YNEE - ECOLI - GREMLIN Contacts

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YNEE - UPF0187 protein YneE

UniProt:	P76146	Sequences: MIVRPQQHWLRRIFVWHGSVLSKISSRLLLNFLFSIAVIFMLPWYTHLGIKFTLAPFSILGVAIAIFLGFRNNAGYARYVEARKLWGQLMIASRSLLREVKTTLPDSASVREFARLQIAFAHCLRMTLRKQPQAEVLAHYLKTEDLQRVLASNSPANRILLIMGEWLAVQRRNGQLSDILFISLNDRLNDISAVLAGCERIAYTPIPFAYTLILHRTVYLFCIMLPFALVVDLHYMTPFISVLISYTFISLDCLAEELEDPFGTENNDLPLDAICNAIEIDLLQMNDEAEIPAKILPDRHYQLT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13813
Length:	304 (277)
Sequences:	1580 (1167)
Seq/√Len:	70.1

ECOLI - YNEE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
85_L	197_G	7.494	1.00
89_L	194_V	4.958	1.00
77_A	84_K	4.382	1.00
91_I	196_A	4.280	1.00
127_T	156_A	3.944	1.00
122_H	125_R	3.553	1.00
112_E	166_W	2.986	1.00
32_F	242_V	2.959	1.00
81_E	200_R	2.919	1.00
114_A	282_L	2.910	1.00
113_F	163_M	2.890	1.00
88_Q	194_V	2.747	1.00
93_S	117_Q	2.692	1.00
120_F	195_L	2.549	1.00
39_I	237_T	2.525	1.00
263_G	268_D	2.523	1.00
257_E	267_N	2.507	1.00
99_E	185_N	2.441	1.00
265_E	268_D	2.351	1.00
77_A	80_V	2.266	1.00
277_A	281_D	2.264	1.00
190_D	193_A	2.239	1.00
111_R	115_R	2.234	1.00
92_A	190_D	2.200	1.00
123_C	159_I	2.189	1.00
36_I	238_P	2.171	1.00
126_M	136_V	2.162	1.00
126_M	131_Q	2.127	1.00
276_N	280_I	2.096	1.00
90_M	274_I	2.050	1.00
28_L	242_V	2.024	1.00
99_E	187_R	2.003	1.00
89_L	124_L	1.978	1.00
97_L	114_A	1.903	1.00
97_L	282_L	1.871	1.00
142_K	145_D	1.863	1.00
91_I	193_A	1.836	1.00
116_L	166_W	1.815	1.00
40_F	44_W	1.786	1.00
162_I	165_E	1.783	1.00
169_V	173_N	1.749	1.00
65_A	69_G	1.746	1.00
179_I	182_I	1.723	1.00
168_A	172_R	1.720	1.00
160_L	192_S	1.711	1.00
57_F	224_M	1.697	1.00
116_L	145_D	1.667	1.00
100_V	110_V	1.633	0.99
125_R	272_D	1.631	0.99
183_S	186_D	1.623	0.99
123_C	155_P	1.609	0.99
98_R	164_G	1.563	0.99
117_Q	163_M	1.550	0.99
145_D	162_I	1.513	0.99
83_R	87_G	1.508	0.99
89_L	191_I	1.467	0.99
164_G	188_L	1.464	0.99
94_R	199_E	1.451	0.99
14_F	18_G	1.441	0.99
186_D	190_D	1.424	0.98
31_N	245_S	1.410	0.98
93_S	278_I	1.398	0.98
98_R	192_S	1.379	0.98
96_L	184_L	1.371	0.98
83_R	204_T	1.362	0.98
81_E	84_K	1.353	0.98
23_K	257_E	1.349	0.98
116_L	163_M	1.341	0.98
135_E	138_A	1.338	0.98
154_S	281_D	1.332	0.98
203_Y	277_A	1.327	0.97
134_A	137_L	1.326	0.97
119_A	141_L	1.322	0.97
120_F	191_I	1.321	0.97
93_S	121_A	1.312	0.97
177_S	180_L	1.298	0.97
212_L	216_R	1.288	0.97
46_T	49_G	1.269	0.97
39_I	43_P	1.253	0.96
99_E	184_L	1.238	0.96
52_F	229_L	1.237	0.96
29_L	33_L	1.234	0.96
95_S	192_S	1.228	0.96
100_V	104_L	1.224	0.96
33_L	40_F	1.221	0.96
96_L	191_I	1.218	0.96
125_R	271_L	1.215	0.96
87_G	91_I	1.211	0.96
80_V	201_I	1.204	0.96
