You can view the list of genes related to a pathway by clicking the correspondinggene models link in the list of reference pathways. You can also download sequence or view multiple alignments with ClustalW.
The page heading shows the KEGG map number for the reference pathway and the name of the reference pathway. Column headings in the list of genes are:
- Protein name JGI's name for the gene, with a link to theProtein Page.
- Protein Id JGI's ID number for the gene, derived from its name, with a link to the Protein Page.
- E-value The expectation value for the association of the gene with the enzyme.
- Top KEGG hit The protein in the KEGG database with the best BLAST alignment to the transcription of the predicted gene. The ID, name, EC number, taxonomy ID, and taxonomy name in the KEGG database are listed.
- EC Num The Enzyme Commission number for the related enzyme.
- Enzyme A description of the related enzyme's action.
- Curated? "Yes" or "No" both link to the annotation, with the current Transcript details if available. From here you can login to annotate the Transcript.
Quick Tips
- To view a diagram of the reference pathway, click theMAP number.
- To see theProtein page for one of the gene models, click the correspondingProt ID.
- To go to the annotation area for a specific gene model, clickYES orNO in theCurated?column.
At the bottom of the list are buttons for retrieving FASTA sequences or ClustalW alignments.
To retrieve sequence in FASTA format:
- Click thecheck box next to each gene for which you want to retrieve sequence.
- ClickRetrieve FASTA.
To retrieve a ClustalW alignment:
- Click thecheck box next to each gene that you want to include in the alignment. (You must choose more than one gene.)
- ClickClustalw.
To clear your selections, clickUncheck all.