DUF4089 - PFAM28P - GREMLIN Contacts

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DUF4089 - Protein of unknown function (DUF4089)

PFAM:	PF13318	Sequences: YVDAAAAALGLPIDPAWRPAVRANLERTARLAALVLEFPLPDEAEPAPVF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	50 (49)
Sequences:	4157 (2535)
Seq/√Len:	362.2
META:	0.928

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
3_D	18_R	4.207	1.00
14_D	17_W	2.902	1.00
17_W	20_A	2.506	1.00
2_V	22_R	2.309	1.00
41_P	44_A	2.233	1.00
31_L	34_L	2.078	1.00
27_R	30_R	2.024	1.00
27_R	31_L	1.737	1.00
33_A	37_E	1.693	1.00
24_N	27_R	1.550	1.00
23_A	27_R	1.513	1.00
28_T	31_L	1.486	1.00
13_I	21_V	1.453	1.00
26_E	30_R	1.449	1.00
6_A	13_I	1.390	1.00
33_A	36_L	1.272	1.00
29_A	33_A	1.250	1.00
2_V	25_L	1.170	1.00
20_A	23_A	1.167	1.00
4_A	7_A	1.141	1.00
24_N	28_T	1.124	1.00
23_A	26_E	1.091	1.00
2_V	13_I	0.961	1.00
5_A	9_L	0.927	1.00
47_A	50_F	0.918	1.00
3_D	15_P	0.918	1.00
7_A	10_G	0.907	1.00
9_L	12_P	0.846	1.00
6_A	9_L	0.846	1.00
26_E	33_A	0.843	1.00
13_I	17_W	0.826	1.00
6_A	11_L	0.816	1.00
17_W	28_T	0.811	1.00
25_L	29_A	0.811	1.00
22_R	26_E	0.800	1.00
15_P	18_R	0.789	1.00
24_N	31_L	0.771	1.00
29_A	32_A	0.757	1.00
31_L	36_L	0.754	1.00
34_L	38_F	0.740	1.00
36_L	39_P	0.702	0.99
28_T	35_V	0.697	0.99
30_R	33_A	0.690	0.99
7_A	12_P	0.682	0.99
11_L	17_W	0.675	0.99
18_R	22_R	0.675	0.99
32_A	35_V	0.669	0.99
17_W	24_N	0.667	0.99
8_A	29_A	0.657	0.99
30_R	34_L	0.643	0.99
34_L	39_P	0.636	0.99
20_A	24_N	0.617	0.98
7_A	25_L	0.607	0.98
23_A	30_R	0.598	0.98
4_A	15_P	0.592	0.98
9_L	17_W	0.591	0.98
10_G	36_L	0.589	0.98
3_D	7_A	0.578	0.98
14_D	19_P	0.574	0.98
6_A	21_V	0.570	0.97
4_A	46_P	0.566	0.97
3_D	6_A	0.565	0.97
46_P	49_V	0.557	0.97
5_A	8_A	0.553	0.97
38_F	43_E	0.550	0.97
5_A	25_L	0.545	0.97
35_V	38_F	0.543	0.97
19_P	23_A	0.539	0.96
44_A	50_F	0.529	0.96
37_E	40_L	0.521	0.96
22_R	25_L	0.518	0.96
14_D	21_V	0.513	0.95
4_A	8_A	0.509	0.95
32_A	39_P	0.500	0.95

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
3al0C	1	0.98	59.1	0.734	Contact Map
4wj3C	1	0.98	51.1	0.746	Contact Map
3ip4C	1	1	50.2	0.747	Contact Map
3h0lC	1	0.98	49.5	0.748	Contact Map
4n0hF	1	0.86	48	0.751	Contact Map
3kfuG	1	0.98	45.6	0.754	Contact Map
3e35A	3	0.74	14.9	0.807	Contact Map
2z6vA	1	0.98	9.4	0.823	Contact Map
2zq5A	1	0.84	9	0.825	Contact Map
3ayxA	2	1	6.8	0.835	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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