DUF3024 - PFAM28P - GREMLIN Contacts

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DUF3024 - Protein of unknown function (DUF3024)

PFAM:	PF11225	Sequences: IESPVAKLRYVKSTGVWKLYWMRRDLKWHRYEPLPPVKSLEELLAEVDEDPTGCFW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (55)
Sequences:	4336 (3099)
Seq/√Len:	417.9
META:	0.944

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_D	29_H	2.834	1.00
46_E	51_P	2.292	1.00
8_L	43_L	2.273	1.00
5_V	56_W	2.201	1.00
19_L	43_L	2.170	1.00
34_L	46_E	2.080	1.00
8_L	47_V	1.842	1.00
22_M	26_L	1.842	1.00
16_V	36_P	1.838	1.00
39_S	42_E	1.643	1.00
37_V	43_L	1.572	1.00
19_L	46_E	1.545	1.00
23_R	29_H	1.439	1.00
4_P	22_M	1.429	1.00
8_L	40_L	1.409	1.00
43_L	47_V	1.355	1.00
18_K	30_R	1.331	1.00
45_A	49_E	1.316	1.00
37_V	42_E	1.236	1.00
22_M	28_W	1.158	1.00
34_L	37_V	1.127	1.00
7_K	20_Y	1.073	1.00
46_E	49_E	1.034	1.00
7_K	28_W	1.032	1.00
21_W	54_C	1.030	1.00
50_D	53_G	1.014	1.00
20_Y	30_R	1.011	1.00
11_V	16_V	1.004	1.00
9_R	28_W	1.000	1.00
41_E	45_A	0.998	1.00
11_V	14_T	0.993	1.00
31_Y	50_D	0.955	1.00
40_L	44_L	0.949	1.00
34_L	43_L	0.914	1.00
4_P	26_L	0.910	1.00
12_K	15_G	0.896	1.00
31_Y	55_F	0.894	1.00
34_L	51_P	0.885	1.00
10_Y	17_W	0.869	1.00
10_Y	15_G	0.864	1.00
4_P	7_K	0.862	1.00
16_V	38_K	0.832	1.00
30_R	35_P	0.828	1.00
50_D	54_C	0.817	1.00
50_D	55_F	0.811	1.00
21_W	25_D	0.805	1.00
8_L	19_L	0.804	1.00
35_P	38_K	0.802	1.00
44_L	48_D	0.772	1.00
34_L	38_K	0.768	1.00
21_W	29_H	0.760	1.00
32_E	52_T	0.741	1.00
14_T	36_P	0.741	1.00
9_R	18_K	0.726	1.00
11_V	18_K	0.711	1.00
28_W	40_L	0.710	1.00
31_Y	46_E	0.696	1.00
3_S	26_L	0.680	1.00
42_E	45_A	0.671	1.00
6_A	47_V	0.670	1.00
47_V	50_D	0.661	0.99
3_S	22_M	0.655	0.99
6_A	19_L	0.644	0.99
19_L	37_V	0.625	0.99
9_R	20_Y	0.623	0.99
11_V	30_R	0.592	0.99
7_K	10_Y	0.582	0.99
14_T	38_K	0.577	0.99
36_P	39_S	0.576	0.99
45_A	48_D	0.576	0.99
14_T	18_K	0.573	0.98
34_L	41_E	0.560	0.98
53_G	56_W	0.546	0.98
35_P	39_S	0.543	0.98
31_Y	51_P	0.543	0.98
6_A	43_L	0.535	0.98
31_Y	54_C	0.534	0.98
2_E	9_R	0.533	0.98
33_P	52_T	0.528	0.97
11_V	33_P	0.516	0.97
19_L	34_L	0.515	0.97
21_W	38_K	0.500	0.96

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
2dk6A	1	0.9107	19.1	0.839	Contact Map
2a90A	1	0.9464	16.8	0.843	Contact Map
4qhwA	1	0.9286	13.8	0.849	Contact Map
1o0sA	4	1	11.5	0.854	Contact Map
1pj3A	4	1	10	0.858	Contact Map
3bowA	1	0.875	6.8	0.869	Contact Map
1qxpA	1	0.8571	6.6	0.869	Contact Map
2r9fA	1	0.875	6.4	0.87	Contact Map
1zivA	1	0.8929	3.8	0.883	Contact Map
2nqaA	3	0.8571	3.8	0.883	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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