Name: Polaribacter porphyrae LNM-20
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133846

Type strain:

Species: Polaribacter porphyrae

Strain Designation: LNM-20

Culture col. no.: LMG 26671, NBRC 108759

NCBI tax ID(s): 1137780 (species)

SI-ID 378088

LMG 26671, NBRC 108759

Special Collections

Literature strains

Section

Polaribacter porphyrae LNM-20 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from thalli of a marine red alga.

Gram-negative
rod-shaped
aerobe
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	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Polaribacter*
	Species	**Polaribacter porphyrae**
	Full Scientific Name (LPSN)	Polaribacter porphyrae Fukui et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30663]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.981

[Ref.: #30663]	Cell length	1.39 µm

[Ref.: #30663]	Cell width	0.37 µm

[Ref.: #30663]	Cell shape	rod-shaped

[Ref.: #30663]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92

[Ref.: #30663]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #30663]			growth	10-30 °C
[Ref.: #30663]			optimum	25 °C

	pH	Kind of pH		pH
[Ref.: #30663]			optimum	7
[Ref.: #30663]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30663]	Oxygen tolerance	aerobe
[Ref.: #69480]	Oxygen tolerance	aerobe Confidence in %90.883

[Ref.: #69480]	Ability of spore formation	no Confidence in %90.333
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30663]		NaCl		growth	02-05	%
[Ref.: #30663]		NaCl		optimum	3	%

[Ref.: #30663]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30663]	2-oxopentanoate ChEBI	+	carbon source
[Ref.: #30663]	acetate ChEBI	+	carbon source
[Ref.: #30663]	alanine ChEBI	+	carbon source
[Ref.: #30663]	alpha-cyclodextrin ChEBI	+	carbon source
[Ref.: #30663]	aspartate ChEBI	+	carbon source
[Ref.: #30663]	dextrin ChEBI	+	carbon source
[Ref.: #30663]	esculin ChEBI	+	hydrolysis
[Ref.: #30663]	galactose ChEBI	+	carbon source
[Ref.: #30663]	glucose ChEBI	+	carbon source
[Ref.: #30663]	glutamate ChEBI	+	carbon source
[Ref.: #30663]	glycine ChEBI	+	carbon source
[Ref.: #30663]	glycogen ChEBI	+	carbon source
[Ref.: #30663]	L-alaninamide ChEBI	+	carbon source
[Ref.: #30663]	lactate ChEBI	+	carbon source
[Ref.: #30663]	lactose ChEBI	+	carbon source
[Ref.: #30663]	maltose ChEBI	+	carbon source
[Ref.: #30663]	mannose ChEBI	+	carbon source
[Ref.: #30663]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #30663]	ornithine ChEBI	+	carbon source
[Ref.: #30663]	proline ChEBI	+	carbon source
[Ref.: #30663]	serine ChEBI	+	carbon source
[Ref.: #30663]	succinate ChEBI	+	carbon source
[Ref.: #30663]	threonine ChEBI	+	carbon source
[Ref.: #30663]	tween 40 ChEBI	+	carbon source
[Ref.: #30663]	uridine ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30663]	acid phosphatase	+	3.1.3.2
[Ref.: #30663]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30663]	catalase	+	1.11.1.6
[Ref.: #30663]	cytochrome oxidase	+	1.9.3.1
[Ref.: #30663]	gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	peptidoglycan biosynthesis	66.67	10 of 15
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	pentose phosphate pathway	45.45	5 of 11
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	oxidative phosphorylation	39.56	36 of 91
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[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
		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.: #30663]	Sample type/isolated from	thalli of a marine red alga
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Host	#Algae	#Red algae

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB695286 (>99% sequence identity) for Polaribacter porphyrae subclade from Microbeatlas

Aquatic Samples	35
Soil Samples	2
Animal Samples	6
Plant Samples
Total Samples	43

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.: #30663]	Polaribacter porphyrae gene for 16S ribosomal RNA, partial sequence, strain: LNM-20	AB695286	1389	GenBank ENA	1137780 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Polaribacter porphyrae NBRC 108759	GCA_002954685	scaffold	GenBank ENA	1137780 tax ID	*
[Ref.: #66792]	Polaribacter porphyrae LMG 26671	GCA_020532745	contig	GenBank ENA	1137780 tax ID	*
[Ref.: #66792]	Polaribacter porphyrae strain NBRC 108759	1137780.3	wgs	PATRIC	1137780 tax ID	*
[Ref.: #66792]	Polaribacter porphyrae NBRC 108759	2895253024	draft	JGI IMG/M	1137780 tax ID	*

[Ref.: #30663]

GC-content

28.6 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Polaribacter porphyrae NBRC 108759 NCBI: GCA_002954685.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Polaribacter porphyrae NBRC 108759 NCBI: GCA_002954685.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.981	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.434	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	90.883	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	90.333	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.981	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	92	yes

Availability in culture collections External links

[Ref.: #30663]

Culture collection no.

LMG 26671, NBRC 108759

[Ref.: #91618]

SI-ID 378088

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Polaribacter porphyrae sp. nov., isolated from the red alga Porphyra yezoensis, and emended descriptions of the genus Polaribacter and two Polaribacter species.	Fukui Y, Abe M, Kobayashi M, Saito H, Oikawa H, Yano Y, Satomi M	Int J Syst Evol Microbiol	10.1099/ijs.0.041434-0	2012	*
Phylogeny	Polaribacter septentrionalilitoris sp. nov., isolated from the biofilm of a stone from the North Sea.	Choo S, Borchert E, Wiese J, Saha M, Kunzel S, Weinberger F, Hentschel U	Int J Syst Evol Microbiol	10.1099/ijsem.0.004290	2020	*
Phylogeny	Polaribacter marinivivus sp. nov., a member of the family Flavobacteriaceae isolated from seawater.	Park S, Park JM, Jung YT, Lee KC, Lee JS, Yoon JH	Antonie Van Leeuwenhoek	10.1007/s10482-014-0283-4	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 )

#30663

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26994 (see below)

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#91618

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-ID378088.1 )

#26994

IJSEM 1665 2013 ( DOI 10.1099/ijs.0.041434-0 , PubMed 22904227 )

* These data were automatically processed and therefore are not curated

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Polaribacter porphyrae NBRC 108759

Polaribacter porphyrae NBRC 108759

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