YEBE - BACSU - GREMLIN Contacts

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YEBE - UPF0316 protein YebE

UniProt:	O34624	Sequences: MMQTILSNGIAMVLIILIINIVYVSFFTIRMILTLKGQRYLAAGISTIEILVYVTGLSLVLDNLDQIQNVIAYALGYGLGVIVGMKIEEKLALGYIMVNVITKELDLDLPKQLREKGYGVTNWVAGGLEGDRTALQILTPRRYELQLYDTIKTLDSKAFIIAYEPKTIHGGFWVKAVKKRRIKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	184 (165)
Sequences:	418 (302)
Seq/√Len:	23.5

BACSU - YEBE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_N	23_Y	5.233	1.00
47_T	78_G	3.606	1.00
102_T	155_D	3.232	1.00
143_Y	146_Q	3.035	1.00
66_Q	69_N	2.992	1.00
119_G	171_G	2.695	0.99
121_T	125_A	2.652	0.99
46_S	77_Y	2.528	0.99
92_A	141_R	2.325	0.97
100_V	137_I	2.312	0.97
151_I	158_A	2.263	0.97
39_R	89_E	2.249	0.97
17_L	79_L	2.098	0.95
26_F	83_V	2.053	0.95
88_E	141_R	2.041	0.95
100_V	109_L	2.036	0.95
26_F	45_I	2.033	0.94
53_Y	57_L	1.966	0.93
24_V	27_F	1.903	0.92
13_V	72_A	1.828	0.91
36_K	164_E	1.784	0.89
118_Y	146_Q	1.778	0.89
88_E	92_A	1.712	0.87
29_I	91_L	1.701	0.87
28_T	76_G	1.700	0.87
44_G	48_I	1.667	0.86
51_L	74_A	1.646	0.85
100_V	151_I	1.596	0.83
82_I	150_T	1.594	0.83
144_E	162_A	1.589	0.83
31_M	137_I	1.585	0.83
51_L	60_V	1.582	0.83
27_F	81_V	1.551	0.81
88_E	94_G	1.545	0.81
54_V	70_V	1.544	0.81
116_K	150_T	1.515	0.80
43_A	85_M	1.505	0.79
23_Y	159_F	1.490	0.79
112_Q	150_T	1.489	0.79
63_N	72_A	1.488	0.79
152_K	169_H	1.476	0.78
71_I	75_L	1.450	0.77
114_R	120_V	1.444	0.77
22_V	52_V	1.444	0.77
24_V	32_I	1.434	0.76
22_V	32_I	1.418	0.75
24_V	49_E	1.409	0.75
51_L	55_T	1.387	0.74
52_V	72_A	1.357	0.72
23_Y	27_F	1.334	0.71
148_Y	166_K	1.323	0.70
21_I	25_S	1.295	0.68
31_M	35_L	1.271	0.67
83_V	150_T	1.259	0.66
46_S	82_I	1.240	0.65
42_A	159_F	1.240	0.65
114_R	129_E	1.234	0.64
43_A	82_I	1.228	0.64
23_Y	56_G	1.214	0.63
32_I	43_A	1.198	0.62
57_L	132_R	1.193	0.62
81_V	85_M	1.181	0.61
51_L	67_I	1.141	0.58
36_K	116_K	1.136	0.58
106_D	169_H	1.131	0.57
102_T	109_L	1.131	0.57
132_R	170_G	1.129	0.57
52_V	96_I	1.123	0.57
53_Y	132_R	1.114	0.56
20_N	25_S	1.113	0.56
96_I	139_T	1.075	0.54
46_S	81_V	1.064	0.53
121_T	127_G	1.064	0.53
27_F	31_M	1.051	0.52
105_L	109_L	1.042	0.51
118_Y	143_Y	1.034	0.51
19_I	56_G	1.032	0.51
99_N	136_Q	1.031	0.50
124_V	133_T	1.022	0.50
90_K	129_E	1.022	0.50
47_T	50_I	1.010	0.49
108_D	111_K	1.007	0.49
39_R	97_M	1.001	0.48
57_L	70_V	0.985	0.47
13_V	70_V	0.971	0.46
86_K	154_L	0.959	0.45
14_L	18_I	0.959	0.45
82_I	99_N	0.958	0.45
21_I	83_V	0.955	0.45
27_F	53_Y	0.951	0.45
102_T	110_P	0.951	0.45
137_I	147_L	0.948	0.45
115_E	145_L	0.942	0.44
47_T	51_L	0.938	0.44
86_K	115_E	0.924	0.43
35_L	66_Q	0.918	0.43
68_Q	72_A	0.917	0.43
21_I	24_V	0.916	0.42
47_T	75_L	0.914	0.42
119_G	159_F	0.898	0.41
62_D	157_K	0.894	0.41
87_I	122_N	0.893	0.41
96_I	166_K	0.891	0.41
28_T	53_Y	0.891	0.41
61_L	87_I	0.879	0.40
54_V	100_V	0.878	0.40
121_T	130_G	0.876	0.40
107_L	111_K	0.868	0.39
20_N	47_T	0.857	0.38
114_R	170_G	0.849	0.38
61_L	64_L	0.846	0.38
16_I	69_N	0.843	0.38
26_F	129_E	0.837	0.37
70_V	121_T	0.834	0.37
99_N	132_R	0.830	0.37
36_K	118_Y	0.829	0.37
89_E	166_K	0.824	0.36
25_S	61_L	0.816	0.36
26_F	66_Q	0.809	0.35
19_I	173_W	0.804	0.35
103_K	140_P	0.796	0.34
114_R	128_L	0.792	0.34
77_Y	81_V	0.787	0.34
100_V	146_Q	0.784	0.34
67_I	103_K	0.783	0.34
