GREMLIN Database
DUF3888 - Protein of unknown function (DUF3888)
PFAM: PF13027 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 88 (85)
Sequences: 539 (444)
Seq/√Len: 48.2
META: 0.56

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
53_E67_K3.0901.00
72_F81_L3.0611.00
3_D39_R2.8501.00
66_G86_H2.8101.00
16_A19_N2.5721.00
39_R48_F2.4521.00
68_D86_H2.4521.00
56_P65_V2.4091.00
70_I81_L2.1761.00
25_L65_V1.8200.99
53_E69_T1.7830.99
25_L58_V1.7310.98
13_I54_V1.7060.98
3_D48_F1.6900.98
28_S57_F1.6700.98
67_K87_L1.6290.98
56_P64_P1.5910.97
9_L74_I1.4690.96
21_Y66_G1.4110.95
56_P69_T1.4030.94
38_K49_E1.3670.94
50_V72_F1.3230.92
5_L8_L1.3170.92
13_I70_I1.2970.92
58_V65_V1.2730.91
73_E80_K1.2590.90
15_K19_N1.2360.90
35_L69_T1.2290.89
57_F62_N1.1870.88
39_R46_F1.1850.88
54_V68_D1.1690.87
33_E53_E1.1690.87
56_P66_G1.1540.86
4_A45_G1.0870.83
21_Y86_H1.0850.82
17_I80_K1.0780.82
56_P68_D1.0600.81
17_I54_V1.0540.81
50_V74_I1.0390.80
52_V74_I1.0330.79
28_S31_D1.0260.79
7_T82_I1.0110.78
74_I79_V1.0020.77
40_V45_G0.9790.75
49_E73_E0.9760.75
73_E82_I0.9550.74
51_T69_T0.9440.73
77_G85_E0.9400.72
59_G62_N0.9220.71
16_A81_L0.9190.71
56_P87_L0.9160.70
33_E37_I0.9100.70
56_P61_H0.9090.70
69_T87_L0.9050.70
25_L56_P0.8920.68
21_Y68_D0.8830.68
16_A84_F0.8630.66
68_D72_F0.8630.66
29_P33_E0.8620.66
48_F55_T0.8480.64
70_I83_K0.8440.64
67_K72_F0.8350.63
22_G27_Y0.8250.62
20_Y86_H0.8230.62
20_Y66_G0.8230.62
67_K73_E0.8190.62
9_L79_V0.8170.62
15_K18_N0.8170.62
59_G65_V0.8090.61
29_P32_V0.7950.59
64_P87_L0.7940.59
36_S51_T0.7910.59
43_F87_L0.7780.58
52_V55_T0.7640.56
9_L52_V0.7590.56
51_T85_E0.7540.55
66_G84_F0.7530.55
68_D87_L0.7510.55
47_D73_E0.7390.54
41_N83_K0.7370.54
27_Y36_S0.7320.53
9_L48_F0.7140.51
41_N45_G0.6920.49
35_L53_E0.6800.48
53_E80_K0.6800.48
34_I73_E0.6740.47
12_Y79_V0.6610.46
43_F46_F0.6590.46
18_N34_I0.6560.46
3_D11_P0.6490.45
37_I77_G0.6480.45
51_T74_I0.6460.45
64_P72_F0.6430.44
61_H66_G0.6420.44
11_P60_P0.6420.44
3_D42_G0.6290.43
36_S47_D0.6210.42
53_E71_T0.6120.41
18_N57_F0.6090.41
26_T57_F0.6070.41
32_V37_I0.6070.41
20_Y24_Y0.5870.39
65_V68_D0.5850.39
42_G45_G0.5850.39
43_F57_F0.5830.38
22_G36_S0.5730.37
20_Y23_E0.5730.37
15_K82_I0.5720.37
40_V47_D0.5700.37
72_F79_V0.5700.37
35_L87_L0.5660.37
19_N83_K0.5420.35
31_D57_F0.5390.34
12_Y38_K0.5300.34
80_K85_E0.5300.34
24_Y38_K0.5240.33
47_D75_S0.5230.33
67_K76_P0.5220.33
35_L41_N0.5210.33
5_L73_E0.5190.33
31_D55_T0.5170.32
40_V54_V0.5120.32
78_G82_I0.5100.32
2_Q60_P0.5080.32
7_T74_I0.5050.31
5_L43_F0.5030.31
41_N80_K0.5010.31
38_K84_F0.5000.31
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  
2d3o1 1 0.5341 34.5 0.872 Contact Map
2nscA 2 0.5341 24.5 0.881 Contact Map
1p9yA 1 0.625 16.5 0.89 Contact Map
1t11A 3 0.875 15.5 0.891 Contact Map
1w26A 1 0.9091 15.5 0.891 Contact Map
2rsxA 1 0.9205 10.2 0.9 Contact Map
4gl6A 1 0.8636 5.3 0.912 Contact Map
4ioyX 1 0.7273 4.5 0.915 Contact Map
3a9lA 2 0.2727 3.7 0.919 Contact Map
4yjwA 1 0.25 3.1 0.922 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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