YIDD - BACSU - GREMLIN Contacts

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YIDD - Putative membrane protein insertion efficiency factor

UniProt:	O34601	Sequences: MKTLFIALIRGYQKFISPLTPPTCRFYPTCSQYGIEAIKTHGALKGGWLTIKRILKCHPFHPGGVDPVPEKKQKH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	75 (67)
Sequences:	2712 (1600)
Seq/√Len:	195.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_G	50_T	4.256	1.00
5_F	43_A	2.685	1.00
6_I	35_I	2.300	1.00
42_G	46_G	2.227	1.00
20_T	23_T	2.078	1.00
13_Q	32_Q	1.998	1.00
26_F	61_H	1.890	1.00
32_Q	36_E	1.764	1.00
48_W	52_K	1.696	1.00
5_F	38_I	1.647	1.00
52_K	56_K	1.644	1.00
11_G	15_F	1.640	1.00
38_I	47_G	1.621	1.00
26_F	62_P	1.609	1.00
27_Y	65_V	1.487	1.00
10_R	13_Q	1.483	1.00
13_Q	35_I	1.424	1.00
35_I	39_K	1.422	1.00
52_K	58_H	1.376	1.00
49_L	69_P	1.350	1.00
10_R	35_I	1.317	1.00
36_E	40_T	1.314	1.00
38_I	50_T	1.283	1.00
7_A	11_G	1.247	1.00
25_R	61_H	1.236	1.00
56_K	61_H	1.195	1.00
9_I	13_Q	1.182	1.00
9_I	38_I	1.151	1.00
9_I	34_G	1.107	1.00
49_L	52_K	1.099	1.00
38_I	43_A	1.098	1.00
26_F	56_K	1.054	1.00
58_H	61_H	1.050	1.00
51_I	55_L	1.040	1.00
15_F	19_L	0.996	1.00
10_R	14_K	0.986	0.99
41_H	68_V	0.983	0.99
15_F	18_P	0.981	0.99
34_G	47_G	0.978	0.99
54_I	58_H	0.953	0.99
3_T	7_A	0.935	0.99
27_Y	32_Q	0.929	0.99
55_L	58_H	0.928	0.99
16_I	20_T	0.911	0.99
32_Q	35_I	0.907	0.99
47_G	51_I	0.901	0.99
36_E	68_V	0.883	0.99
41_H	45_K	0.877	0.99
6_I	39_K	0.844	0.98
41_H	69_P	0.838	0.98
37_A	68_V	0.825	0.98
43_A	47_G	0.819	0.98
50_T	54_I	0.814	0.98
6_I	10_R	0.813	0.98
49_L	68_V	0.772	0.97
7_A	10_R	0.758	0.97
34_G	38_I	0.742	0.96
36_E	67_P	0.739	0.96
4_L	7_A	0.723	0.96
16_I	23_T	0.698	0.95
9_I	35_I	0.696	0.95
25_R	62_P	0.695	0.95
38_I	46_G	0.694	0.95
19_L	22_P	0.688	0.95
36_E	39_K	0.687	0.95
12_Y	16_I	0.675	0.94
17_S	21_P	0.671	0.94
27_Y	63_G	0.657	0.93
60_F	65_V	0.633	0.92
12_Y	20_T	0.633	0.92
16_I	22_P	0.632	0.92
26_F	67_P	0.620	0.91
9_I	54_I	0.614	0.91
5_F	8_L	0.613	0.91
37_A	49_L	0.612	0.91
48_W	55_L	0.612	0.91
52_K	55_L	0.598	0.90
34_G	54_I	0.595	0.89
5_F	47_G	0.582	0.88
9_I	12_Y	0.579	0.88
44_L	55_L	0.570	0.87
6_I	38_I	0.570	0.87
15_F	20_T	0.569	0.87
3_T	39_K	0.558	0.86
52_K	61_H	0.555	0.86
4_L	8_L	0.554	0.86
16_I	21_P	0.545	0.85
46_G	50_T	0.542	0.84
4_L	44_L	0.541	0.84
11_G	14_K	0.536	0.84
45_K	49_L	0.534	0.84
44_L	47_G	0.532	0.83
61_H	64_G	0.525	0.83
17_S	29_T	0.525	0.83
10_R	39_K	0.520	0.82
14_K	60_F	0.519	0.82
21_P	25_R	0.510	0.81
8_L	11_G	0.507	0.80
26_F	58_H	0.504	0.80
16_I	19_L	0.500	0.79

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
4fccA	5	0.8533	31.4	0.908	Contact Map
3mw9A	5	0.8533	11.6	0.924	Contact Map
1bgvA	5	0.9067	10.8	0.926	Contact Map
3qpiA	1	0.4667	6.1	0.933	Contact Map
2bmaA	5	0.8533	5.7	0.934	Contact Map
2tmgA	5	0.9067	5.6	0.935	Contact Map
3r3jA	5	0.8533	5.4	0.935	Contact Map
2jlnA	1	0.2667	5.4	0.935	Contact Map
3k92A	5	0.84	5.2	0.935	Contact Map
3aoeE	3	0.8533	4.9	0.937	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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