YPBE - BACSU - GREMLIN Contacts

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YPBE - Uncharacterized protein YpbE

UniProt:	P50731	Sequences: MTNMSRVERRKAQNLYEDQNAALADDYVDDGESLPTRQSVKNQREQKKKQGKTKTPLFTVLAVIFVFVPVIVLVTLFYLKSHPDNHDDYEDVFIDSSQSKYEVVPKSEDKNDTADTKETALQKESKKEPEDSKPKEQTAADKKQTAVAEKEDSPNKEEATAAAASSSQSTVQQQEQPAEPVQNVPNRVVKHTVQKKETLYRISMKYYKSRTGEEKIRAYNHLNGNDVYTGQVLDIPLMDE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	240 (216)
Sequences:	262 (260)
Seq/√Len:	17.7

BACSU - YPBE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
191_H	197_E	4.014	1.00
191_H	206_Y	3.984	1.00
217_R	224_G	3.703	1.00
201_R	205_K	3.543	1.00
216_I	235_I	3.328	0.99
216_I	236_P	3.310	0.99
212_G	235_I	2.835	0.98
217_R	222_L	2.644	0.97
37_R	41_K	2.586	0.97
25_D	29_D	2.570	0.97
211_T	216_I	2.490	0.96
197_E	225_N	2.401	0.95
198_T	202_I	2.375	0.95
198_T	201_R	2.259	0.93
222_L	233_L	2.231	0.93
152_D	155_N	2.195	0.92
57_L	65_F	2.178	0.92
219_Y	234_D	2.137	0.91
201_R	204_M	2.090	0.90
212_G	215_K	1.978	0.87
165_S	169_S	1.894	0.85
197_E	214_E	1.876	0.84
61_L	65_F	1.867	0.84
219_Y	236_P	1.856	0.84
212_G	216_I	1.845	0.83
212_G	236_P	1.829	0.83
34_L	37_R	1.724	0.79
217_R	233_L	1.712	0.78
216_I	219_Y	1.707	0.78
191_H	202_I	1.694	0.77
199_L	211_T	1.682	0.77
69_P	219_Y	1.657	0.76
212_G	219_Y	1.654	0.76
210_R	213_E	1.647	0.75
204_M	212_G	1.563	0.71
198_T	204_M	1.546	0.70
39_S	42_N	1.542	0.70
219_Y	235_I	1.537	0.70
164_A	167_S	1.527	0.69
59_T	63_V	1.516	0.69
191_H	216_I	1.504	0.68
206_Y	235_I	1.499	0.68
228_Y	231_Q	1.488	0.67
198_T	211_T	1.471	0.66
217_R	225_N	1.464	0.66
206_Y	211_T	1.452	0.65
197_E	232_V	1.449	0.65
206_Y	215_K	1.440	0.65
190_K	203_S	1.437	0.65
69_P	75_T	1.431	0.64
198_T	210_R	1.410	0.63
136_E	141_D	1.408	0.63
199_L	216_I	1.383	0.62
27_Y	30_D	1.383	0.62
71_I	223_N	1.363	0.60
102_E	107_S	1.346	0.59
34_L	40_V	1.345	0.59
135_K	143_K	1.335	0.59
64_I	67_F	1.329	0.58
152_D	160_T	1.309	0.57
161_A	171_V	1.309	0.57
220_N	230_G	1.304	0.57
199_L	224_G	1.294	0.56
53_T	65_F	1.279	0.55
191_H	235_I	1.275	0.55
127_K	149_E	1.238	0.53
213_E	224_G	1.235	0.53
166_S	169_S	1.225	0.52
193_V	233_L	1.223	0.52
17_E	21_A	1.199	0.50
134_P	138_T	1.196	0.50
109_D	117_K	1.188	0.50
193_V	202_I	1.177	0.49
155_N	158_E	1.177	0.49
213_E	234_D	1.164	0.48
205_K	222_L	1.159	0.48
213_E	227_V	1.153	0.48
38_Q	41_K	1.130	0.46
32_E	40_V	1.130	0.46
59_T	192_T	1.125	0.46
210_R	231_Q	1.117	0.46
37_R	40_V	1.101	0.45
113_T	121_L	1.094	0.44
210_R	229_T	1.093	0.44
135_K	150_K	1.090	0.44
142_K	155_N	1.089	0.44
216_I	225_N	1.088	0.44
32_E	39_S	1.085	0.44
71_I	75_T	1.084	0.44
165_S	168_Q	1.081	0.43
56_P	232_V	1.076	0.43
200_Y	223_N	1.066	0.42
23_L	27_Y	1.065	0.42
130_E	173_Q	1.061	0.42
61_L	79_L	1.059	0.42
54_K	236_P	1.058	0.42
126_K	135_K	1.056	0.42
58_F	190_K	1.053	0.42
