Name: Chondromyces crocatus Cm c5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 12016

Type strain:

Species: Chondromyces crocatus

Strain Designation: Cm c5

Culture col. no.: DSM 14714, JCM 12616

Strain history: DSM 14714 <-- H. Reichenbach Cm c5.

NCBI tax ID(s): 52 (species)

SI-ID 297613

DSM 14714, JCM 12616

Other strains from Chondromyces crocatus

C. crocatus Cm c2, DSM 14606

Section

Chondromyces crocatus Cm c5 is a spore-forming, mesophilic, Gram-negative bacterium that was isolated from soil.

Gram-negative
spore-forming
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	*Deltaproteobacteria*
	Order	*Myxococcales*
	Family	*Polyangiaceae*
	Genus	*Chondromyces*
	Species	**Chondromyces crocatus**
	Full Scientific Name (LPSN)	Chondromyces crocatus Berkeley and Curtis 1874 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.945

Multimedia content

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Caption:

swarm on agar medium 9

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

CY-AGAR (DSMZ Medium 67)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

VY/2 AGAR (DSMZ Medium 9)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5499]			growth	30 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #5499]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	yes Confidence in %93
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.252

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	alanine metabolism	93.1	27 of 29
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	glycolysis	88.24	15 of 17
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	urea cycle	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	lysine metabolism	76.19	32 of 42
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	70.59	12 of 17
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	polyamine pathway	69.57	16 of 23
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	ascorbate metabolism	59.09	13 of 22
[Ref.: #66794]	oxidative phosphorylation	57.14	52 of 91
[Ref.: #66794]	mevalonate metabolism	57.14	4 of 7
[Ref.: #66794]	androgen and estrogen metabolism	56.25	9 of 16
[Ref.: #66794]	allantoin degradation	55.56	5 of 9
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	arachidonic acid metabolism	50	9 of 18
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	daunorubicin biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	vitamin B12 metabolism	26.47	9 of 34
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
		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.: #5499]	Sample type/isolated from	soil
[Ref.: #5499]	Geographic location (country and/or sea, region)	Parana
[Ref.: #5499]	Country	Brazil
[Ref.: #5499]	Country ISO 3 Code	BRA
[Ref.: #5499]	Continent	Middle and South America

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Country	Brazil
[Ref.: #67770]	Country ISO 3 Code	BRA
[Ref.: #67770]	Continent	Middle and South America
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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

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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.: #5499]	Chondromyces crocatus strain Cm c5 16S ribosomal RNA gene, partial sequence	GU207874	1497	ENA	52 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Chondromyces crocatus Cm c5	GCA_001189295	complete	GenBank	52 tax ID	*
[Ref.: #66792]	Chondromyces crocatus strain Cm c5	52.12	complete	PATRIC	52 tax ID	*
[Ref.: #66792]	Chondromyces crocatus Cm c5	2648501185	complete	JGI IMG/M	52 tax ID	*
[Ref.: #66792]	Chondromyces crocatus Cm c5	2582581503	draft	JGI IMG/M	52 tax ID	*

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: Chondromyces crocatus Cm c5 NCBI: GCA_001189295.1
[Ref.: #69481]	spore-forming	yes	93	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Chondromyces crocatus Cm c5 NCBI: GCA_001189295.1
[Ref.: #69480]	motile	no	81.961	no
[Ref.: #69480]	flagellated	no	95.695	no
[Ref.: #69480]	gram-positive	no	93.067	no
[Ref.: #69480]	anaerobic	no	97.06	no
[Ref.: #69480]	aerobic	yes	83.491	no
[Ref.: #69480]	halophile	no	88.172	no
[Ref.: #69480]	spore-forming	no	73.92	no
[Ref.: #69480]	thermophile	no	99.149	no
[Ref.: #69480]	glucose-util	yes	79.729	no
[Ref.: #69480]	glucose-ferment	no	90.868	no

Availability in culture collections External links

[Ref.: #5499]

Culture collection no.

