Name: Rubidibacter lacunae UTEXL2944
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134365

Type strain:

Species: Rubidibacter lacunae

Strain Designation: UTEXL2944

Culture col. no.: KCTC 40015, KORDI 51-2

NCBI tax ID(s): 582515 (strain), 582514 (species)

SI-ID 349896

KCTC 40015

Section

Rubidibacter lacunae UTEXL2944 is a mesophilic, rod-shaped bacterium that was isolated from seawater.

rod-shaped
mesophilic
16S sequence
Bacteria

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Cyanobacteriota*
	Class	*Cyanophyceae*
	Order	*Chroococcales*
	Family	*Aphanothecaceae*
	Genus	*Rubidibacter*
	Species	**Rubidibacter lacunae**
	Full Scientific Name (LPSN)	Rubidibacter lacunae Choi et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32624]	Cell length	2.5-4.7 µm

[Ref.: #32624]	Cell width	0.9-1.5 µm

[Ref.: #32624]	Cell shape	rod-shaped

[Ref.: #32624]	Motility	no

[Ref.: #32624]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #32624]			growth	25-35 °C
[Ref.: #32624]			optimum	30 °C

[Ref.: #32624]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #32624]			optimum	7
[Ref.: #32624]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32624]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32624]		NaCl		growth	02-07	%
[Ref.: #32624]		NaCl		optimum	02-07	%

[Ref.: #32624]

Observation

aggregates in chains

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	vitamin E metabolism	100	4 of 4
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	chlorophyll metabolism	94.44	17 of 18
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	purine metabolism	78.72	74 of 94
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	lipid A biosynthesis	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	polyamine pathway	65.22	15 of 23
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	60.71	17 of 28
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	O-antigen biosynthesis	60	3 of 5
[Ref.: #66794]	pyrimidine metabolism	60	27 of 45
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	alanine metabolism	51.72	15 of 29
[Ref.: #66794]	oxidative phosphorylation	51.65	47 of 91
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	ginsenoside metabolism	31.25	5 of 16
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[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.: #32624]	Sample type/isolated from	seawater
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF126149 (>99% sequence identity) for Rubidibacter lacunae subclade from Microbeatlas

Aquatic Samples	54
Soil Samples	1
Animal Samples	5
Plant Samples	1
Total Samples	61

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.: #32624]	Rubidibacter lacunae KORDI 51-2 16S ribosomal RNA gene, partial sequence	EF126149	1359	GenBank	582515 tax ID

[Ref.: #32624]

GC-content

60.5 mol%

Availability in culture collections External links

[Ref.: #32624]

Culture collection no.

KCTC 40015, KORDI 51-2

[Ref.: #91912]

SI-ID 349896

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Cyanochelins, an Overlooked Class of Widely Distributed Cyanobacterial Siderophores, Discovered by Silent Gene Cluster Awakening.	Galica T, Borbone N, Mares J, Kust A, Caso A, Esposito G, Saurav K, Hajek J, Rehakova K, Urajova P, Costantino V, Hrouzek P	Appl Environ Microbiol	10.1128/AEM.03128-20	2021	*
Genetics	Draft genome sequence of Rubidibacter lacunae strain KORDI 51-2(T), a cyanobacterium isolated from seawater of Chuuk lagoon.	Choi DH, Ryu JY, Kwon KK, Lee JH, Kim C, Lee CM, Noh JH	Stand Genomic Sci	10.4056/sigs.4398180	2013	*
Phylogeny	Rubidibacter lacunae gen. nov., sp. nov., a unicellular, phycoerythrin-containing cyanobacterium isolated from seawater of Chuuk lagoon, Micronesia.	Choi DH, Noh JH, Lee CM, Rho S	Int J Syst Evol Microbiol	10.1099/ijs.0.65798-0	2008	*

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 )

#32624

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 #28835 (see below)

#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 .

#91912

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-ID349896.1 )

#28835

IJSEM 2807 2008 ( DOI 10.1099/ijs.0.65798-0 , PubMed 19060063 )

* These data were automatically processed and therefore are not curated

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