DUF4169 - PFAM28P - GREMLIN Contacts

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DUF4169 - Domain of unknown function (DUF4169)

PFAM:	PF13770	Sequences: AEIVNLRRARKAKARAEKEAQAAANRARFGRTKAERALDEAEAERARRDLDGHRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	55 (55)
Sequences:	7971 (5621)
Seq/√Len:	758.0
META:	0.925

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_R	39_D	2.844	1.00
45_R	49_D	2.431	1.00
49_D	53_H	1.948	1.00
38_L	42_E	1.940	1.00
19_E	26_R	1.893	1.00
33_K	37_A	1.648	1.00
31_R	35_E	1.586	1.00
8_R	12_A	1.403	1.00
24_A	28_R	1.278	1.00
46_A	49_D	1.268	1.00
32_T	35_E	1.260	1.00
13_K	17_E	1.249	1.00
14_A	17_E	1.248	1.00
43_A	47_R	1.239	1.00
21_Q	24_A	1.234	1.00
17_E	21_Q	1.214	1.00
12_A	16_A	1.209	1.00
25_N	29_F	1.200	1.00
20_A	23_A	1.190	1.00
37_A	40_E	1.179	1.00
44_E	48_R	1.166	1.00
40_E	44_E	1.151	1.00
9_A	12_A	1.145	1.00
35_E	39_D	1.136	1.00
47_R	51_D	1.136	1.00
23_A	26_R	1.131	1.00
39_D	42_E	1.122	1.00
38_L	41_A	1.117	1.00
42_E	45_R	1.106	1.00
14_A	18_K	1.105	1.00
43_A	46_A	1.088	1.00
6_L	10_R	1.079	1.00
42_E	46_A	1.064	1.00
37_A	41_A	1.064	1.00
18_K	21_Q	1.054	1.00
48_R	52_G	1.047	1.00
46_A	50_L	1.034	1.00
22_A	26_R	1.026	1.00
16_A	19_E	1.020	1.00
21_Q	25_N	1.002	1.00
2_E	26_R	0.996	1.00
9_A	13_K	0.973	1.00
7_R	19_E	0.943	1.00
25_N	28_R	0.936	1.00
13_K	16_A	0.918	1.00
44_E	47_R	0.910	1.00
50_L	53_H	0.905	1.00
40_E	43_A	0.882	1.00
41_A	45_R	0.868	1.00
36_R	40_E	0.826	1.00
16_A	20_A	0.823	1.00
41_A	44_E	0.817	1.00
17_E	20_A	0.808	1.00
39_D	43_A	0.776	1.00
28_R	43_A	0.750	1.00
4_V	9_A	0.747	1.00
23_A	27_A	0.714	1.00
24_A	27_A	0.698	1.00
48_R	51_D	0.697	1.00
19_E	23_A	0.692	1.00
12_A	19_E	0.681	1.00
45_R	48_R	0.678	1.00
51_D	54_R	0.664	1.00
6_L	9_A	0.652	1.00
20_A	24_A	0.650	1.00
32_T	36_R	0.644	1.00
31_R	34_A	0.633	1.00
4_V	7_R	0.630	1.00
28_R	39_D	0.627	1.00
6_L	13_K	0.623	1.00
10_R	13_K	0.620	1.00
49_D	52_G	0.608	1.00
50_L	55_R	0.592	1.00
38_L	45_R	0.562	1.00
7_R	11_K	0.557	1.00
52_G	55_R	0.542	1.00
5_N	8_R	0.528	1.00
29_F	36_R	0.526	1.00
29_F	33_K	0.519	1.00
34_A	38_L	0.518	1.00
35_E	38_L	0.512	1.00
15_R	19_E	0.500	1.00

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
2nysA	2	0	4.5	0.858	Contact Map
1ne3A	1	0.3455	2.3	0.879	Contact Map
3o2uA	1	0.8909	1.2	0.896	Contact Map
4rb5B	1	1	1.1	0.898	Contact Map
3bbnB	1	1	1.1	0.899	Contact Map
2nvuC	1	0.8727	1	0.901	Contact Map
4wjwA	2	0.5455	0.9	0.904	Contact Map
4ujpG	1	0.4727	0.9	0.904	Contact Map
4ftbA	7	0.4545	0.8	0.907	Contact Map
4qvrA	1	0.8	0.8	0.907	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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