DSM 14714, JCM 12616

[Ref.: #81235]

SI-ID 297613

Literature:

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

Topic	Title	Authors	Journal	DOI	Year
Genetics	Crocadepsins-Depsipeptides from the Myxobacterium Chondromyces crocatus Found by a Genome Mining Approach.	Surup F, Viehrig K, Rachid S, Plaza A, Maurer CK, Hartmann RW, Muller R	ACS Chem Biol	10.1021/acschembio.7b00900	2017	*
Metabolism	Structure and Biosynthesis of Crocagins: Polycyclic Posttranslationally Modified Ribosomal Peptides from Chondromyces crocatus.	Viehrig K, Surup F, Volz C, Herrmann J, Abou Fayad A, Adam S, Kohnke J, Trauner D, Muller R	Angew Chem Int Ed Engl	10.1002/anie.201612640	2017	*
Metabolism	Genome Analysis of the Fruiting Body-Forming Myxobacterium Chondromyces crocatus Reveals High Potential for Natural Product Biosynthesis.	Zaburannyi N, Bunk B, Maier J, Overmann J, Muller R	Appl Environ Microbiol	10.1128/AEM.03011-15	2016	*
Metabolism	Biosynthesis of crocacin involves an unusual hydrolytic release domain showing similarity to condensation domains.	Muller S, Rachid S, Hoffmann T, Surup F, Volz C, Zaburannyi N, Muller R	Chem Biol	10.1016/j.chembiol.2014.05.012	2014	*
Phylogeny	Designation of type strains for seven species of the order Myxococcales and proposal for neotype strains of Cystobacter ferrugineus, Cystobacter minus and Polyangium fumosum.	Lang E, Reichenbach H	Int J Syst Evol Microbiol	10.1099/ijs.0.056440-0	2013	*
Phylogeny	An unusual thioesterase promotes isochromanone ring formation in ajudazol biosynthesis.	Buntin K, Weissman KJ, Muller R	Chembiochem	10.1002/cbic.200900712	2010	*
Metabolism	Biosynthesis of thuggacins in myxobacteria: comparative cluster analysis reveals basis for natural product structural diversity.	Buntin K, Irschik H, Weissman KJ, Luxenburger E, Blocker H, Muller R	Chem Biol	10.1016/j.chembiol.2010.02.013	2010	*
Metabolism	Characterization of a novel type of oxidative decarboxylase involved in the biosynthesis of the styryl moiety of chondrochloren from an acylated tyrosine.	Rachid S, Revermann O, Dauth C, Kazmaier U, Muller R	J Biol Chem	10.1074/jbc.M109.079707	2010	*
Metabolism	Unusual chemistry in the biosynthesis of the antibiotic chondrochlorens.	Rachid S, Scharfe M, Blocker H, Weissman KJ, Muller R	Chem Biol	10.1016/j.chembiol.2008.11.005	2009	*
Metabolism	Biosynthesis of (R)-beta-tyrosine and its incorporation into the highly cytotoxic chondramides produced by Chondromyces crocatus.	Rachid S, Krug D, Weissman KJ, Muller R	J Biol Chem	10.1074/jbc.M703439200	2007	*
Genetics	Molecular and biochemical studies of chondramide formation-highly cytotoxic natural products from Chondromyces crocatus Cm c5.	Rachid S, Krug D, Kunze B, Kochems I, Scharfe M, Zabriskie TM, Blocker H, Muller R	Chem Biol	10.1016/j.chembiol.2006.06.002	2006	*
Metabolism	The biosynthesis of branched dialkylpyrazines in myxobacteria.	Nawrath T, Dickschat JS, Kunze B, Schulz S	Chem Biodivers	10.1002/cbdv.201000158	2010	*

References

#5499

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14714

#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 )

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#81235

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-ID297613.1 )

* These data were automatically processed and therefore are not curated

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