DUF2389 - PFAM28P - GREMLIN Contacts

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DUF2389 - Tryptophan-rich protein (DUF2389)

PFAM:	PF09493	Sequences: SKWTAVKPINKEKHFLVTEVEDEEGKVVWVELEAVLSKRISFRIDWRELKDSSKWLQGWK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	60 (58)
Sequences:	2692 (1603)
Seq/√Len:	210.5
META:	0.847

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_R	42_F	2.930	1.00
29_W	43_R	2.918	1.00
31_E	41_S	2.778	1.00
12_E	39_R	2.303	1.00
31_E	43_R	2.270	1.00
12_E	37_S	2.144	1.00
51_D	54_K	2.109	1.00
18_T	41_S	2.041	1.00
11_K	36_L	2.003	1.00
48_E	54_K	1.961	1.00
19_E	31_E	1.866	1.00
34_A	37_S	1.682	1.00
33_E	38_K	1.672	1.00
16_L	33_E	1.643	1.00
32_L	42_F	1.583	1.00
45_D	48_E	1.446	1.00
9_I	12_E	1.438	1.00
22_D	26_K	1.413	1.00
29_W	45_D	1.410	1.00
33_E	41_S	1.402	1.00
6_V	56_L	1.367	1.00
21_E	25_G	1.255	1.00
22_D	25_G	1.209	1.00
20_V	27_V	1.205	1.00
20_V	29_W	1.163	1.00
5_A	8_P	1.155	1.00
12_E	36_L	1.070	1.00
18_T	31_E	1.028	1.00
9_I	42_F	1.016	1.00
7_K	54_K	0.993	1.00
19_E	41_S	0.971	1.00
52_S	57_Q	0.962	1.00
23_E	28_V	0.951	1.00
32_L	44_I	0.945	0.99
12_E	42_F	0.943	0.99
17_V	30_V	0.876	0.99
23_E	44_I	0.865	0.99
37_S	57_Q	0.810	0.98
28_V	57_Q	0.784	0.98
26_K	42_F	0.768	0.98
5_A	9_I	0.760	0.98
30_V	45_D	0.743	0.97
33_E	37_S	0.734	0.97
1_S	17_V	0.710	0.96
30_V	49_L	0.698	0.96
24_E	57_Q	0.667	0.95
36_L	42_F	0.658	0.94
24_E	28_V	0.646	0.94
44_I	51_D	0.640	0.94
18_T	33_E	0.639	0.94
1_S	10_N	0.635	0.93
55_W	58_G	0.634	0.93
4_T	55_W	0.634	0.93
19_E	33_E	0.620	0.93
26_K	53_S	0.619	0.92
14_H	17_V	0.614	0.92
55_W	59_W	0.614	0.92
21_E	29_W	0.612	0.92
45_D	50_K	0.609	0.92
11_K	46_W	0.606	0.92
13_K	37_S	0.604	0.92
5_A	37_S	0.602	0.91
50_K	56_L	0.592	0.91
2_K	5_A	0.583	0.90
48_E	51_D	0.578	0.90
20_V	25_G	0.563	0.88
47_R	54_K	0.560	0.88
26_K	30_V	0.558	0.88
8_P	33_E	0.552	0.88
9_I	54_K	0.548	0.87
25_G	29_W	0.543	0.87
26_K	45_D	0.533	0.86
8_P	13_K	0.531	0.85
38_K	48_E	0.526	0.85
17_V	32_L	0.525	0.85
52_S	56_L	0.524	0.85
2_K	59_W	0.523	0.85
20_V	43_R	0.520	0.84
30_V	44_I	0.520	0.84
13_K	56_L	0.518	0.84
47_R	50_K	0.517	0.84
39_R	49_L	0.513	0.83
8_P	12_E	0.512	0.83
23_E	30_V	0.510	0.83
17_V	33_E	0.507	0.83
18_T	39_R	0.500	0.82
38_K	52_S	0.500	0.82

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
2x5rA	2	0.7333	6.8	0.876	Contact Map
2lt3A	1	0.6	3.8	0.89	Contact Map
3v22V	1	0.6667	2.2	0.902	Contact Map
2jrmA	1	0.7	2.2	0.903	Contact Map
1eexG	1	0.9667	1.7	0.909	Contact Map
3bqoB	1	0	1.7	0.909	Contact Map
4cvuA	2	0.9667	1.6	0.91	Contact Map
4ipuA	1	0.8167	1.5	0.912	Contact Map
3znvA	1	0.9333	1.3	0.914	Contact Map
1iwpG	1	0.9833	1.3	0.914	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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