DUF3320 - PFAM28P - GREMLIN Contacts

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DUF3320 - Protein of unknown function (DUF3320)

PFAM:	PF11784	Sequences: DEFHEPAYRAELAELIAEVVEVEGPIHEDELARRVARAWGLQRAGSRIRE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	50 (47)
Sequences:	5300 (3862)
Seq/√Len:	563.3
META:	0.909

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_E	34_R	2.209	1.00
32_A	44_A	2.194	1.00
16_I	31_L	2.053	1.00
15_L	39_W	1.999	1.00
28_E	32_A	1.956	1.00
15_L	38_A	1.808	1.00
23_E	34_R	1.779	1.00
20_V	24_G	1.717	1.00
17_A	21_E	1.647	1.00
18_E	22_V	1.583	1.00
36_A	44_A	1.510	1.00
16_I	35_V	1.392	1.00
3_F	41_L	1.377	1.00
33_R	36_A	1.377	1.00
26_I	31_L	1.341	1.00
8_Y	39_W	1.312	1.00
26_I	30_E	1.263	1.00
15_L	35_V	1.251	1.00
45_G	48_I	1.238	1.00
2_E	7_A	1.234	1.00
3_F	12_L	1.100	1.00
13_A	17_A	1.094	1.00
41_L	48_I	1.039	1.00
2_E	5_E	1.019	1.00
12_L	35_V	1.015	1.00
29_D	49_R	1.000	1.00
18_E	21_E	0.987	1.00
23_E	30_E	0.961	1.00
36_A	41_L	0.961	1.00
11_E	14_E	0.940	1.00
19_V	23_E	0.923	1.00
36_A	42_Q	0.910	1.00
19_V	34_R	0.888	1.00
14_E	17_A	0.883	1.00
19_V	30_E	0.880	1.00
9_R	13_A	0.875	1.00
18_E	38_A	0.850	1.00
14_E	18_E	0.841	1.00
32_A	36_A	0.829	1.00
10_A	14_E	0.806	1.00
19_V	35_V	0.800	1.00
41_L	44_A	0.780	1.00
44_A	49_R	0.780	1.00
20_V	26_I	0.770	1.00
29_D	32_A	0.753	1.00
27_H	30_E	0.716	1.00
42_Q	45_G	0.708	1.00
30_E	33_R	0.706	1.00
11_E	17_A	0.684	1.00
7_A	11_E	0.682	1.00
2_E	8_Y	0.660	1.00
10_A	13_A	0.658	1.00
29_D	33_R	0.646	1.00
33_R	47_R	0.642	1.00
35_V	39_W	0.635	1.00
4_H	8_Y	0.631	1.00
19_V	38_A	0.611	1.00
10_A	17_A	0.600	1.00
8_Y	11_E	0.595	1.00
11_E	18_E	0.580	1.00
19_V	31_L	0.578	1.00
5_E	8_Y	0.568	0.99
32_A	49_R	0.540	0.99
7_A	39_W	0.534	0.99
3_F	48_I	0.527	0.99
9_R	27_H	0.526	0.99
11_E	15_L	0.521	0.99
22_V	40_G	0.513	0.99
16_I	20_V	0.512	0.99
12_L	39_W	0.500	0.99

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
4nmnA	3	0.94	12.9	0.809	Contact Map
1b79A	3	0.98	11.9	0.811	Contact Map
3bgwA	3	0.94	10.2	0.817	Contact Map
2ahqA	1	0.98	10	0.818	Contact Map
1knvA	4	0.44	9.4	0.82	Contact Map
2q6tA	1	0.98	9.2	0.82	Contact Map
2lznA	1	0.98	8.6	0.823	Contact Map
2r5uA	5	0.98	8.6	0.823	Contact Map
4f0zA	1	0.98	7.9	0.826	Contact Map
3gxvA	4	0.98	7.9	0.826	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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