Reverse Methanogenesis and Respiration in Methanotrophic Archaea

Table 2

Domain based (meta)genome comparison of selected metagenomes of methanotrophs and selected genomes of other archaea. Domain abundance in every (meta)genome is indicated by numbers. S-AOM performing ANME include ANME-1-s [40], ANME-1-m [41], and ANME-2a [42]. N-AOM performing ANME include ANME-2d-h [28] and ANME-2d-a [43]. The acetoclastic (A) and methylotrophic (M) methanogens include Methanosarcina acetivorans C2A (AM), Methanosaeta concilii GP6 (A), Methanococcoides burtonii DSM6242 (M-1), Methanolobus tindarius DSM2278 (M-2), and Methanohalophilus mahii DSM5219 (M-3). Hydrogenotrophic methanogens (H) include Methanospirillum hungatei JF-1 (H-1), Methanobacterium formicicum DSM3637 (H-2), Methanococcus maripaludis C5 (H-3), and Methanoregula formicica SMSP (H-4). The sulfate-reducing archaeon (S) is Archaeoglobus fulgidus DSM 4304.

	InterPro ID	ANME-1 S	ANME-1 M	ANME-2a	ANME-2d H	ANME-2d A	AM	A	M-1	M-2	M-3	H-1	H-2	H-3	H-4	S
Central pathway
Mcr, alpha subunit, N-terminal	IPR003183	4	2	1	1	1	1	1	1	1	1	1	2	1	2	0
Mcr, alpha subunit, N-terminal subdomain 1	IPR015811	2	3	1	1	1	1	1	1	1	1	1	2	1	2	0
Mcr, alpha subunit, N-terminal subdomain 2	IPR015823	2	2	2	2	2	2	2	2	2	2	2	4	2	4	0
Mcr, alpha subunit, C-terminal	IPR009047	3	2	1	1	1	1	1	1	1	1	1	2	1	2	0
Mcr, alpha/beta subunit, C-terminal	IPR008924	6	4	2	2	2	2	2	2	2	2	2	4	2	4	0
Mcr, alpha/beta subunit, domain 2, C-terminal	IPR022681	9	6	3	3	3	3	3	3	3	3	3	6	3	6	0
Mcr, beta subunit	IPR003179	1	2	1	1	1	1	1	1	1	1	1	2	1	2	0
Mcr, beta subunit, C-terminal	IPR022679	3	2	1	1	1	1	1	1	1	1	1	2	1	2	0
Mcr, beta subunit, N-terminal	IPR022680	4	2	1	1	1	1	1	1	1	1	1	2	1	2	0
Mcr, gamma subunit	IPR003178	14	8	4	4	4	4	4	4	4	4	4	8	4	8	0
Mcr, protein C	IPR007687	2	1	1	1	1	1	1	1	1	1	1	1	1	1	0
Mcr, protein C-like	IPR026327	5	2	2	2	2	2	2	1	2	2	2	2	2	1	0
Mcr, protein D	IPR003901	0	0	3	6	6	3	3	3	3	3	3	9	3	6	0
Mcr, ferredoxin-like fold	IPR009024	12	6	3	3	3	3	3	3	3	3	3	6	3	6	0
5,10-methylenetetrahydromethanopterin reductase	IPR019946	0	0	2	1	1	1	1	1	1	1	1	1	1	1	1
Acetoclastic methanogenesis
CO dehydrogenase/acetyl-CoA synthase complex alpha subunit	IPR004460	0	1	1	1	1	3	1	1	1	1	1	1	1	1	2
CO dehydrogenase/acetyl-CoA synthase complex beta subunit	IPR004461	13	4	2	2	2	4	4	2	2	2	2	2	2	4	2
CO dehydrogenase/acetyl-CoA synthase delta subunit	IPR004486	5	1	1	1	1	2	1	1	1	1	1	1	1	1	1
CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel	IPR016041	11	2	5	3	2	4	2	2	3	3	3	2	2	5	2
CO dehydrogenase b subunit/acetyl-CoA synthase epsilon subunit	IPR003704	3	2	2	2	2	4	2	2	2	2	2	2	2	2	4
