Enzyme Genome & Database Mining Services

CD Biosynsis offers comprehensive Enzyme Genome & Database Mining Services, designed to efficiently search and analyze vast biological data (genomic, transcriptomic, and environmental metagenomic datasets) to discover novel biocatalysts. Utilizing advanced bioinformatics and computational tools, we identify, classify, and prioritize enzyme candidates with desirable properties such as high activity, thermal stability, or unique substrate specificity. Our services move beyond simple sequence homology to provide deep insight into enzyme function, phylogenetic relationships, and evolutionary potential, delivering validated targets ready for Gene Synthesis and subsequent Enzyme Engineering. This is an essential first step for any project requiring novel or highly optimized enzymes.

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Systematic Search for High-Value Biocatalysts

The vast majority of microbial diversity remains uncultured, representing a massive untapped source of novel enzymes. Our Genome & Database Mining platform is engineered to leverage this untapped potential, allowing researchers to explore novel enzyme scaffolds and functions that have evolved under unique environmental pressures. We apply sophisticated algorithms to predict enzyme activity, stability, and cellular localization from sequence data alone. This data-driven approach drastically reduces the time and cost associated with random screening and ensures that the top candidates are selected for downstream wet-lab validation, integrating seamlessly with our Enzyme Metagenomic Library Screening Service and in silico prediction tools.

Data Mining and Predictive Bioinformatics

Metagenomic and Genomic Analysis Functional and Structural Prediction Evolutionary Profiling and Selection

Data Sourcing and Library Preparation

Accessing Uncharted Enzyme Diversity

Enzyme Metagenomic Library Screening Service

In silico processing of large metagenomic datasets (soil, water, gut microbiome) to identify and classify novel open reading frames (ORFs) and functional gene clusters.

Comparative Genomics

Analysis of publicly available and proprietary sequenced microbial genomes to find homologs or orthologs with unique functional potential.

Substrate Specific Databases

Mining specialized databases (e.g., BRENDA, KEGG) for enzymes with defined activities that can be adapted for new applications.

Predictive and Computational Tools

Prioritizing Function from Sequence

In Silico Enzyme Candidate Selection Service

Using advanced computational modeling, including homology modeling and molecular docking, to predict the three-dimensional structure and active site pocket of candidates.

Catalytic Mechanism Prediction

Identification of key catalytic residues and prediction of the reaction mechanism based on sequence motif analysis and machine learning.

Property Scoring

Scoring candidates based on predicted thermostability, optimal pH, and predicted expression feasibility in common host systems.

Evolutionary Context and Targeting

Understanding Enzyme Development

Enzyme Phylogenetic & Evolutionary Analysis Service

Construction of detailed phylogenetic trees to identify evolutionary relationships, pinpointing enzymes that may represent functional divergence or ancestral traits.

Targeted Sequence Synthesis

Selection of the most promising enzyme genes for Gene Synthesis and immediate cloning, bypassing random screening.

Pathway Reconstruction

Identification of entire biosynthetic pathways or gene clusters from environmental or genomic data to discover synergistic enzymes.

Database Mining and Candidate Funnel

A systematic process from sequence data to functional enzyme gene.

Data Acquisition and Filtering

Deep Bioinformatics Analysis

Prioritization and Selection

Delivery

Data Input: Collection of genomic or metagenomic data from the client or public sources.

Filtering: Initial quality control and removal of redundant or low-quality sequences.

Enzyme Phylogenetic & Evolutionary Analysis Service: Functional annotation and evolutionary profiling.

Prediction: Use of In Silico Enzyme Candidate Selection Service to model structure and predict activity/stability.

Scoring: Candidates ranked based on novelty, predicted activity, and industrial relevance.

Enzyme Metagenomic Library Screening Service: Final selection of top enzyme genes for synthesis.

Codon Optimization: Sequence refinement for optimal expression in a target host.
Delivery: Final gene sequences, QC data, and detailed bioinformatics report.
Optional: Gene Synthesis and Cloning into expression vector.

Mining the Next Generation of Biocatalysts

High-Confidence Prediction

Computational tools accurately predict enzyme function and stability, reducing experimental failure rates.

Access to Dark Matter

Unlocks novel enzyme families from uncultured microbial and environmental metagenomes.

Evolutionary Insight

Phylogenetic analysis helps target enzymes with high evolvability or unique catalytic mechanisms.

Accelerated Lead Time

Replaces months of traditional screening with weeks of computational and targeted gene synthesis.

Client Testimonials on Enzyme Genome & Database Mining

"The metagenomic analysis identified three highly unique lipases from a soil sample that were missed by our internal homology searches. This opened a completely new direction for our project."

Dr. Samuel Liu, R&D Director

"The In Silico Enzyme Candidate Selection Service provided a very small, high-confidence list of targets. We validated the top candidate in the lab, and it worked flawlessly."

Ms. Janet Chen, Lead Bioengineer

"The detailed phylogenetic analysis helped us choose an ancestral enzyme variant that was highly promiscuous, making it an ideal starting point for our directed evolution campaign."

Dr. Kenji Tanaka, Principal Scientist

"Their ability to quickly process vast amounts of genomic data and prioritize genes based on predicted thermal stability saved us immense time and resources on wet-lab screening."

Mr. Alex Johnson, Research Manager

"The integrated service of mining and subsequent gene synthesis provided a seamless transition from bioinformatics to functional enzyme production."

Dr. Maria Gomez, Group Leader

FAQs about Enzyme Genome & Database Mining Services

Still have questions?

What types of data can you analyze?

We analyze genomic, transcriptomic, and environmental metagenomic sequence data, as well as protein structure and functional databases.

What makes your Metagenomic Library Screening Service effective?

Our Enzyme Metagenomic Library Screening Service uses advanced computational filtering and deep learning models to bypass traditional cloning limits, focusing on finding novel, high-potential enzymes directly from environmental DNA.

Can you predict the function of a completely unknown enzyme sequence?

Yes. By using homology modeling, active site prediction, and In Silico Enzyme Candidate Selection Service, we can infer function, stability, and optimal reaction conditions even for sequences with low identity to known enzymes.

How does phylogenetic analysis help enzyme discovery?

The Enzyme Phylogenetic & Evolutionary Analysis Service helps identify enzyme variants that are distantly related, suggesting potentially unique functions or high evolvability, which are key for successful Enzyme Engineering.

How much does Metabolic Engineering services cost?

The cost of Metabolic Engineering services depends on the project scope, complexity of the target compound, the host organism chosen, and the required yield optimization. We provide customized quotes after a detailed discussion of your specific research objectives.

Do your engineered strains meet regulatory standards?

We adhere to high quality control standards in all strain construction and optimization processes. While we do not handle final regulatory approval, our detailed documentation and compliance with best laboratory practices ensure your engineered strains are prepared for necessary regulatory filings (e.g., GRAS, FDA).

What to look for when selecting the best gene editing service?

We provide various gene editing services such as CRISPR-sgRNA library generation, stable transformation cell line generation, gene knockout cell line generation, and gene point mutation cell line generation. Users are free to select the type of service that suits their research.

Does gene editing allow customisability?

Yes, we offer very customised gene editing solutions such as AAV vector capsid directed evolution, mRNA vector gene delivery, library creation, promoter evolution and screening, etc.

What is the process for keeping data private and confidential?

We adhere to the data privacy policy completely, and all customer data and experimental data are kept confidential.