193_A	196_A	1.190	0.95
124_L	195_L	1.178	0.95
100_V	113_F	1.172	0.95
153_N	280_I	1.169	0.95
170_Q	175_Q	1.162	0.95
109_S	166_W	1.159	0.94
111_R	288_E	1.149	0.94
254_L	258_L	1.148	0.94
71_R	259_E	1.139	0.94
92_A	194_V	1.139	0.94
76_Y	80_V	1.137	0.94
87_G	196_A	1.134	0.94
208_F	212_L	1.128	0.94
139_H	142_K	1.126	0.94
39_I	230_V	1.125	0.94
95_S	187_R	1.114	0.93
138_A	150_L	1.114	0.93
192_S	195_L	1.114	0.93
84_K	200_R	1.105	0.93
69_G	248_F	1.094	0.93
96_L	117_Q	1.091	0.92
115_R	283_L	1.089	0.92
35_S	39_I	1.087	0.92
102_T	165_E	1.087	0.92
36_I	39_I	1.086	0.92
143_T	148_R	1.082	0.92
69_G	73_N	1.079	0.92
101_K	104_L	1.078	0.92
21_L	28_L	1.071	0.92
127_T	154_S	1.061	0.91
146_L	150_L	1.058	0.91
67_F	251_L	1.056	0.91
125_R	275_C	1.055	0.91
23_K	38_V	1.050	0.91
154_S	199_E	1.048	0.91
101_K	285_M	1.036	0.90
71_R	75_G	1.032	0.90
33_L	36_I	1.015	0.89
213_I	250_S	1.011	0.89
105_P	172_R	1.009	0.89
90_M	278_I	0.998	0.89
45_Y	50_I	0.993	0.88
34_F	38_V	0.993	0.88
259_E	268_D	0.992	0.88
96_L	113_F	0.984	0.88
115_R	286_N	0.981	0.88
83_R	200_R	0.976	0.88
109_S	170_Q	0.961	0.87
56_P	60_L	0.960	0.87
167_L	181_F	0.954	0.86
101_K	110_V	0.951	0.86
171_R	180_L	0.951	0.86
260_D	268_D	0.947	0.86
196_A	199_E	0.942	0.86
34_F	223_I	0.937	0.85
250_S	257_E	0.934	0.85
33_L	37_A	0.930	0.85
128_L	198_C	0.927	0.85
281_D	284_Q	0.918	0.84
235_Y	255_A	0.918	0.84
153_N	284_Q	0.916	0.84
35_S	241_S	0.914	0.84
65_A	157_N	0.911	0.84
81_E	85_L	0.906	0.83
200_R	204_T	0.901	0.83
126_M	133_Q	0.897	0.83
37_A	288_E	0.894	0.83
43_P	49_G	0.887	0.82
279_E	283_L	0.885	0.82
86_W	278_I	0.878	0.81
116_L	159_I	0.876	0.81
21_L	274_I	0.867	0.81
89_L	120_F	0.866	0.81
72_N	210_Y	0.864	0.80
85_L	198_C	0.862	0.80
24_I	249_I	0.862	0.80
174_G	178_D	0.859	0.80
90_M	199_E	0.859	0.80
80_V	87_G	0.852	0.79
91_I	278_I	0.849	0.79
246_Y	251_L	0.848	0.79
112_E	145_D	0.846	0.79
89_L	163_M	0.845	0.79
25_S	30_L	0.844	0.79
32_F	35_S	0.842	0.79
154_S	195_L	0.841	0.79
181_F	221_F	0.840	0.78
276_N	279_E	0.839	0.78
114_A	286_N	0.831	0.78
222_C	267_N	0.830	0.78
28_L	35_S	0.830	0.78
19_S	212_L	0.827	0.77
35_S	238_P	0.824	0.77
45_Y	177_S	0.822	0.77
196_A	278_I	0.821	0.77
109_S	175_Q	0.819	0.77
117_Q	191_I	0.816	0.76
69_G	72_N	0.808	0.76
88_Q	190_D	0.808	0.76
42_L	230_V	0.805	0.75
83_R	269_L	0.805	0.75
92_A	191_I	0.805	0.75
129_R	271_L	0.803	0.75
222_C	249_I	0.802	0.75
49_G	231_V	0.800	0.75
43_P	46_T	0.800	0.75
94_R	196_A	0.796	0.75
87_G	200_R	0.794	0.74
206_I	258_L	0.794	0.74
51_K	231_V	0.787	0.74
92_A	187_R	0.787	0.74
117_Q	121_A	0.786	0.74
126_M	132_P	0.784	0.74
79_Y	258_L	0.783	0.73
118_I	280_I	0.783	0.73
36_I	186_D	0.778	0.73
118_I	282_L	0.778	0.73
