DUF3343 - PFAM28P - GREMLIN Contacts

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DUF3343 - Protein of unknown function (DUF3343)

PFAM:	PF11823	Sequences: YYVITFHSTHHALRAEKLLKEAGIPVRLIPVPREISSGCGLALRFPLEDLEAVERLLEEAGIEPEGIYE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	69 (66)
Sequences:	7511 (5498)
Seq/√Len:	676.7
META:	0.884

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
2_Y	47_L	2.547	1.00
45_F	53_V	2.510	1.00
31_V	42_A	2.360	1.00
49_D	52_A	2.266	1.00
50_L	54_E	2.226	1.00
4_I	45_F	2.199	1.00
29_I	44_R	1.771	1.00
46_P	49_D	1.728	1.00
15_A	57_L	1.719	1.00
15_A	43_L	1.712	1.00
55_R	59_E	1.602	1.00
19_L	53_V	1.508	1.00
8_S	11_H	1.485	1.00
18_L	60_A	1.480	1.00
22_A	56_L	1.469	1.00
16_E	20_K	1.450	1.00
26_V	43_L	1.430	1.00
6_F	15_A	1.391	1.00
24_I	52_A	1.388	1.00
7_H	65_E	1.323	1.00
7_H	11_H	1.289	1.00
52_A	55_R	1.260	1.00
3_V	29_I	1.252	1.00
45_F	50_L	1.211	1.00
16_E	26_V	1.162	1.00
54_E	58_E	1.157	1.00
25_P	49_D	1.091	1.00
19_L	43_L	1.080	1.00
2_Y	45_F	1.075	1.00
22_A	52_A	1.057	1.00
14_R	18_L	1.052	1.00
28_L	41_L	1.025	1.00
33_R	36_S	1.025	1.00
33_R	38_G	1.014	1.00
12_A	38_G	1.013	1.00
56_L	60_A	1.013	1.00
9_T	41_L	1.006	1.00
18_L	22_A	0.982	1.00
19_L	26_V	0.973	1.00
56_L	59_E	0.958	1.00
51_E	54_E	0.943	1.00
18_L	21_E	0.939	1.00
31_V	40_G	0.939	1.00
5_T	31_V	0.927	1.00
38_G	41_L	0.923	1.00
22_A	59_E	0.916	1.00
29_I	42_A	0.914	1.00
51_E	55_R	0.908	1.00
12_A	41_L	0.870	1.00
22_A	60_A	0.869	1.00
20_K	26_V	0.811	1.00
11_H	14_R	0.808	1.00
7_H	63_E	0.791	1.00
18_L	56_L	0.781	1.00
57_L	64_P	0.772	1.00
19_L	45_F	0.769	1.00
25_P	46_P	0.768	1.00
9_T	13_L	0.760	1.00
12_A	28_L	0.757	1.00
10_H	38_G	0.755	1.00
9_T	30_P	0.742	1.00
24_I	56_L	0.740	1.00
31_V	37_S	0.738	1.00
11_H	63_E	0.732	1.00
4_I	57_L	0.719	1.00
47_L	50_L	0.717	1.00
30_P	41_L	0.716	1.00
10_H	41_L	0.716	1.00
54_E	67_I	0.715	1.00
28_L	43_L	0.711	1.00
52_A	56_L	0.690	1.00
4_I	64_P	0.687	1.00
55_R	58_E	0.686	1.00
4_I	53_V	0.677	1.00
10_H	13_L	0.661	1.00
17_K	21_E	0.659	1.00
24_I	53_V	0.657	1.00
64_P	67_I	0.647	1.00
24_I	49_D	0.640	1.00
5_T	42_A	0.631	1.00
15_A	19_L	0.630	1.00
19_L	24_I	0.629	1.00
27_R	44_R	0.623	1.00
14_R	17_K	0.619	1.00
10_H	14_R	0.619	1.00
58_E	61_G	0.618	1.00
6_F	12_A	0.612	1.00
9_T	12_A	0.608	1.00
32_P	35_I	0.586	1.00
13_L	16_E	0.585	1.00
4_I	67_I	0.563	1.00
2_Y	50_L	0.562	1.00
5_T	10_H	0.554	1.00
36_S	40_G	0.554	1.00
21_E	60_A	0.532	1.00
32_P	42_A	0.524	1.00
5_T	35_I	0.511	0.99
45_F	49_D	0.509	0.99
5_T	38_G	0.500	0.99

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
2hfvA	1	0.9855	59.1	0.783	Contact Map
2gqcA	1	0.913	47.1	0.798	Contact Map
2lepA	1	0.8986	46	0.799	Contact Map
4w4mA	1	0.8841	37	0.81	Contact Map
4hddA	6	0.913	34.5	0.813	Contact Map
3j6da	3	0.8116	31.2	0.817	Contact Map
2l69A	1	1	28.5	0.821	Contact Map
1vr9A	1	0	24.5	0.826	Contact Map
4o9uB	2	0.7971	20.7	0.833	Contact Map
1djlA	1	0.7971	15.5	0.841	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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