DUF1992 - PFAM28P - GREMLIN Contacts

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DUF1992 - Domain of unknown function (DUF1992)

PFAM:	PF09350	Sequences: LAERRIREAMERGEFDNLPGAGKPLPLDDPYDPLVPEELRLAYRILKNAGFLPPELELRKEIEALEELLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	70 (67)
Sequences:	10211 (5563)
Seq/√Len:	679.7
META:	0.871

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_E	12_R	2.872	1.00
59_R	63_E	2.611	1.00
7_R	11_E	2.500	1.00
44_R	48_N	2.468	1.00
4_R	8_E	2.262	1.00
7_R	10_M	2.170	1.00
16_D	21_A	1.808	1.00
53_P	56_L	1.798	1.00
39_L	43_Y	1.788	1.00
1_L	5_R	1.622	1.00
10_M	16_D	1.622	1.00
54_P	57_E	1.587	1.00
64_A	68_L	1.577	1.00
64_A	67_E	1.570	1.00
17_N	21_A	1.450	1.00
52_L	60_K	1.442	1.00
9_A	14_E	1.436	1.00
37_E	40_R	1.398	1.00
40_R	43_Y	1.378	1.00
32_D	35_V	1.357	1.00
3_E	7_R	1.341	1.00
5_R	8_E	1.327	1.00
57_E	61_E	1.279	1.00
20_G	24_P	1.274	1.00
52_L	57_E	1.262	1.00
9_A	15_F	1.248	1.00
4_R	7_R	1.232	1.00
32_D	44_R	1.200	1.00
63_E	67_E	1.181	1.00
41_L	44_R	1.180	1.00
6_I	10_M	1.178	1.00
20_G	23_K	1.163	1.00
63_E	66_E	1.121	1.00
52_L	56_L	1.121	1.00
55_E	59_R	1.070	1.00
2_A	5_R	1.053	1.00
10_M	15_F	1.015	1.00
54_P	58_L	1.002	1.00
36_P	40_R	0.972	1.00
29_D	33_P	0.945	1.00
39_L	42_A	0.911	1.00
35_V	40_R	0.904	1.00
58_L	66_E	0.894	1.00
28_D	47_K	0.878	1.00
20_G	26_P	0.874	1.00
62_I	66_E	0.841	1.00
62_I	65_L	0.837	1.00
47_K	50_G	0.837	1.00
13_G	16_D	0.834	1.00
60_K	64_A	0.823	1.00
35_V	43_Y	0.819	1.00
56_L	63_E	0.814	1.00
15_F	18_L	0.808	1.00
4_R	11_E	0.786	1.00
36_P	39_L	0.784	1.00
34_L	37_E	0.779	1.00
56_L	59_R	0.765	1.00
65_L	68_L	0.762	1.00
2_A	10_M	0.748	1.00
43_Y	55_E	0.739	1.00
27_L	32_D	0.724	1.00
40_R	44_R	0.718	1.00
29_D	44_R	0.713	1.00
17_N	20_G	0.695	1.00
42_A	45_I	0.689	1.00
18_L	21_A	0.671	1.00
57_E	60_K	0.668	1.00
26_P	33_P	0.665	1.00
29_D	40_R	0.660	1.00
10_M	14_E	0.652	1.00
55_E	65_L	0.636	1.00
35_V	38_E	0.635	1.00
46_L	51_F	0.626	1.00
18_L	22_G	0.615	1.00
65_L	69_L	0.612	1.00
8_E	11_E	0.611	1.00
8_E	14_E	0.605	1.00
45_I	50_G	0.603	1.00
45_I	49_A	0.602	1.00
46_L	49_A	0.598	1.00
48_N	51_F	0.596	1.00
18_L	23_K	0.583	1.00
66_E	69_L	0.581	1.00
3_E	6_I	0.563	1.00
10_M	21_A	0.555	1.00
59_R	68_L	0.544	1.00
27_L	39_L	0.543	1.00
58_L	61_E	0.543	1.00
15_F	21_A	0.530	1.00
61_E	64_A	0.527	1.00
60_K	63_E	0.525	1.00
20_G	25_L	0.524	1.00
46_L	52_L	0.517	0.99
52_L	55_E	0.517	0.99
58_L	62_I	0.515	0.99
46_L	54_P	0.512	0.99
61_E	65_L	0.509	0.99
2_A	46_L	0.503	0.99
39_L	45_I	0.501	0.99
5_R	12_R	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
4jadA	5	0.9571	49.7	0.817	Contact Map
4tvmA	2	0.5143	44.6	0.822	Contact Map
3msuA	2	0.9571	43.6	0.824	Contact Map
1a59A	2	0.9286	42.9	0.824	Contact Map
4xghA	5	0.5857	42.6	0.825	Contact Map
2h12A	4	0.9714	40.8	0.827	Contact Map
3hwkA	5	0.9286	38.7	0.829	Contact Map
3tqgA	2	0.9286	31.4	0.837	Contact Map
1vgmA	2	0.9571	31	0.837	Contact Map
1o7xA	2	0.9429	30.8	0.838	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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