DUF423 - PFAM28P - GREMLIN Contacts

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DUF423 - Protein of unknown function (DUF423)

PFAM:	PF04241	Sequences: ALGAFGAHGLKGRLSALAVFETAVRYQMYHALALLAVGLLARPPSRLLRWAGWLFLAGIVLFSGSLYLLALTGIRWLGAITPIGGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	86 (86)
Sequences:	25250 (16243)
Seq/√Len:	1751.6
META:	0.904

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_E	25_R	4.275	1.00
27_Q	67_Y	3.662	1.00
25_R	29_Y	2.893	1.00
65_S	81_T	2.869	1.00
33_A	55_F	2.746	1.00
6_G	20_F	2.247	1.00
76_W	79_A	2.230	1.00
18_A	21_E	2.102	1.00
50_W	53_W	2.022	1.00
19_V	66_L	1.819	1.00
3_G	26_Y	1.804	1.00
16_A	19_V	1.775	1.00
5_F	9_G	1.736	1.00
69_L	78_G	1.665	1.00
47_L	50_W	1.572	1.00
29_Y	32_L	1.538	1.00
24_V	27_Q	1.495	1.00
2_L	20_F	1.493	1.00
19_V	69_L	1.489	1.00
37_V	55_F	1.457	1.00
61_L	79_A	1.437	1.00
49_R	53_W	1.383	1.00
50_W	54_L	1.302	1.00
34_L	56_L	1.259	1.00
46_R	50_W	1.245	1.00
68_L	72_T	1.230	1.00
30_H	55_F	1.187	1.00
36_A	39_L	1.160	1.00
22_T	25_R	1.154	1.00
27_Q	59_I	1.148	1.00
79_A	83_I	1.141	1.00
34_L	59_I	1.136	1.00
77_L	80_I	1.093	1.00
40_L	43_P	1.055	1.00
51_A	55_F	1.038	1.00
28_M	32_L	1.030	1.00
47_L	51_A	1.029	1.00
38_G	52_G	1.025	1.00
32_L	36_A	1.022	1.00
53_W	57_A	1.010	1.00
16_A	70_A	0.997	1.00
16_A	73_G	0.991	1.00
31_A	59_I	0.990	1.00
59_I	63_S	0.986	1.00
37_V	51_A	0.942	1.00
14_L	70_A	0.931	1.00
18_A	25_R	0.930	1.00
48_L	51_A	0.924	1.00
43_P	48_L	0.916	1.00
30_H	33_A	0.915	1.00
30_H	59_I	0.910	1.00
39_L	48_L	0.910	1.00
37_V	52_G	0.907	1.00
23_A	70_A	0.906	1.00
7_A	22_T	0.885	1.00
19_V	70_A	0.879	1.00
23_A	63_S	0.875	1.00
24_V	28_M	0.834	1.00
34_L	38_G	0.831	1.00
57_A	61_L	0.816	1.00
14_L	17_L	0.802	1.00
10_L	20_F	0.796	1.00
34_L	37_V	0.773	1.00
45_S	51_A	0.772	1.00
61_L	65_S	0.770	1.00
66_L	69_L	0.767	1.00
42_R	45_S	0.763	1.00
37_V	48_L	0.761	1.00
68_L	74_I	0.761	1.00
34_L	52_G	0.755	1.00
44_P	49_R	0.753	1.00
20_F	24_V	0.741	1.00
52_G	56_L	0.728	1.00
35_L	38_G	0.727	1.00
46_R	49_R	0.724	1.00
31_A	38_G	0.723	1.00
9_G	13_R	0.722	1.00
78_G	83_I	0.717	1.00
74_I	77_L	0.707	1.00
35_L	39_L	0.703	1.00
40_L	48_L	0.701	1.00
41_A	44_P	0.700	1.00
24_V	31_A	0.699	1.00
56_L	59_I	0.695	1.00
45_S	48_L	0.693	1.00
68_L	77_L	0.687	1.00
72_T	75_R	0.685	1.00
33_A	36_A	0.678	1.00
44_P	48_L	0.674	1.00
36_A	40_L	0.663	1.00
28_M	31_A	0.659	1.00
41_A	48_L	0.657	1.00
31_A	35_L	0.651	1.00
22_T	26_Y	0.647	1.00
2_L	24_V	0.645	1.00
72_T	77_L	0.644	1.00
82_P	85_G	0.639	1.00
20_F	23_A	0.636	1.00
18_A	22_T	0.635	1.00
69_L	81_T	0.634	1.00
53_W	56_L	0.624	1.00
34_L	55_F	0.621	1.00
72_T	79_A	0.619	1.00
9_G	12_G	0.618	1.00
45_S	49_R	0.615	1.00
69_L	75_R	0.606	1.00
61_L	83_I	0.599	1.00
65_S	69_L	0.595	1.00
17_L	21_E	0.590	1.00
13_R	17_L	0.590	1.00
20_F	27_Q	0.588	1.00
37_V	40_L	0.580	1.00
12_G	17_L	0.578	1.00
44_P	47_L	0.576	1.00
59_I	64_G	0.576	1.00
68_L	71_L	0.574	1.00
54_L	57_A	0.574	1.00
26_Y	66_L	0.556	1.00
11_K	18_A	0.548	1.00
6_G	9_G	0.548	1.00
66_L	70_A	0.542	1.00
56_L	60_V	0.536	1.00
24_V	29_Y	0.535	1.00
5_F	10_L	0.528	1.00
65_S	80_I	0.520	1.00
16_A	71_L	0.514	1.00
5_F	69_L	0.511	1.00
11_K	15_S	0.511	1.00
13_R	16_A	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
1v54K	1	0.5	9.6	0.874	Contact Map
2y69K	1	0.5	4.4	0.893	Contact Map
2e84A	1	0.186	1.7	0.914	Contact Map
2cvcA	1	0.1395	1.5	0.916	Contact Map
1z1nX	1	0.1279	1.3	0.919	Contact Map
4q2eA	2	1	1.1	0.924	Contact Map
4o9uB	2	0.7674	1	0.925	Contact Map
2q1fA	1	0.2209	0.9	0.927	Contact Map
4ru0A	1	0.186	0.9	0.927	Contact Map
2losA	1	0.7791	0.8	0.929	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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