DUF1542 - PFAM28P - GREMLIN Contacts

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DUF1542 - Domain of Unknown Function (DUF1542)

PFAM:	PF07564	Sequences: KKAEIDADPDLTDEEKAAAKAEVDAAADAAKAAIDNATTNDAVDQAKTNGITAINAVNPPAVAKPAAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	68 (67)
Sequences:	3612 (1983)
Seq/√Len:	242.2
META:	0.501

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_D	20_K	2.793	1.00
13_D	17_A	2.155	1.00
26_A	57_V	1.935	1.00
2_K	24_D	1.912	1.00
27_A	31_K	1.871	1.00
17_A	21_A	1.819	1.00
12_T	15_E	1.781	1.00
39_T	42_A	1.761	1.00
41_D	45_Q	1.598	1.00
3_A	7_A	1.593	1.00
28_D	32_A	1.578	1.00
26_A	29_A	1.492	1.00
21_A	25_A	1.464	1.00
47_K	51_I	1.459	1.00
45_Q	49_N	1.458	1.00
30_A	50_G	1.444	1.00
33_A	36_N	1.397	1.00
32_A	36_N	1.397	1.00
18_A	22_E	1.347	1.00
52_T	56_A	1.334	1.00
24_D	28_D	1.322	1.00
48_T	52_T	1.268	1.00
46_A	50_G	1.234	1.00
46_A	49_N	1.232	1.00
49_N	53_A	1.200	1.00
25_A	29_A	1.186	1.00
37_A	46_A	1.176	1.00
1_K	4_E	1.160	1.00
40_N	44_D	1.090	1.00
53_A	56_A	1.089	1.00
62_V	65_P	1.064	1.00
38_T	42_A	1.055	1.00
22_E	25_A	1.046	1.00
29_A	33_A	1.008	1.00
8_D	11_L	1.007	1.00
40_N	43_V	0.999	1.00
43_V	47_K	0.977	1.00
44_D	48_T	0.977	1.00
19_A	59_P	0.966	1.00
44_D	47_K	0.963	1.00
31_K	35_D	0.947	1.00
62_V	66_A	0.938	1.00
30_A	33_A	0.933	1.00
5_I	23_V	0.925	1.00
4_E	58_N	0.918	1.00
52_T	55_N	0.906	1.00
28_D	31_K	0.905	1.00
3_A	6_D	0.897	1.00
29_A	32_A	0.897	1.00
63_A	66_A	0.884	1.00
26_A	53_A	0.881	0.99
18_A	21_A	0.873	0.99
8_D	61_A	0.865	0.99
21_A	24_D	0.864	0.99
23_V	27_A	0.854	0.99
20_K	24_D	0.848	0.99
42_A	45_Q	0.842	0.99
58_N	61_A	0.837	0.99
2_K	20_K	0.836	0.99
2_K	6_D	0.833	0.99
32_A	35_D	0.832	0.99
22_E	26_A	0.827	0.99
6_D	16_K	0.820	0.99
11_L	19_A	0.809	0.99
5_I	16_K	0.803	0.99
19_A	22_E	0.790	0.99
2_K	23_V	0.783	0.99
8_D	19_A	0.777	0.99
19_A	57_V	0.776	0.99
19_A	58_N	0.765	0.99
25_A	28_D	0.754	0.98
26_A	30_A	0.739	0.98
49_N	52_T	0.736	0.98
61_A	65_P	0.726	0.98
14_E	17_A	0.726	0.98
20_K	23_V	0.724	0.98
14_E	18_A	0.718	0.98
1_K	11_L	0.698	0.97
51_I	55_N	0.669	0.97
1_K	58_N	0.668	0.97
4_E	7_A	0.661	0.96
45_Q	48_T	0.658	0.96
41_D	44_D	0.654	0.96
8_D	58_N	0.651	0.96
19_A	60_P	0.637	0.96
33_A	46_A	0.620	0.95
23_V	57_V	0.585	0.93
15_E	18_A	0.571	0.92
37_A	43_V	0.564	0.92
24_D	27_A	0.562	0.92
11_L	61_A	0.562	0.92
11_L	15_E	0.553	0.91
22_E	57_V	0.551	0.91
13_D	16_K	0.549	0.91
1_K	59_P	0.547	0.90
1_K	57_V	0.546	0.90
27_A	34_I	0.539	0.90
9_P	16_K	0.533	0.89
37_A	42_A	0.526	0.89
48_T	51_I	0.500	0.86

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
2dgjA	4	0.6324	38.7	0.726	Contact Map
2ynqA	2	0.6029	34.8	0.733	Contact Map
4kjmA	4	0.6471	29.6	0.742	Contact Map
4gwpC	1	0	18.7	0.765	Contact Map
1zdaA	1	0.3824	5.7	0.814	Contact Map
2marA	1	0.6471	5.5	0.815	Contact Map
2j5yA	1	0.7647	5.5	0.816	Contact Map
1l6xB	1	0.3971	4.1	0.827	Contact Map
1gjsA	1	0.7941	3.6	0.832	Contact Map
2fs1A	1	0.7941	3.5	0.832	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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