DUF3099 - PFAM28P - GREMLIN Contacts

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DUF3099 - Protein of unknown function (DUF3099)

PFAM:	PF11298	Sequences: LITSAPRSLSEDIRRRQRRYLISMGIRTVCFVLAVVVYRVHPGWLAWVLVVGAVVLPYVAVVIANAGRPRRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	72 (70)
Sequences:	3651 (1905)
Seq/√Len:	227.7
META:	0.795

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_R	18_R	3.251	1.00
21_L	25_G	2.558	1.00
30_C	52_G	2.491	1.00
13_I	17_Q	2.290	1.00
33_L	49_L	2.273	1.00
37_V	49_L	2.167	1.00
7_R	15_R	2.034	1.00
9_L	13_I	1.986	1.00
7_R	11_E	1.890	1.00
34_A	50_V	1.772	1.00
15_R	19_R	1.659	1.00
43_G	47_W	1.480	1.00
24_M	60_A	1.472	1.00
17_Q	21_L	1.471	1.00
18_R	21_L	1.444	1.00
19_R	63_I	1.424	1.00
33_L	36_V	1.404	1.00
31_F	53_A	1.379	1.00
22_I	26_I	1.378	1.00
18_R	22_I	1.367	1.00
44_W	48_V	1.361	1.00
8_S	11_E	1.357	1.00
23_S	28_T	1.353	1.00
14_R	17_Q	1.317	1.00
58_Y	62_V	1.309	1.00
42_P	46_A	1.294	1.00
37_V	42_P	1.290	1.00
59_V	62_V	1.280	1.00
50_V	54_V	1.213	1.00
33_L	37_V	1.197	1.00
42_P	45_L	1.159	1.00
34_A	46_A	1.157	1.00
7_R	12_D	1.133	1.00
28_T	32_V	1.078	1.00
41_H	46_A	1.075	1.00
23_S	59_V	1.069	1.00
34_A	49_L	1.057	1.00
12_D	15_R	0.954	1.00
55_V	59_V	0.943	1.00
11_E	15_R	0.938	1.00
10_S	13_I	0.932	1.00
62_V	66_A	0.926	1.00
30_C	53_A	0.921	1.00
25_G	29_V	0.915	1.00
37_V	46_A	0.909	0.99
26_I	30_C	0.901	0.99
45_L	48_V	0.901	0.99
6_P	12_D	0.877	0.99
22_I	25_G	0.854	0.99
1_L	47_W	0.815	0.99
29_V	53_A	0.804	0.99
37_V	43_G	0.803	0.99
37_V	41_H	0.790	0.99
66_A	69_P	0.779	0.98
1_L	58_Y	0.777	0.98
63_I	66_A	0.774	0.98
11_E	17_Q	0.764	0.98
9_L	12_D	0.758	0.98
61_V	64_A	0.755	0.98
48_V	52_G	0.750	0.98
47_W	51_V	0.747	0.98
26_I	52_G	0.743	0.98
52_G	56_L	0.726	0.98
63_I	69_P	0.715	0.97
53_A	58_Y	0.714	0.97
19_R	23_S	0.713	0.97
29_V	55_V	0.709	0.97
32_V	36_V	0.704	0.97
51_V	55_V	0.703	0.97
41_H	45_L	0.700	0.97
1_L	5_A	0.685	0.96
66_A	70_R	0.681	0.96
2_I	13_I	0.674	0.96
23_S	56_L	0.662	0.96
1_L	23_S	0.647	0.95
27_R	61_V	0.647	0.95
28_T	31_F	0.643	0.95
31_F	54_V	0.641	0.95
10_S	14_R	0.621	0.94
27_R	30_C	0.609	0.93
2_I	5_A	0.605	0.93
43_G	53_A	0.603	0.93
38_Y	41_H	0.599	0.93
46_A	50_V	0.593	0.92
9_L	68_R	0.590	0.92
56_L	59_V	0.589	0.92
24_M	57_P	0.588	0.92
15_R	63_I	0.585	0.92
37_V	45_L	0.579	0.92
29_V	33_L	0.574	0.91
23_S	60_A	0.569	0.91
61_V	65_N	0.566	0.91
35_V	46_A	0.557	0.90
49_L	52_G	0.550	0.89
25_G	28_T	0.537	0.88
37_V	40_V	0.535	0.88
19_R	32_V	0.534	0.88
4_S	9_L	0.531	0.88
59_V	63_I	0.530	0.88
21_L	28_T	0.529	0.87
35_V	50_V	0.525	0.87
43_G	46_A	0.510	0.85
6_P	10_S	0.508	0.85
27_R	57_P	0.504	0.85
54_V	58_Y	0.500	0.84

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
3wdoA	1	1	12.6	0.883	Contact Map
4umwA	1	1	7.3	0.895	Contact Map
4f4cA	1	1	7.1	0.895	Contact Map
3zdqA	2	1	6.6	0.897	Contact Map
4ry2A	2	1	6.4	0.898	Contact Map
4q9hA	1	0.9028	6.4	0.898	Contact Map
3b5xA	2	1	5.6	0.901	Contact Map
3j09A	2	0.9722	5	0.903	Contact Map
4a82A	2	1	4.8	0.904	Contact Map
4q4hB	1	1	4.6	0.904	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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