GREMLIN Database
Plasmid_RAQPRD - Plasmid protein of unknown function (Plasmid_RAQPRD)
PFAM: PF09686 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 77 (75)
Sequences: 927 (596)
Seq/√Len: 68.8
META: 0.676

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
16_L49_L3.9371.00
5_E42_Y3.3581.00
40_F56_I3.2501.00
41_D44_R3.1591.00
27_E46_R2.7911.00
20_E53_R2.5631.00
13_L53_R2.2871.00
12_I19_L2.2411.00
48_D55_G2.0861.00
20_E46_R1.9771.00
23_I45_L1.9701.00
2_D6_R1.9001.00
9_L56_I1.6470.99
59_Y63_P1.5490.99
11_R15_Q1.5430.99
12_I22_L1.4620.99
31_D36_A1.4100.98
38_Y66_Q1.4010.98
24_E46_R1.2970.97
32_P52_I1.2560.96
22_L45_L1.2320.96
13_L17_D1.2170.96
6_R49_L1.1750.95
59_Y62_P1.1730.95
55_G75_G1.1680.94
5_E9_L1.1570.94
55_G64_R1.1290.93
8_Q11_R1.1210.93
35_G49_L1.0580.91
4_A8_Q1.0410.90
51_R69_D1.0250.89
26_A30_A1.0230.89
17_D53_R1.0230.89
8_Q25_R0.9890.88
13_L60_L0.9840.87
44_R62_P0.9780.87
27_E57_Q0.9720.87
62_P65_A0.9330.85
51_R58_D0.9190.84
4_A29_Q0.8990.82
42_Y49_L0.8960.82
30_A42_Y0.8830.81
41_D62_P0.8610.79
24_E32_P0.8570.79
15_Q59_Y0.8570.79
45_L52_I0.8340.77
10_A36_A0.8330.77
40_F59_Y0.8320.77
63_P73_L0.8310.77
36_A73_L0.8200.76
44_R70_P0.8180.76
8_Q22_L0.8110.75
7_E10_A0.7880.73
19_L45_L0.7850.73
13_L73_L0.7810.72
15_Q65_A0.7650.71
70_P74_R0.7640.71
38_Y44_R0.7560.70
13_L57_Q0.7540.70
19_L28_A0.7520.70
18_A56_I0.7510.69
4_A7_E0.7360.68
11_R19_L0.7360.68
5_E30_A0.7100.65
50_E54_Q0.7100.65
15_Q19_L0.7090.65
26_A35_G0.7080.65
43_D47_Q0.7050.65
44_R75_G0.6900.63
41_D64_R0.6830.62
5_E12_I0.6700.61
47_Q60_L0.6700.61
5_E26_A0.6690.61
23_I27_E0.6670.60
25_R32_P0.6620.60
25_R28_A0.6550.59
14_R17_D0.6370.57
38_Y41_D0.6190.55
15_Q53_R0.6130.54
23_I43_D0.5980.52
32_P35_G0.5980.52
27_E31_D0.5970.52
7_E63_P0.5960.52
24_E28_A0.5940.52
58_D68_R0.5930.52
4_A33_D0.5930.52
7_E41_D0.5870.51
32_P46_R0.5850.51
39_R47_Q0.5840.50
3_A38_Y0.5830.50
39_R74_R0.5820.50
15_Q39_R0.5810.50
22_L25_R0.5670.48
12_I30_A0.5620.48
56_I76_D0.5610.48
14_R36_A0.5590.47
47_Q51_R0.5570.47
17_D70_P0.5530.47
60_L67_P0.5520.47
39_R51_R0.5460.46
33_D36_A0.5440.46
42_Y63_P0.5430.46
59_Y73_L0.5400.45
38_Y64_R0.5300.44
55_G59_Y0.5290.44
71_P74_R0.5260.44
23_I46_R0.5200.43
13_L29_Q0.5190.43
16_L55_G0.5170.42
60_L64_R0.5140.42
14_R47_Q0.5130.42
29_Q35_G0.5000.41
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  
1dd5A 1 0.5584 6.3 0.883 Contact Map
1is1A 1 0.5714 6.1 0.884 Contact Map
1iseA 1 0.5584 5.5 0.886 Contact Map
4kddA 1 0.5714 5.2 0.888 Contact Map
1t92A 2 0.5584 5.1 0.888 Contact Map
2kepA 1 0.5714 4.7 0.89 Contact Map
4jkvA 2 1 4.6 0.89 Contact Map
4qinA 2 1 4.5 0.891 Contact Map
1ge9A 1 0.6104 4.5 0.891 Contact Map
1eh1A 1 0.5844 4.4 0.891 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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