YVLD - BACSU - GREMLIN Contacts

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YVLD - Uncharacterized membrane protein YvlD

UniProt:	O34648	Sequences: MVKWAVSILVNALLLIVIDGYIDSIHISSIGAAIIASLILSILNVLIKPLLIIFTLPVTMVTLGLFLFVINAITLMMTASIMGDSFQIDGFGTAIWASVILSVFHLLIQKGILEPLRKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	119 (110)
Sequences:	1506 (1125)
Seq/√Len:	107.2

BACSU - YVLD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_T	67_L	3.730	1.00
72_A	95_I	2.947	1.00
75_L	101_L	2.899	1.00
18_I	101_L	2.709	1.00
43_L	78_T	2.499	1.00
68_F	95_I	2.341	1.00
22_I	93_T	2.305	1.00
75_L	97_A	2.288	1.00
52_I	67_L	2.280	1.00
53_I	56_L	2.208	1.00
18_I	100_I	2.198	1.00
91_F	95_I	2.077	1.00
48_K	52_I	2.013	1.00
43_L	74_T	1.986	1.00
15_L	36_A	1.942	1.00
73_I	76_M	1.940	1.00
82_M	85_S	1.914	1.00
25_I	97_A	1.864	1.00
16_I	33_A	1.655	1.00
72_A	91_F	1.641	1.00
14_L	108_I	1.575	1.00
26_H	89_D	1.565	1.00
55_T	67_L	1.521	1.00
40_L	78_T	1.494	1.00
4_W	38_L	1.489	1.00
22_I	100_I	1.479	1.00
52_I	55_T	1.436	1.00
92_G	96_W	1.414	1.00
75_L	88_I	1.412	1.00
15_L	101_L	1.391	1.00
10_V	108_I	1.298	0.99
82_M	86_F	1.296	0.99
52_I	70_I	1.268	0.99
93_T	97_A	1.185	0.99
15_L	97_A	1.169	0.99
91_F	94_A	1.162	0.99
104_F	108_I	1.161	0.99
4_W	8_I	1.158	0.99
51_L	74_T	1.148	0.98
24_S	89_D	1.139	0.98
32_A	82_M	1.138	0.98
100_I	104_F	1.097	0.98
98_S	102_S	1.080	0.98
71_N	102_S	1.079	0.98
97_A	101_L	1.064	0.97
12_A	34_I	1.060	0.97
56_L	59_T	1.059	0.97
16_I	20_G	1.050	0.97
65_L	69_V	1.041	0.97
66_F	69_V	1.040	0.97
39_I	82_M	1.025	0.97
8_I	38_L	1.007	0.96
79_A	88_I	1.002	0.96
77_M	80_S	1.000	0.96
59_T	66_F	0.998	0.96
14_L	18_I	0.995	0.96
12_A	47_I	0.988	0.96
79_A	87_Q	0.986	0.96
14_L	104_F	0.976	0.96
36_A	86_F	0.967	0.96
27_I	33_A	0.963	0.95
90_G	93_T	0.957	0.95
88_I	97_A	0.938	0.95
55_T	66_F	0.938	0.95
28_S	32_A	0.930	0.94
25_I	79_A	0.928	0.94
52_I	56_L	0.923	0.94
56_L	60_M	0.894	0.93
59_T	70_I	0.890	0.93
7_S	109_Q	0.886	0.93
22_I	96_W	0.886	0.93
30_I	33_A	0.885	0.93
17_V	104_F	0.880	0.93
43_L	47_I	0.868	0.92
8_I	37_S	0.868	0.92
41_S	105_H	0.865	0.92
25_I	75_L	0.855	0.92
75_L	79_A	0.848	0.91
55_T	74_T	0.826	0.90
8_I	11_N	0.813	0.89
39_I	78_T	0.811	0.89
16_I	27_I	0.810	0.89
25_I	86_F	0.801	0.89
48_K	102_S	0.797	0.88