190_K	234_D	1.049	0.41
127_K	143_K	1.043	0.41
59_T	212_G	1.041	0.41
197_E	206_Y	1.032	0.40
131_D	136_E	1.024	0.40
142_K	147_V	1.023	0.40
19_Q	22_A	1.021	0.40
123_K	132_S	1.012	0.39
164_A	174_Q	1.009	0.39
73_L	235_I	1.007	0.39
72_V	78_Y	1.006	0.39
197_E	201_R	0.999	0.39
66_V	72_V	0.983	0.38
200_Y	204_M	0.981	0.37
215_K	236_P	0.979	0.37
29_D	216_I	0.977	0.37
92_V	96_S	0.970	0.37
210_R	234_D	0.968	0.37
41_K	44_R	0.960	0.36
38_Q	45_E	0.955	0.36
74_V	82_H	0.950	0.36
210_R	236_P	0.947	0.36
24_A	27_Y	0.942	0.35
191_H	211_T	0.940	0.35
198_T	212_G	0.940	0.35
65_F	198_T	0.937	0.35
34_L	38_Q	0.933	0.35
16_Y	27_Y	0.933	0.35
38_Q	42_N	0.932	0.35
56_P	67_F	0.924	0.34
211_T	236_P	0.919	0.34
69_P	215_K	0.919	0.34
120_A	136_E	0.917	0.34
50_Q	66_V	0.915	0.34
169_S	176_Q	0.911	0.34
199_L	225_N	0.910	0.34
120_A	161_A	0.909	0.33
176_Q	184_V	0.909	0.33
129_P	145_T	0.908	0.33
56_P	61_L	0.906	0.33
204_M	213_E	0.905	0.33
64_I	218_A	0.900	0.33
131_D	137_Q	0.896	0.33
215_K	219_Y	0.892	0.33
115_D	149_E	0.889	0.32
100_K	115_D	0.888	0.32
136_E	151_E	0.882	0.32
38_Q	190_K	0.880	0.32
54_K	68_V	0.875	0.32
211_T	215_K	0.874	0.32
216_I	233_L	0.873	0.32
59_T	231_Q	0.873	0.32
30_D	33_S	0.866	0.31
210_R	219_Y	0.861	0.31
178_A	182_Q	0.857	0.31
23_L	26_D	0.857	0.31
23_L	33_S	0.856	0.31
164_A	173_Q	0.851	0.30
206_Y	229_T	0.847	0.30
136_E	154_P	0.847	0.30
206_Y	212_G	0.844	0.30
58_F	74_V	0.836	0.30
59_T	236_P	0.834	0.30
191_H	212_G	0.833	0.29
179_E	182_Q	0.827	0.29
39_S	233_L	0.821	0.29
59_T	234_D	0.819	0.29
97_S	100_K	0.819	0.29
83_P	227_V	0.818	0.29
194_Q	205_K	0.817	0.29
18_D	25_D	0.816	0.29
55_T	64_I	0.815	0.29
203_S	234_D	0.807	0.28
136_E	139_A	0.806	0.28
202_I	211_T	0.793	0.27
213_E	228_Y	0.793	0.27
95_D	98_Q	0.792	0.27
159_A	172_Q	0.789	0.27
126_K	136_E	0.787	0.27
166_S	179_E	0.784	0.27
134_P	156_K	0.783	0.27
211_T	235_I	0.780	0.27
132_S	141_D	0.779	0.27
199_L	222_L	0.775	0.27
125_S	157_E	0.769	0.26
51_G	65_F	0.767	0.26
191_H	219_Y	0.767	0.26
130_E	156_K	0.764	0.26
199_L	202_I	0.760	0.26
56_P	227_V	0.759	0.26
61_L	66_V	0.750	0.25
133_K	146_A	0.749	0.25
73_L	236_P	0.746	0.25
196_K	229_T	0.742	0.25
206_Y	216_I	0.739	0.25
122_Q	133_K	0.735	0.25
129_P	140_A	0.734	0.25
54_K	216_I	0.731	0.25
111_N	175_E	0.728	0.24
55_T	233_L	0.726	0.24
113_T	167_S	0.726	0.24
77_F	81_S	0.718	0.24
87_D	108_E	0.717	0.24
120_A	137_Q	0.716	0.24
98_Q	101_Y	0.716	0.24
25_D	28_V	0.712	0.24
147_V	159_A	0.710	0.24
150_K	156_K	0.706	0.23
53_T	68_V	0.704	0.23
138_T	156_K	0.703	0.23
158_E	165_S	0.699	0.23
123_K	135_K	0.694	0.23
145_T	148_A	0.691	0.23
170_T	174_Q	0.691	0.23
157_E	173_Q	0.689	0.23
33_S	37_R	0.688	0.23
108_E	176_Q	0.687	0.23
50_Q	62_A	0.684	0.23
171_V	181_V	0.681	0.22
84_D	87_D	0.680	0.22
227_V	231_Q	0.675	0.22
29_D	32_E	0.673	0.22
130_E	192_T	0.669	0.22
108_E	136_E	0.668	0.22
