Name: Parafilimonas terrae 5GHs7-2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 130806

Type strain:

Species: Parafilimonas terrae

Strain Designation: 5GHs7-2

Culture col. no.: DSM 28286, KACC 17343

Strain history: <- K. Soon-Wo, KACC; 5GHs7-2

NCBI tax ID(s): 1465490 (species)

SI-ID 401467

DSM 28286

Special Collections

DSMZ

Section

Parafilimonas terrae 5GHs7-2 is a Gram-negative bacterium that was isolated from greenhouse soil.

Gram-negative
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Chitinophagia*
	Order	*Chitinophagales*
	Family	*Chitinophagaceae*
	Genus	*Parafilimonas*
	Species	**Parafilimonas terrae**
	Full Scientific Name (LPSN)	Parafilimonas terrae Kim et al. 2014

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22113]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #22113]

Culture medium growth

[Ref.: #22113]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22113]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22113]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	degradation of pentoses	71.43	20 of 28
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	degradation of sugar acids	68	17 of 25
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	carotenoid biosynthesis	59.09	13 of 22
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	daunorubicin biosynthesis	44.44	4 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	oxidative phosphorylation	41.76	38 of 91
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #22113]	Sample type/isolated from	greenhouse soil
[Ref.: #22113]	Geographic location (country and/or sea, region)	Wanju-gun, Yongjin-myeon
[Ref.: #22113]	Country	Republic of Korea
[Ref.: #22113]	Country ISO 3 Code	KOR
[Ref.: #22113]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Greenhouse
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KF934397 (>99% sequence identity) for Parafilimonas terrae from Microbeatlas

Aquatic Samples	7
Soil Samples	80
Animal Samples	6
Plant Samples
Total Samples	93

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #22113]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #22113]	Parafilimonas terrae strain 5GHs7-2 16S ribosomal RNA gene, partial sequence	KF934397	1461	GenBank ENA	1465490 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Parafilimonas terrae DSM 28286	GCA_900115755	contig	GenBank ENA	1465490 tax ID	*
[Ref.: #66792]	Parafilimonas terrae strain DSM 28286	1465490.12	wgs	PATRIC	1465490 tax ID	*
[Ref.: #66792]	Parafilimonas terrae DSM 28286	2693429887	draft	JGI IMG/M	1465490 tax ID	*

[Ref.: #22113]

GC-content

47.6 mol%

fluorimetric

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Parafilimonas terrae strain DSM 28286 PATRIC: 1465490.12
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	86.234	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.737	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	85.232	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	87.338	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.147	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	85	no

Availability in culture collections External links

[Ref.: #22113]

Culture collection no.

DSM 28286, KACC 17343

[Ref.: #89294]

SI-ID 401467

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ilyomonas limi gen. nov., sp. nov., a new member of the family Chitinophagaceae isolated from mud.	Chhetri G, Kim J, Kim H, Kim I, Kim MK, Seo T	Antonie Van Leeuwenhoek	10.1007/s10482-019-01300-9	2019	*
Phylogeny	Parafilimonas rhizosphaerae sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.).	Cho H, Ahn JH, Weon HY, Joa JH, Hong SB, Seok SJ, Kim JS, Kwon SW, Kim SJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001945	2017	*
Phylogeny	Filimonas aurantiibacter sp. nov., an orange-pigmented bacterium isolated from lake water and emended description of the genus Filimonas.	Albert RA, Waas NE, Pavlons SC, Pearson JL, Roecker J, Tewalt N, Cleeve N, Rossello-Mora R, Busse HJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001305	2016	*
Phylogeny	Parafilimonas terrae gen. nov., sp. nov., isolated from greenhouse soil.	Kim SJ, Park JH, Lim JM, Ahn JH, Anandham R, Weon HY, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.061945-0	2014	*

References

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#22113

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28286

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#89294

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID401467.1 )

* These data were automatically processed and therefore are not curated

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Parafilimonas terrae strain DSM 28286

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