YUID - BACSU - GREMLIN Contacts

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YUID - Uncharacterized membrane protein YuiD

UniProt:	O32107	Sequences: MELLTNFPLLSSLAAIIFAQVIKVPIQFIVSRKLDWSLVTSTGGMPSSHSAAVTALSTGVALEHGLDSSLFAVSAIFAVITMFDATGVRRHAGEQATVINKLVIDFNRFVNEAKDFPKAAEKEKQKKLKELLGHQPIEVFFGGLTGILLTLVLAYFFM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	158 (141)
Sequences:	863 (570)
Seq/√Len:	48.0

BACSU - YUID

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_S	78_A	4.598	1.00
92_A	132_L	4.030	1.00
38_L	41_S	3.141	1.00
57_S	74_S	3.023	1.00
42_T	83_F	2.975	1.00
61_A	66_L	2.800	1.00
11_S	55_A	2.762	1.00
70_L	73_V	2.735	1.00
100_N	130_E	2.732	1.00
82_M	143_G	2.627	1.00
64_H	69_S	2.544	1.00
18_F	145_T	2.128	1.00
45_M	141_F	2.113	1.00
42_T	132_L	2.020	1.00
90_R	94_E	1.953	0.99
12_S	55_A	1.872	0.99
50_S	54_T	1.869	0.99
11_S	153_L	1.803	0.99
54_T	143_G	1.793	0.99
15_A	55_A	1.748	0.99
95_Q	99_I	1.717	0.98
88_V	132_L	1.712	0.98
50_S	144_L	1.699	0.98
64_H	70_L	1.544	0.97
62_L	154_A	1.541	0.97
22_I	26_I	1.505	0.96
58_T	147_I	1.494	0.96
91_H	132_L	1.493	0.96
142_G	146_G	1.473	0.96
82_M	139_V	1.471	0.96
60_V	69_S	1.460	0.95
73_V	77_F	1.458	0.95
22_I	145_T	1.420	0.95
16_I	52_A	1.382	0.94
57_S	75_A	1.346	0.93
22_I	141_F	1.345	0.93
90_R	138_E	1.285	0.91
60_V	73_V	1.269	0.91
7_F	150_T	1.267	0.91
17_I	81_T	1.245	0.90
27_Q	35_D	1.219	0.89
53_V	77_F	1.213	0.89
16_I	25_P	1.207	0.88
104_I	127_K	1.202	0.88
85_A	143_G	1.190	0.88
135_Q	138_E	1.182	0.87
10_L	15_A	1.166	0.87
96_A	100_N	1.157	0.86
100_N	128_L	1.154	0.86
88_V	95_Q	1.152	0.86
16_I	41_S	1.150	0.86
53_V	78_A	1.140	0.85
50_S	82_M	1.119	0.84
17_I	153_L	1.109	0.84
14_A	33_K	1.092	0.83
55_A	59_G	1.090	0.83
56_L	77_F	1.085	0.82
91_H	135_Q	1.084	0.82
50_S	141_F	1.080	0.82
52_A	76_I	1.078	0.82
96_A	128_L	1.068	0.81
73_V	137_I	1.061	0.81
90_R	93_G	1.049	0.80
43_G	49_H	1.049	0.80
86_T	136_P	1.039	0.80
91_H	96_A	1.038	0.79
34_L	91_H	1.034	0.79
19_A	42_T	1.033	0.79
60_V	68_S	1.028	0.79
57_S	71_F	1.017	0.78
107_N	138_E	1.013	0.78
95_Q	98_V	1.009	0.77
78_A	81_T	1.001	0.77
90_R	135_Q	0.994	0.76
10_L	14_A	0.989	0.76
61_A	71_F	0.985	0.76
87_G	96_A	0.975	0.75
42_T	48_S	0.965	0.74
14_A	17_I	0.956	0.74
20_Q	48_S	0.948	0.73
15_A	51_A	0.937	0.72
24_V	38_L	0.931	0.72
45_M	137_I	0.925	0.71
5_T	10_L	0.920	0.71
75_A	79_V	0.917	0.70
56_L	73_V	0.911	0.70
63_E	66_L	0.907	0.70
12_S	59_G	0.905	0.69
77_F	99_I	0.894	0.68
80_I	124_K	0.891	0.68
60_V	74_S	0.885	0.68
99_I	103_V	0.880	0.67
53_V	56_L	0.880	0.67
42_T	88_V	0.874	0.67
98_V	103_V	0.874	0.67
15_A	19_A	0.864	0.66
11_S	59_G	0.858	0.65
92_A	96_A	0.843	0.64
27_Q	31_S	0.843	0.64
120_A	123_E	0.836	0.63
12_S	56_L	0.831	0.63
15_A	80_I	0.830	0.63
21_V	39_V	0.828	0.62
24_V	41_S	0.828	0.62
126_K	129_K	0.820	0.62
87_G	92_A	0.819	0.62
87_G	100_N	0.816	0.61
