GREMLIN Database
DUF504 - Protein of unknown function (DUF504)
PFAM: PF04457 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 55 (55)
Sequences: 2254 (1724)
Seq/√Len: 232.5
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
44_E54_E3.7161.00
5_D13_K2.2721.00
2_G14_R2.2401.00
12_I43_R2.1521.00
2_G12_I2.0631.00
16_P19_E1.9591.00
2_G44_E1.9321.00
4_Y43_R1.9201.00
31_E34_E1.8841.00
46_Y51_V1.8681.00
4_Y9_P1.7451.00
8_A11_D1.6771.00
7_G11_D1.6391.00
5_D8_A1.5011.00
29_V36_S1.3921.00
14_R46_Y1.3921.00
24_E29_V1.3731.00
3_Y24_E1.2451.00
29_V34_E1.1771.00
51_V54_E1.1661.00
27_F36_S1.1271.00
1_I20_I1.1131.00
22_F29_V1.0821.00
4_Y7_G1.0781.00
8_A13_K1.0481.00
47_Y50_E1.0401.00
4_Y11_D1.0231.00
30_E33_E1.0161.00
44_E51_V0.9901.00
15_V28_F0.9721.00
47_Y55_R0.9601.00
21_V34_E0.9591.00
32_G35_H0.9301.00
2_G46_Y0.9271.00
19_E30_E0.9241.00
24_E36_S0.9131.00
20_I28_F0.8760.99
21_V33_E0.8280.99
2_G43_R0.8030.99
1_I18_S0.7990.99
17_G47_Y0.7950.99
17_G45_I0.7890.99
23_L26_S0.7790.99
23_L28_F0.7710.98
17_G25_G0.7650.98
5_D11_D0.7620.98
7_G10_G0.7580.98
5_D26_S0.7310.98
2_G53_W0.6920.97
30_E34_E0.6860.97
23_L39_Y0.6730.96
27_F39_Y0.6660.96
18_S47_Y0.6610.96
15_V32_G0.6590.96
1_I4_Y0.6560.96
14_R22_F0.6510.96
18_S25_G0.6400.95
5_D53_W0.6290.95
28_F36_S0.6230.94
24_E27_F0.6220.94
40_H53_W0.6220.94
13_K17_G0.6130.94
23_L42_I0.6110.94
46_Y52_I0.6100.94
30_E45_I0.6000.93
52_I55_R0.5970.93
20_I49_G0.5780.92
10_G55_R0.5780.92
28_F42_I0.5750.92
30_E37_I0.5680.91
25_G55_R0.5540.90
4_Y35_H0.5430.89
3_Y47_Y0.5410.89
28_F39_Y0.5370.89
35_H55_R0.5340.88
43_R52_I0.5320.88
23_L27_F0.5260.88
6_R55_R0.5200.87
37_I44_E0.5130.86
10_G39_Y0.5110.86
22_F39_Y0.5080.86
21_V32_G0.5000.85
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

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  
4c9sA 5 0.9091 22.3 0.803 Contact Map
3dc8A 3 0.9636 12.6 0.824 Contact Map
3sfwA 3 0.9636 10.4 0.83 Contact Map
4lcqA 3 0.9636 8.2 0.838 Contact Map
1nfgA 3 0.9636 8.1 0.838 Contact Map
3griA 1 0.9636 7.6 0.841 Contact Map
3g5kA 3 0.4 7.2 0.842 Contact Map
3hm7A 2 0.9636 6.8 0.844 Contact Map
2gwnA 1 0.9636 6 0.847 Contact Map
1gkpA 4 0.9636 6 0.847 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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