Micromonospora rifamycinica AM105 | Type strain | DSM 44983, CGMCC 4.2495, JCM 15474

Caption:

Medium 554 28°C

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

Culture medium

CZAPEK PEPTONE AGAR (DSMZ Medium 83)

Culture medium growth

Medium recipe at MediaDive

Culture medium link

Culture medium composition

Culture medium

N-Z-AMINE-MEDIUM (DSMZ Medium 554)

Culture medium growth

Medium recipe at MediaDive

Culture medium link

Culture medium composition

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

Culture medium growth

Medium recipe provided by DSMZ

Culture medium link

Culture medium

ISP 2

Culture medium growth

Culture medium composition

Culture medium

ISP 3

Culture medium growth

Culture medium composition

Culture medium

ISP 4

Culture medium growth

Culture medium composition

Culture medium

ISP 5

Culture medium growth

Culture medium composition

Culture medium

ISP 6

Culture medium growth

Culture medium composition

Culture medium

ISP 7

Culture medium growth

Culture medium composition

		Temperature
[Ref.: #12141]	growth	28 °C
[Ref.: #20148]	optimum	28 °C
[Ref.: #31840]	growth	20-37 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #12141]	Temperature range	mesophilic
[Ref.: #20148]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31840]

Oxygen tolerance

aerobe

[Ref.: #31840]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.665

What are isolation sources categories?

Name of produced compound

refamycin

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31840]		NaCl		growth	0-3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #20148]	arabinose ChEBI	+
[Ref.: #20148]	cellulose ChEBI	+
[Ref.: #20148]	fructose ChEBI	+
[Ref.: #20148]	glucose ChEBI	+
[Ref.: #31840]	glucose ChEBI	+	carbon source
[Ref.: #20148]	mannitol ChEBI	-
[Ref.: #20148]	myo-inositol ChEBI	-
[Ref.: #31840]	nitrate ChEBI	+	reduction
[Ref.: #20148]	raffinose ChEBI	-
[Ref.: #20148]	rhamnose ChEBI	-
[Ref.: #20148]	sucrose ChEBI	+
[Ref.: #20148]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #67770]		rifamycin S ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	+	3.2.1.31	* from API zym
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #20148]	929	not determinedn.d.	+	+	+	-	+	-	-	+	-	+	+	+	+	+	+	+	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	urea cycle	84.62	11 of 13
[Ref.: #66794]	methionine metabolism	80.77	21 of 26
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	3-phenylpropionate degradation	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	oxidative phosphorylation	71.43	65 of 91
[Ref.: #66794]	degradation of pentoses	71.43	20 of 28
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	octane oxidation	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]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	carotenoid biosynthesis	63.64	14 of 22
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	glycine metabolism	60	6 of 10
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	elloramycin biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	aclacinomycin biosynthesis	57.14	4 of 7
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	androgen and estrogen metabolism	56.25	9 of 16
[Ref.: #66794]	daunorubicin biosynthesis	55.56	5 of 9
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
		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.: #12141]	Sample type/isolated from	marine mangrove sediment
[Ref.: #12141]	Geographic location (country and/or sea, region)	Hainan
[Ref.: #12141]	Country	China
[Ref.: #12141]	Country ISO 3 Code	CHN
[Ref.: #12141]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Mangrove sediment
[Ref.: #67770]	Geographic location (country and/or sea, region)	South China Sea
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Mangrove
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

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

[Ref.: #12141]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #20148]	Biosafety level	1	German classification

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.: #12141]	Micromonospora rifamycinica strain AM105 16S ribosomal RNA gene, partial sequence	AY561829	1475	ENA	291594 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Micromonospora rifamycinica AM105	GCA_001542325	contig	GenBank	291594 tax ID
[Ref.: #66792]	Micromonospora rifamycinica DSM 44983	GCA_900090265	chromosome	GenBank	291594 tax ID	*
[Ref.: #66792]	Micromonospora rifamycinica strain DSM 44983	291594.5	complete	PATRIC	291594 tax ID	*
[Ref.: #66792]	Micromonospora rifamycinica DSM 44983	2623620551	draft	JGI IMG/M	291594 tax ID	*
[Ref.: #66792]	Micromonospora rifamycinica AM105	2728369151	draft	JGI IMG/M	291594 tax ID	*

[Ref.: #12141]	GC-content	71 mol%
[Ref.: #67770]	GC-content	71 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	72.99 mol%	genome sequence analysis

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: Micromonospora rifamycinica strain DSM 44983 PATRIC: 291594.5
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Micromonospora rifamycinica strain DSM 44983 PATRIC: 291594.5
[Ref.: #69480]	gram-positive	yes	89.309	yes
[Ref.: #69480]	anaerobic	no	99.503	yes
[Ref.: #69480]	halophile	no	94.556	no
[Ref.: #69480]	spore-forming	yes	96.7	yes
[Ref.: #69480]	glucose-util	yes	88.03	no
[Ref.: #69480]	motile	no	94.814	no
[Ref.: #69480]	flagellated	no	97.667	no
[Ref.: #69480]	aerobic	yes	94.764	yes
[Ref.: #69480]	thermophile	no	98.223	yes
[Ref.: #69480]	glucose-ferment	no	90.205	no

Availability in culture collections External links