About AADB

AADB (pH Stress Resistance Gene Database) focuses on microbial genes and functional systems that enable adaptation to extreme pH environments, including both acidic and alkaline conditions. Rather than treating acid and alkali resistance as separate phenomena, AADB organizes genes into functional systems involved in pH homeostasis, proton flux regulation, cytoplasmic buffering, membrane remodeling, and stress response pathways that collectively determine microbial survival across a wide pH spectrum.

The database provides a curated and searchable resource for researchers studying microbial adaptation mechanisms, evolutionary biology, and biotechnological applications related to pH stress resistance. AADB prioritizes quality over quantity, focusing on curated, non-redundant, and experimentally supported sequences to ensure high-confidence annotations.

AADB organizes genes into functional systems involved in pH homeostasis and stress response. These systems work collectively to maintain cellular pH balance and enable survival under extreme pH conditions (both acidic and alkaline).

The database currently includes 11 core pH stress resistance systems, including glutamate decarboxylase systems, antiporter systems, acid-activated chaperones, alkaline resistance mechanisms, pH response regulators, and various metabolic pathways. These systems are not mutually exclusive; many organisms employ multiple mechanisms simultaneously to achieve robust pH stress resistance.

For detailed descriptions of each functional system, including their molecular mechanisms, pH ranges, and biological roles, see Functional Systems.

Data Sources

• Multi-environment microbial genome data (human body, ocean, soil, extreme environments)
• Published pH resistance-related research literature
• Functionally verified high-quality sequence data from public databases
• Experimentally supported sequences with documented pH resistance functions

Quality Control

• Sequence Quality: Strict sequence quality control standards
• Functional Specificity: Functional specificity verification through literature review
• Deduplication: Sequence deduplication processing to ensure uniqueness
• Format Standardization: Consistent FASTA format and annotation standards
• Curated, Non-redundant: Focus on high-confidence, experimentally supported sequences

The database prioritizes quality over quantity, ensuring that each sequence has clear functional relevance to pH stress resistance mechanisms.

Data Collection

Sequences were collected from multiple sources including NCBI GenBank, UniProt, and published research articles. Each sequence was verified for functional relevance to pH stress resistance through literature review and functional annotation analysis.

Functional Classification

Genes were classified into functional systems based on their molecular mechanisms and biological roles in pH homeostasis. Classification considers:

• Enzymatic activity (e.g., decarboxylases, ureases)
• Transport function (e.g., antiporters, channels)
• Regulatory roles (e.g., transcription factors, sigma factors)
• Protective functions (e.g., chaperones, stress proteins)

Database Building

The BLAST database was constructed using NCBI BLAST+ tools with protein sequences in FASTA format. Sequences were aligned and annotated to provide comprehensive metadata including species, functional system classification, pH range, and environment information.

Research Applications

• pH Resistance Gene Identification: Identify genes involved in pH stress resistance through sequence similarity search
• Functional Annotation: Annotate unknown sequences based on similarity to characterized pH resistance genes
• Evolutionary Analysis: Study the evolution of pH resistance mechanisms across different species
• Comparative Genomics: Compare pH resistance gene repertoires across organisms

Biotechnological Applications

• Strain Engineering: Identify candidate genes for engineering pH-resistant microbial strains
• Probiotic Development: Screen for pH-resistant probiotic candidates
• Industrial Fermentation: Identify genes for improving acid/alkali tolerance in fermentation processes

AADB focuses on experimentally supported pH stress resistance genes and functional systems. While this curated approach ensures high confidence annotations, the database is not intended to be exhaustive. The prioritization of quality over quantity means that some potentially relevant sequences may not be included if they lack sufficient experimental validation or functional characterization.

Future versions will expand sequence coverage and incorporate additional environmental and mechanistic dimensions as more experimentally validated data becomes available. Users should be aware that the database represents a curated snapshot of current knowledge and may not capture all pH resistance mechanisms across all microbial species.

If you use AADB in your research, please cite:

For questions, suggestions, or to report issues:

• Email: jytu@bu.edu
• GitHub Issues: Report issues on GitHub
• Documentation: Full Documentation