Pseudoalteromonas rubra (DSM 6842, ATCC 29570, LMG 2876)

Cell morphology

Multimedia

• @ref:	2850
  multimedia content:	DSM_6842.jpg
  multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_6842.jpg
  caption:	Micrograph of DSM 6842.
  intellectual property rights:	Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
  manual_annotation:	1

• @ref:	2850
  multimedia content:	DSM_6842-1.jpg
  multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_6842-1.jpg
  caption:	DSM 6842 grown on DSMZ medium 514.
  intellectual property rights:	Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
2850	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
42026	Marine agar (MA)			Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
122286	CIP Medium 13		Medium recipe at CIP

Culture temp

Oxygen tolerance

Spore formation

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
122286	4853 ChEBI	esculin	-	hydrolysis
122286	17632 ChEBI	nitrate	-	reduction
122286	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122286	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
122286	15688 ChEBI	acetoin	-
122286	17234 ChEBI	glucose

Enzymes

@ref	Value	Activity	Ec
122286	alcohol dehydrogenase	-	1.1.1.1
122286	beta-galactosidase	-	3.2.1.23
122286	caseinase	+	3.4.21.50
122286	catalase	+	1.11.1.6
122286	gelatinase	+
122286	lecithinase	-
122286	lysine decarboxylase	-	4.1.1.18
122286	ornithine decarboxylase	-	4.1.1.17
122286	oxidase	+
122286	tryptophan deaminase	-
122286	urease	-	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	biotin biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	enterobactin biosynthesis	100	3 of 3
66794	glycogen metabolism	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	butanoate fermentation	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	ubiquinone biosynthesis	100	7 of 7
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	photosynthesis	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	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	tyrosine metabolism	85.71	12 of 14
66794	proline metabolism	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	cellulose degradation	80	4 of 5
66794	starch degradation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	glutathione metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	NAD metabolism	77.78	14 of 18
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	purine metabolism	74.47	70 of 94
66794	flavin biosynthesis	73.33	11 of 15
66794	citric acid cycle	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	methionine metabolism	69.23	18 of 26
66794	histidine metabolism	68.97	20 of 29
66794	octane oxidation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	tryptophan metabolism	65.79	25 of 38
66794	glycolysis	64.71	11 of 17
66794	vitamin B6 metabolism	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	urea cycle	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	polyamine pathway	60.87	14 of 23
66794	propionate fermentation	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	non-pathway related	57.89	22 of 38
66794	lysine metabolism	54.76	23 of 42
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	kanosamine biosynthesis II	50	1 of 2
66794	arachidonic acid metabolism	50	9 of 18
66794	cyclohexanol degradation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	sphingosine metabolism	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	oxidative phosphorylation	43.96	40 of 91
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	carotenoid biosynthesis	40.91	9 of 22
66794	vitamin K metabolism	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	degradation of pentoses	39.29	11 of 28
66794	degradation of hexoses	38.89	7 of 18
66794	degradation of sugar alcohols	37.5	6 of 16
66794	carnitine metabolism	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	phenol degradation	35	7 of 20
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	sulfoquinovose degradation	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	methane metabolism	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	vitamin B12 metabolism	32.35	11 of 34
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	d-xylose degradation	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	degradation of sugar acids	24	6 of 25

Isolation source categories

Isolation

Taxonmaps

69479

Global distribution of 16S sequence X82147 (>99% sequence identity) for Pseudoalteromonas from Microbeatlas

Aquatic Samples	2485
Soil Samples	55
Animal Samples	574
Plant Samples	64
Total Samples	3178

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM23829v4 assembly for Pseudoalteromonas rubra DSM 6842	chromosome	GCA_000238295	43658.31	2541047006	43658	78.5
66792	Pseudoalteromonas rubra ATCC 29570	contig		1117318.14		1117318	66.4

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
2850	A.rubra 16S rRNA gene (ATCC 29570T)	X82147	1426		1117318
124043	Pseudoalteromonas rubra gene for 16S ribosomal RNA, partial sequence, strain: TKA09_02.	LC275063	1447		43658

