Name: Pontibaca methylaminivorans GRP21
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13856

Type strain:

Species: Pontibaca methylaminivorans

Strain Designation: GRP21

Culture col. no.: DSM 21219, KCTC 22497

Strain history: <- SG Kim, KRIBB

NCBI tax ID(s): 515897 (species)

SI-ID 370649

DSM 21219, KCTC 22497

Section

Pontibaca methylaminivorans GRP21 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from coastal sediment.

Gram-negative
ovoid-shaped
facultative anaerobe
mesophilic
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Pontibaca*
	Species	**Pontibaca methylaminivorans**
	Full Scientific Name (LPSN)	Pontibaca methylaminivorans Kim et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29756]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.985

[Ref.: #29756]	Cell length	0.9-1.6 µm

[Ref.: #29756]	Cell width	0.7-1.3 µm

[Ref.: #29756]	Cell shape	ovoid-shaped

[Ref.: #29756]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %94.939

[Ref.: #29756]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15521]

Culture medium

TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)

[Ref.: #15521]

Culture medium growth

[Ref.: #15521]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15521]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15521]	growth	28 °C
[Ref.: #29756]	growth	15-37 °C
[Ref.: #29756]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #15521]	Temperature range	mesophilic
[Ref.: #29756]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29756]			optimum	07-08
[Ref.: #29756]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29756]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #29756]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.983

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29756]		NaCl		growth	0.5-10	%
[Ref.: #29756]		NaCl		optimum	02-03	%

[Ref.: #29756]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29756]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #29756]	acetate ChEBI	+	carbon source
[Ref.: #29756]	nitrate ChEBI	+	reduction
[Ref.: #29756]	serine ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #29756]	catalase	+	1.11.1.6
[Ref.: #29756]	cytochrome oxidase	+	1.9.3.1
[Ref.: #29756]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	purine metabolism	62.77	59 of 94
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	60.71	17 of 28
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	55.56	5 of 9
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	lipid metabolism	51.61	16 of 31
[Ref.: #66794]	pyrimidine metabolism	51.11	23 of 45
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	tryptophan metabolism	42.11	16 of 38
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of sugar acids	28	7 of 25
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[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.: #15521]	Sample type/isolated from	coastal sediment
[Ref.: #15521]	Geographic location (country and/or sea, region)	East Sea
[Ref.: #15521]	Country	Republic of Korea
[Ref.: #15521]	Country ISO 3 Code	KOR
[Ref.: #15521]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From sea water
[Ref.: #67771]	Geographic location (country and/or sea, region)	the east sea
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Coast

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ505788 (>99% sequence identity) for Pontibaca methylaminivorans subclade from Microbeatlas

Aquatic Samples	423
Soil Samples	147
Animal Samples	375
Plant Samples	48
Total Samples	993

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

[Ref.: #15521]

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.: #15521]	Pontibaca methylaminivorans partial 16S rRNA gene, isolate GRP21	AJ505788	1434	ENA	515897 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pontibaca methylaminivorans DSM 21219	GCA_900156525	contig	GenBank	515897 tax ID	*
[Ref.: #66792]	Pontibaca methylaminivorans strain DSM 21219	515897.3	wgs	PATRIC	515897 tax ID	*
[Ref.: #66792]	Pontibaca methylaminivorans DSM 21219	2681812934	draft	JGI IMG/M	515897 tax ID	*

[Ref.: #15521]	GC-content	64.8 mol%
[Ref.: #29756]	GC-content	64.8-65.6 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pontibaca methylaminivorans strain DSM 21219 PATRIC: 515897.3
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pontibaca methylaminivorans strain DSM 21219 PATRIC: 515897.3
[Ref.: #69480]	gram-positive	no	98.246	yes
[Ref.: #69480]	anaerobic	no	95.159	yes
[Ref.: #69480]	halophile	yes	54.03	no
[Ref.: #69480]	spore-forming	no	95.139	yes
[Ref.: #69480]	glucose-util	no	58.763	no
[Ref.: #69480]	aerobic	yes	77.704	no
[Ref.: #69480]	thermophile	no	82.577	yes
[Ref.: #69480]	flagellated	no	91.282	no
[Ref.: #69480]	motile	no	60.94	no
[Ref.: #69480]	glucose-ferment	no	86.882	no

Availability in culture collections External links

[Ref.: #15521]

Culture collection no.

DSM 21219, KCTC 22497

[Ref.: #83032]

SI-ID 370649

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pontibaca salina sp. nov., isolated from marine sediment.	Bo JS, Wang S, Song XZ, Du ZJ	Arch Microbiol	10.1007/s00203-021-02434-z	2021	*
Phylogeny	Pukyongiella litopenaei gen. nov., sp. nov., a novel bacterium isolated from the gut content of a whiteleg shrimp Litopenaeus vannamei.	Kim YS, Kim SE, Kim SJ, Jung HK, Kim KH	Int J Syst Evol Microbiol	10.1099/ijsem.0.004269	2020	*
Phylogeny	Roseovarius spongiae sp. nov., a bacterium isolated from marine sponge.	Zhuang L, Luo L	Int J Syst Evol Microbiol	10.1099/ijsem.0.003750	2020	*
Phylogeny	Oceaniglobus indicus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from surface seawater.	Li J, Huang Z, Lai Q, Liu X, Wang G, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.002275	2017	*
Phylogeny	Oceaniovalibus guishaninsula gen. nov., sp. nov., a marine bacterium of the family Rhodobacteraceae.	Liu K, Zong R, Li Q, Fu Y, Xu Y, Wang Y, Jiao N	Curr Microbiol	10.1007/s00284-012-0081-z	2012	*
Phylogeny	Pontibaca methylaminivorans gen. nov., sp. nov., a member of the family Rhodobacteraceae.	Kim KK, Lee JS, Lee KC, Oh HM, Kim SG	Int J Syst Evol Microbiol	10.1099/ijs.0.020172-0	2009	*

References

#15521

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21219

#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 )

#29756

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 #26137 (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 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#83032

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-ID370649.1 )

#26137

IJSEM 2170 2010 ( DOI 10.1099/ijs.0.020172-0 , PubMed 19897619 )

* These data were automatically processed and therefore are not curated

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Pontibaca methylaminivorans strain DSM 21219

Pontibaca methylaminivorans strain DSM 21219

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