YRBF - BACSU - GREMLIN Contacts

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YRBF - UPF0092 membrane protein YrbF

UniProt:	O32052	Sequences: MMTGTLGTLVPIILMFAVLYFLLIRPQQKQQKAVRQMQEELKKGDSVVTIGGLHGTVDSIDESKVVIKTGDNTRLTFDRRAIREVSAAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	89 (79)
Sequences:	2316 (1545)
Seq/√Len:	173.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_Q	40_E	2.700	1.00
69_T	75_L	2.332	1.00
34_V	38_Q	2.103	1.00
33_A	36_Q	2.102	1.00
12_I	16_F	2.068	1.00
54_H	78_D	2.059	1.00
19_L	23_L	2.042	1.00
29_K	33_A	1.951	1.00
18_V	22_L	1.837	1.00
9_L	13_I	1.795	1.00
66_V	74_R	1.742	1.00
41_L	82_I	1.722	1.00
36_Q	39_E	1.681	1.00
35_R	39_E	1.673	1.00
53_L	75_L	1.659	1.00
70_G	73_T	1.526	1.00
31_Q	35_R	1.517	1.00
47_V	67_I	1.487	1.00
46_S	56_T	1.484	1.00
41_L	57_V	1.465	1.00
50_I	81_A	1.459	1.00
30_Q	33_A	1.449	1.00
28_Q	31_Q	1.431	1.00
14_L	17_A	1.356	1.00
8_T	12_I	1.355	1.00
53_L	69_T	1.333	1.00
10_V	14_L	1.310	1.00
6_L	11_P	1.277	1.00
54_H	64_K	1.277	1.00
7_G	11_P	1.270	1.00
28_Q	32_K	1.259	1.00
15_M	19_L	1.180	1.00
16_F	24_I	1.177	1.00
12_I	15_M	1.159	1.00
66_V	76_T	1.156	1.00
13_I	17_A	1.147	1.00
6_L	10_V	1.134	1.00
25_R	29_K	1.126	1.00
69_T	73_T	1.102	1.00
53_L	77_F	1.077	1.00
65_V	82_I	1.040	0.99
58_D	74_R	1.026	0.99
7_G	10_V	1.010	0.99
11_P	14_L	0.999	0.99
60_I	79_R	0.983	0.99
16_F	19_L	0.981	0.99
64_K	76_T	0.956	0.99
68_K	71_D	0.943	0.99
56_T	68_K	0.942	0.99
54_H	59_S	0.928	0.99
50_I	83_R	0.927	0.99
11_P	15_M	0.926	0.99
55_G	67_I	0.920	0.99
24_I	28_Q	0.908	0.99
30_Q	34_V	0.897	0.98
78_D	81_A	0.896	0.98
27_Q	31_Q	0.889	0.98
68_K	74_R	0.877	0.98
42_K	45_D	0.874	0.98
68_K	72_N	0.839	0.98
31_Q	34_V	0.839	0.98
12_I	19_L	0.838	0.98
8_T	11_P	0.813	0.97
23_L	28_Q	0.804	0.97
67_I	77_F	0.803	0.97
41_L	60_I	0.790	0.97
25_R	28_Q	0.786	0.96
49_T	67_I	0.784	0.96
9_L	12_I	0.772	0.96
48_V	54_H	0.759	0.96
61_D	76_T	0.745	0.95
49_T	77_F	0.743	0.95
78_D	84_E	0.736	0.95
37_M	40_E	0.735	0.95
48_V	84_E	0.734	0.95
14_L	18_V	0.724	0.94
25_R	33_A	0.712	0.94
61_D	64_K	0.702	0.93
37_M	83_R	0.679	0.92
70_G	75_L	0.662	0.91
64_K	78_D	0.659	0.91
43_K	58_D	0.656	0.91
43_K	59_S	0.648	0.90
58_D	68_K	0.646	0.90
65_V	79_R	0.644	0.90
71_D	74_R	0.643	0.90
37_M	46_S	0.640	0.90
14_L	23_L	0.634	0.89
17_A	21_F	0.632	0.89
54_H	76_T	0.627	0.89
47_V	82_I	0.619	0.88
37_M	45_D	0.612	0.88
68_K	76_T	0.608	0.87
34_V	37_M	0.605	0.87
21_F	25_R	0.599	0.87
20_Y	66_V	0.596	0.86
51_G	77_F	0.593	0.86
69_T	77_F	0.589	0.86
70_G	74_R	0.587	0.86
34_V	50_I	0.581	0.85
46_S	54_H	0.579	0.85
46_S	78_D	0.577	0.85
12_I	17_A	0.575	0.84
66_V	71_D	0.575	0.84
8_T	16_F	0.570	0.84
46_S	64_K	0.555	0.82
57_V	60_I	0.553	0.82
77_F	81_A	0.542	0.81
65_V	77_F	0.540	0.80
7_G	12_I	0.534	0.80
7_G	14_L	0.534	0.80
50_I	80_R	0.525	0.79
18_V	23_L	0.509	0.76
10_V	20_Y	0.504	0.76
49_T	53_L	0.504	0.76
49_T	82_I	0.502	0.76
15_M	18_V	0.501	0.75
15_M	71_D	0.500	0.75

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
2rddB	1	0.4157	99.3	0.603	Contact Map
4hczA	1	0.5843	67.4	0.882	Contact Map
1zq1A	2	0.6404	60.4	0.888	Contact Map
4hw9A	3	0.764	46.8	0.896	Contact Map
1dbgA	1	0.7191	39.1	0.901	Contact Map
5ajiA	3	0.764	39.1	0.901	Contact Map
3udcA	3	0.764	31.9	0.906	Contact Map
3lrxA	3	0.427	30.9	0.906	Contact Map
4l5gA	1	0.5955	30.6	0.906	Contact Map
1u1sA	3	0.6404	27.6	0.908	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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