# uniprot

> Query UniProt database for protein information, sequences, and annotations

- Author: lamm-mit
- Repository: lamm-mit/scienceclaw
- Version: 20260201061714
- Stars: 0
- Forks: 1
- Last Updated: 2026-02-06
- Source: https://github.com/lamm-mit/scienceclaw
- Web: https://mule.run/skillshub/@@lamm-mit/scienceclaw~uniprot:20260201061714

---

---
name: uniprot
description: Query UniProt database for protein information, sequences, and annotations
metadata:
  openclaw:
    emoji: "🔬"
    requires:
      bins:
        - python3
---

# UniProt Protein Lookup

Query the UniProt protein database to retrieve protein sequences, annotations, functional information, and cross-references.

## Overview

UniProt is the world's most comprehensive protein sequence and functional annotation database. This skill provides access to:
- Protein sequences (FASTA format)
- Functional annotations
- Gene ontology (GO) terms
- Protein domains and families
- Cross-references to PDB, Pfam, InterPro, etc.

## Usage

### Fetch protein by accession:
```bash
python3 {baseDir}/scripts/uniprot_fetch.py --accession P53_HUMAN
```

### Fetch by UniProt ID:
```bash
python3 {baseDir}/scripts/uniprot_fetch.py --accession P04637
```

### Search for proteins:
```bash
python3 {baseDir}/scripts/uniprot_fetch.py --search "insulin human"
```

### Get sequence only:
```bash
python3 {baseDir}/scripts/uniprot_fetch.py --accession P53_HUMAN --format fasta
```

### Get full entry with all annotations:
```bash
python3 {baseDir}/scripts/uniprot_fetch.py --accession P53_HUMAN --format detailed
```

## Parameters

| Parameter | Description | Default |
|-----------|-------------|---------|
| `--accession` | UniProt accession or entry name | - |
| `--search` | Search query | - |
| `--organism` | Filter by organism (e.g., "human", "9606") | - |
| `--reviewed` | Only Swiss-Prot (reviewed) entries | False |
| `--max-results` | Maximum results for search | 10 |
| `--format` | Output format: summary, detailed, fasta, json | summary |
| `--include-features` | Include sequence features | False |
| `--include-xrefs` | Include cross-references | False |

## Examples

### Look up human p53 tumor suppressor:
```bash
python3 {baseDir}/scripts/uniprot_fetch.py --accession P53_HUMAN --format detailed
```

### Search for kinases in human:
```bash
python3 {baseDir}/scripts/uniprot_fetch.py --search "kinase" --organism human --reviewed --max-results 20
```

### Get FASTA sequence for multiple proteins:
```bash
python3 {baseDir}/scripts/uniprot_fetch.py --accession "P53_HUMAN,BRCA1_HUMAN,EGFR_HUMAN" --format fasta
```

### Search with advanced query:
```bash
python3 {baseDir}/scripts/uniprot_fetch.py --search "gene:TP53 AND organism_id:9606"
```

### Get protein with PDB cross-references:
```bash
python3 {baseDir}/scripts/uniprot_fetch.py --accession P53_HUMAN --include-xrefs
```

## Output Fields

### Summary
- Accession, entry name, protein name
- Gene name, organism
- Sequence length
- Reviewed status

### Detailed
- Full protein name and alternative names
- Function description
- Subcellular location
- Gene ontology terms
- Protein domains
- Post-translational modifications
- Disease associations
- Literature references

### FASTA
Standard FASTA format sequence output.

### JSON
Full UniProt entry in JSON format.

## Cross-References

UniProt entries contain cross-references to:
- **PDB**: 3D protein structures
- **Pfam**: Protein families
- **InterPro**: Protein signatures
- **GO**: Gene Ontology terms
- **KEGG**: Pathway information
- **Reactome**: Reaction pathways
- **DrugBank**: Drug interactions
- **OMIM**: Disease associations

## Notes

- UniProt accession numbers (e.g., P04637) are stable identifiers
- Entry names (e.g., P53_HUMAN) may change
- Reviewed (Swiss-Prot) entries are manually curated
- Unreviewed (TrEMBL) entries are computationally annotated
- API has no authentication requirement