SeqBench

E. coli (K-12) Codon Usage

For every amino acid with more than one synonymous codon, E. coli (K-12)uses some codons far more often than others. The table below shows each codon's usage fraction — the share of that amino acid's codons it accounts for — with the preferred (most-used) codon highlighted.

Amino acid1-letter3-letterCodonFraction
AlanineAAlaGCT11%
AlanineAAlaGCC31%
AlanineAAlaGCA21%
AlanineAAlaGCG38%preferred
ArginineRArgCGT36%
ArginineRArgCGC44%preferred
ArginineRArgCGA7%
ArginineRArgCGG7%
ArginineRArgAGA2%
ArginineRArgAGG3%
AsparagineNAsnAAT47%
AsparagineNAsnAAC53%preferred
Aspartic acidDAspGAT65%preferred
Aspartic acidDAspGAC35%
CysteineCCysTGT42%
CysteineCCysTGC58%preferred
Glutamic acidEGluGAA70%preferred
Glutamic acidEGluGAG30%
GlutamineQGlnCAA30%
GlutamineQGlnCAG70%preferred
GlycineGGlyGGT29%
GlycineGGlyGGC46%preferred
GlycineGGlyGGA13%
GlycineGGlyGGG12%
HistidineHHisCAT55%preferred
HistidineHHisCAC45%
IsoleucineIIleATT58%preferred
IsoleucineIIleATC35%
IsoleucineIIleATA7%
LeucineLLeuTTA15%
LeucineLLeuTTG12%
LeucineLLeuCTT12%
LeucineLLeuCTC10%
LeucineLLeuCTA5%
LeucineLLeuCTG46%preferred
LysineKLysAAA73%preferred
LysineKLysAAG27%
MethionineMMetATG100%preferred
PhenylalanineFPheTTT57%preferred
PhenylalanineFPheTTC43%
ProlinePProCCT17%
ProlinePProCCC13%
ProlinePProCCA14%
ProlinePProCCG55%preferred
SerineSSerTCT11%
SerineSSerTCC11%
SerineSSerTCA15%
SerineSSerTCG16%
SerineSSerAGT14%
SerineSSerAGC33%preferred
ThreonineTThrACT16%
ThreonineTThrACC47%preferred
ThreonineTThrACA13%
ThreonineTThrACG24%
TryptophanWTrpTGG100%preferred
TyrosineYTyrTAT53%preferred
TyrosineYTyrTAC47%
ValineVValGTT25%
ValineVValGTC18%
ValineVValGTA17%
ValineVValGTG40%preferred
Stop*StopTAA64%
Stop*StopTAG0%
Stop*StopTGA36%

Optimize a protein for E. coli

Paste a protein sequence and every residue is rewritten with its preferred E. coli codon — the same engine behind the full Codon Optimizer tool, scoped to this one organism.

Frequently asked questions

What is the preferred codon for each amino acid in E. coli?

The codon with the highest usage fraction for that amino acid in E. coli (K-12) — highlighted in green in the table below. It's the codon a codon optimizer picks when rewriting a gene for this host.

What's a rare codon to avoid in E. coli?

AGA (Arginine) is used only 2% of the time among its synonymous codons in E. coli (K-12) — a run of codons like this can slow translation if the matching tRNA is scarce.

How do I codon-optimize a gene for E. coli?

Paste the protein sequence into the tool below (or the full Codon Optimizer), and every residue is rewritten with its most-used codon in E. coli (K-12) — the encoded protein is unchanged, only the DNA sequence changes.

Are these values exact?

These fractions are reference approximations derived from the Kazusa Codon Usage Database for E. coli (K-12). For critical work, verify against your specific expression system rather than treating any single table as definitive.