Protein Sequence(s)

Raw sequence or multi-FASTA format. Input limit: 500,000 characters.

Options

Add copies of to each sequence

💡 Quick Summary

Protein Molecular Weight calculates the theoretical molecular weight (in kDa) for one or more protein sequences. Residue weights are water-subtracted values; 18.015 Da is added for the N- and C-terminal groups. Common epitope and affinity tags can be appended to each sequence before calculation.

📋 How to Use

Paste one or more protein sequences (raw or FASTA) into the text area.
Optionally add a fusion/epitope tag: choose the number of copies and the tag from the dropdowns.
Click Submit. Results appear as a table with Name, Length, and MW (kDa).
Click Load Example to analyse two sample sequences.
Use Copy All to copy the tabular results to your clipboard.

🧮 Formulas & Logic

MW (Da)

Sum of residue weights (water-subtracted) + 18.015 Da (terminal H and OH groups)

MW (kDa)

MW (Da) / 1000

📊 Result Interpretation

< 10 kDa

Small peptide or domain fragment.

10 – 50 kDa

Typical range for most single-domain proteins and enzymes.

50 – 150 kDa

Large or multi-domain proteins.

> 150 kDa

Very large proteins; consider whether the sequence is complete.

🔬 Applications

Predicting expected band size on SDS-PAGE gels
Estimating stoichiometry for protein complexes
Verifying sequence integrity after cloning or mutation
Comparing MW of wild-type vs. tagged or truncated variants
Evaluating the mass contribution of common affinity tags (His6, GST, etc.)

⚠️ Common Mistakes & Warnings

Theoretical estimate only

The calculated MW assumes a fully unfolded protein and does not account for post-translational modifications, disulfide bonds, glycosylation, lipid anchors, or prosthetic groups.

Only standard amino acids counted

Non-standard characters (B, Z, X, *, gaps) are stripped before calculation. Only the 20 canonical amino acids contribute to the molecular weight.

Tag length is included in reported length

When a fusion tag is added, the reported sequence length includes the appended tag residues.

❓ Frequently Asked Questions

Why does this value differ from the database entry?

Databases often report the MW of the mature processed form (after signal peptide cleavage or propeptide removal). This tool calculates MW from the exact sequence you provide. Post-translational modifications such as glycosylation can add significant mass not reflected here.

Why does my SDS-PAGE band run at a different MW than calculated?

SDS-PAGE separates proteins by apparent MW, which can deviate from the calculated value due to anomalous SDS binding, proline-rich regions, or membrane protein behaviour. The calculated MW is the more accurate value.

What is the difference between average and monoisotopic mass?

This tool uses average residue weights (as in the original Sequence Manipulation Suite), which are appropriate for SDS-PAGE comparison. Monoisotopic masses (using the most abundant isotope of each element) are used for high-resolution mass spectrometry.