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Table 3 Overview of rules for classification of fungal secondary metabolite megasynthases used in synthaser

From: Synthaser: a CD-Search enabled Python toolkit for analysing domain architecture of fungal secondary metabolite megasynth(et)ases

   

Domain rules

Rename rules

Rule name

Domains

Evaluator

Class

Families

From

To

Before

After

Hybrid PKS-NRPS

KS, A, C, ACP

0 and (1 or 2)

  

ACP

T

 

A, C

     

T

ACP

A, C

KS

Thiolase

KS

0

KS

cd00829, cd00751,

PLN02287

    

HMG-CoA synthase

KS

0

KS

TIGR01833

    

beta subunit

AT, ER, DH

0 and 1 and 2

ER

COG4981

    

alpha subunit

AT, KR, ACPS

0 and 1 and 2

KR

cd08950

    

FAS

KS

0

KS

COG0304, cd00834,

cd00830, TIGR03150

    

NRPS-like

A, C, ACP

0 or 1

  

ACP

T

  

NRPS

A, ACP, C

0 and 2

  

ACP

T

  

Type III

KS

0

KS

cd00831

    

Non-reducing PKS

SAT, PT

0 and 1

      

Partially-reducing PKS

DH, ER, KR

0 or 1 or 2

KR

smart00822, cl00100

    
   

ER

smart00829, cd05195

    
   

DH

smart00826

    

Highly-reducing PKS

DH, ER, KR

0 and 1 and 2

KR

smart00822, cl00100

    
   

ER

smart00829, cd05195

    

Type I PKS

AT

0

AT

smart00827, cl08282

    

Multi-modular PKS

KS, KS

0 and 1

      

PKS

KS

0

KS

smart00825, cd00833,

cd00831

    
  1. Overview of rules for classification of fungal secondary metabolite megasynthases used in synthaser. Each rule is comprised of a name, a set of domain classes, an evaluator, domain filters which specify valid domain families for a given domain class, and rename rules, which specify domain classes which should be renamed in certain contexts