201	0.32
192_K	197_G	1.201	0.32
177_G	192_K	1.199	0.32
202_L	234_G	1.188	0.32
115_G	118_G	1.185	0.32
38_S	95_L	1.175	0.31
125_V	245_Q	1.168	0.31
195_I	227_R	1.135	0.30
165_Q	239_V	1.132	0.30
209_D	215_V	1.128	0.29
131_R	184_I	1.105	0.29
220_A	238_T	1.103	0.29
158_A	231_D	1.099	0.28
118_G	216_Y	1.087	0.28
85_L	206_Y	1.064	0.27
49_I	155_Q	1.063	0.27
36_I	221_Y	1.058	0.27
64_L	200_N	1.055	0.27
225_A	229_N	1.032	0.26
112_M	150_V	1.030	0.26
85_L	136_I	1.019	0.25
213_D	241_K	1.016	0.25
65_W	158_A	1.013	0.25
137_F	181_L	1.007	0.25
74_D	131_R	1.004	0.25
36_I	112_M	1.003	0.25
158_A	197_G	1.001	0.25
213_D	217_E	1.001	0.25
83_I	126_F	0.996	0.25
124_Y	194_P	0.987	0.24
42_D	48_V	0.985	0.24
144_D	236_V	0.984	0.24
36_I	203_S	0.978	0.24
158_A	173_L	0.977	0.24
50_D	84_Q	0.974	0.24
141_V	179_E	0.971	0.24
64_L	120_A	0.969	0.24
119_G	205_L	0.961	0.23
207_P	216_Y	0.960	0.23
42_D	47_G	0.957	0.23
38_S	51_E	0.952	0.23
56_G	172_D	0.948	0.23
112_M	199_V	0.946	0.23
179_E	224_I	0.941	0.23
149_S	178_R	0.937	0.23
132_Q	190_V	0.937	0.23
211_D	249_F	0.935	0.23
76_R	166_N	0.927	0.22
50_D	75_G	0.927	0.22
154_N	186_N	0.906	0.22
185_Y	189_G	0.905	0.22
79_Q	173_L	0.900	0.22
210_F	237_Q	0.897	0.21
227_R	232_S	0.897	0.21
102_G	217_E	0.894	0.21
39_T	237_Q	0.893	0.21
54_L	238_T	0.889	0.21
148_Y	181_L	0.886	0.21
50_D	172_D	0.882	0.21
41_G	52_V	0.881	0.21
36_I	57_N	0.880	0.21
37_V	110_V	0.876	0.21
116_G	119_G	0.875	0.21
176_K	247_F	0.873	0.21
160_V	189_G	0.867	0.21
73_R	105_I	0.867	0.21
184_I	195_I	0.867	0.21
212_R	251_R	0.867	0.21
93_P	210_F	0.863	0.20
177_G	240_L	0.863	0.20
45_G	191_L	0.861	0.20
176_K	231_D	0.861	0.20
114_T	221_Y	0.860	0.20
152_Y	181_L	0.859	0.20
78_H	239_V	0.850	0.20
109_A	125_V	0.848	0.20
56_G	229_N	0.845	0.20
52_V	100_M	0.842	0.20
125_V	137_F	0.842	0.20
43_V	111_V	0.838	0.20
113_D	220_A	0.838	0.20
160_V	219_L	0.834	0.20
168_T	203_S	0.833	0.20
100_M	108_V	0.820	0.19
120_A	200_N	0.820	0.19
116_G	224_I	0.819	0.19
51_E	163_H	0.818	0.19
78_H	106_E	0.817	0.19
142_L	240_L	0.816	0.19
83_I	156_Y	0.816	0.19
68_I	184_I	0.816	0.19
100_M	131_R	0.815	0.19
107_D	131_R	0.810	0.19
76_R	246_R	0.810	0.19
117_S	229_N	0.808	0.19
34_A	128_Y	0.805	0.19
78_H	146_L	0.803	0.19
155_Q	163_H	0.800	0.19
150_V	247_F	0.799	0.19
81_Q	128_Y	0.793	0.18
157_K	231_D	0.792	0.18
148_Y	199_V	0.789	0.18
154_N	190_V	0.786	0.18
73_R	104_K	0.785	0.18
47_G	103_D	0.785	0.18
61_G	66_R	0.782	0.18
62_S	214_G	0.782	0.18
178_R	208_V	0.781	0.18
156_Y	254_V	0.780	0.18
154_N	171_L	0.777	0.18
143_N	247_F	0.776	0.18
52_V	76_R	0.775	0.18
224_I	236_V	0.771	0.18
95_L	132_Q	0.771	0.18
138_N	247_F	0.768	0.18
98_G	110_V	0.767	0.18
102_G	203_S	0.765	0.18
195_I	201_P	0.765	0.18
202_L	253_T	0.765	0.18
145_E	176_K	0.764	0.18
93_P	228_Y	0.756	0.17
39_T	97_L	0.755	0.17
118_G	226_G	0.747	0.17
171_L	245_Q	0.747	0.17
184_I	244_G	0.739	0.17
56_G	189_G	0.737	0.17
77_T	242_W	0.733	0.17
35_I	125_V	0.731	0.17
188_Q	213_D	0.726	0.17
169_Y	203_S	0.722	0.16
50_D	53_F	0.722	0.16
101_T	193_M	0.722	0.16
201_P	204_G	0.721	0.16
53_F	208_V	0.721	0.16
33_R	238_T	0.720	0.16
175_Y	234_G	0.713	0.16
91_Y	117_S	0.712	0.16
94_S	244_G	0.712	0.16
152_Y	183_E	0.709	0.16
61_G	132_Q	0.708	0.16
55_T	221_Y	0.707	0.16
120_A	225_A	0.703	0.16
172_D	189_G	0.702	0.16
119_G	222_Q	0.702	0.16
143_N	224_I	0.699	0.16