Methylotrophic methanogenesis
Methyltransferase MtaA/CmuA	IPR006360	0	0	0	0	0	7	0	4	5	6	0	0	1	0	0
Methanol-cobalamin methyltransferase, B subunit	IPR021079	0	0	0	0	0	3	0	2	2	2	0	0	0	0	0
Monomethylamine methyltransferase MtmB	IPR008031	3	0	0	0	0	12	0	12	21	15	0	0	0	0	0
Trimethylamine methyltransferase	IPR010426	11	0	0	0	0	4	0	5	2	2	0	0	0	0	0
Dimethylamine methyltransferase MtbB	IPR012653	0	0	0	0	0	9	0	6	6	6	0	0	0	0	0
Trimethylamine methyltransferase, Methanosarcina	IPR012740	0	0	0	0	0	2	0	1	1	1	0	0	0	0	0
Methylamine methyltransferase corrinoid protein reductive activase	IPR026339	0	0	0	0	0	4	0	2	2	2	0	0	0	0	0
C-type cytochromes
Di-haem cytochrome, transmembrane, nitrate reduction	IPR016174	2	0	4	3	7	4	0	0	4	0	1	1	0	0	1
Doubled CXXCH motif	IPR010177	33	0	3	2	3	0	0	0	0	0	0	0	0	0	0
Cytochrome c-like domain	IPR009056	2	0	6	0	17	15	0	4	8	6	0	0	0	0	4
Class III cytochrome C (tetraheme cytochrome)	IPR020942	2	0	0	3	3	0	0	0	0	0	0	0	0	0	0
Tetraheme cytochrome domain, flavocytochrome c3 (Shewanella)	IPR012286	4	0	4	5	4	2	0	0	1	0	1	0	0	0	2
Octaheme c-type cytochrome	IPR024673	1	0	2	0	0	0	0	0	2	2	0	0	0	0	1
Methanogenesis multiheme c-type cytochrome	IPR027594	0	0	1	0	0	1	0	1	1	1	0	0	0	0	0
Multiheme cytochrome	IPR011031	78	15	52	80	73	3	0	6	8	14	0	0	0	1	7
S-layer domains
S-layer family duplication domain	IPR006457	13	0	29	16	26	34	19	16	44	17	0	0	0	0	0
Sarcinarray family protein	IPR026476	0	0	6	0	4	1	0	0	2	1	0	0	0	0	0
S-layer homology domain	IPR001119	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0
Cell export and cell adhesion
HYR domain	IPR003410	1	5	2	0	0	0	0	0	0	0	0	0	0	0	0
CARDB domain	IPR011635	64	14	15	6	6	30	4	1	4	0	9	0	0	3	8
Collagen-binding surface protein Cna-like, B-type domain	IPR008454	4	1	2	1	8	0	6	0	2	2	0	0	0	0	0
von Willebrand factor, type A	IPR002035	55	28	17	32	14	37	23	17	42	9	28	8	0	27	7
VWA N-terminal	IPR013608	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0
Adhesion lipoprotein	IPR006128	8	4	4	5	0	0	5	3	0	4	4	5	0	0	0
Adhesin B	IPR006129	0	3	4	5	0	0	3	0	0	4	0	3	0	0	0
Invasin/intimin cell-adhesion fragments	IPR008964	17	0	3	2	6	7	0	2	7	0	1	2	0	2	2
Putative cell wall binding repeat 2	IPR007253	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0
Archaeosortase A	IPR014522	2	0	1	2	2	1	1	1	1	1	1	0	0	2	1
Archaeosortase B	IPR026430	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
Archaeosortase C	IPR022504	0	0	1	2	1	0	0	1	1	0	0	0	0	0	0
Exosortase/archaeosortase domain	IPR026392	5	0	2	5	3	1	1	2	2	2	1	0	1	2	1
Exosortase, EpsH	IPR013426	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0
