Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine

Table 3 DNA replication proteins compared to the corresponding components in Thermoplasmatales, MG-II and DHEV2

	"Ca. M. alvus"	"Ca. M. intestinalis"	M. luminyensis	MG-II	DHEV2	Thermoplasmatales
ATP-dependent DNA ligase	AGI85913	AGN25909	WP_019176428	X	■	■
Orc1/Cdc6	AGI84758 (1)	AGN25419 (1)	WP_019178385 (1)	■■	■	■■
Orc1/Cdc6	AGI85775 (2)	AGN27158 (2)	WP_019178317 (2)	■■	■	■■
DNA Pol D large subunit (DPL)	AGI85099	AGN26720	WP_019177373	■	■	■
DNA Pol D small subunit (DPS)	AGI84772	AGN27082	WP_019178373	■	■	■
FEN-1	AGI85207	AGN26626	WP_019176843	■	■	■
GINS 51	AGI84890	AGN27100	X	X	■	■
GINS 23	X	X	X	X	X	X
DNA Gyrase subunit B	[AGI86382]	[AGY50228]	[WP_019178436]	[■]	[■]	[■]
DNA Gyrase subunit A	[AGI86381]	[AGN27159]	[WP_019178437]	[■]	[■]	[■]
MCM	AGI86392	AGN26346	WP_019178416	■	■	■
MCM	AGI86392	AGN27203	WP_019178416	■	■	■
PCNA	AGI84935	AGN27068	WP_019176118	■	■	■
DNA Pol B	AGI86264	AGN26701	WP_019177962	■	■	■
DNA Pol B	AGI86264	AGN26701	WP_019177491	■	■	■
Primase large subunit (PriL)	AGI84820	AGN27177	WP_019178297	■	■	■
Primase small subunit (PriS)	AGI86400	AGY50234	WP_019178400	■	■	■
RFC large subunit	AGI85559	AGN26596	WP_019176873	■	■	■
RFC small subunit	AGI85778	AGN26166	WP_019177244	■	■	■
RNaseH II	AGI86158	AGN25790	WP_019177553	■	■	■
TopoVI subunit A	AGI85998	AGN26743	WP_019177592	■	■	X
TopoVI subunit B	AGI85997	AGN26742	WP_019177591	■	■	X
Topo IB	X	X	X	X	X	X
SSB	X	X	X	X	■	■
RPA2	AGI84916	AGN25568	WP_019178149	■	■	■
RPA2	AGI84916	AGY50184	WP_019177069	■	■	■
rpa2A (rp associated protein)	AGI84915	AGN25567	WP_019178150	■	■	■
NAD-dependent DNA ligase	[AGI85455]	X	X	[■]	X	X

Proteins in brackets indicate horizontal transfers from bacteria; Proteins in italics indicate fast evolving additional copies likely representing decaying paralogs, genes horizontally transferred among archaea, or homologs arising from integration of foreign elements. Absent proteins (or unavailable due to genome incompleteness) are indicated by an X. (1) and (2) in front of the Orc1/Cdc6 protein accession numbers indicate the Orc1/Cdc6.1 and Orc1/Cdc6.2, respectively.

ISSN: 1471-2164