193_M	196_E	0.698	0.16
125_V	217_E	0.698	0.16
50_D	145_E	0.693	0.16
74_D	97_L	0.687	0.16
62_S	91_Y	0.685	0.16
97_L	244_G	0.681	0.15
183_E	225_A	0.673	0.15
52_V	149_S	0.667	0.15
34_A	249_F	0.659	0.15
93_P	191_L	0.659	0.15
110_V	215_V	0.657	0.15
96_F	216_Y	0.651	0.15
64_L	224_I	0.647	0.15
219_L	237_Q	0.646	0.15
206_Y	219_L	0.645	0.15
117_S	228_Y	0.644	0.15
162_S	203_S	0.643	0.15
208_V	249_F	0.638	0.14
99_D	107_D	0.637	0.14
93_P	172_D	0.635	0.14
192_K	240_L	0.635	0.14
32_S	193_M	0.633	0.14
241_K	254_V	0.631	0.14
36_I	55_T	0.629	0.14
184_I	227_R	0.626	0.14
111_V	121_I	0.625	0.14
191_L	194_P	0.624	0.14
56_G	205_L	0.622	0.14
75_G	100_M	0.621	0.14
125_V	168_T	0.612	0.14
112_M	122_Y	0.611	0.14
108_V	216_Y	0.611	0.14
107_D	221_Y	0.609	0.14
39_T	215_V	0.603	0.14
108_V	128_Y	0.603	0.14
175_Y	244_G	0.603	0.14
208_V	215_V	0.600	0.14
194_P	197_G	0.599	0.14
181_L	192_K	0.595	0.14
29_P	187_S	0.592	0.13
167_E	173_L	0.592	0.13
207_P	218_L	0.592	0.13
170_I	203_S	0.591	0.13
169_Y	204_G	0.588	0.13
118_G	229_N	0.588	0.13
103_D	107_D	0.587	0.13
109_A	216_Y	0.586	0.13
93_P	252_Q	0.584	0.13
157_K	172_D	0.583	0.13
45_G	240_L	0.582	0.13
119_G	228_Y	0.581	0.13
139_S	212_R	0.580	0.13
144_D	201_P	0.578	0.13
48_V	166_N	0.577	0.13
51_E	215_V	0.577	0.13
94_S	217_E	0.577	0.13
106_E	167_E	0.575	0.13
224_I	234_G	0.574	0.13
43_V	169_Y	0.574	0.13
79_Q	186_N	0.573	0.13
70_L	228_Y	0.573	0.13
121_I	165_Q	0.573	0.13
75_G	197_G	0.571	0.13
94_S	151_R	0.571	0.13
126_F	174_T	0.569	0.13
118_G	188_Q	0.567	0.13
126_F	234_G	0.567	0.13
110_V	164_Q	0.567	0.13
150_V	160_V	0.565	0.13
219_L	224_I	0.565	0.13
92_N	119_G	0.564	0.13
102_G	107_D	0.561	0.13
101_T	242_W	0.561	0.13
76_R	136_I	0.555	0.13
103_D	170_I	0.554	0.13
100_M	217_E	0.552	0.13
158_A	233_L	0.551	0.13
148_Y	229_N	0.550	0.13
149_S	190_V	0.546	0.12
104_K	186_N	0.542	0.12
67_N	193_M	0.541	0.12
143_N	197_G	0.540	0.12
162_S	197_G	0.537	0.12
146_L	240_L	0.536	0.12
43_V	173_L	0.533	0.12
194_P	242_W	0.532	0.12
55_T	162_S	0.532	0.12
116_G	226_G	0.532	0.12
50_D	117_S	0.531	0.12
145_E	171_L	0.531	0.12
65_W	193_M	0.531	0.12
136_I	155_Q	0.530	0.12
104_K	176_K	0.529	0.12
113_D	130_N	0.529	0.12
77_T	247_F	0.528	0.12
169_Y	234_G	0.525	0.12
150_V	199_V	0.524	0.12
163_H	246_R	0.524	0.12
94_S	154_N	0.523	0.12
115_G	228_Y	0.523	0.12
151_R	238_T	0.522	0.12
72_I	106_E	0.522	0.12
83_I	236_V	0.522	0.12
44_T	100_M	0.518	0.12
159_S	173_L	0.517	0.12
52_V	238_T	0.517	0.12
43_V	128_Y	0.517	0.12
234_G	254_V	0.516	0.12
41_G	181_L	0.515	0.12
35_I	243_N	0.514	0.12
119_G	172_D	0.514	0.12
178_R	181_L	0.513	0.12
161_I	188_Q	0.507	0.12
199_V	223_R	0.505	0.12
54_L	64_L	0.504	0.12
214_G	217_E	0.504	0.12
35_I	68_I	0.504	0.12
70_L	110_V	0.504	0.12
146_L	158_A	0.503	0.12
79_Q	147_K	0.502	0.12
248_M	254_V	0.500	0.12

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
3ijeA	1	0.7901	92.9	0.932	Contact Map
4o9xA	1	0.8321	92.2	0.934	Contact Map
2bwrA	1	0.6031	88.7	0.939	Contact Map
4iglA	1	0.7863	87.2	0.94	Contact Map
4um9A	1	0.8092	86.8	0.941	Contact Map
4a7kA	2	0.7061	82	0.944	Contact Map
3vi3A	1	0.7863	75.8	0.947	Contact Map
2zuxA	1	0.8206	72.7	0.949	Contact Map
4nehA	1	0.8053	65.6	0.951	Contact Map
4pj2A	1	0.4542	65	0.951	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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