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. 2014 Oct 23;10(10):e1003898. doi: 10.1371/journal.pcbi.1003898

Table 1. Definitions of terms and counts for locus and genome categories analyzed using LoClass.

Term Definition Count
Locus Super-type The largest cluster of loci where all contained loci encode the same signature enzyme or are syntenic to these loci while encoding no alternative signature enzyme. 15
Locus Type A more stringent cluster of loci; in addition to conserved signature enzymes, these loci typically are syntenic to one another, indicating common origin. 23
Locus (Sub)type The most stringent clustering of loci, where many syntenic loci of the same type are separated into smaller groups; these typically vary by genes encoding ancillary functions. 30
Prospective BMC Locus Region of a genome including BMC shell protein genes within 20 kb of each other and all other genes within 10 kb upstream and downstream. 580
Envelope Region of a Prospective BMC Locus that includes only the BMC shell protein genes and genes encoded between them. -
Satellite loci Prospective BMC Loci that are predicted to encode a subset of shell components for a BMC and no other BMC-related genes (Materials and Methods). 149
Satellite-like loci Prospective BMC Loci that meet most but not all of the criteria established for satellite loci or encode other BMC-related genes. 21
Confirmed BMC Loci All Prospective BMC Loci which are of the same Locus Type as a locus whose function has been experimentally elucidated. 335
Candidate BMC Loci All Prospective BMC Loci that are not putative satellite, satellite-like, or Confirmed BMC Loci. 75
Carboxysome loci Confirmed Loci encoding the carboxysome. 87
Metabolosome loci Candidate/Confirmed Loci that, of the core metabolosome enzymes, encode at least a core AldDH or are members of a Locus Type where the majority of loci do. These loci presumably encapsulate catabolic reactions (Fig. 1B). 312
Metabolosome loci with an incomplete core Metabolosome loci that are of a Locus Type where the majority of loci do not encode a core AlcDH and/or PTAC. 22
BMC-containing genomes Genomes that contain any Prospective BMC Loci. 329
Satellite-containing genomes Genomes containing at least one putative satellite locus. 77

Counts for Locus super-types, types, and sub-types include loci from IMG that were analyzed manually. Due to the fragmentation of most IMG loci, these were excluded from all other counts.