DUF378 - PFAM28P - GREMLIN Contacts

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DUF378 - Domain of unknown function (DUF378)

PFAM:	PF04070	Sequences: KTLDKIALILVIIGGLNWGLVGLFNFDLVAAIFGGSMSALSRIVYILVGLAALYLIVLLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	60 (56)
Sequences:	12649 (8035)
Seq/√Len:	1073.7
META:	0.926

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_G	52_A	3.212	1.00
23_L	46_I	2.909	1.00
26_F	31_A	2.435	1.00
30_A	41_S	2.343	1.00
11_V	55_L	2.322	1.00
4_D	54_Y	2.038	1.00
25_N	42_R	1.818	1.00
8_L	55_L	1.786	1.00
11_V	15_G	1.773	1.00
27_D	30_A	1.707	1.00
2_T	6_I	1.561	1.00
38_S	41_S	1.548	1.00
22_G	46_I	1.516	1.00
14_G	48_V	1.487	1.00
39_A	43_I	1.477	1.00
7_A	55_L	1.292	1.00
7_A	54_Y	1.265	1.00
20_L	28_L	1.245	1.00
18_W	45_Y	1.222	1.00
12_I	52_A	1.219	1.00
19_G	49_G	1.194	1.00
55_L	58_L	1.160	1.00
2_T	5_K	1.149	1.00
10_L	51_A	1.060	1.00
21_V	27_D	1.021	1.00
24_F	42_R	1.019	1.00
17_N	27_D	0.997	1.00
5_K	55_L	0.980	1.00
5_K	9_I	0.973	1.00
33_F	38_S	0.940	1.00
20_L	26_F	0.938	1.00
37_M	41_S	0.923	1.00
27_D	41_S	0.920	1.00
4_D	55_L	0.920	1.00
54_Y	57_V	0.913	1.00
7_A	51_A	0.908	1.00
53_L	57_V	0.893	1.00
25_N	37_M	0.890	1.00
30_A	45_Y	0.864	1.00
42_R	46_I	0.842	1.00
50_L	54_Y	0.813	1.00
5_K	57_V	0.806	1.00
17_N	28_L	0.791	1.00
22_G	49_G	0.779	1.00
29_V	44_V	0.776	1.00
22_G	42_R	0.776	1.00
14_G	18_W	0.763	1.00
4_D	8_L	0.752	1.00
5_K	8_L	0.731	1.00
29_V	41_S	0.731	1.00
8_L	12_I	0.728	1.00
30_A	36_S	0.725	1.00
31_A	39_A	0.713	1.00
18_W	29_V	0.707	1.00
8_L	58_L	0.706	1.00
4_D	57_V	0.698	1.00
33_F	40_L	0.676	1.00
13_I	48_V	0.661	1.00
16_L	52_A	0.657	1.00
27_D	45_Y	0.644	1.00
18_W	48_V	0.644	1.00
33_F	44_V	0.642	1.00
34_G	38_S	0.633	1.00
33_F	41_S	0.632	1.00
47_L	51_A	0.627	1.00
36_S	41_S	0.622	1.00
11_V	52_A	0.614	1.00
39_A	42_R	0.603	1.00
30_A	38_S	0.600	1.00
3_L	54_Y	0.585	1.00
51_A	55_L	0.581	1.00
12_I	55_L	0.573	1.00
12_I	16_L	0.556	1.00
4_D	9_I	0.546	1.00
40_L	44_V	0.542	1.00
21_V	36_S	0.537	1.00
17_N	20_L	0.534	1.00
40_L	43_I	0.534	1.00
17_N	48_V	0.531	1.00
34_G	41_S	0.523	1.00
18_W	44_V	0.514	1.00
10_L	47_L	0.508	1.00
29_V	33_F	0.506	1.00
12_I	56_I	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
3j1rA	5	0.4167	2.1	0.877	Contact Map
1oahA	2	0	2	0.88	Contact Map
3pjzA	2	0.8833	1.6	0.885	Contact Map
4ev6A	3	0.8667	1.4	0.889	Contact Map
4q4hB	1	0.9667	1.4	0.889	Contact Map
4pl0A	2	1	1.3	0.891	Contact Map
3zdqA	2	1	1.2	0.893	Contact Map
3j9pD	4	1	1.2	0.895	Contact Map
3bz1X	1	0.5	1.1	0.896	Contact Map
4i0uA	4	0.8667	1	0.898	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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