130_E	135_K	0.667	0.22
162_A	177_P	0.667	0.22
189_V	205_K	0.667	0.22
99_S	117_K	0.667	0.22
172_Q	183_N	0.665	0.22
198_T	236_P	0.660	0.21
227_V	233_L	0.660	0.21
24_A	29_D	0.657	0.21
36_T	41_K	0.657	0.21
168_Q	171_V	0.656	0.21
41_K	45_E	0.655	0.21
172_Q	176_Q	0.653	0.21
125_S	155_N	0.652	0.21
130_E	138_T	0.649	0.21
96_S	165_S	0.646	0.21
29_D	42_N	0.644	0.21
118_E	151_E	0.642	0.21
119_T	128_E	0.639	0.21
52_K	55_T	0.639	0.21
48_K	186_N	0.634	0.20
124_E	130_E	0.633	0.20
20_N	33_S	0.632	0.20
70_V	202_I	0.629	0.20
24_A	34_L	0.625	0.20
32_E	38_Q	0.624	0.20
149_E	155_N	0.623	0.20
124_E	137_Q	0.623	0.20
68_V	83_P	0.622	0.20
128_E	131_D	0.621	0.20
90_E	96_S	0.620	0.20
205_K	212_G	0.619	0.20
67_F	233_L	0.619	0.20
191_H	236_P	0.617	0.20
191_H	234_D	0.616	0.20
90_E	95_D	0.607	0.19
63_V	70_V	0.603	0.19
73_L	225_N	0.600	0.19
197_E	202_I	0.597	0.19
76_L	213_E	0.595	0.19
198_T	206_Y	0.594	0.19
129_P	175_E	0.593	0.19
211_T	214_E	0.592	0.19
174_Q	182_Q	0.589	0.19
152_D	158_E	0.586	0.19
200_Y	213_E	0.584	0.19
193_V	230_G	0.582	0.18
126_K	165_S	0.581	0.18
119_T	136_E	0.580	0.18
70_V	76_L	0.580	0.18
39_S	214_E	0.579	0.18
157_E	178_A	0.578	0.18
94_I	99_S	0.577	0.18
35_P	191_H	0.576	0.18
49_K	215_K	0.575	0.18
39_S	45_E	0.573	0.18
48_K	56_P	0.572	0.18
211_T	231_Q	0.570	0.18
200_Y	226_D	0.570	0.18
218_A	221_H	0.569	0.18
227_V	234_D	0.567	0.18
73_L	78_Y	0.565	0.18
29_D	40_V	0.564	0.18
204_M	229_T	0.564	0.18
123_K	178_A	0.561	0.18
192_T	236_P	0.560	0.18
25_D	40_V	0.559	0.18
157_E	163_A	0.559	0.18
219_Y	225_N	0.557	0.18
193_V	220_N	0.556	0.18
89_Y	93_F	0.555	0.17
25_D	31_G	0.553	0.17
55_T	68_V	0.550	0.17
204_M	210_R	0.549	0.17
32_E	41_K	0.547	0.17
128_E	156_K	0.547	0.17
58_F	67_F	0.544	0.17
59_T	213_E	0.544	0.17
111_N	115_D	0.540	0.17
225_N	229_T	0.540	0.17
63_V	74_V	0.539	0.17
117_K	126_K	0.534	0.17
122_Q	125_S	0.534	0.17
57_L	61_L	0.529	0.17
122_Q	137_Q	0.526	0.16
200_Y	227_V	0.524	0.16
89_Y	92_V	0.522	0.16
132_S	137_Q	0.521	0.16
193_V	223_N	0.521	0.16
79_L	228_Y	0.521	0.16
136_E	140_A	0.520	0.16
154_P	175_E	0.518	0.16
206_Y	234_D	0.518	0.16
187_R	200_Y	0.516	0.16
25_D	216_I	0.516	0.16
191_H	198_T	0.514	0.16
55_T	59_T	0.512	0.16
53_T	57_L	0.507	0.16
72_V	219_Y	0.507	0.16
139_A	149_E	0.506	0.16
59_T	219_Y	0.502	0.16
25_D	196_K	0.502	0.16
127_K	137_Q	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
2mkxA	1	0.2125	99.4	0.727	Contact Map
2djpA	1	0.2667	99.4	0.73	Contact Map
2mpwA	1	0.3042	99.2	0.747	Contact Map
2ltfA	1	0.2167	99.2	0.752	Contact Map
1e0gA	1	0.2	99.1	0.76	Contact Map
4pxvA	1	0.1958	99.1	0.763	Contact Map
4uz3A	1	0.2083	99.1	0.766	Contact Map
4b8vA	2	0.2292	98.9	0.783	Contact Map
2l9yA	1	0.4625	98.7	0.794	Contact Map
4lzhA	1	0.2792	98.7	0.798	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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