UniProt

Introduction

So you need protein sequences, functions, domains, or disease associations? Welcome to UniProt — the world's most comprehensive protein database, and your one-stop shop for everything protein-related.

Universal Protein Resource — a collaboration between three major institutions since 2002:

What it gives you:

• Protein sequences and functions
• Domains, families, PTMs
• Disease associations and variants
• Subcellular localization
• Cross-references to 180+ external databases
• Proteomes for complete organisms
• BLAST, Align, ID mapping tools

The UniProt Structure

UniProt isn't just one database — it's a collection:

                    UniProt
                       │
       ┌───────────────┼───────────────┐
       │               │               │
   UniProtKB        UniRef         UniParc
   (Knowledge)    (Clusters)      (Archive)
       │
   ┌───┴───┐
   │       │
Swiss-Prot TrEMBL
(Reviewed) (Unreviewed)

Swiss-Prot vs TrEMBL: Know the Difference

This is the most important distinction in UniProt:

UniProt Identifiers

Accession Numbers

The primary identifier — stable and persistent:

P05067      (6 characters: 1 letter + 5 alphanumeric)
A0A024RBG1  (10 characters: newer format)

Entry Names

Human-readable format: GENE_SPECIES

APP_HUMAN    → Amyloid precursor protein, Human
INS_HUMAN    → Insulin, Human
SPIKE_SARS2  → Spike protein, SARS-CoV-2

Protein Existence Levels

UniProt classifies how confident we are that a protein actually exists:

Query syntax: existence:1 (for protein-level evidence)

Annotation Score

A 1-5 score indicating annotation completeness (not accuracy!):

UniProt Search Syntax

UniProt uses a field-based query syntax. The general format:

field:value

Basic Query Structure

term1 AND term2 AND (term3 OR term4)

Boolean operators: AND, OR, NOT (can be uppercase or lowercase)

Key Search Fields

Organism and Taxonomy

Common taxonomy IDs:

• Human: 9606
• Mouse: 10090
• Rat: 10116
• Zebrafish: 7955
• E. coli K12: 83333
• Yeast: 559292

Review Status and Existence

Enzyme Classification (EC Numbers)

Proteomes

Finding proteome IDs: Go to UniProt → Proteomes → Search your organism

Cross-References (External Databases)

Function and Annotation

Gene Ontology

Sequence Properties

Building Complex Queries

Pattern 1: Reviewed + Organism + Function

reviewed:true AND organism_id:9606 AND cc_function:"kinase"

Pattern 2: Multiple EC Numbers

(ec:3.4.21.*) OR (ec:3.4.22.*)

Pattern 3: Multiple Organisms

(organism_id:10116) OR (organism_id:7955)

Pattern 4: Proteome + Database Cross-Reference

proteome:UP000005640 AND (database:pdb OR database:smr) AND reviewed:true

Pattern 5: Complex Boolean Logic

For "exactly two of three conditions" (A, B, C):

((A AND B) OR (B AND C) OR (A AND C)) NOT (A AND B AND C)

Practice Exercises

Exercise 1: Protein Existence Statistics

Q: (1) What percentage of TrEMBL entries have evidence at "protein level"? (2) What percentage of Swiss-Prot entries have evidence at "protein level"?

(1) (existence:1) AND (reviewed:false)
(2) (existence:1) AND (reviewed:true)

Exercise 2: EC Numbers + Multiple Organisms

Q: Retrieve all reviewed proteins annotated as either:

• Cysteine endopeptidases (EC 3.4.22.*)
• Serine endopeptidases (EC 3.4.21.*)

From: Rattus norvegicus [10116] and Danio rerio [7955]

How many?

