DUF308 - PFAM28P - GREMLIN Contacts

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DUF308 - Short repeat of unknown function (DUF308)

PFAM:	PF03729	Sequences: LLGILAIVAGILALAWPGITLLALVLLLGAWLLVSGIFEIVAAFRLRGEGGGGRWWLLLSGILSILLGVLLLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	73 (72)
Sequences:	56161 (38200)
Seq/√Len:	4501.9
META:	0.913

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_A	31_W	2.896	1.00
30_A	34_V	2.475	1.00
33_L	68_G	2.371	1.00
11_I	15_A	2.170	1.00
26_L	30_A	2.149	1.00
12_L	16_W	2.119	1.00
35_S	39_E	2.093	1.00
36_G	65_I	1.983	1.00
13_A	20_T	1.926	1.00
43_A	58_L	1.867	1.00
40_I	61_G	1.799	1.00
49_E	52_G	1.713	1.00
28_L	32_L	1.628	1.00
41_V	45_R	1.507	1.00
22_L	26_L	1.401	1.00
31_W	35_S	1.391	1.00
43_A	61_G	1.377	1.00
39_E	60_S	1.373	1.00
16_W	19_I	1.358	1.00
62_I	66_L	1.337	1.00
37_I	41_V	1.331	1.00
64_S	67_L	1.314	1.00
32_L	67_L	1.303	1.00
55_W	59_L	1.289	1.00
60_S	64_S	1.281	1.00
50_G	53_G	1.228	1.00
2_L	35_S	1.224	1.00
23_A	27_L	1.205	1.00
47_R	54_R	1.196	1.00
36_G	61_G	1.140	1.00
4_I	8_V	1.130	1.00
58_L	62_I	1.115	1.00
39_E	57_L	1.110	1.00
6_A	9_A	1.098	1.00
18_G	22_L	1.073	1.00
23_A	26_L	1.045	1.00
51_G	54_R	1.012	1.00
39_E	61_G	1.006	1.00
8_V	12_L	1.004	1.00
40_I	44_F	1.003	1.00
18_G	21_L	0.997	1.00
54_R	58_L	0.982	1.00
42_A	57_L	0.971	1.00
33_L	65_I	0.958	1.00
57_L	60_S	0.954	1.00
21_L	25_V	0.937	1.00
52_G	55_W	0.937	1.00
39_E	64_S	0.918	1.00
41_V	44_F	0.894	1.00
40_I	65_I	0.889	1.00
29_G	68_G	0.888	1.00
42_A	45_R	0.874	1.00
66_L	70_L	0.870	1.00
36_G	64_S	0.854	1.00
66_L	69_V	0.837	1.00
19_I	23_A	0.836	1.00
30_A	72_L	0.828	1.00
2_L	60_S	0.822	1.00
9_A	27_L	0.785	1.00
29_G	71_L	0.774	1.00
46_L	49_E	0.773	1.00
53_G	56_W	0.770	1.00
40_I	58_L	0.769	1.00
9_A	31_W	0.766	1.00
3_G	7_I	0.760	1.00
2_L	39_E	0.757	1.00
47_R	50_G	0.753	1.00
6_A	13_A	0.752	1.00
2_L	9_A	0.748	1.00
22_L	25_V	0.723	1.00
8_V	11_I	0.709	1.00
56_W	60_S	0.691	1.00
45_R	48_G	0.670	1.00
42_A	46_L	0.667	1.00
7_I	11_I	0.666	1.00
16_W	20_T	0.666	1.00
2_L	6_A	0.655	1.00
67_L	70_L	0.653	1.00
19_I	22_L	0.646	1.00
69_V	72_L	0.635	1.00
43_A	54_R	0.634	1.00
60_S	67_L	0.632	1.00
38_F	42_A	0.622	1.00
17_P	24_L	0.622	1.00
50_G	54_R	0.612	1.00
48_G	52_G	0.605	1.00
30_A	38_F	0.605	1.00
25_V	71_L	0.601	1.00
58_L	61_G	0.601	1.00
43_A	55_W	0.601	1.00
28_L	67_L	0.594	1.00
59_L	63_L	0.576	1.00
44_F	58_L	0.568	1.00
51_G	55_W	0.565	1.00
5_L	9_A	0.559	1.00
9_A	28_L	0.557	1.00
43_A	57_L	0.553	1.00
15_A	18_G	0.549	1.00
57_L	64_S	0.546	1.00
39_E	42_A	0.544	1.00
1_L	4_I	0.544	1.00
36_G	68_G	0.537	1.00
35_S	64_S	0.535	1.00
65_I	69_V	0.527	1.00
25_V	32_L	0.519	1.00
23_A	31_W	0.511	1.00
60_S	63_L	0.510	1.00
6_A	35_S	0.500	1.00

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
4o6mA	2	0.9589	7.6	0.774	Contact Map
4o6yA	2	1	5.6	0.787	Contact Map
3owqA	1	0	3.3	0.809	Contact Map
3pjzA	2	0.9041	3.2	0.81	Contact Map
4ytpD	1	0.9863	2.8	0.817	Contact Map
4k0jA	3	0.9726	2.7	0.818	Contact Map
4mt1A	3	1	2.6	0.82	Contact Map
4dx5A	3	1	2.5	0.822	Contact Map
4c7rA	3	1	2.5	0.822	Contact Map
4djkA	2	0.9726	2.4	0.822	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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