DUF4287 - PFAM28P - GREMLIN Contacts

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DUF4287 - Domain of unknown function (DUF4287)

PFAM:	PF14117	Sequences: SFQAYIDNIEKKTGKSLEEWLALAKKSGLTVKHGEIVAWLKEEHGLGHGHANAIVHVAKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	60 (55)
Sequences:	11507 (5681)
Seq/√Len:	766.1
META:	0.94

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_A	42_E	2.411	1.00
32_K	35_E	2.254	1.00
15_K	19_E	2.088	1.00
4_A	8_N	1.874	1.00
16_S	19_E	1.840	1.00
41_K	48_H	1.750	1.00
3_Q	7_D	1.718	1.00
15_K	23_L	1.666	1.00
24_A	58_A	1.553	1.00
21_L	58_A	1.531	1.00
46_L	54_I	1.463	1.00
27_S	39_W	1.441	1.00
21_L	25_K	1.376	1.00
34_G	38_A	1.373	1.00
5_Y	50_H	1.346	1.00
37_V	51_A	1.327	1.00
36_I	55_V	1.314	1.00
23_L	39_W	1.295	1.00
27_S	43_E	1.295	1.00
24_A	36_I	1.256	1.00
47_G	50_H	1.213	1.00
7_D	11_K	1.201	1.00
10_E	16_S	1.190	1.00
20_W	44_H	1.189	1.00
12_K	50_H	1.147	1.00
5_Y	9_I	1.127	1.00
24_A	54_I	1.110	1.00
33_H	52_N	1.107	1.00
39_W	43_E	1.102	1.00
23_L	44_H	1.073	1.00
18_E	22_A	1.052	1.00
29_L	35_E	1.019	1.00
30_T	35_E	1.007	1.00
8_N	11_K	0.987	1.00
7_D	10_E	0.978	1.00
29_L	36_I	0.963	1.00
53_A	57_V	0.933	1.00
24_A	40_L	0.919	1.00
33_H	37_V	0.918	1.00
21_L	57_V	0.905	1.00
22_A	26_K	0.892	1.00
35_E	38_A	0.886	1.00
29_L	39_W	0.875	1.00
48_H	52_N	0.851	1.00
33_H	55_V	0.851	1.00
21_L	24_A	0.799	1.00
18_E	21_L	0.797	1.00
38_A	41_K	0.787	1.00
37_V	48_H	0.774	1.00
19_E	23_L	0.769	1.00
23_L	27_S	0.762	1.00
5_Y	8_N	0.760	1.00
8_N	12_K	0.752	1.00
4_A	7_D	0.752	1.00
19_E	22_A	0.746	1.00
49_G	53_A	0.732	1.00
6_I	17_L	0.727	1.00
49_G	52_N	0.715	1.00
28_G	36_I	0.714	1.00
17_L	21_L	0.709	1.00
37_V	52_N	0.701	1.00
33_H	56_H	0.676	1.00
27_S	36_I	0.654	1.00
20_W	23_L	0.653	1.00
39_W	44_H	0.639	1.00
24_A	39_W	0.638	1.00
15_K	20_W	0.633	1.00
9_I	50_H	0.628	1.00
37_V	41_K	0.625	1.00
10_E	19_E	0.592	1.00
47_G	53_A	0.591	1.00
33_H	36_I	0.589	1.00
22_A	25_K	0.584	1.00
34_G	37_V	0.577	1.00
9_I	53_A	0.577	1.00
46_L	50_H	0.570	1.00
55_V	58_A	0.540	1.00
38_A	48_H	0.533	1.00
17_L	57_V	0.528	1.00
8_N	50_H	0.507	1.00
52_N	55_V	0.506	1.00
12_K	47_G	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
1xb2B	1	0.9667	46.1	0.8	Contact Map
3avxA	1	0.95	33.4	0.815	Contact Map
3gbgA	1	0.9333	31.8	0.818	Contact Map
2cp9A	1	0.8833	31.1	0.818	Contact Map
1zq1C	1	0.9833	27.2	0.823	Contact Map
4pc3C	1	0.95	27	0.824	Contact Map
2d6fC	1	0.9833	26.5	0.824	Contact Map
1aipC	2	0.95	26.4	0.825	Contact Map
1dd4C	7	0.6667	19.2	0.836	Contact Map
3ip4B	1	0.9833	18.6	0.836	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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