Table 1.

Annotated domains of TAAs, divided into functional classes. Where the structure of a domain is known, the Protein Data Bank accession code is given in square brackets

Domain name	Structure	Prediction	PFAM
Class: signal peptide
Autotransporter signal peptide	–	HMMER	–
Class: head
Ylhead	Beta-solenoid [1p9h]	HMMER/rules	Hep_Hag
HIM1, HIM2a	Insert within last Ylhead repeat before the neck	HMMER	–
Trp-ring	Beta-meander [1s7m]	HMMER	–
GIN	Beta-prism [1s7m]	HMMER	–
FxG	Unknown	HMMER	X_fast-SP-rel
Class: stalk
Right-handed stalks	Right handed CC	HMMER	–
Left-handed stalks	Left-handed coiled coil	Marcoil/rules	DUF1079b
FGG	Coiled-coil variant	HMMER/rules	–
Class: connector
Neck	Loop [1p9h]	HMMER	HIM
HANS	Unknown	HMMER/rules	–
DALL1, 2, 3	Unknown	HMMER	–
ISneck1	Neck with an inserted domain [1s7m]	HMMER	–
ISneck2a	Neck with an short insertion	HMMER	- (HIM)c
Class: anchor
Membrane anchor	Beta-barrel occluded by CC	HMMER	YadA

^aDUF1079 is a motif in the left-handed stalks of Moraxella UspA1 and UspA2.

^bThese domains were added as a result of the manual benchmark annotation and were not used for benchmarking.

^cPFAM HIM definition annotates only first half of this motif.