Methanosalsum zhilinae (DSM 4017, NBRC 107636, OCM 62)

Multimedia

• @ref:	66793
  multimedia content:	EM_DSM_4017_1.jpg
  multimedia.multimedia content:	EM_DSM_4017_1.jpg
  caption:	electron microscopic image
  intellectual property rights:	© HZI/Manfred Rohde
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
1575	METHANOSALSUM ZHILINAE MEDIUM (DSMZ Medium 396)		Medium recipe at MediaDive	Name: METHANOSALSUM ZHILINAE MEDIUM (DSMZ Medium 396) Composition: MgCl2 x 6 H2O 3.5 g/l NaHCO3 3.0 g/l Trypticase peptone 2.0 g/l Trimethylamine-HCl 2.0 g/l Na2CO3 2.0 g/l Yeast extract 2.0 g/l KCl 1.0 g/l NH4Cl 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l K2HPO4 0.4 g/l Na2S x 9 H2O 0.25 g/l MgSO4 x 7 H2O 0.015 g/l Nitrilotriacetic acid 0.0075 g/l NaCl 0.005 g/l MnSO4 x H2O 0.0025 g/l CoSO4 x 7 H2O 0.0009 g/l ZnSO4 x 7 H2O 0.0009 g/l Sodium resazurin 0.0005 g/l CaCl2 x 2 H2O 0.0005 g/l FeSO4 x 7 H2O 0.0005 g/l NiCl2 x 6 H2O 0.00015 g/l AlK(SO4)2 x 12 H2O 0.0001 g/l Na2MoO4 x 2 H2O 5e-05 g/l CuSO4 x 5 H2O 5e-05 g/l H3BO3 5e-05 g/l Na2WO4 x 2 H2O 2e-06 g/l Na2SeO3 x 5 H2O 1.5e-06 g/l Distilled water

Culture temp

Oxygen tolerance

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	methanofuran biosynthesis	100	5 of 5
66794	ubiquinone biosynthesis	100	7 of 7
66794	factor 420 biosynthesis	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	ribulose monophosphate pathway	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	methanogenesis from CO2	83.33	10 of 12
66794	flavin biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	palmitate biosynthesis	77.27	17 of 22
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	purine metabolism	73.4	69 of 94
66794	pentose phosphate pathway	72.73	8 of 11
66794	heme metabolism	71.43	10 of 14
66794	coenzyme M biosynthesis	70	7 of 10
66794	starch degradation	70	7 of 10
66794	phenylalanine metabolism	69.23	9 of 13
66794	vitamin B12 metabolism	67.65	23 of 34
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	valine metabolism	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	gluconeogenesis	62.5	5 of 8
66794	pyrimidine metabolism	62.22	28 of 45
66794	vitamin B1 metabolism	61.54	8 of 13
66794	NAD metabolism	61.11	11 of 18
66794	threonine metabolism	60	6 of 10
66794	myo-inositol biosynthesis	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	d-mannose degradation	55.56	5 of 9
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	serine metabolism	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	methionine metabolism	53.85	14 of 26
66794	sulfopterin metabolism	50	2 of 4
66794	non-pathway related	50	19 of 38
66794	alginate biosynthesis	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	Entner Doudoroff pathway	50	5 of 10
66794	tyrosine metabolism	50	7 of 14
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	biotin biosynthesis	50	2 of 4
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	lysine metabolism	47.62	20 of 42
66794	tryptophan metabolism	47.37	18 of 38
66794	leucine metabolism	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	lipid metabolism	45.16	14 of 31
66794	cysteine metabolism	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	citric acid cycle	42.86	6 of 14
66794	propanol degradation	42.86	3 of 7
66794	oxidative phosphorylation	41.76	38 of 91
66794	carotenoid biosynthesis	40.91	9 of 22
66794	urea cycle	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	isoprenoid biosynthesis	34.62	9 of 26
66794	alanine metabolism	34.48	10 of 29
66794	cyanate degradation	33.33	1 of 3
66794	formaldehyde oxidation	33.33	1 of 3
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	degradation of hexoses	33.33	6 of 18
66794	lipid A biosynthesis	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	glutathione metabolism	28.57	4 of 14
66794	mevalonate metabolism	28.57	2 of 7
66794	vitamin B6 metabolism	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	polyamine pathway	26.09	6 of 23
66794	degradation of pentoses	25	7 of 28
66794	catecholamine biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	CMP-KDO biosynthesis	25	1 of 4
66794	butanoate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	chlorophyll metabolism	22.22	4 of 18

Isolation source categories

Isolation

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM21799v1 assembly for Methanosalsum zhilinae DSM 4017	complete	GCA_000217995	679901.8	2502790017	679901	98.6

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
1575	Methanosalsum zhilinae strain DSM 4017 16S ribosomal RNA gene, partial sequence	FJ224366	1427		679901

GC content

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly.	Llorens-Mares T, Liu Z, Allen LZ, Rusch DB, Craig MT, Dupont CL, Bryant DA, Casamayor EO.	ISME J	10.1038/ismej.2016.93	2017
	Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis.	Zuo G, Xu Z, Hao B.	Life (Basel)	10.3390/life5010949	2015
	Evolution of the B-Block Binding Subunit of TFIIIC That Binds to the Internal Promoter for RNA Polymerase III.	Matsutani S.	Int J Evol Biol	10.1155/2014/609865	2014
Metabolism	The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism.	Hove-Jensen B, Brodersen DE, Manav MC.	Microbiol Mol Biol Rev	10.1128/mmbr.00040-18	2019
Metabolism	Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage.	de Crecy-Lagard V, Forouhar F, Brochier-Armanet C, Tong L, Hunt JF.	Biol Direct	10.1186/1745-6150-7-32	2012
	Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors.	Tatarinova T, Salih B, Dien Bard J, Cohen I, Bolshoy A.	Biomed Res Int	10.1155/2015/786861	2015
	Horizontal gene transfer drives the evolution of Rh50 permeases in prokaryotes.	Matassi G.	BMC Evol Biol	10.1186/s12862-016-0850-6	2017
Metabolism	Phylogenomic reconstruction of archaeal fatty acid metabolism.	Dibrova DV, Galperin MY, Mulkidjanian AY.	Environ Microbiol	10.1111/1462-2920.12359	2014
	Methods of combinatorial optimization to reveal factors affecting gene length.	Bolshoy A, Tatarinova T.	Bioinform Biol Insights	10.4137/bbi.s10525	2012