Table 5. Summary of Pfam domains.

Accession	ID	Description	Occurrence
Protein domains in the reference transcriptome
PF00069.19	Pkinase	Protein kinase domain	507
PF00076.16	RRM_1	RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)	237
PF01535.14	PPR	pentatricopeptide repeat	220
PF00400.26	WD40	WD domain, G-beta repeat	203
PF07714.1	Pkinase_Tyr	Protein tyrosine kinase	199
PF07727.8	RVT_2	Reverse transcriptase (RNA-dependent DNA polymerase)	190
PF00067.16	p450	Cytochrome P450	148
PF12854.1	PPR_1	Pentatricopeptide repeat	142
PF00665.20	rve	Integrase core domain	93
PF00004.23	AAA	ATPase family associated with various cellular activities (AAA)	90
PF00270.23	DEAD	DEAD/DEAH box helicase	90
PF00271.25	Helicase_C	Helicase conserved C-terminal domain	80
PF00153.21	Mito_carr	Mitochondrial carrier protein	77
PF00481.15	PP2C	Protein phosphatase 2C	75
PF00036.26	efhand	EF hand	74
	Other domains		18 055
Protein domains in candidate genes for hydrocarbon biosynthesis
PF00501	AMP-binding	AMP-binding enzyme	62
PF01061	ABC2_membrane	ABC-2 type transporter	43
PF00106	adh_short	short chain dehydrogenase	35
PF00378	ECH	Enoyl-CoA hydratase/isomerase family	23
PF01553	Acyltransferase	Acyltransferase	13
PF03405.8	FA_desaturase_2	Fatty acid desaturase	13
PF08392.1	FAE1_CUT1_RppA	FAE1/Type III polyketide synthase-like protein	13
PF07993	NAD_binding_4	Male sterility protein	13
	Other domains		60
Protein domains in candidate genes for anthocyanin biosynthesis
PF03171	2OG-FeII_Oxy	2OG-Fe(II) oxygenase superfamily	63
PF00201	UDPGT	UDP-glucoronosyl and UDP-glucosyl transferase	19
PF02797	Chal_sti_synt_C	Chalcone and stilbene synthases, C-terminal domain	10
PF00195	Chal_sti_synt_N	Chalcone and stilbene synthases, N-terminal domain	7
PF02431	Chalcone	Chalcone-flavanone isomerase	4

Highly abundant protein domains in the Ophrys reference transcriptome and among candidate genes for hydrocarbon and anthocyanin biosynthesis. ‘Occurrence’ lists the number of transcripts matching a given domain.