106_L	110_K	0.794	0.88
48_K	67_L	0.785	0.88
89_D	93_T	0.777	0.87
39_I	81_I	0.772	0.87
68_F	71_N	0.770	0.87
92_G	95_I	0.770	0.87
30_I	34_I	0.769	0.87
76_M	80_S	0.765	0.86
3_K	7_S	0.754	0.86
29_S	33_A	0.751	0.85
22_I	97_A	0.750	0.85
39_I	43_L	0.750	0.85
72_A	76_M	0.749	0.85
5_A	9_L	0.743	0.85
17_V	20_G	0.735	0.84
65_L	95_I	0.726	0.83
69_V	95_I	0.726	0.83
17_V	108_I	0.725	0.83
95_I	98_S	0.719	0.83
38_L	45_V	0.718	0.83
105_H	109_Q	0.717	0.83
38_L	42_I	0.714	0.82
46_L	52_I	0.709	0.82
17_V	21_Y	0.701	0.81
58_V	67_L	0.697	0.81
33_A	86_F	0.693	0.80
50_L	80_S	0.693	0.80
53_I	60_M	0.687	0.80
14_L	17_V	0.686	0.80
18_I	22_I	0.681	0.79
73_I	90_G	0.669	0.78
67_L	109_Q	0.667	0.78
25_I	101_L	0.658	0.77
4_W	7_S	0.655	0.77
75_L	85_S	0.653	0.76
19_D	86_F	0.637	0.75
63_L	110_K	0.633	0.74
76_M	94_A	0.630	0.74
15_L	105_H	0.624	0.73
17_V	81_I	0.622	0.73
15_L	27_I	0.616	0.72
26_H	70_I	0.611	0.71
37_S	73_I	0.601	0.70
53_I	61_V	0.600	0.70
2_V	103_V	0.592	0.69
47_I	74_T	0.588	0.69
18_I	93_T	0.587	0.68
52_I	59_T	0.582	0.68
20_G	108_I	0.576	0.67
40_L	82_M	0.575	0.67
32_A	37_S	0.574	0.67
37_S	85_S	0.571	0.66
32_A	78_T	0.568	0.66
79_A	82_M	0.568	0.66
43_L	106_L	0.567	0.66
49_P	66_F	0.565	0.65
4_W	11_N	0.564	0.65
15_L	86_F	0.560	0.65
31_G	103_V	0.559	0.65
63_L	109_Q	0.558	0.65
6_V	16_I	0.556	0.64
73_I	77_M	0.550	0.63
55_T	59_T	0.548	0.63
9_L	16_I	0.545	0.63
41_S	45_V	0.542	0.62
62_T	70_I	0.537	0.62
58_V	70_I	0.536	0.61
38_L	82_M	0.536	0.61
40_L	48_K	0.535	0.61
7_S	17_V	0.535	0.61
10_V	14_L	0.524	0.60
23_D	28_S	0.521	0.59
6_V	10_V	0.514	0.58
20_G	30_I	0.513	0.58
108_I	112_I	0.512	0.58
22_I	36_A	0.509	0.58
47_I	67_L	0.508	0.57
8_I	42_I	0.507	0.57
101_L	106_L	0.504	0.57
99_V	103_V	0.502	0.57
14_L	21_Y	0.500	0.56

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
3qnqA	2	0.9748	12	0.93	Contact Map
2kv5A	1	0.2689	9.6	0.933	Contact Map
4b19A	1	0.2521	6.9	0.937	Contact Map
4czbA	2	0.9832	6.1	0.939	Contact Map
4oh3A	2	0.9748	4.5	0.943	Contact Map
4cz8A	2	0.958	4.1	0.944	Contact Map
3wajA	1	0.9496	2.8	0.948	Contact Map
4rp9A	2	0.8319	2.3	0.95	Contact Map
3wdoA	1	0.9664	2.3	0.95	Contact Map
2ksfA	1	0.8403	2.1	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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