Table 10.
List of Regex terms part 1 that likely indicate toxicity found in a control set of bacterial proteins
| Category | Regex Pattern | Rationale |
|---|---|---|
| Secretion System Effectors | (?i)(T7SS effector.*toxin) T9SS.*sorting domain T9SS.*target domain | Identifies effector proteins secreted via type 7 and type 9 secretion systems, which are commonly linked to toxins. |
| Pore-Forming Toxins | pore-forming | Identifies toxins that disrupt membranes, potentially forming pores in host cells. |
| Chemotaxis Inhibitors | chemotaxis-inhibiting | Identifies proteins that likely inhibit bacterial chemotaxis. |
| Secretion System Proteins | Dot/Icm secretion system protein | Identifies proteins from the Dot/Icm secretion system. |
| Effector Toxins of Types III, IV and VI | (?i)(effector.*(type III|type IV|type VI|T6SS|T4SS|T3SS|type 3|type 4|type 6)) ((type III|type IV|type VI|T6SS|T4SS|T3SS|type 3|type 4|type 6).*effector) | Identifies effector proteins related to Type III, IV, and VI secretion systems, commonly associated with delivering proteins directly into host cells. |
| Known Toxin Subunits | (?i)(toxin ADP-ribosyltransferase subunit ArtA|cytolethal distending toxin subunit B family protein | two-peptide bacteriocin plantaricin EF subunit PlnE |putative AB5 enterotoxin ADP-ribosylating subunit YtxA|alpha-xenorhabdolysin family binary toxin subunit A|alpha-xenorhabdolysin family binary toxin subunit B|Shiga toxin A subunit|cytolethal distending toxin subunit B family|Shiga toxin 2 subunit A) | Identifies known toxic subunits of large, multi-component toxins. |
| General Toxin Keywords | (?i)(toxin/[|toxin,|toxin;|toxin protein|toxin peptide| toxin B (plasmid)|toxin 1|toxin 2| toxin 5|toxin of|toxin component|toxin-like|toxin-type| toxin*.family|toxin*.domain| family*.toxin| pre-toxin|polymorphic toxin) | Captures generic mentions of “toxin” in protein descriptions, including common family or component annotations. The regex search for the keyword “toxin” on its own is not sufficient due to component words like e.g.: “antitoxins”, which are not toxins. |
| Colicin and Bacteriocins | colicin-like pore-forming|colicin-like bacteriocin| bacteriocin/[| bacteriocin,| bacteriocin.*domain| bacteriocin.*family| bacteriocin-like| bacteriocin class| bacteriocin fulvocin C-related | Identifies colicin-like and bacteriocin-related proteins. |
| Hemolysins and Leukocidins | hemolysin/[| hemolysin domain| hemolysin.*family| hemolysin-type| hemolysin*.precursor| hemolysin-type| leukocidin | Identifies probable hemolysins and leukocidins. |
| Cytotoxins and Cytolysins | cytotoxin/[|cytotoxin.*domain| cytotoxin.*family| cytolysin| cytotoxix | Captures probable cytotoxins and cytolysins. |
| Pyrocines | pyocin/[| pyocin.*domain| pyocin protein| pyocin large subunit family protei| pyocin.*cytotoxin | Captures likely pyrocines. |