GREMLIN Database
PT-VENN - Pre-toxin domain with VENN motif
PFAM: PF04829 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 52 (50)
Sequences: 1100 (631)
Seq/√Len: 89.2
META: 0.535

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
28_G33_D2.8781.00
20_A41_G2.8341.00
42_K46_E2.8341.00
3_D8_E2.5601.00
5_T8_E2.4731.00
21_G38_A2.1091.00
20_A37_G1.9281.00
11_T14_A1.8651.00
16_S19_A1.7751.00
30_S33_D1.7201.00
6_E10_Q1.6911.00
16_S44_A1.5151.00
17_T42_K1.4070.99
24_G32_A1.3170.99
29_G33_D1.3050.99
35_V38_A1.1830.98
17_T38_A1.1400.97
36_A40_A1.1220.97
35_V39_Q1.0860.96
39_Q43_N1.0320.95
15_L37_G1.0200.94
10_Q14_A1.0190.94
20_A49_Y0.9460.92
23_A32_A0.9360.91
18_L25_G0.9060.90
6_E9_K0.9010.90
7_E11_T0.8830.89
16_S31_T0.8650.88
8_E11_T0.8630.88
37_G47_N0.8520.87
19_A22_L0.8440.86
11_T26_L0.8360.86
31_T35_V0.8290.85
45_V49_Y0.8230.85
13_S17_T0.8200.85
16_S20_A0.8090.84
5_T11_T0.7950.83
25_G34_A0.7840.82
19_A40_A0.7650.81
43_N47_N0.7590.80
36_A39_Q0.7570.80
34_A38_A0.7470.79
8_E49_Y0.7230.77
31_T43_N0.7210.77
11_T15_L0.7030.75
13_S42_K0.6990.74
12_I21_G0.6980.74
18_L21_G0.6950.74
14_A17_T0.6940.74
22_L26_L0.6850.73
24_G41_G0.6850.73
17_T22_L0.6800.72
9_K42_K0.6760.72
4_L34_A0.6730.71
11_T35_V0.6670.71
18_L27_A0.6560.70
9_K34_A0.6290.66
13_S16_S0.6280.66
4_L43_N0.6210.65
3_D7_E0.6140.64
44_A49_Y0.5950.62
17_T20_A0.5950.62
15_L34_A0.5920.62
40_A43_N0.5880.61
5_T18_L0.5740.59
4_L47_N0.5700.59
33_D39_Q0.5680.59
27_A33_D0.5670.58
19_A35_V0.5660.58
30_S36_A0.5370.54
13_S50_L0.5250.53
32_A35_V0.5190.52
17_T44_A0.5160.51
13_S44_A0.5060.50
17_T34_A0.5000.49
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  
3agxA 2 0.3462 30.1 0.801 Contact Map
3lz8A 2 0.5385 15.6 0.826 Contact Map
3anwB 1 0.5 15.3 0.826 Contact Map
3wolA 2 0.9231 15.1 0.826 Contact Map
4j80A 2 0.4231 9 0.843 Contact Map
3kdwA 2 0.9423 8.2 0.846 Contact Map
4y04A 2 0.9423 7.1 0.85 Contact Map
4b2nA 1 0.3654 5.9 0.856 Contact Map
1vzvA 2 0.9423 5.6 0.858 Contact Map
3e9lA 1 0.3462 5.4 0.858 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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