Amino acid composition
v1.0.0Calculate the percentage and frequency of each amino acid in protein sequences
Calculate the percentage and frequency of each amino acid in protein sequences
Paste a protein sequence or upload a FASTA file to calculate the frequency of each of the 20 standard amino acids. The results contain one row per sequence, its residue count, and all 20 amino acid columns. Leave Show percentage enabled for percentages, or turn it off for exact counts.
For the human insulin B chain:
>insulin-B human insulin B chain
FVNQHLCGSHLVEALYLVCGERGFFYTPKTThe result has ID = insulin-B and Residues = 30. Selected columns are shown below; the result table includes all 20 residues.
| Column | Percentage mode (default) | Count mode |
|---|---|---|
Cys (C) | 6.67 | 2 |
Gly (G) | 10 | 3 |
Leu (L) | 13.33 | 4 |
Tyr (Y) | 6.67 | 2 |
Trp (W) | 0 | 0 |
These counts agree with ExPASy ProtParam. Percentages use the same count divided by sequence length, with two decimal places of rounding. The table can display trailing zeros, for example 6.670, without adding calculation precision.
Give each sequence its own FASTA header, with sequence data starting on the following line:
>insulin-B human insulin B chain
FVNQHLCGSHLVEALYLVCGERGFFYTPKT
>insulin-A human insulin A chain
GIVEQCCTSICSLYQLENYCNWith Show percentage turned off, the selected results are:
| ID | Residues | Cys (C) | Gly (G) | Leu (L) | Tyr (Y) |
|---|---|---|---|---|---|
| insulin-B | 30 | 2 | 3 | 4 | 2 |
| insulin-A | 21 | 4 | 1 | 2 | 2 |
Each sequence has its own denominator. The sequences are not combined into a pooled composition.
| Input | Accepted content |
|---|---|
| Pasted text | One plain protein sequence, or multiple FASTA records. Wrapped lines belong to the same sequence until the next FASTA header. |
| Files | Text files with extensions .fasta, .fa, .fas, or .txt, up to 50 MiB per file. |
| Residues | Standard one-letter codes: ACDEFGHIKLMNPQRSTVWY. Uppercase and lowercase are accepted. |
| Formatting | Whitespace, blank lines, invisible document characters and lines starting with # are ignored. Position numbers separated by whitespace at the beginning or end of sequence lines are ignored. |
| Unsupported input | Ambiguous codes B, Z, X, J; non-standard codes U, O; gaps, stop symbols, embedded numbers and punctuation. These cause an error rather than being removed. |
Guest runs accept up to 5 sequences, free accounts up to 100, and paid plans have no sequence-count cap. The file-size limit still applies.
A plain sequence receives the ID Sequence. Put any name or description after >; a plain-text name such as GFP uses valid residue letters and would be counted as part of the sequence. Do not paste spreadsheet columns, database annotations or structure records directly. Empty FASTA records are rejected, including a header with no sequence beneath it.
| Setting | Default | Behavior |
|---|---|---|
Show percentage | On | On: amino acid columns contain percentages from 0 to 100, rounded to two decimal places. Off: they contain exact integer counts. Residues always contains the sequence length. |
| Column or action | Meaning |
|---|---|
ID | The header text before the first space or pipe. For example, >sample kinase gives sample; >sp|P01308|INS_HUMAN gives sp. |
Residues | Total number of standard amino acids in that record. |
| Amino acid columns | Three-letter labels with one-letter codes, such as Ala (A) and Cys (C). Every amino acid appears, including those with zero counts. |
| Download | Export the table through the shared download control as CSV, JSON or Excel. |
If multiple records produce the same ID, the tool shows a warning and keeps a separate result for each record. Use distinct identifiers before any space or pipe when names must be distinguishable. The table supports sorting and searching.
For amino acid type , count its occurrences in a sequence of residues:
Counts sum exactly to Residues. Rounded percentages can sum slightly above or below 100%. The method matches the standard count and percentage definitions in Biopython's ProteinAnalysis reference. No mass weighting or prediction model is involved.
Composition describes residue abundance, without positions or order. It can reveal enrichment or depletion when compared with an appropriate reference, but it does not establish structure, solubility, disorder or function. A reference distribution should match the organism and protein class being studied.
GRAVY uses residue abundances and hydropathy values. The instability index additionally depends on adjacent residue pairs, so identical composition does not imply an identical instability score. Modifications, disulfide bonds and chain connectivity are not represented in this composition table.
| Goal | Tool |
|---|---|
| Count residues or compare their percentages across proteins | Amino acid composition |
| Calculate several protein properties together | Protein parameters |
| Prepare named FASTA records from text | TXT to FASTA |
| Convert spreadsheet sequence columns | CSV to FASTA |
| Extract protein sequences from a structure file | PDB to FASTA |
Gaps and unknown residues are rejected. Resolve them from the source sequence before analysis. If you deliberately remove residues, the remaining sequence has a different length and percentage denominator; the calculator does not make that choice automatically.
Yes. Reordering residues preserves every count and percentage while potentially changing structure and function. Composition alone cannot identify a protein or describe where a residue occurs.
It treats the input as protein. A string made only of A, C, G and T is also valid protein lettering, so check that the submitted sequence is the intended protein sequence.
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