YLMG - BACSU - GREMLIN Contacts

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YLMG - Uncharacterized membrane protein YlmG

UniProt:	O31729	Sequences: MILYQVFSVLSLLITIYSFALIIYIFMSWVPSTRETAVGRFLASICEPYLEPFRKIIPPIAMLDISPIVAILVLRFATTGLWGLYRMIAF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	90 (80)
Sequences:	1588 (1132)
Seq/√Len:	126.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_Y	46_C	3.089	1.00
53_F	70_A	3.044	1.00
47_E	51_E	2.894	1.00
20_A	46_C	2.464	1.00
60_I	65_I	2.327	1.00
68_I	75_R	2.305	1.00
20_A	45_I	2.085	1.00
14_I	78_T	2.050	1.00
21_L	46_C	2.042	1.00
14_I	74_L	2.004	1.00
11_S	78_T	1.957	1.00
52_P	56_I	1.931	1.00
53_F	73_V	1.839	1.00
59_P	62_M	1.833	1.00
21_L	70_A	1.817	1.00
47_E	54_R	1.638	1.00
40_R	44_S	1.638	1.00
75_R	78_T	1.576	1.00
20_A	42_L	1.514	1.00
54_R	64_D	1.466	1.00
11_S	15_T	1.422	1.00
76_F	80_G	1.396	1.00
41_F	45_I	1.375	1.00
49_Y	70_A	1.361	1.00
54_R	59_P	1.306	1.00
68_I	71_I	1.246	1.00
72_L	79_T	1.192	0.99
15_T	78_T	1.163	0.99
22_I	71_I	1.160	0.99
49_Y	52_P	1.128	0.99
29_W	63_L	1.121	0.99
15_T	19_F	1.115	0.99
50_L	67_P	1.109	0.99
10_L	85_Y	1.094	0.99
18_S	75_R	1.089	0.99
19_F	23_I	1.088	0.99
7_F	82_W	1.057	0.98
79_T	83_G	0.985	0.98
7_F	85_Y	0.979	0.97
75_R	79_T	0.976	0.97
10_L	18_S	0.941	0.97
26_F	75_R	0.920	0.96
30_V	33_T	0.904	0.96
18_S	74_L	0.899	0.96
59_P	65_I	0.895	0.96
50_L	70_A	0.876	0.95
22_I	74_L	0.869	0.95
13_L	17_Y	0.858	0.95
33_T	39_G	0.848	0.94
17_Y	74_L	0.848	0.94
24_Y	50_L	0.836	0.94
31_P	39_G	0.823	0.93
72_L	76_F	0.823	0.93
80_G	83_G	0.820	0.93
59_P	64_D	0.820	0.93
8_S	12_L	0.815	0.93
25_I	68_I	0.811	0.93
12_L	16_I	0.807	0.93
30_V	58_P	0.797	0.92
25_I	62_M	0.797	0.92
25_I	67_P	0.785	0.92
15_T	75_R	0.784	0.92
57_I	69_V	0.767	0.91
58_P	66_S	0.763	0.90
56_I	61_A	0.762	0.90
27_M	36_T	0.759	0.90
50_L	66_S	0.758	0.90
33_T	36_T	0.758	0.90
21_L	71_I	0.754	0.90
82_W	85_Y	0.749	0.90
78_T	82_W	0.739	0.89
15_T	38_V	0.738	0.89
27_M	39_G	0.736	0.89
24_Y	47_E	0.733	0.89
76_F	79_T	0.733	0.89
25_I	29_W	0.695	0.86
61_A	65_I	0.687	0.85
80_G	84_L	0.679	0.84
17_Y	48_P	0.676	0.84
21_L	50_L	0.664	0.83
16_I	20_A	0.661	0.83
65_I	68_I	0.656	0.82
62_M	65_I	0.652	0.82
40_R	43_A	0.645	0.81
25_I	59_P	0.645	0.81
30_V	42_L	0.637	0.80
71_I	75_R	0.637	0.80
11_S	14_I	0.636	0.80
28_S	64_D	0.636	0.80
60_I	66_S	0.636	0.80
57_I	60_I	0.628	0.80
55_K	58_P	0.628	0.80
15_T	18_S	0.623	0.79
26_F	38_V	0.619	0.79
17_Y	45_I	0.618	0.78
29_W	65_I	0.611	0.78
60_I	77_A	0.610	0.78
24_Y	43_A	0.607	0.77
49_Y	53_F	0.600	0.76
57_I	61_A	0.598	0.76
7_F	10_L	0.592	0.75
24_Y	39_G	0.588	0.75
35_E	40_R	0.567	0.72
28_S	67_P	0.559	0.71
26_F	33_T	0.554	0.71
52_P	80_G	0.553	0.70
16_I	55_K	0.551	0.70
17_Y	20_A	0.547	0.70
30_V	62_M	0.546	0.70
34_R	76_F	0.546	0.70
69_V	73_V	0.546	0.70
15_T	63_L	0.539	0.69
33_T	37_A	0.536	0.68
58_P	69_V	0.531	0.67
49_Y	56_I	0.526	0.67
33_T	40_R	0.514	0.65
58_P	61_A	0.508	0.64
19_F	29_W	0.507	0.64
74_L	78_T	0.501	0.63
49_Y	77_A	0.500	0.63

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
1ku5A	2	0.5	3.4	0.914	Contact Map
3tiaA	3	0	3.1	0.916	Contact Map
1nmbN	1	0	2.7	0.918	Contact Map
4b7jA	3	0	1.6	0.928	Contact Map
1ciiA	1	0.4667	1.3	0.932	Contact Map
2mm4A	1	0.3556	1	0.937	Contact Map
4p6vD	1	0.8556	0.9	0.938	Contact Map
2lotA	1	0.3667	0.9	0.938	Contact Map
4lxjA	1	0.4889	0.8	0.94	Contact Map
4pirA	3	0.3111	0.8	0.941	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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