51_A	102_L	0.807	0.60
58_T	80_I	0.805	0.60
61_A	67_D	0.803	0.60
94_E	97_T	0.803	0.60
46_P	49_H	0.797	0.59
29_I	144_L	0.788	0.59
20_Q	23_K	0.782	0.58
59_G	150_T	0.768	0.57
12_S	53_V	0.766	0.56
60_V	70_L	0.744	0.54
66_L	150_T	0.739	0.54
94_E	138_E	0.738	0.54
45_M	51_A	0.735	0.53
25_P	108_R	0.734	0.53
38_L	42_T	0.733	0.53
38_L	48_S	0.730	0.53
7_F	11_S	0.728	0.53
48_S	56_L	0.719	0.52
98_V	128_L	0.719	0.52
33_K	129_K	0.714	0.51
23_K	46_P	0.711	0.51
13_L	79_V	0.707	0.51
54_T	137_I	0.697	0.50
15_A	27_Q	0.696	0.49
19_A	48_S	0.687	0.49
20_Q	129_K	0.685	0.48
43_G	46_P	0.684	0.48
60_V	64_H	0.682	0.48
74_S	81_T	0.681	0.48
9_L	12_S	0.679	0.48
105_D	127_K	0.674	0.47
8_P	129_K	0.671	0.47
5_T	73_V	0.667	0.47
17_I	36_W	0.666	0.46
21_V	151_L	0.659	0.46
13_L	18_F	0.652	0.45
92_A	130_E	0.651	0.45
126_K	149_L	0.650	0.45
14_A	51_A	0.642	0.44
17_I	21_V	0.639	0.44
109_F	123_E	0.635	0.43
29_I	138_E	0.631	0.43
54_T	78_A	0.627	0.43
8_P	16_I	0.625	0.42
14_A	18_F	0.623	0.42
16_I	95_Q	0.622	0.42
25_P	154_A	0.622	0.42
85_A	93_G	0.620	0.42
88_V	140_F	0.615	0.41
28_F	33_K	0.613	0.41
23_K	49_H	0.606	0.41
7_F	59_G	0.603	0.40
45_M	132_L	0.602	0.40
4_L	10_L	0.601	0.40
62_L	66_L	0.600	0.40
87_G	90_R	0.600	0.40
54_T	64_H	0.599	0.40
96_A	131_L	0.592	0.39
148_L	151_L	0.590	0.39
18_F	132_L	0.589	0.39
58_T	62_L	0.587	0.39
33_K	36_W	0.586	0.39
83_F	132_L	0.584	0.38
91_H	97_T	0.583	0.38
30_V	61_A	0.569	0.37
25_P	29_I	0.563	0.36
19_A	145_T	0.563	0.36
36_W	122_K	0.562	0.36
95_Q	128_L	0.561	0.36
11_S	15_A	0.559	0.36
10_L	152_V	0.557	0.36
48_S	51_A	0.555	0.36
67_D	140_F	0.554	0.36
71_F	92_A	0.547	0.35
74_S	78_A	0.546	0.35
17_I	152_V	0.542	0.34
77_F	81_T	0.540	0.34
53_V	57_S	0.540	0.34
14_A	21_V	0.539	0.34
82_M	145_T	0.536	0.34
105_D	138_E	0.534	0.34
20_Q	142_G	0.534	0.34
58_T	150_T	0.531	0.34
94_E	124_K	0.528	0.33
90_R	130_E	0.526	0.33
25_P	40_T	0.526	0.33
69_S	74_S	0.522	0.33
82_M	85_A	0.522	0.33
14_A	153_L	0.522	0.33
78_A	82_M	0.521	0.33
80_I	105_D	0.521	0.33
75_A	80_I	0.521	0.33
50_S	126_K	0.518	0.32
24_V	88_V	0.517	0.32
62_L	151_L	0.515	0.32
106_F	120_A	0.512	0.32
28_F	34_L	0.511	0.32
86_T	131_L	0.509	0.32
24_V	68_S	0.508	0.31
21_V	88_V	0.508	0.31
122_K	148_L	0.507	0.31
54_T	73_V	0.505	0.31
16_I	80_I	0.503	0.31
28_F	129_K	0.501	0.31
21_V	153_L	0.500	0.31

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
4px7A	1	0.7089	95.6	0.895	Contact Map
4citA	1	0.8101	95	0.899	Contact Map
2ipbA	2	0.7025	94.3	0.902	Contact Map
1d2tA	5	0.7025	93.1	0.907	Contact Map
3w36A	2	0.8734	87.2	0.918	Contact Map
1qi9A	2	0.8418	86.1	0.92	Contact Map
3bb0A	1	0.8797	80.8	0.925	Contact Map
1up8A	9	0.8354	75.3	0.928	Contact Map
2jlnA	1	0.6646	14.7	0.953	Contact Map
4tl1A	2	0.2025	9	0.958	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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