DUF2798 - PFAM28P - GREMLIN Contacts

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DUF2798 - Protein of unknown function (DUF2798)

PFAM:	PF11391	Sequences: LIMSGLMSFIMSGVATLINLGFGPGFLARWLKAWLIAWPVAFPTVLLVAPLVRRLVARL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (58)
Sequences:	6212 (4012)
Seq/√Len:	526.7
META:	0.816

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_P	43_P	3.342	1.00
20_L	29_R	2.270	1.00
8_S	34_W	2.262	1.00
17_L	22_F	2.073	1.00
25_G	29_R	2.007	1.00
52_V	56_V	1.998	1.00
4_S	38_W	1.865	1.00
4_S	42_F	1.644	1.00
23_G	29_R	1.530	1.00
14_V	40_V	1.522	1.00
49_A	53_R	1.510	1.00
51_L	54_R	1.445	1.00
9_F	31_L	1.419	1.00
15_A	19_N	1.380	1.00
16_T	20_L	1.373	1.00
11_M	15_A	1.364	1.00
38_W	42_F	1.350	1.00
2_I	52_V	1.331	1.00
28_A	32_K	1.320	1.00
7_M	11_M	1.300	1.00
35_L	39_P	1.299	1.00
31_L	35_L	1.277	1.00
45_V	49_A	1.258	1.00
27_L	31_L	1.229	1.00
18_I	32_K	1.199	1.00
18_I	36_I	1.189	1.00
20_L	23_G	1.185	1.00
13_G	30_W	1.170	1.00
43_P	47_L	1.067	1.00
53_R	57_A	1.065	1.00
8_S	41_A	1.053	1.00
3_M	49_A	1.051	1.00
7_M	41_A	1.046	1.00
44_T	48_V	1.032	1.00
9_F	34_W	1.028	1.00
25_G	28_A	1.003	1.00
6_L	48_V	0.984	1.00
1_L	42_F	0.966	1.00
10_I	44_T	0.949	1.00
54_R	58_R	0.943	1.00
32_K	36_I	0.927	1.00
51_L	55_L	0.924	1.00
42_F	46_L	0.891	1.00
4_S	8_S	0.890	1.00
24_P	28_A	0.886	1.00
17_L	26_F	0.859	1.00
3_M	45_V	0.829	1.00
13_G	38_W	0.775	1.00
32_K	35_L	0.759	1.00
13_G	17_L	0.752	1.00
30_W	38_W	0.744	1.00
2_I	56_V	0.722	1.00
21_G	25_G	0.709	1.00
15_A	33_A	0.701	1.00
15_A	18_I	0.697	1.00
13_G	26_F	0.677	1.00
9_F	13_G	0.666	1.00
14_V	18_I	0.656	1.00
12_S	30_W	0.650	1.00
19_N	24_P	0.649	1.00
11_M	41_A	0.637	1.00
2_I	6_L	0.629	1.00
19_N	33_A	0.628	1.00
7_M	15_A	0.617	1.00
5_G	38_W	0.611	1.00
50_P	54_R	0.611	1.00
29_R	32_K	0.599	1.00
16_T	26_F	0.584	0.99
37_A	49_A	0.583	0.99
8_S	15_A	0.579	0.99
54_R	57_A	0.577	0.99
31_L	34_W	0.576	0.99
15_A	45_V	0.576	0.99
15_A	37_A	0.573	0.99
5_G	34_W	0.562	0.99
20_L	25_G	0.560	0.99
6_L	51_L	0.554	0.99
46_L	49_A	0.545	0.99
19_N	29_R	0.544	0.99
28_A	31_L	0.544	0.99
24_P	27_L	0.543	0.99
12_S	15_A	0.540	0.99
2_I	55_L	0.524	0.99
19_N	32_K	0.522	0.99
8_S	45_V	0.509	0.98
33_A	37_A	0.508	0.98
10_I	45_V	0.500	0.98

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
4il3A	1	1	14.2	0.809	Contact Map
4aw6A	2	1	8.7	0.827	Contact Map
3w9iA	3	0.9831	6	0.838	Contact Map
4k0jA	3	0.9831	5.5	0.842	Contact Map
4mt1A	3	0.9831	5	0.845	Contact Map
4pd6A	3	0.8814	4.7	0.846	Contact Map
4dx5A	3	0.9831	3.6	0.854	Contact Map
3ne5A	3	0.9322	3.6	0.855	Contact Map
4j72A	2	0.5424	3.2	0.859	Contact Map
4u4vA	1	0.8814	1.6	0.879	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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