Subsystem: Heme Biosynthesis: protoporphyrin- and coproporphyrin-dependent pathways
This subsystem's description is:
You are now in the Subsystem viewer of the SEED database. The narrow green banner above provides links to genome analysis tools and data. Please use them to see -
I. The “Spreadsheet” Tab: contains a Table where each row represents a genome, each column corresponds to a Functional Role (protein family), and each cell is populated with the gene(s)/protein(s) that implement this Functional Role in each organism. Each gene/protein is identified with a blue number – the Protein-Encoding Gene (PEG) ID - which is linked to an underlying detailed PEG page. The Spreadsheet can be sorted: by taxonomy, by the pattern of PEGs absence/presence, or by gene clustering pattern, or alphabetically by organism. It can also be filtered: pls use "Limit Display" Tab on the “Spreadsheet” page to limit by a specific taxonomic group, OR/AND use column headings to see only genomes with a specific protein family present/absent. Cells highlighted with the same color within the same row (genome) indicate genes that are co-localized on the chromosome.
II. The “Functional Roles” Tab: contains the list of protein families included in this Subsystem, and explains abbreviations used in the heading of the Subsystem Spreadsheet. Note "Subsets" (in the leftmost column), which group some Functional Roles together. Subsets allow to further customize Subsystem Spreadsheet view: to limit it to columns that are included in a selected SubSet, or to collapse isofunctional protein family into a single column for clearity, eic. Use "Limit Display" tab on the “Spreadsheet” page to do this
III. "Variant codes" are assigned to every organism in the Subsystem spreadsheet. They attempt to capture in a brief form the type of heme biosynthesis pathway that can be predicted to operate in this organism based on its genome data, and any notable exceptions or observations. Hover over them in the spreadsheet to read detailed discretion of each code. All Variant codes are also listed below on this page (Under "Variants")
V. The representative set of 982 diverse eubacterial and archaeal genomes is included in this Subsystem. It accurately represents the immense diversity of ~12,000 prokaryotic organisms with sequenced genomes currently in the SEED database, and it is not skewed by an overabundance of genomes for a handful of microbial genera (medically or industrially important) such as Enterobacteriaceae, Staphylococci, Mycobacteria, etc.
VI. To limit the Spreadsheet to photosynthetic organisms only please use the right-most Column headings (ChlL or ChlN) and set it to "non-empty". This will reduce the Spreadsheet to show only the organisms capable of (bacterio)chlorophyll biosynthesis
VI. Further help in navigating the SEED database is available here -
For more information, please check out the description and the additional notes tabs, below
|Literature References||Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin. Dailey HA Proceedings of the National Academy of Sciences of the United States of America 2015 Feb 17||25646457|
|Diagram||Functional Roles||Subsystem Spreadsheet||Description||Additional Notes|