42_L	231_V	0.775	0.73
89_L	218_V	0.771	0.72
148_R	229_L	0.767	0.72
67_F	252_D	0.766	0.72
82_A	267_N	0.758	0.71
222_C	247_T	0.758	0.71
118_I	279_E	0.757	0.71
211_T	215_H	0.757	0.71
33_L	151_A	0.752	0.70
217_T	247_T	0.752	0.70
36_I	40_F	0.751	0.70
115_R	145_D	0.748	0.70
196_A	252_D	0.746	0.70
214_L	217_T	0.744	0.70
25_S	120_F	0.742	0.69
125_R	129_R	0.742	0.69
36_I	220_L	0.740	0.69
105_P	109_S	0.739	0.69
87_G	179_I	0.737	0.69
72_N	222_C	0.736	0.69
166_W	170_Q	0.735	0.69
219_Y	223_I	0.733	0.68
260_D	265_E	0.731	0.68
237_T	267_N	0.730	0.68
42_L	51_K	0.729	0.68
108_A	138_A	0.722	0.67
270_P	281_D	0.722	0.67
30_L	220_L	0.722	0.67
24_I	62_V	0.721	0.67
109_S	112_E	0.717	0.67
254_L	259_E	0.715	0.66
246_Y	257_E	0.715	0.66
87_G	199_E	0.711	0.66
252_D	259_E	0.709	0.66
37_A	235_Y	0.708	0.66
250_S	269_L	0.708	0.66
75_G	258_L	0.707	0.66
129_R	272_D	0.705	0.65
86_W	271_L	0.703	0.65
67_F	75_G	0.701	0.65
79_Y	82_A	0.700	0.65
38_V	241_S	0.700	0.65
252_D	255_A	0.699	0.65
178_D	182_I	0.698	0.65
84_K	97_L	0.695	0.64
74_A	251_L	0.693	0.64
70_F	210_Y	0.691	0.64
143_T	147_Q	0.690	0.64
211_T	270_P	0.688	0.64
31_N	249_I	0.687	0.63
112_E	116_L	0.686	0.63
100_V	103_T	0.685	0.63
17_H	109_S	0.685	0.63
87_G	277_A	0.684	0.63
16_W	19_S	0.684	0.63
65_A	250_S	0.684	0.63
24_I	247_T	0.683	0.63
72_N	255_A	0.681	0.63
134_A	155_P	0.681	0.63
148_R	151_A	0.680	0.63
153_N	286_N	0.679	0.62
171_R	178_D	0.679	0.62
149_V	162_I	0.678	0.62
85_L	194_V	0.678	0.62
193_A	285_M	0.676	0.62
128_L	201_I	0.675	0.62
62_V	227_F	0.675	0.62
75_G	89_L	0.674	0.62
71_R	258_L	0.671	0.62
213_I	216_R	0.670	0.61
110_V	114_A	0.667	0.61
30_L	137_L	0.662	0.61
147_Q	151_A	0.662	0.61
61_G	67_F	0.660	0.60
161_L	285_M	0.654	0.60
78_R	83_R	0.654	0.60
75_G	181_F	0.653	0.59
283_L	287_D	0.650	0.59
139_H	144_E	0.649	0.59
81_E	87_G	0.648	0.59
86_W	225_L	0.642	0.58
212_L	215_H	0.640	0.58
263_G	269_L	0.640	0.58
88_Q	193_A	0.639	0.58
123_C	137_L	0.638	0.58
35_S	237_T	0.637	0.58
205_P	267_N	0.637	0.58
95_S	221_F	0.636	0.57
107_S	151_A	0.636	0.57
204_T	260_D	0.636	0.57
87_G	278_I	0.636	0.57
80_V	83_R	0.635	0.57
64_I	258_L	0.634	0.57
111_R	286_N	0.631	0.57
25_S	29_L	0.627	0.56
226_P	241_S	0.627	0.56
68_L	251_L	0.625	0.56
119_A	159_I	0.624	0.56
62_V	221_F	0.622	0.56
75_G	110_V	0.615	0.55
177_S	274_I	0.612	0.55
120_F	124_L	0.609	0.54
240_I	255_A	0.609	0.54
74_A	206_I	0.609	0.54
127_T	281_D	0.607	0.54
160_L	188_L	0.606	0.54
106_D	115_R	0.605	0.54
201_I	274_I	0.601	0.53
58_S	82_A	0.600	0.53
67_F	72_N	0.600	0.53
96_L	100_V	0.600	0.53
264_T	271_L	0.593	0.52
24_I	28_L	0.590	0.52
51_K	73_N	0.590	0.52
93_S	191_I	0.590	0.52
39_I	235_Y	0.588	0.52