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Stress	In vitro study of the modulatory effects of heat-killed bacterial biomass on aquaculture bacterioplankton communities.	Sousa JMG, Louvado A, Coelho FJRC, Oliveira V, Oliveira H, Cleary DFR, Gomes NCM.	Sci Rep	10.1038/s41598-022-23439-8	2022
	Total Synthesis of the Repeating Units of Highly Functionalized O-Antigens of Pseudomonas aeruginosa ATCC 27577, O10, and O19	Yang X, Zhang H, Zhao Q, Li Q, Li T, Gao J.	JACS Au		2024
Metabolism	Co-occurrence of enzyme domains guides the discovery of an oxazolone synthetase.	de Rond T, Asay JE, Moore BS.	Nat Chem Biol	10.1038/s41589-021-00808-4	2021
Metabolism	Culturing marine bacteria from the genus Pseudoalteromonas on a cotton scaffold alters secondary metabolite production.	Timmermans ML, Picott KJ, Ucciferri L, Ross AC.	Microbiologyopen	10.1002/mbo3.724	2019
Enzymology	Deciphering the biosynthesis of a novel lipid in Mycobacterium tuberculosis expands the known roles of the nitroreductase superfamily.	Grigg JC, Copp JN, Krekhno JMC, Liu J, Ibrahimova A, Eltis LD.	J Biol Chem	10.1016/j.jbc.2023.104924	2023
	A mixed-valent Fe(II)Fe(III) species converts cysteine to an oxazolone/thioamide pair in methanobactin biosynthesis.	Park YJ, Jodts RJ, Slater JW, Reyes RM, Winton VJ, Montaser RA, Thomas PM, Dowdle WB, Ruiz A, Kelleher NL, Bollinger JM, Krebs C, Hoffman BM, Rosenzweig AC.	Proc Natl Acad Sci U S A	10.1073/pnas.2123566119	2022
	Biosynthetic potential of the global ocean microbiome.	Paoli L, Ruscheweyh HJ, Forneris CC, Hubrich F, Kautsar S, Bhushan A, Lotti A, Clayssen Q, Salazar G, Milanese A, Carlstrom CI, Papadopoulou C, Gehrig D, Karasikov M, Mustafa H, Larralde M, Carroll LM, Sanchez P, Zayed AA, Cronin DR, Acinas SG, Bork P, Bowler C, Delmont TO, Gasol JM, Gossert AD, Kahles A, Sullivan MB, Wincker P, Zeller G, Robinson SL, Piel J, Sunagawa S.	Nature	10.1038/s41586-022-04862-3	2022
Enzymology	Exploring regulation genes involved in the expression of L-amino acid oxidase in Pseudoalteromonas sp. Rf-1.	Yu Z, Wang J, Lin J, Zhao M, Qiu J.	PLoS One	10.1371/journal.pone.0122741	2015
	An Indonesian Marine Bacterium, Pseudoalteromonas rubra, Produces Antimicrobial Prodiginine Pigments.	Setiyono E, Adhiwibawa MAS, Indrawati R, Prihastyanti MNU, Shioi Y, Brotosudarmo THP.	ACS Omega	10.1021/acsomega.9b04322	2020
	Synthesis of Cycloprodigiosin Identifies the Natural Isolate as a Scalemic Mixture.	Johnson RE, de Rond T, Lindsay VN, Keasling JD, Sarpong R.	Org Lett	10.1021/acs.orglett.5b01527	2015
Genetics	Distribution in microbial genomes of genes similar to lodA and goxA which encode a novel family of quinoproteins with amino acid oxidase activity.	Campillo-Brocal JC, Chacon-Verdu MD, Lucas-Elio P, Sanchez-Amat A.	BMC Genomics	10.1186/s12864-015-1455-y	2015
Biotechnology	An Overview on Industrial and Medical Applications of Bio-Pigments Synthesized by Marine Bacteria.	Nawaz A, Chaudhary R, Shah Z, Dufosse L, Fouillaud M, Mukhtar H, Haq IU.	Microorganisms	10.3390/microorganisms9010011	2020
	Distribution of dehalogenation activity in subseafloor sediments of the Nankai Trough subduction zone.	Futagami T, Morono Y, Terada T, Kaksonen AH, Inagaki F.	Philos Trans R Soc Lond B Biol Sci	10.1098/rstb.2012.0249	2013
Metabolism	Structure, Chemical Synthesis, and Biosynthesis of Prodiginine Natural Products.	Hu DX, Withall DM, Challis GL, Thomson RJ.	Chem Rev	10.1021/acs.chemrev.6b00024	2016
Metabolism	New prodigiosin-like pigment from Alteromonas rubra.	Gerber NN, Gauthier MJ.	Appl Environ Microbiol	10.1128/aem.37.6.1176-1179.1979	1979
Enzymology	Novel Salt-Tolerant Leucine Dehydrogenase from Marine Pseudoalteromonas rubra DSM 6842.	Chen R, Liao YT, Gao TT, Zhang YM, Lu LH, Wang CH	Mol Biotechnol	10.1007/s12033-022-00505-0	2022
Genetics	Genome sequence of the cycloprodigiosin-producing bacterial strain Pseudoalteromonas rubra ATCC 29570(T).	Xie BB, Shu YL, Qin QL, Rong JC, Zhang XY, Chen XL, Zhou BC, Zhang YZ	J Bacteriol	10.1128/JB.06822-11	2012
Genetics	Structure of a polysaccharide from the lipopolysaccharides of Vibrio vulnificus strains CECT 5198 and S3-I2-36, which is remarkably similar to the O-polysaccharide of Pseudoalteromonas rubra ATCC 29570.	Shashkov AS, Senchenkova SN, Chizhov AO, Knirel YA, Esteve C, Alcaide E, Merino S, Tomas JM	Carbohydr Res	10.1016/j.carres.2009.06.035	2009
Genetics	The structure of the O-polysaccharide of the Pseudoalteromonas rubra ATCC 29570T lipopolysaccharide containing a keto sugar.	Kilcoyne M, Shashkov AS, Knirel YA, Gorshkova RP, Nazarenko EL, Ivanova EP, Gorshkova NM, Senchenkova SN, Savage AV	Carbohydr Res	10.1016/j.carres.2005.07.007	2005
	Spartinivicinus ruber gen. nov., sp. nov., a Novel Marine Gammaproteobacterium Producing Heptylprodigiosin and Cycloheptylprodigiosin as Major Red Pigments.	Huang Z, Dong L, Lai Q, Liu J.	Front Microbiol	10.3389/fmicb.2020.02056	2020
Phylogeny	Classification of a Violacein-Producing Psychrophilic Group of Isolates Associated with Freshwater in Antarctica and Description of Rugamonas violacea sp. nov.	Sedlacek I, Holochova P, Sobotka R, Busse HJ, Svec P, Kralova S, Sedo O, Pilny J, Stankova E, Koublova V, Sedlar K.	Microbiol Spectr	10.1128/spectrum.00452-21	2021
Phylogeny	Pseudoalteromonas bacteriolytica sp. nov., a marine bacterium that is the causative agent of red spot disease of Laminaria japonica.	Sawabe T, Makino H, Tatsumi M, Nakano K, Tajima K, Iqbal MM, Yumoto I, Ezura Y, Christen R	Int J Syst Bacteriol	10.1099/00207713-48-3-769	1998