Proximity between Rubisco or Prk and other genetic features on DNA molecules in CBB-positive genomes.

The columns contain the consensus rank (’Rank’; see S5 Dataset), feature type (’Feature_Type’; DeepEC or Pfam), feature ID (’Feature’), feature name (’Name’), the Calvin cycle feature to which distance was measured (‘cFeature’), whether the genetic feature and Prk or Rubisco are on the same strand (‘Strand’; Same or Opposite), the minimum observed distance in number of genes (‘minD’), the median observed distance in number of genes (‘medD’), the maximum observed distance in number of genes (‘maxD’), the average distance in number of genes (‘meanD’), the number of occurrences of the feature in the particular configuration described by the row (‘Count’), number of occurrences on a chromosome (‘locChr’), number of occurrences on a plasmid (‘locPsm’), number of occurrences on an unknown DNA molecule type (‘locUnk’; e.g. a contig of a draft genome), fraction of genes located on a plasmid (‘fracPsm’; ‘locPsm’ divided by the sum of ‘locPsm’ and ‘locChr’), feature description (’Description’; the DESC line from the Pfam HMM database, or the full list of enzyme names from KEGG for DeepEC), and the KEGG EC of the entry (’KEGG_EC’). Note that some DeepEC ECs were transferred to one or more new ECs in KEGG, as indicated by a discrepancy between ’Feature’ (if ’Feature_Type’ is DeepEC) and ’KEGG_EC’. A single feature can therefore be listed more than once. The table has been sorted by increasing median distance (‘medD’) followed by decreasing number of occurrences (‘Count’). Only features located on the same DNA molecule as Rubisco or Prk were included, and only CBB-positive genomes were considered. All DNA molecules were considered as linear due to the many genomes in a state of unplaced scaffolds, which may place certain features further way from Rubisco and Prk compared to if the DNA molecule would have been modeled as a circle. Rubisco and Prk, representing ORFs that were identified by the specific method for Rubisco and Prk identification described in the Materials and methods, are included as features in order to show the proximity between Rubisco and Prk.
(XLSX)