Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases

Table 1 Summary of the TnpA_Y1 family subclasses properties

Subclass^a	Subclass size	Subclass coverage	Median full length	Key motifs^b			Length	Core domain				Protein tail domain			Intra-genomique copies		REP	Taxonomic distribution
				Key motifs^b				Sequence insertion^c				Proximal		Distal	Intra-genomique copies
				HuH	W	Y		β1:αA	αB	β3:αC	αC:β4	hmm^d	motif	hmm^d	Mean	Identity^e
1.1	2620	22.42	152	DH[VI]H	W[TS]	Y[IV]ENQ	117								4.8	99.4	small subterminal DNA hairpin structures	Archaea Bacteria
1.2	101	3.83	148	DH[IV]H	WQ	YIKNQKEHH	112					30			1.7	36.2	no	Cyanobacteria Bacteroidetes
2.1 (1)	493	14.9	238	NHVH NH[YF]H	W[EQ] FQ	YIELNP Y[IV]HLNP	111					53	SS	49 37 69	1.9	49.2	no	Bacteria prevalence in ε, β, δ proteobacteria
2.2 (2)	270	6.71	165	DHLH	WE	YIHYNP	111				10	33	SS		1.5	42.3	long long with bulge	Proteobacteria
2.3	224	2.88	325	NHYH	WE	YVDLNP	172	10		55		21	TS	61	3.9	74.8	no	Chromatiales Alteromonadales
2.4 (4)	124	4.94	194	NH[IFV]H	WQ	YIxNNP	146		8	yes^f					1.5	40.1	long double foot inserted in tnpAREP	Cyanobacteria Bacteroidetes and various phyla
2.5 (3)	87	2.21	151	DH[LF]H	WQ	YI[VI]ANP	111					20			1.6	55.3	short few long	Xanthomonad Pseudomonad
2.6 (5)	63	2.51	179	NH[LIV]H	WQ	YIH[QN]NP	135				21	29	SS		1.8	40.7	atypical secondary structures	Bacteroidetes
2.7	36	1.84	213	[ND]HVH	WQ	YI[LR][NQ]NP	102								1.2	37.4	long	Cyanobacteria and few other phyla
2.8	8	0.37	199	NHYH	W[YH]	YIHYNP	112								1.0	na	long	Cyanobacteria
3	14	0.29	178	NHVH	W[TA]	YV[VI][AENY]EQ	155								1.2	60.7	atypical secondary structures	Planctomycetes Acidobacteria Proteobacteria

ISSN: 1471-2164