Sequence Logos

Visualization of conserved motifs in 2A peptides

Overview

Sequence logos visualize the conservation pattern at each position in aligned 2A peptides. Height indicates information content (conservation), and letter size shows relative amino acid frequency.

Class 1 Sequence Logo

class1_seqs <- read_stockholm_sequences(class1_path)
message(sprintf("Loaded %d Class 1 sequences", length(class1_seqs)))

Loaded 35265 Class 1 sequences

ggseqlogo(class1_seqs, method = "prob") +
  labs(
    title = "Class 1 2A Peptide",
    x = "Position",
    y = "Probability"
  ) +
  theme_logo() +
  theme(
    plot.title = element_text(hjust = 0.5, size = 14, face = "bold"),
    axis.title = element_text(size = 10)
  )

Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
ℹ The deprecated feature was likely used in the ggseqlogo package.
  Please report the issue at <https://github.com/omarwagih/ggseqlogo/issues>.

Figure 1: Class 1 2A peptide sequence logo showing conserved GDVE central motif and NPGP C-terminal motif

Expected Conservation Pattern

Position:  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18
Consensus: L  L  x  x  x  x  G  D  V  E  x  x  x  x  N  P  G  P
                          ^^^^^^^               ^^^^^^^^^^
                          Central               C-terminal

Key positions: - Positions 7-10: GDVE central motif - Positions 15-18: NPGP C-terminal motif

Class 2 Sequence Logo

class2_seqs <- read_stockholm_sequences(class2_path)
message(sprintf("Loaded %d Class 2 sequences", length(class2_seqs)))

Loaded 709 Class 2 sequences

ggseqlogo(class2_seqs, method = "prob") +
  labs(
    title = "Class 2 2A Peptide",
    x = "Position",
    y = "Probability"
  ) +
  theme_logo() +
  theme(
    plot.title = element_text(hjust = 0.5, size = 14, face = "bold"),
    axis.title = element_text(size = 10)
  )

Figure 2: Class 2 2A peptide sequence logo showing conserved N-terminal tryptophan, EEGIE central motif, and PNPGP C-terminal motif

Expected Conservation Pattern

Position:  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19
Consensus: W  x  x  x  x  E  E  G  I  E  x  x  x  P  N  P  G  P  x
           ^              ^^^^^^^^^^^        ^^^^^^^^^^^^^^
           N-terminal     Central            C-terminal

Key positions: - Position 1: Invariant tryptophan (W) - Positions 6-10: EEGIE central motif - Positions 14-18: PNPGP C-terminal motif

Interpretation Guide

Feature	Meaning
Tall letters	Highly conserved position
Short letters	Variable position
Stack height	Information content (bits)
Letter order	Frequency (top = most common)

Conservation by Iteration

Track how conservation patterns change through iterative refinement:

Iteration	Sequences	Avg. Conservation
Seed	~10	High
Iter 1	~100	Medium
Iter 2	~500	Lower (more diversity)
Final (curated)	~200	Medium-High

Position-Specific Features

Critical Residues

Position	Residue	Function	Tolerance
-1	G	Cleavage site	None
0	P	Cleavage site	None
-2	G	Positioning	Low
-3	P/N	Efficiency	Medium

Variable Regions

• Positions 2-6: Allow diversity
• Positions 11-14: Linker region
• Tolerate substitutions without losing function