DUF2516 - PFAM28P - GREMLIN Contacts

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DUF2516 - Protein of unknown function (DUF2516)

PFAM:	PF10724	Sequences: SVQGLVLLVLGLAALVVEVWAFVDALRRPADAFVAAGKLTKPAWLAILGVALLLGLLGFGGPLGLLGLIAVVAALVYLVDVRPALREVQGGG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	92 (88)
Sequences:	3011 (2041)
Seq/√Len:	217.6
META:	0.79

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_L	43_A	4.249	1.00
75_L	79_V	3.758	1.00
24_D	28_R	3.205	1.00
22_F	49_G	2.667	1.00
47_I	73_A	2.634	1.00
42_P	46_A	2.471	1.00
18_E	55_G	2.320	1.00
46_A	50_V	2.217	1.00
25_A	33_F	2.153	1.00
24_D	77_Y	2.147	1.00
45_L	49_G	2.108	1.00
5_L	9_V	1.812	1.00
43_A	47_I	1.799	1.00
82_R	86_R	1.798	1.00
14_A	71_V	1.792	1.00
26_L	45_L	1.737	1.00
28_R	33_F	1.652	1.00
30_A	34_V	1.600	1.00
25_A	45_L	1.570	1.00
8_L	12_L	1.568	1.00
39_L	47_I	1.567	1.00
19_V	52_L	1.527	1.00
85_L	88_V	1.496	1.00
17_V	78_L	1.433	1.00
20_W	78_L	1.425	1.00
85_L	89_Q	1.354	1.00
25_A	48_L	1.335	1.00
18_E	74_A	1.326	1.00
65_L	69_I	1.309	1.00
16_V	20_W	1.268	1.00
71_V	75_L	1.177	1.00
43_A	46_A	1.137	1.00
28_R	77_Y	1.135	1.00
18_E	71_V	1.105	1.00
4_G	8_L	1.104	1.00
19_V	23_V	1.043	1.00
81_V	85_L	1.036	1.00
22_F	48_L	0.986	1.00
38_K	84_A	0.985	1.00
13_A	16_V	0.983	1.00
22_F	26_L	0.979	1.00
84_A	87_E	0.972	1.00
72_V	76_V	0.966	1.00
51_A	73_A	0.966	1.00
64_G	67_G	0.959	1.00
86_R	90_G	0.932	0.99
18_E	67_G	0.928	0.99
54_L	66_L	0.896	0.99
62_P	67_G	0.891	0.99
29_P	32_A	0.870	0.99
13_A	17_V	0.864	0.99
14_A	18_E	0.859	0.99
48_L	52_L	0.858	0.99
53_L	57_L	0.838	0.99
55_G	71_V	0.824	0.99
55_G	70_A	0.823	0.99
18_E	70_A	0.821	0.99
5_L	8_L	0.819	0.99
7_L	11_G	0.798	0.98
74_A	78_L	0.792	0.98
30_A	42_P	0.785	0.98
54_L	70_A	0.783	0.98
68_L	71_V	0.778	0.98
20_W	82_R	0.772	0.98
28_R	89_Q	0.760	0.98
3_Q	7_L	0.755	0.98
17_V	71_V	0.750	0.98
51_A	74_A	0.748	0.98
17_V	75_L	0.745	0.98
60_G	64_G	0.736	0.97
87_E	90_G	0.730	0.97
76_V	84_A	0.728	0.97
38_K	83_P	0.724	0.97
15_L	52_L	0.722	0.97
3_Q	6_V	0.722	0.97
21_A	78_L	0.716	0.97
8_L	11_G	0.715	0.97
38_K	80_D	0.714	0.97
33_F	77_Y	0.714	0.97
33_F	85_L	0.713	0.97
23_V	27_R	0.697	0.96
38_K	81_V	0.687	0.96
48_L	69_I	0.679	0.96
47_I	50_V	0.667	0.95
17_V	74_A	0.654	0.95
9_V	13_A	0.652	0.95
50_V	54_L	0.649	0.95
15_L	19_V	0.646	0.94
20_W	24_D	0.634	0.94
55_G	74_A	0.634	0.94
32_A	85_L	0.611	0.93
22_F	45_L	0.609	0.93
34_V	37_G	0.606	0.92
63_L	67_G	0.599	0.92
61_G	64_G	0.596	0.92
67_G	79_V	0.592	0.91
86_R	89_Q	0.589	0.91
64_G	68_L	0.579	0.91
11_G	68_L	0.578	0.90
62_P	68_L	0.574	0.90
68_L	72_V	0.572	0.90
46_A	49_G	0.572	0.90
4_G	59_F	0.567	0.90
49_G	56_L	0.565	0.89
80_D	84_A	0.560	0.89
15_L	18_E	0.559	0.89
24_D	82_R	0.553	0.88
80_D	83_P	0.551	0.88
52_L	56_L	0.548	0.88
22_F	52_L	0.545	0.88
21_A	48_L	0.542	0.87
31_D	88_V	0.536	0.87
78_L	82_R	0.536	0.87
2_V	5_L	0.534	0.87
62_P	65_L	0.530	0.86
27_R	82_R	0.528	0.86
54_L	60_G	0.527	0.86
35_A	88_V	0.525	0.86
81_V	84_A	0.523	0.86
18_E	52_L	0.523	0.86
51_A	75_L	0.522	0.85
34_V	40_T	0.516	0.85
61_G	67_G	0.515	0.85
51_A	70_A	0.513	0.84
33_F	38_K	0.510	0.84
43_A	84_A	0.509	0.84
48_L	74_A	0.509	0.84
48_L	77_Y	0.507	0.84
76_V	83_P	0.506	0.84
59_F	62_P	0.505	0.84
77_Y	82_R	0.502	0.83
60_G	67_G	0.500	0.83

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	0.3478	9	0.896	Contact Map
3wajA	1	0.9348	8	0.899	Contact Map
3rceA	1	0.8696	7.3	0.9	Contact Map
4qndA	2	0.4022	3.7	0.914	Contact Map
3j2wE	1	0.5	3.4	0.915	Contact Map
4mndA	2	0.837	3.4	0.915	Contact Map
2f93B	2	0.5543	3.3	0.916	Contact Map
2j6pA	4	0.3478	3	0.917	Contact Map
3ayfA	2	0.4674	2.3	0.922	Contact Map
3ixzA	1	1	2.1	0.924	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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