Pichia (K. phaffii) Codon Usage

For every amino acid with more than one synonymous codon, Pichia (K. phaffii)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 acid	1-letter	3-letter	Codon	Fraction
Alanine	A	Ala	GCT	45%preferred
Alanine	A	Ala	GCC	26%
Alanine	A	Ala	GCA	23%
Alanine	A	Ala	GCG	6%
Arginine	R	Arg	CGT	16%
Arginine	R	Arg	CGC	5%
Arginine	R	Arg	CGA	10%
Arginine	R	Arg	CGG	5%
Arginine	R	Arg	AGA	48%preferred
Arginine	R	Arg	AGG	16%
Asparagine	N	Asn	AAT	48%
Asparagine	N	Asn	AAC	52%preferred
Aspartic acid	D	Asp	GAT	58%preferred
Aspartic acid	D	Asp	GAC	42%
Cysteine	C	Cys	TGT	64%preferred
Cysteine	C	Cys	TGC	36%
Glutamic acid	E	Glu	GAA	56%preferred
Glutamic acid	E	Glu	GAG	44%
Glutamine	Q	Gln	CAA	61%preferred
Glutamine	Q	Gln	CAG	39%
Glycine	G	Gly	GGT	44%preferred
Glycine	G	Gly	GGC	14%
Glycine	G	Gly	GGA	33%
Glycine	G	Gly	GGG	10%
Histidine	H	His	CAT	56%preferred
Histidine	H	His	CAC	44%
Isoleucine	I	Ile	ATT	50%preferred
Isoleucine	I	Ile	ATC	31%
Isoleucine	I	Ile	ATA	18%
Leucine	L	Leu	TTA	16%
Leucine	L	Leu	TTG	33%preferred
Leucine	L	Leu	CTT	17%
Leucine	L	Leu	CTC	8%
Leucine	L	Leu	CTA	11%
Leucine	L	Leu	CTG	15%
Lysine	K	Lys	AAA	47%
Lysine	K	Lys	AAG	53%preferred
Methionine	M	Met	ATG	100%preferred
Phenylalanine	F	Phe	TTT	54%preferred
Phenylalanine	F	Phe	TTC	46%
Proline	P	Pro	CCT	35%
Proline	P	Pro	CCC	15%
Proline	P	Pro	CCA	42%preferred
Proline	P	Pro	CCG	9%
Serine	S	Ser	TCT	29%preferred
Serine	S	Ser	TCC	20%
Serine	S	Ser	TCA	18%
Serine	S	Ser	TCG	9%
Serine	S	Ser	AGT	15%
Serine	S	Ser	AGC	9%
Threonine	T	Thr	ACT	40%preferred
Threonine	T	Thr	ACC	26%
Threonine	T	Thr	ACA	24%
Threonine	T	Thr	ACG	11%
Tryptophan	W	Trp	TGG	100%preferred
Tyrosine	Y	Tyr	TAT	47%
Tyrosine	Y	Tyr	TAC	53%preferred
Valine	V	Val	GTT	42%preferred
Valine	V	Val	GTC	23%
Valine	V	Val	GTA	15%
Valine	V	Val	GTG	19%
Stop	*	Stop	TAA	50%
Stop	*	Stop	TAG	31%
Stop	*	Stop	TGA	19%

Optimize a protein for Pichia

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

Optimize a protein for Pichia

Frequently asked questions

What is the preferred codon for each amino acid in Pichia?

The codon with the highest usage fraction for that amino acid in Pichia (K. phaffii) — 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 Pichia?

CGG (Arginine) is used only 5% of the time among its synonymous codons in Pichia (K. phaffii) — a run of codons like this can slow translation if the matching tRNA is scarce.

How do I codon-optimize a gene for Pichia?

Paste the protein sequence into the tool below (or the full Codon Optimizer), and every residue is rewritten with its most-used codon in Pichia (K. phaffii) — 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 Pichia (K. phaffii). For critical work, verify against your specific expression system rather than treating any single table as definitive.