A new sequence logo generator by using reduced amino acid clusters
With a bacteriolytic function, lysozyme C (LYC) is ubiquitous from chickens to humans. we collected 21 lysozyme C (LYC) aligned sequences from chickens to humans. Then, after RaacLogo treatment (polar/Neutrall/hydrophobicity, RKEDQN, GASTPHY, CLVIMFW), the reduced letters make the logo very neat and simple, reflecting the high sequence homology. Although the amino acid coding of LYC changed greatly in the evolution from chicken to human, we can see that the overall amino acid properties of LYC remained unchanged after reduction, and the homologous function of LYC was maintained.
| Parameter | RaacLogo Type 54 |
|---|---|
| Cluster | RKEDQNGASTPHYCLVIMFW
PolarNeutralHydrophobicity |
| Edit | RaacLogo Analysis |
Cluster: RKEDQNGASTPHYCLVIMFW
The typical CXXC domain is rich in basic amino acids and highly conserved among species and combines with a CpG sequence. It has seven amino acids that bind to DNA and stabilizes the spatial conformation through two Zn2+ ions that coordinate with four cysteines (C4-type zinc finger). In the natural logo, the eight cysteines are extremely conserved, while the other amino acids are clearly differentiated. In the reduced logo, the overall effect is good but some jumbled amino acids are always divided into two groups: K and A. This means that the properties of these amino acid sites have changed dramatically. This may be the cause of functional differentiation of paralogs.
| Parameter | RaacLogo Type 54 |
|---|---|
| Cluster | KRANCQGHILMFPSTWYVDE PositiveNeutralNegative (Charge) |
| Edit | RaacLogo Analysis |
Cluster: KRANCQGHILMFPSTWYVDE
Double-stranded b-helix (DSBH) domain is the catalytic core of demethylase, depending on Fe-2OG. It is the vital executor of the dynamic changes between methylation and demethylation in the plants and animals. Homologous peptides of 35 amino acids were selected to demonstrate the reduction of enzyme proteins by RaacLogo. The results showed that RAAC could effectively reduce the chaotic motif into a simple logo to reflect the conservatism of the paralogs.
| Parameter | RaacLogo Type 7 |
|---|---|
| Cluster | WCGPHNDERQKASTFYVMIL HeterocyclicSulfydrylNo chiralOthersAromaticAliphatic |
| Edit | RaacLogo Analysis |
Cluster: WCGPHNDERQKASTFYVMIL
The POU (Pit-Oct-Unc) protein family is an evolutionary ancient group of transcription factors (TFs) that bind specific DNA sequences to direct gene expression programs. We collected 30 POU aligned sequences and obtained the natural logo and Raaclogo. The results showed that various amino acid site differences could be effectively reduced by rational strategies. For example, 7-E/R/D/K is reduced to 7-P, and 65-L/V/I is reduced to 65-V.
| Parameter | RaacLogo Type 7 |
|---|---|
| Cluster | WCGPHNDERQKASTFYVMIL HeterocyclicSulfydrylNo chiralOthersAromaticAliphatic |
| Edit | RaacLogo Analysis |
Cluster: WCGPHNDERQKASTFYVMIL
G-protein-coupled receptors (GPCRs), one of the largest protein superfamilies, are key mediators linking extracellular ligands to downstream signals and are the most common targets for pharmaceutical drug development. The G protein family has a large number of members, and its sites and functions are extremely diverse. Therefore, the logo of its protein sequence appears disordered. After RaacLogo reduction, most of the sites became very conservative, which verified the law of homologous differentiation.
| Parameter | RaacLogo Type 7 |
|---|---|
| Cluster | WCGPHNDERQKASTFYVMIL HeterocyclicSulfydrylNo chiralOthersAromaticAliphatic |
| Edit | RaacLogo Analysis |
Cluster: WCGPHNDERQKASTFYVMIL