GREMLIN Database
DUF3060 - Protein of unknown function (DUF3060)
PFAM: PF11259 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 58 (56)
Sequences: 3900 (2913)
Seq/√Len: 389.3
META: 0.885

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
23_N40_N2.6931.00
20_S37_S2.5561.00
22_S39_S2.4961.00
4_S22_S2.3791.00
24_N41_N2.2381.00
25_T42_T2.1671.00
5_N23_N2.1531.00
3_G6_N1.9551.00
2_S20_S1.8991.00
45_Y50_P1.8811.00
37_S55_S1.8561.00
4_S39_S1.7551.00
18_T35_T1.6661.00
6_N24_N1.5401.00
29_D46_K1.5171.00
27_T44_T1.5071.00
7_T25_T1.4891.00
2_S37_S1.4761.00
5_N40_N1.3771.00
19_V26_V1.1931.00
14_C17_V1.1721.00
21_G24_N1.1681.00
28_V45_Y1.1601.00
16_S35_T1.1051.00
31_V34_I1.0511.00
10_L14_C1.0461.00
13_S30_S1.0421.00
9_T27_T0.9841.00
50_P54_D0.9321.00
11_T29_D0.9231.00
19_V36_V0.9231.00
13_S32_D0.8801.00
14_C31_V0.8771.00
34_I43_V0.8611.00
15_D32_D0.8531.00
8_V26_V0.8371.00
10_L45_Y0.8251.00
14_C32_D0.8071.00
30_S46_K0.8061.00
3_G38_G0.8031.00
36_V43_V0.7901.00
35_T53_S0.7871.00
10_L17_V0.7851.00
14_C29_D0.7751.00
11_T46_K0.7641.00
30_S33_T0.7611.00
1_V8_V0.7321.00
26_V43_V0.7281.00
16_S33_T0.7131.00
11_T14_C0.7071.00
32_D49_D0.7021.00
30_S47_S0.6991.00
5_N16_S0.6650.99
28_V34_I0.6600.99
4_S23_N0.6570.99
7_T42_T0.6510.99
51_K55_S0.6390.99
35_T44_T0.6310.99
10_L28_V0.6280.99
28_V43_V0.6190.99
2_S55_S0.6150.99
36_V55_S0.6000.99
15_D50_P0.5960.98
28_V31_V0.5950.98
27_T48_G0.5920.98
30_S54_D0.5780.98
46_K49_D0.5580.98
12_G45_Y0.5560.98
1_V55_S0.5560.98
17_V31_V0.5540.98
36_V54_D0.5520.98
27_T54_D0.5440.97
7_T27_T0.5410.97
8_V18_T0.5280.97
16_S30_S0.5190.96
17_V28_V0.5160.96
15_D33_T0.5150.96
44_T47_S0.5140.96
19_V24_N0.5130.96
7_T16_S0.5090.96
36_V45_Y0.5070.96
4_S21_G0.5020.96
50_P53_S0.5010.96
15_D18_T0.5000.96
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

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  
3ultA 1 0.8793 15.5 0.757 Contact Map
4mtkA 4 0.9828 6.8 0.793 Contact Map
3petA 2 0.9655 5.1 0.805 Contact Map
4opwA 1 0.9828 3.5 0.82 Contact Map
4yguA 3 0.9828 2.9 0.827 Contact Map
3lycA 2 0.9828 2.9 0.827 Contact Map
3jx8A 4 0.9655 1.7 0.848 Contact Map
3h09A 1 0.9828 1.7 0.848 Contact Map
2ks0A 2 0.8448 1.6 0.849 Contact Map
1wthA 3 0.931 1.6 0.849 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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