uniprot

Compare original and translation side by side

🇺🇸

Original

English

🇨🇳

Translation

Chinese

UniProt Database Access

UniProt 数据库访问

Note: This skill uses the UniProt REST API directly. No Modal deployment needed - all operations run locally via HTTP requests.

注意：本技能直接调用UniProt REST API，无需部署Modal——所有操作均通过HTTP请求在本地运行。

Fetching Sequences

获取序列

By Accession

通过登录号

bash

undefined

bash

undefined

FASTA format

FASTA格式

curl "https://rest.uniprot.org/uniprotkb/P00533.fasta"

JSON format with annotations

带注释的JSON格式

curl "https://rest.uniprot.org/uniprotkb/P00533.json"

undefined

curl "https://rest.uniprot.org/uniprotkb/P00533.json"

undefined

Using Python

使用Python

python

import requests

def get_uniprot_sequence(accession):
    """Fetch sequence from UniProt."""
    url = f"https://rest.uniprot.org/uniprotkb/{accession}.fasta"
    response = requests.get(url)
    if response.ok:
        lines = response.text.strip().split('\n')
        header = lines[0]
        sequence = ''.join(lines[1:])
        return header, sequence
    return None, None

python

import requests

def get_uniprot_sequence(accession):
    """从UniProt获取序列。"""
    url = f"https://rest.uniprot.org/uniprotkb/{accession}.fasta"
    response = requests.get(url)
    if response.ok:
        lines = response.text.strip().split('\n')
        header = lines[0]
        sequence = ''.join(lines[1:])
        return header, sequence
    return None, None

Getting Annotations

获取注释信息

Full Entry

完整条目

python

def get_uniprot_entry(accession):
    """Fetch full UniProt entry as JSON."""
    url = f"https://rest.uniprot.org/uniprotkb/{accession}.json"
    response = requests.get(url)
    return response.json() if response.ok else None

entry = get_uniprot_entry("P00533")
print(f"Protein: {entry['proteinDescription']['recommendedName']['fullName']['value']}")

python

def get_uniprot_entry(accession):
    """以JSON格式获取完整的UniProt条目。"""
    url = f"https://rest.uniprot.org/uniprotkb/{accession}.json"
    response = requests.get(url)
    return response.json() if response.ok else None

entry = get_uniprot_entry("P00533")
print(f"蛋白质: {entry['proteinDescription']['recommendedName']['fullName']['value']}")

Domain Boundaries

结构域边界

python

def get_domains(accession):
    """Extract domain annotations."""
    entry = get_uniprot_entry(accession)
    domains = []

    for feature in entry.get('features', []):
        if feature['type'] == 'Domain':
            domains.append({
                'name': feature.get('description', ''),
                'start': feature['location']['start']['value'],
                'end': feature['location']['end']['value']
            })

    return domains

python

def get_domains(accession):
    """提取结构域注释信息。"""
    entry = get_uniprot_entry(accession)
    domains = []

    for feature in entry.get('features', []):
        if feature['type'] == 'Domain':
            domains.append({
                'name': feature.get('description', ''),
                'start': feature['location']['start']['value'],
                'end': feature['location']['end']['value']
            })

    return domains

Example: EGFR domains

示例：EGFR结构域

domains = get_domains("P00533")

[{'name': 'Kinase', 'start': 712, 'end': 979}, ...]

undefined

undefined

Searching UniProt

搜索UniProt

By Gene Name

通过基因名称

python

def search_uniprot(query, organism=None, limit=10):
    """Search UniProt by query."""
    url = "https://rest.uniprot.org/uniprotkb/search"
    params = {
        "query": query,
        "format": "json",
        "size": limit
    }
    if organism:
        params["query"] += f" AND organism_id:{organism}"

    response = requests.get(url, params=params)
    return response.json()['results']

python

def search_uniprot(query, organism=None, limit=10):
    """通过查询语句搜索UniProt。"""
    url = "https://rest.uniprot.org/uniprotkb/search"
    params = {
        "query": query,
        "format": "json",
        "size": limit
    }
    if organism:
        params["query"] += f" AND organism_id:{organism}"

    response = requests.get(url, params=params)
    return response.json()['results']