208_F	257_E	0.587	0.52
16_W	20_V	0.586	0.51
202_A	260_D	0.585	0.51
28_L	147_Q	0.582	0.51
45_Y	48_L	0.582	0.51
180_L	183_S	0.581	0.51
122_H	272_D	0.581	0.51
243_L	250_S	0.578	0.50
209_A	260_D	0.577	0.50
68_L	254_L	0.574	0.50
60_L	241_S	0.573	0.50
23_K	209_A	0.571	0.50
55_A	241_S	0.569	0.49
29_L	38_V	0.566	0.49
122_H	279_E	0.565	0.49
33_L	189_N	0.565	0.49
159_I	280_I	0.564	0.49
82_A	201_I	0.564	0.49
67_F	256_E	0.560	0.48
16_W	23_K	0.560	0.48
115_R	165_E	0.559	0.48
138_A	175_Q	0.559	0.48
171_R	273_A	0.558	0.48
45_Y	75_G	0.558	0.48
33_L	43_P	0.558	0.48
66_I	212_L	0.555	0.48
264_T	272_D	0.555	0.48
111_R	173_N	0.554	0.48
39_I	238_P	0.554	0.48
195_L	205_P	0.554	0.48
246_Y	254_L	0.552	0.47
82_A	209_A	0.552	0.47
213_I	254_L	0.549	0.47
69_G	251_L	0.548	0.47
125_R	136_V	0.547	0.47
34_F	47_H	0.547	0.47
213_I	222_C	0.544	0.46
79_Y	204_T	0.544	0.46
167_L	171_R	0.544	0.46
158_R	162_I	0.544	0.46
195_L	199_E	0.542	0.46
208_F	267_N	0.541	0.46
157_N	285_M	0.541	0.46
120_F	281_D	0.539	0.46
66_I	211_T	0.538	0.46
58_S	149_V	0.537	0.46
119_A	137_L	0.536	0.45
97_L	101_K	0.535	0.45
128_L	204_T	0.533	0.45
42_L	69_G	0.532	0.45
217_T	243_L	0.531	0.45
146_L	149_V	0.531	0.45
162_I	169_V	0.530	0.45
119_A	123_C	0.529	0.45
81_E	128_L	0.529	0.45
127_T	152_S	0.529	0.45
16_W	21_L	0.529	0.45
84_K	259_E	0.527	0.44
92_A	193_A	0.527	0.44
134_A	140_Y	0.527	0.44
20_V	26_S	0.525	0.44
143_T	146_L	0.524	0.44
65_A	213_I	0.523	0.44
233_L	270_P	0.523	0.44
53_T	232_D	0.520	0.43
55_A	58_S	0.520	0.43
72_N	253_C	0.519	0.43
102_T	105_P	0.518	0.43
89_L	198_C	0.518	0.43
127_T	131_Q	0.518	0.43
81_E	203_Y	0.518	0.43
42_L	49_G	0.515	0.43
99_E	164_G	0.514	0.43
86_W	275_C	0.514	0.43
30_L	223_I	0.510	0.42
146_L	151_A	0.510	0.42
269_L	272_D	0.510	0.42
63_A	241_S	0.509	0.42
123_C	156_A	0.508	0.42
87_G	90_M	0.507	0.42
88_Q	116_L	0.507	0.42
106_D	109_S	0.507	0.42
57_F	160_L	0.507	0.42
88_Q	196_A	0.507	0.42
273_A	276_N	0.506	0.42
65_A	170_Q	0.504	0.42
107_S	110_V	0.504	0.42
105_P	138_A	0.503	0.41
121_A	269_L	0.502	0.41
167_L	283_L	0.502	0.41
251_L	257_E	0.502	0.41
30_L	82_A	0.500	0.41
171_R	181_F	0.500	0.41
91_I	281_D	0.500	0.41

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
4wd8A	3	0.8882	100	0.121	Contact Map
4rdqA	5	0.9704	100	0.323	Contact Map
2mi2A	1	0.227	7.9	0.971	Contact Map
2mn6B	2	0.1447	4.4	0.974	Contact Map
4p4hI	3	0.3125	4.3	0.974	Contact Map
4o9lA	1	0.3092	4.1	0.974	Contact Map
2l16A	1	0.1612	3.9	0.975	Contact Map
4xk8I	1	0.0954	3.3	0.976	Contact Map
1lqbD	2	0.0592	3.2	0.976	Contact Map
2azeC	2	0.1447	3.2	0.976	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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