Peptides

Peptide Data

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    sources:

        Profile Plot

        Profile Plot

        Peptide Heatmap

        Section Heatmap

        Protein Sequence

        Example Searches

        Iron Stress in Prochlorococcus:

        Background: A component of the iron transport system, IdiA, has been well characterized in marine cyanobacterium increasing in abundance when iron availability is low (Webb et al., 2001). This protein was used as a biomarker of iron stress and shown to be more abundant across the Central Pacific Ocean in Saito et al., 2014.

        Search: entering the term “iron” into the product name search field yields all proteins with iron in the title. IdIA is usually annotated as “afuA putative ABC transporter”. Currently it shows up ~5th in the list of search results (ranked by # of spectral counts) for results from the ProteOMZ expedition. Clicking Sequence brings up the amino acid sequence of the protein, and the BLAST button below it connects to NCBI to searching the sequence in GenBank. The Section button produces a ocean section of the distribution of the protein across the Central Pacific showing iron stress in Prochlorococcus throughout this region. Also, checking box to the left of the protein and clicking Profile button generates vertical profiles from this data set. Additional features connect to outside resources, such as Sequence, which opens a box with a BLAST sequence alignment link, the Expedition link connects to the BCO-DMO Project page for other datasets and expedition information, the UniProt link connects to EBI’s informatics resources.

        The peptide link brings up a peptide data table and allows profile visualization, and taxonomic least common ancestor analysis of each peptide by searching the genomic, metagenomic, and MAG database within the linked METATRYP software, with visualized tree and heatmaps can be generated for the selected peptides.

        External Sites:

        NCBI Taxonomy Browser View Website
        Pfam Search View Website
        KO (Kegg Orthology) View Website
        RCSB Protein Data Bank View Website
        ExPASy Bioinformatics Resource Portal View Website
        UniProt ID View Website

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