GPMAW lite – Protein Sequence Calculator (and much more)

Protein molecular weight calculator
Alphalyse
Apr 10. 2017

When working with proteins, you often need to make simple bioinformatics calculations on a specific protein sequence – and for this purpose, the GPMAW protein sequence calculator is perfect.
For example, to find out:

  • What is the molecular weight of bovine serum albumin (BSA)?
  • What is the amino acid composition in my protein?
  • How many N-glycosylation sites are present in my protein?
  • What peptides does trypsin cleavage generate?

Questions like these are typical. Therefore, Alphalyse launched GPMAW lite bioinformatics tool to make these calculations quickly.

There are three different ways to enter a sequence into GPMAW lite;

1. Either enter the known accession number from either NCBI or UNIPROT. The sequence will be retrieved into the sequence window automatically. With the NCBI and UniProt lookup function, you can easily find the accession number for any known protein from any organism.

2. Alternatively, paste the sequence directly into the protein sequence calculator window.

3. Or, you can type in the sequence using one letter AA code.

GPMAW lite functions

The cleanup function is helpful if your sequence contains numbers. It also works with spaces or lower case letters. You can perform several different bioinformatics analyses when the protein sequence has been entered. First, select the analysis you would like to have completed. Next, click Calculate.

The protein’s name and sequence are shown at the top of the analysis results. In addition, you can use the Colorize function to highlight specific amino acid residues and potential N-glycosylations sites.

The Protein Information table provides all the basic information about your protein. These include Molecular Weight (mono-isotopic and average mass of non-reduced protein), theoretically calculated molar absorbance, and extinction coefficient. It also shows the isoelectric point and hydrophobicity index. 

The Amino Acid Composition function shows an amino acid composition table. It includes numbers and percentages of individual amino acids. If the sequence contains any unusual amino acids, it will also be visible in this table.

The protease Digest lists all peptides formed by complete theoretical digestion using the chosen protease. The table contains info about the peptide sequence and MH+ (mono-isotopic molecular weight of the protonated peptide in reduced form). You will also see the isoelectric point pI and expected retention time in an HPLC run (reversed phase) for each peptide. It is possible to sort all columns. You do so by clicking the header of the column. The columns can thus show peptides by position, HPLC retention time, or mass.

protein mw calculation

Why use the GPMAW lite protein sequence calculator?

In conclusion, GPMAW lite is an online software for simple and easy bioinformatics calculations on protein amino acid sequences as an alternative to complete protein sequence analysis.

You can access GPMAW lite free from any browser, computer, smartphone, or tablet at our website.

Check out the GPMAW lite protein calculator >>>

Compute the pI/Mw from protein amino acid sequence or accession number: https://web.expasy.org/compute_pi/

Get help with protein MW determination by mass spectrometry:
Molecular Weight Determination and Intact Mass Analysis

More posts about Bioinformatics
  • Useful Protein Molecular Weight Calculator – kDa to pmol/µg

  • GPMAW lite – Protein Sequence Calculator (and much more)

About Alphalyse

Alphalyse uses expertise in the field of protein chemistry and bioinformatics, combined with top-of-the-line mass spectrometry equipment, to provide protein analysis services globally.

Alphalyse aims to deliver high quality data and customer service to all of our clients in a fast and convenient way.

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