Pichia pastoris Codon Usage Table

See the most used codons, highest-fraction synonymous codons, and full codon usage frequencies for Pichia pastoris.

Use frequency to find the most common codons in this organism, and use fraction to compare synonymous codon preference within the same amino acid family.

Escherichia coli Saccharomyces cerevisiae Arabidopsis thaliana Caenorhabditis elegans Cricetulus griseus Drosophila melanogaster Homo sapiens Spodoptera frugiperda Mus musculus Nicotiana tabacum Pichia pastoris Sus scrofa Rattus norvegicus Streptomyces Zea mays

Choose Organism and Display

These settings control the summary cards and the full codon usage table below.

Top Codons by Frequency

Codons ranked by frequency per 1,000 codons in the selected organism.

GAA

Amino acid: E

Fraction 0.58

Freq 40.2

GAT

Amino acid: D

Fraction 0.59

Freq 37.2

AAG

Amino acid: K

Fraction 0.53

Freq 34.4

ATT

Amino acid: I

Fraction 0.51

Freq 31.7

TTG

Amino acid: L

Fraction 0.33

Freq 31.4

AAA

Amino acid: K

Fraction 0.47

Freq 30.2

GCT

Amino acid: A

Fraction 0.45

Freq 29.6

GAG

Amino acid: E

Fraction 0.42

Freq 29.6

Top Codons by Fraction

Synonymous codons ranked by fraction. Stop codons and single-codon amino acids are excluded.

TGT

Amino acid: C

Fraction 0.65

Freq 8.3

CAA

Amino acid: Q

Fraction 0.62

Freq 23.9

GAT

Amino acid: D

Fraction 0.59

Freq 37.2

GAA

Amino acid: E

Fraction 0.58

Freq 40.2

TTT

Amino acid: F

Fraction 0.56

Freq 23.9

TAC

Amino acid: Y

Fraction 0.55

Freq 18.3

CAT

Amino acid: H

Fraction 0.54

Freq 10.5

AAG

Amino acid: K

Fraction 0.53

Freq 34.4

Preferred Codons by Amino Acid

One preferred codon per amino acid, ranked by frequency to surface practical defaults.

GAA

Amino acid: E

Fraction 0.58

Freq 40.2

GAT

Amino acid: D

Fraction 0.59

Freq 37.2

AAG

Amino acid: K

Fraction 0.53

Freq 34.4

ATT

Amino acid: I

Fraction 0.51

Freq 31.7

TTG

Amino acid: L

Fraction 0.33

Freq 31.4

GCT

Amino acid: A

Fraction 0.45

Freq 29.6

GTT

Amino acid: V

Fraction 0.42

Freq 26.7

GGT

Amino acid: G

Fraction 0.43

Freq 26.6

Pichia pastoris (Yeast): (Genetic code: Standard)

Print-friendly 2-column table in genetic code order. Frequency is shown per 1,000 codons.

Triplet	Amino acid	Fraction	Frequency/Thousand	Number	Triplet	Amino acid	Fraction	Frequency/Thousand	Number
TTT TTC TTA TTG	F F L L	0.56 0.44 0.15 0.33	23.9 19.1 14.9 31.4	1,013 810 634 1,332	TCT TCC TCA TCG	S S S S	0.29 0.20 0.19 0.09	23.5 16.3 15.6 7.2	996 693 663 305
TAT TAC TAA TAG	Y Y * *	0.45 0.55 0.53 0.29	14.7 18.3 0.9 0.5	622 777 38 21	TGT TGC TGA TGG	C C * W	0.65 0.35 0.18 1.00	8.3 4.5 0.3 9.9	353 191 13 418
CTT CTC CTA CTG	L L L L	0.17 0.08 0.12 0.16	16.0 7.6 11.2 15.3	677 321 475 648	CCT CCC CCA CCG	P P P P	0.35 0.16 0.40 0.10	15.3 6.7 17.1 4.1	648 285 725 172
CAT CAC CAA CAG	H H Q Q	0.54 0.46 0.62 0.38	10.5 8.9 23.9 14.5	447 378 1,015 616	CGT CGC CGA CGG	R R R R	0.16 0.05 0.11 0.05	6.9 2.3 4.6 2.2	291 99 195 93
ATT ATC ATA ATG	I I I M	0.51 0.31 0.18 1.00	31.7 19.3 11.5 19.2	1,347 819 486 813	ACT ACC ACA ACG	T T T T	0.40 0.24 0.25 0.11	23.3 13.7 14.3 6.3	989 580 605 267
AAT AAC AAA AAG	N N K K	0.48 0.52 0.47 0.53	23.5 25.7 30.2 34.4	998 1,090 1,280 1,460	AGT AGC AGA AGG	S S R R	0.15 0.09 0.47 0.16	12.1 7.4 19.9 6.6	514 315 846 281
GTT GTC GTA GTG	V V V V	0.42 0.23 0.16 0.20	26.7 14.5 10.1 12.8	1,131 615 430 543	GCT GCC GCA GCG	A A A A	0.45 0.25 0.24 0.06	29.6 16.7 15.9 3.7	1,256 707 675 158
GAT GAC GAA GAG	D D E E	0.59 0.41 0.58 0.42	37.2 26.2 40.2 29.6	1,578 1,110 1,706 1,255	GGT GGC GGA GGG	G G G G	0.43 0.14 0.32 0.10	26.6 8.6 20.0 6.4	1,130 365 849 271

Showing 64 entries for Pichia pastoris (Yeast).

Frequency is measured per 1,000 codons. Fraction compares codons that encode the same amino acid.

Questions this table can answer

Which codons are most common in Pichia pastoris?

Which synonymous codons are preferred in Pichia pastoris?

Which codons should be checked before expression design?

How to use this page

Use the summary cards to find the most used and highest-fraction codons quickly.

Switch sorting in the full table when you want to compare by frequency, fraction, or count.

Use the full organism list and search codons/amino acids on the Codon Usage Frequency Table.

FAQ

What are the most used codons in Pichia pastoris?

Use the "Most Used Codons" section to see which codons appear most often in Pichia pastoris. The ranking is based on frequency per 1,000 codons.

Which codons have the highest fraction in Pichia pastoris?

Use the "Highest Fraction Codons" section to compare synonymous codons for the same amino acid. Single-codon amino acids and stop codons are excluded so the ranking reflects codon preference rather than trivial 1.00 values.

What is the difference between codon frequency and codon fraction in Pichia pastoris?

Frequency measures how often a codon appears per 1,000 codons in the dataset. Fraction measures how strongly that codon is preferred relative to alternative codons encoding the same amino acid.

How should I use this Pichia pastoris codon usage table for optimization?

Start with the preferred-codon summaries to identify likely defaults, then review the full table below before making codon optimization or expression design decisions.