((ec:3.4.21.*) OR (ec:3.4.22.*)) AND ((organism_id:10116) OR (organism_id:7955)) AND (reviewed:true)

Exercise 3: Proteome + Structure Cross-References

Q: Retrieve all reviewed entries from the Human Reference Proteome that have either:

• A PDB structure, OR
• A Swiss-Model Repository structure

How many?

proteome:UP000005640 AND ((database:pdb) OR (database:smr)) AND (reviewed:true)

Exercise 4: Complex Boolean — "Exactly Two of Three"

Q: Find all reviewed entries with exactly two of these three properties:

• Function: "ion transport" (CC field)
• Subcellular location: "cell membrane" (SL-0039)
• GO term: "cell adhesion" (GO:0007155)

(cc_function:"ion transport" AND cc_scl_term:SL-0039) OR (cc_scl_term:SL-0039 AND go:0007155) OR (cc_function:"ion transport" AND go:0007155) NOT (cc_function:"ion transport" AND cc_scl_term:SL-0039 AND go:0007155) AND (reviewed:true)

⚠️ Common UniProt Search Mistakes

Mistake #1: Forgetting reviewed:true

❌ organism_id:9606 AND ec:3.4.21.*
   → Returns millions of TrEMBL entries

✓ organism_id:9606 AND ec:3.4.21.* AND reviewed:true
   → Returns curated Swiss-Prot entries only

Mistake #2: Wrong Parentheses Grouping

❌ ec:3.4.21.* OR ec:3.4.22.* AND organism_id:9606
   → Parsed as: ec:3.4.21.* OR (ec:3.4.22.* AND organism_id:9606)
   → Gets ALL serine peptidases from ANY organism

✓ (ec:3.4.21.* OR ec:3.4.22.*) AND organism_id:9606
   → Gets both types, but only from human

Rule: Always use parentheses to make grouping explicit!

Mistake #3: Confusing Taxonomy Fields

organism_id:9606    → Works ✓
organism_name:human → Works ✓
taxonomy:human      → Doesn't work as expected

Best practice: Use organism_id with the NCBI taxonomy ID for precision.

Mistake #4: Missing Quotes Around Phrases

❌ cc_function:ion transport
   → Searches for "ion" in function AND "transport" anywhere

✓ cc_function:"ion transport"
   → Searches for the phrase "ion transport" in function

Mistake #5: Using Wrong Field for Cross-References

❌ pdb:1ABC
   → Not a valid field

✓ database:pdb AND xref:pdb-1ABC
   → Correct way to search for specific PDB

Or to find ANY protein with PDB:

database:pdb

Quick Reference: Common Query Patterns

By Organism

organism_id:9606                           # Human
organism_id:10090                          # Mouse
(organism_id:9606) OR (organism_id:10090)  # Human OR Mouse

By Enzyme Class

ec:1.1.1.1              # Exact EC
ec:1.1.1.*              # All in 1.1.1.x
ec:1.*                  # All oxidoreductases

By Evidence Level

reviewed:true                    # Swiss-Prot only
reviewed:false                   # TrEMBL only
existence:1                      # Protein-level evidence
existence:1 AND reviewed:true    # Best quality

By Database Cross-Reference

database:pdb                     # Has any PDB structure
database:smr                     # Has Swiss-Model
database:ensembl                 # Has Ensembl link
(database:pdb) OR (database:smr) # Has any 3D structure

By Proteome

proteome:UP000005640    # Human reference proteome
proteome:UP000000589    # Mouse reference proteome
proteome:UP000000625    # E. coli K12 proteome

By Function/Location

cc_function:"kinase"              # Function contains "kinase"
cc_scl_term:SL-0039               # Cell membrane
keyword:phosphoprotein            # UniProt keyword
go:0007155                        # GO term by ID
go:"cell adhesion"                # GO term by name

Entry Sections Quick Reference

A UniProtKB entry contains these sections:

Tools Available in UniProt

Download Formats

Automatic Annotation Systems

For TrEMBL entries, annotations come from:

Evidence codes (ECO):

• ECO:0000269 — Experimental evidence
• ECO:0000305 — Curator inference
• ECO:0000256 — Sequence model (automatic)
• ECO:0000259 — InterPro match (automatic)

TL;DR

• UniProt = protein database = Swiss-Prot (reviewed, high quality) + TrEMBL (unreviewed, comprehensive)
• Always add reviewed:true when you need reliable annotations
• Query syntax: field:value with AND, OR, NOT
• Use parentheses to group OR conditions properly
• Common fields: organism_id, ec, reviewed, existence, database, proteome, go
• Wildcards: Use * for EC numbers (e.g., ec:3.4.21.*)
• Protein existence: Level 1 = experimental evidence, Level 5 = uncertain

Now go find some proteins! 🧬