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Annotation
Annotation modules in Conduit are organized according to the source of the annotations.
Most modules rely on UniProt to generate proteomes and associated functional annotations. These annotations are automatically applied whenever UniProt-derived data is used to define the search space.
MAGs (Metagenome-Assembled Genomes), on the other hand, do not depend on UniProt and are handled via separate pipelines (see below).
UniProt-derived modules provide a rich set of functional annotations for proteins. The external references provided by uniprot are then used to query the relevent database for a functional description of the xref in question. The following functional terms are supported.
| Annotation Type | Description | Example |
|---|---|---|
| GO Terms | Gene Ontology terms describing molecular function, biological process, and cellular component. | — |
| KEGG Pathways | Maps proteins to organism-specific metabolic and signaling pathways. |
ecj00540 — Lipopolysaccharide biosynthesis (E. coli K-12) |
| KEGG Map Pathways | Non-organism-specific pathway annotations, useful for cross-species comparisons. |
map00540 — Lipopolysaccharide biosynthesis |
| KEGG Orthology (KO) | Assigns KEGG orthologs for functional grouping of proteins. |
K03643 — LPS-assembly lipoprotein |
| Pfam | Annotates proteins with families and domains using sequence alignments and profile HMMs. Helps identify known structural/functional domains. | — |
| CAZy | Carbohydrate-Active Enzyme annotations. Provides: • Class: broad enzyme category • Family: specific enzymatic activity |
— |
| EggNOG | Orthology-based annotations linking proteins to evolutionary and functional categories. Each protein can have multiple codes (~20 functional descriptors). | — |
Additional annotation sources can be added in the future, allowing Conduit to expand functional characterization beyond the currently supported sets.
MAGs are annotated using pipelines that do not rely on UniProt, enabling Conduit to handle:
- Experimental-specific genomes
- Environments with limited UniProt coverage
Details of MAG annotation pipelines will be updated here once finalized.