Exosortase EpsH-related	IPR019127	4	2	2	3	2	1	1	2	1	1	1	0	1	2	1
Archaeosortase family protein ArtE	IPR026485	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
Cell wall hydrolase/autolysin, catalytic	IPR002508	2	2	1	0	0	0	0	0	0	0	0	0	0	1	0
PEF-CTERM protein sorting domain	IPR017474	0	0	3	4	1	0	0	10	19	0	0	0	0	0	0
PGF-pre-PGF domain	IPR026453	1	1	18	9	8	24	0	7	21	11	0	0	0	1	1
PGF-CTERM archaeal protein-sorting signal	IPR026371	9	4	6	2	1	2	0	2	1	2	1	0	0	1	3
LPXTG cell wall anchor domain	IPR019931	3	0	1	0	0	0	1	1	0	0	0	0	0	0	0
VPXXXP-CTERM protein sorting domain	IPR026428	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0
Cellulosome-related/Dockerin
Cellulosome anchoring protein, cohesin domain	IPR002102	80	77	52	4	12	2	0	4	15	3	1	1	0	0	4
Dockerin domain	IPR016134	149	112	44	4	6	5	17	2	4	0	9	0	0	0	2
Dockerin type I repeat	IPR002105	1	0	5	0	0	0	0	0	0	0	0	0	0	0	1
Carbohydrate-binding domains
Carbohydrate-binding domain	IPR008965	50	42	39	2	6	2	0	3	13	2	3	0	1	0	2
Carbohydrate-binding-like fold	IPR013784	14	5	3	10	19	0	0	0	0	1	3	0	0	6	1
Carbohydrate-binding, CenC-like	IPR003305	1	0	7	0	17	0	0	0	0	0	0	0	0	0	0
Carbohydrate-binding/sugar hydrolysis domain	IPR006633	27	22	5	2	2	27	3	7	8	8	0	5	2	1	8
Carbohydrate-binding domain, family 9	IPR010502	1	0	0	0	2	0	0	0	0	0	0	0	0	0	0
Bacteroidetes-associated carbohydrate-binding often N-terminal	IPR024361	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
Carbohydrate binding module, xylan-binding domain	IPR031768	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
Galactose-binding domain-like	IPR008979	12	1	17	6	39	4	4	2	1	3	0	0	0	0	0
Menaquinones
3-Demethylubiquinone-9 3-methyltransferase	IPR028973	0	0	0	3	3	0	0	0	0	0	0	1	0	0	0
Succinate dehydrogenase/fumarate reductase, flavoprotein subunit	IPR014006	0	0	1	2	1	0	0	0	0	1	0	0	0	0	1
UbiE/COQ5 methyltransferase	IPR004033	3	0	0	2	2	1	0	1	0	0	0	0	0	0	0
UbiE/COQ5 methyltransferase, conserved site	IPR023576	3	0	0	2	2	0	0	0	1	0	0	0	0	0	0
NrfD family	IPR005614	3	0	0	4	3	0	0	0	0	0	0	0	0	0	3
Futalosine hydrolase	IPR019963	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0
Cyclic dehypoxanthine futalosine synthase	IPR022431	1	1	0	1	1	0	0	0	0	0	0	0	0	0	1
Aminodeoxyfutalosine synthase	IPR022432	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0
Menaquinone synthesis (chorismate dehydratase & naphthoate synthase)	IPR003773	8	6	0	2	2	0	0	0	0	0	0	0	0	0	2
FO synthase, subunit 2	IPR020050	3	3	1	3	3	2	1	2	1	2	2	2	2	2	3
Phenazines
Phenazine biosynthesis PhzF protein	IPR003719	1	1	4	0	0	2	0	0	0	0	0	0	0	2	0