DUF4124 - PFAM28P - GREMLIN Contacts

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DUF4124 - Domain of unknown function (DUF4124)

PFAM:	PF13511	Sequences: LLLLLAAAAAAAQIYKWVDADGVVHYSDTPPPAGAKAETVEPAPPPAAPAPAAAAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (51)
Sequences:	37404 (30232)
Seq/√Len:	4233.4
META:	0.95

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_K	24_V	4.710	1.00
18_V	24_V	4.339	1.00
17_W	25_H	3.133	1.00
17_W	31_P	2.912	1.00
19_D	23_V	2.652	1.00
17_W	27_S	2.445	1.00
19_D	25_H	1.569	1.00
31_P	34_G	1.413	1.00
27_S	30_P	1.315	1.00
16_K	26_Y	1.294	1.00
17_W	24_V	1.272	1.00
7_A	10_A	1.257	1.00
38_E	42_P	1.250	1.00
8_A	11_A	1.172	1.00
31_P	35_A	1.163	1.00
9_A	12_A	1.047	1.00
45_P	48_A	1.037	1.00
15_Y	27_S	1.019	1.00
42_P	45_P	1.013	1.00
6_A	9_A	1.012	1.00
7_A	11_A	0.961	1.00
33_A	36_K	0.904	1.00
33_A	37_A	0.901	1.00
41_E	44_P	0.899	1.00
48_A	51_P	0.886	1.00
14_I	26_Y	0.882	1.00
31_P	36_K	0.882	1.00
48_A	52_A	0.872	1.00
49_P	52_A	0.865	1.00
17_W	28_D	0.865	1.00
32_P	37_A	0.861	1.00
6_A	10_A	0.860	1.00
10_A	13_Q	0.847	1.00
47_A	50_A	0.841	1.00
26_Y	29_T	0.806	1.00
46_P	49_P	0.806	1.00
15_Y	29_T	0.793	1.00
32_P	35_A	0.769	1.00
11_A	14_I	0.734	1.00
25_H	28_D	0.728	1.00
45_P	49_P	0.726	1.00
21_D	25_H	0.709	1.00
4_L	7_A	0.708	1.00
17_W	20_A	0.706	1.00
14_I	17_W	0.702	1.00
4_L	8_A	0.701	1.00
31_P	37_A	0.700	1.00
34_G	37_A	0.684	1.00
44_P	47_A	0.680	1.00
43_A	46_P	0.665	1.00
5_L	9_A	0.646	1.00
2_L	5_L	0.639	1.00
6_A	11_A	0.631	1.00
17_W	32_P	0.624	1.00
47_A	51_P	0.623	1.00
40_V	43_A	0.616	1.00
6_A	12_A	0.615	1.00
42_P	47_A	0.614	1.00
13_Q	30_P	0.605	1.00
37_A	40_V	0.600	1.00
17_W	37_A	0.594	1.00
43_A	47_A	0.586	1.00
44_P	52_A	0.580	1.00
15_Y	30_P	0.575	1.00
42_P	46_P	0.572	1.00
35_A	38_E	0.571	1.00
14_I	28_D	0.563	1.00
3_L	6_A	0.558	1.00
44_P	48_A	0.551	1.00
15_Y	28_D	0.543	1.00
5_L	30_P	0.541	1.00
2_L	6_A	0.537	1.00
14_I	29_T	0.526	1.00
5_L	10_A	0.515	1.00
38_E	41_E	0.507	1.00
32_P	38_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
1qwyA	1	0.9821	14.2	0.79	Contact Map
4iiwA	4	0.6786	13.7	0.791	Contact Map
3ab4A	7	0.9643	9.5	0.806	Contact Map
2r1fA	4	0.8929	8.2	0.811	Contact Map
3tviA	2	0.9643	7.6	0.814	Contact Map
1e19A	2	0.9643	7.3	0.816	Contact Map
4axsA	2	0.9643	6.6	0.82	Contact Map
2cdqA	2	0.9643	6.4	0.821	Contact Map
3c1mA	3	0.9643	6.1	0.822	Contact Map
2a1fA	5	0.875	6.1	0.823	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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