How to Use the Asparaginase Database

The Asparaginase Database asparaginase classification

Experimentally Studied Proteins and Swiss-Prot Sequences Tables

Table Features

Information Overview: Provides data and references for l‑asparginases - classification, sequence, structure, source organism, cellular location and enzyme kinetics
Interactive Links: Click on family codes, accession numbers, or enzyme kinetics data for relevant publications
Selection Tools: Use checkboxes to select individual entries or all entries at once
Download Options: Export selected data (Tab-separated, UniProt IDs, or copy the sequence IDs to clipboard for easy UniProt ID mapping)

Table Descriptions

Fam (Family)

Classification code in the format Class-Clan-Family (e.g., 1-1-1). Links to detailed family pages.

Alt (Alternative)

Historical or alternative names, classifications or abbreviations used in the literature.

AN (Accession Number)

UniProt accession number linking to the protein entry.

Name

UniProt entry name, provided only for Swiss-Prot entries.

Enzyme Commission numbers. Inferred from homology where necessary. May not reflect all subsidiary activities.

Organism

Source organism name as reported in the original studies or UniProt.

Cell-Loc (Cellular Location)

Subcellular localization as reported in the original studies or UniProt.

AAs (Amino Acids)

Number of amino acid residues of the unprocessed proteins.

Structure

Quaternary organization as reported in the Protein Data Bank or alternative structural information provided in original studies.

PDB

Protein Data Bank IDs when 3D structure is available. Links directly to selected PDB entry or to the UniProt structure section for all structures.

K_m

Michaelis constant for l‑asparagine substrate in millimolar (mM). Indicates enzyme-substrate affinity.

V_max

Maximum reaction velocity for l‑asparagine in μmol/min/mg protein. Indicates maximum catalytic capacity under saturating conditions.

K_cat

Turnover number for l‑asparagine in s^-1. Represents the number of substrate molecules converted per enzyme molecule per second.

Links

Any coloured text is a link to a detailed l‑asparaginase family page, database or the original publication.

Tooltip with additional or specifying information.

Example Entry

Fam	Alt	AN	Name	EC	Organism	Cell-Loc	AAs	Structure	PDB	K_m	V_max	K_cat
1-1-3	EcAII	P00805	ASPG2_ECOLI	3.5.1.1	Escherichia coli	Periplasm	348	Homo tetramer	3ECA PDBs	0.015	-	24

How to Use BLAST Search

The BLAST page allows you to search your protein sequence against The Asparaginase Database to find similar asparaginases, identify experimentally studied asparaginases related to your query, and classify your asparaginase into a class, clan and family. Enter your sequence in FASTA format (e.g., >my_sequence followed by the amino acid sequence) or simply paste a plain amino acid sequence, then click Run BLAST. The search is automatically performed against all three asparaginase subdatabases in parallel: UniRef100 Sequences, Experimentally Studied Proteins, and Swiss-Prot Sequences.

Search Parameters:

E-value: Maximum expect value threshold (default: 0.001). Lower values return more stringent matches.
Hits: Maximum number of hits to return (default: 250).
Matrix: Scoring matrix for alignment (default: BLOSUM62).
Output: Result format. Keep at 0 - Pairwise for full functionality.

Understanding Results:

Classification Summary: Analyses the top 10 or 50 UniRef100 hits when either of those hit limits is selected; otherwise, it analyses up to the top 100. The summary shows how many of the analysed hits belong to each asparaginase class, clan and family.
Classification Prediction: A prediction is shown only when at least 10 UniRef100 hits are available, the selected E-value threshold is 0.1 or lower, and at least 80% of the analysed hits belong to the same class, clan and family.
Top 3 Hits: Displays the best matches from UniRef100, Experimentally Studied Proteins, and Swiss-Prot databases.
Identity: Percentage of identical amino acids in the alignment.
Score (bits): Bit score representing alignment quality. Higher scores indicate better matches.

The raw BLAST output for each database can be copied using the copy button. The corresponding sequence tables below each output are automatically filtered to show only the matching entries.

Please treat the predicted classification as a suggestion. Predictions may be less reliable for divergent, short, partial or low-quality sequences.

How to Download Sequences from Tables?

You can easily download data from the tables and UniRef100 l‑asparaginases directly from The Asparaginase Database. To specifically download sequences of Experimentally Studied Proteins or Swiss-Prot l‑asparaginases, use the ID mapping option, which copies the sequence IDs to your clipboard and opens UniProt ID Mapping. Simply paste the sequences, map them, and then download or align them directly on UniProt. Please note that e.g. UniParc sequences cannot be mapped using the default mapping settings.

Conserved Motifs

Selected conserved sequence motifs are presented for classes and families. They were determined from an alignment of representative sequences that generally have relatively low mutual sequence identity. The random selection was refined by removing significant outliers and adding a selected reference sequence. The resulting motifs are presented with amino acid frequencies in the representative sequences and are mapped to the positions in the reference sequence. These percentages can indicate strong trends in the families, but do not reflect every single sequence, as each family has a large number of sequences.

More Help

Please contact us at info@asparaginasedb.com if you need additional assistance, have feedback to share, or would like to submit your data for inclusion.

The Asparaginase Database Help