34_T	54_V	0.780	0.33
117_G	120_V	0.770	0.33
61_L	166_K	0.769	0.33
77_Y	155_D	0.768	0.33
23_Y	144_E	0.766	0.33
34_T	51_L	0.765	0.33
132_R	138_L	0.761	0.32
60_V	141_R	0.755	0.32
149_D	152_K	0.755	0.32
164_E	168_I	0.754	0.32
35_L	155_D	0.754	0.32
160_I	163_Y	0.754	0.32
69_N	72_A	0.743	0.31
30_R	49_E	0.738	0.31
114_R	135_L	0.737	0.31
94_G	141_R	0.735	0.31
132_R	163_Y	0.733	0.31
142_R	162_A	0.732	0.31
20_N	27_F	0.730	0.30
35_L	135_L	0.722	0.30
36_K	171_G	0.722	0.30
14_L	108_D	0.717	0.30
23_Y	79_L	0.710	0.29
79_L	96_I	0.708	0.29
159_F	164_E	0.706	0.29
33_L	155_D	0.706	0.29
33_L	87_I	0.705	0.29
40_Y	68_Q	0.700	0.29
125_A	141_R	0.698	0.29
101_I	130_G	0.693	0.28
128_L	151_I	0.693	0.28
13_V	69_N	0.691	0.28
55_T	58_S	0.686	0.28
41_L	44_G	0.685	0.28
114_R	137_I	0.676	0.27
40_Y	67_I	0.673	0.27
125_A	134_A	0.672	0.27
58_S	66_Q	0.668	0.27
88_E	93_L	0.666	0.27
93_L	146_Q	0.665	0.27
23_Y	47_T	0.662	0.27
25_S	87_I	0.661	0.26
56_G	163_Y	0.661	0.26
77_Y	136_Q	0.659	0.26
164_E	171_G	0.659	0.26
23_Y	42_A	0.657	0.26
38_Q	41_L	0.655	0.26
112_Q	116_K	0.655	0.26
111_K	115_E	0.655	0.26
29_I	90_K	0.652	0.26
46_S	142_R	0.646	0.26
19_I	144_E	0.643	0.26
23_Y	75_L	0.641	0.25
109_L	112_Q	0.640	0.25
11_A	55_T	0.638	0.25
103_K	160_I	0.635	0.25
17_L	48_I	0.634	0.25
46_S	73_Y	0.631	0.25
82_I	125_A	0.630	0.25
56_G	106_D	0.630	0.25
123_W	134_A	0.628	0.25
12_M	152_K	0.624	0.25
54_V	88_E	0.622	0.24
46_S	57_L	0.614	0.24
23_Y	57_L	0.608	0.24
75_L	86_K	0.608	0.24
56_G	161_I	0.605	0.24
114_R	122_N	0.603	0.23
37_G	100_V	0.600	0.23
53_Y	70_V	0.594	0.23
99_N	155_D	0.590	0.23
22_V	116_K	0.585	0.23
12_M	83_V	0.583	0.22
116_K	146_Q	0.582	0.22
13_V	142_R	0.578	0.22
16_I	28_T	0.578	0.22
101_I	134_A	0.577	0.22
48_I	56_G	0.573	0.22
60_V	88_E	0.573	0.22
48_I	112_Q	0.573	0.22
82_I	139_T	0.571	0.22
17_L	74_A	0.569	0.22
138_L	165_P	0.556	0.21
107_L	153_T	0.555	0.21
71_I	79_L	0.554	0.21
102_T	135_L	0.553	0.21
62_D	77_Y	0.544	0.21
37_G	97_M	0.543	0.21
120_V	165_P	0.541	0.20
101_I	125_A	0.541	0.20
34_T	169_H	0.539	0.20
98_V	166_K	0.537	0.20
132_R	160_I	0.536	0.20
107_L	115_E	0.535	0.20
26_F	167_T	0.534	0.20
139_T	143_Y	0.532	0.20
58_S	79_L	0.531	0.20
144_E	159_F	0.530	0.20
54_V	132_R	0.527	0.20
45_I	54_V	0.526	0.20
37_G	64_L	0.526	0.20
64_L	151_I	0.523	0.20
45_I	105_L	0.521	0.20
21_I	55_T	0.521	0.20
91_L	143_Y	0.519	0.19
25_S	50_I	0.519	0.19
51_L	111_K	0.518	0.19
32_I	36_K	0.517	0.19
56_G	77_Y	0.515	0.19
64_L	67_I	0.515	0.19
34_T	82_I	0.515	0.19
14_L	118_Y	0.514	0.19
138_L	168_I	0.514	0.19
33_L	119_G	0.513	0.19
52_V	107_L	0.512	0.19
44_G	112_Q	0.510	0.19
39_R	140_P	0.509	0.19
32_I	93_L	0.507	0.19
112_Q	157_K	0.507	0.19
20_N	42_A	0.504	0.19
87_I	100_V	0.502	0.19
114_R	127_G	0.502	0.19
47_T	113_L	0.500	0.19

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
3hluA	2	0.3804	99.6	0.764	Contact Map
2dclA	5	0.4674	88.7	0.925	Contact Map
4rleA	3	0.5163	75.7	0.936	Contact Map
4rwwA	3	0.4239	60.7	0.942	Contact Map
1o51A	3	0.3913	60.5	0.942	Contact Map
4usiA	3	0.4728	55.7	0.944	Contact Map
3m05A	3	0.4185	53.3	0.945	Contact Map
4affA	3	0.4565	53.2	0.945	Contact Map
4wk1A	3	0.4402	52	0.945	Contact Map
2gw8A	3	0.4348	49	0.946	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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