The epsSMASH hierarchy of rules#

The rules used in epsSMASH are divided into three strictness levels: strict, relaxed, and loose. The default is 'loose'.

Strict rules#

Created using epsProtocol. They require the core genes of a system to be present, but the minimum requirement can be met by other genes. Some deviation from the literature is allowed. Includes Synthase-, Wzx/Wzy- ABC transporter- and Sucrase-dependent systems.

Relaxed rules#

Less strict versions of the synthase-dependent rules found in the strict rules. These all require the synthase gene of their respective system to be present, and usually one other gene necessary for the synthase complex. All rules have "-like" added to their name.

Loose rules#

Made in order to capture the diversity of exoPS BGCs that do not fit the strict or relaxed rules. Wzx/Wzy- and ABC-transporter-dependent BGCs produce the majority of extracellular polysaccharides, and only a few of them have been described in literature.

We know that all Wzx/Wzy- and ABC-transport-dependent systems need an outer membrane protein (OPX), a polysaccharide co-polymerase (PCP) as well as several glycosyltransferases. The loose rules take advantage of the many HMMs that were created for these genes for the relaxed Wzx/Wzy-dependent rules, and uses them to detect putative exoPS BGCs.

The loose rules are the only rules that do not give a name to the detected BGCs, as they are not yet described in literature.

Rule strictness	Protocol	BGC genes required	BGC synteny requirement in epsProtocol	exoPS BGC categories (?)
Strict	epsProtocol	All	Minimal deviation from literature allowed	Synthase-dependent Sucrase-dependent Wzx/Wzy-dependent ABC transporter-dependent
Relaxed	epsProtocol	Core genes + minimum requirement	Deviation from literature allowed	Synthase-dependent-like
Loose	Manual	Core genes (Not system specific)	Not applicable	Wzy-dependent-putative ABC-transporter-dependent-putative (CPS, LPS, undescribed exoPS)

Read more about the strict, relaxed and loose rules in the rules glossary.