Search for human EGFR

搜索人类EGFR

results = search_uniprot("EGFR", organism=9606)

undefined

results = search_uniprot("EGFR", organism=9606)

undefined

By Sequence Similarity (BLAST)

通过序列相似性（BLAST）

python

undefined

python

undefined

Use UniProt BLAST

使用UniProt BLAST

https://www.uniprot.org/blast

undefined

undefined

Cross-References

交叉引用

Get PDB Structures

获取PDB结构

python

def get_pdb_references(accession):
    """Get PDB structures for UniProt entry."""
    entry = get_uniprot_entry(accession)
    pdbs = []

    for xref in entry.get('uniProtKBCrossReferences', []):
        if xref['database'] == 'PDB':
            pdbs.append({
                'pdb_id': xref['id'],
                'method': xref.get('properties', [{}])[0].get('value', ''),
                'chains': xref.get('properties', [{}])[1].get('value', '')
            })

    return pdbs

python

def get_pdb_references(accession):
    """获取UniProt条目的PDB结构信息。"""
    entry = get_uniprot_entry(accession)
    pdbs = []

    for xref in entry.get('uniProtKBCrossReferences', []):
        if xref['database'] == 'PDB':
            pdbs.append({
                'pdb_id': xref['id'],
                'method': xref.get('properties', [{}])[0].get('value', ''),
                'chains': xref.get('properties', [{}])[1].get('value', '')
            })

    return pdbs

Example: PDB structures for EGFR

示例：EGFR的PDB结构

pdbs = get_pdb_references("P00533")

undefined

pdbs = get_pdb_references("P00533")

undefined

Common Use Cases

常见使用场景

Target Selection

靶点选择

python

undefined

python

undefined

1. Find protein by name

1. 通过名称查找蛋白质

results = search_uniprot("insulin receptor", organism=9606)

results = search_uniprot("胰岛素受体", organism=9606)

2. Get accession

2. 获取登录号

accession = results[0]['primaryAccession'] # e.g., P06213

accession = results[0]['primaryAccession'] # 例如：P06213

3. Get domains

3. 获取结构域

domains = get_domains(accession)

4. Find PDB structure

4. 查找PDB结构

pdbs = get_pdb_references(accession)

5. Download best structure for design

5. 下载最优结构用于设计

undefined

undefined

Sequence Alignment Info

序列比对信息

python

def get_sequence_variants(accession):
    """Get natural variants from UniProt."""
    entry = get_uniprot_entry(accession)
    variants = []

    for feature in entry.get('features', []):
        if feature['type'] == 'Natural variant':
            variants.append({
                'position': feature['location']['start']['value'],
                'original': feature.get('alternativeSequence', {}).get('originalSequence', ''),
                'variant': feature.get('alternativeSequence', {}).get('alternativeSequences', [''])[0],
                'description': feature.get('description', '')
            })

    return variants

python

def get_sequence_variants(accession):
    """从UniProt获取自然变异体信息。"""
    entry = get_uniprot_entry(accession)
    variants = []

    for feature in entry.get('features', []):
        if feature['type'] == 'Natural variant':
            variants.append({
                'position': feature['location']['start']['value'],
                'original': feature.get('alternativeSequence', {}).get('originalSequence', ''),
                'variant': feature.get('alternativeSequence', {}).get('alternativeSequences', [''])[0],
                'description': feature.get('description', '')
            })

    return variants

API Reference

API参考

Endpoint	Description
`/uniprotkb/{id}.fasta`	FASTA sequence
`/uniprotkb/{id}.json`	Full entry JSON
`/uniprotkb/search`	Search entries
`/uniprotkb/stream`	Batch download

端点	描述
`/uniprotkb/{id}.fasta`	FASTA格式序列
`/uniprotkb/{id}.json`	完整条目JSON格式
`/uniprotkb/search`	条目搜索
`/uniprotkb/stream`	批量下载

Troubleshooting

故障排除

Entry not found: Check accession format (e.g., P00533) Rate limits: Add delay between requests Large downloads: Use stream endpoint with pagination

Next: Use sequence with

esm

for embeddings or

colabfold

for structure.

未找到条目：检查登录号格式（例如：P00533） 速率限制：在请求之间添加延迟 大文件下载：使用stream端点并分页

下一步：将序列与

esm

结合用于嵌入，或与

colabfold

结合用于结构分析。