Aminobacterium colombiense (DSM 12261, ALA-1)

Cell morphology

Multimedia

• @ref:	66793
  manual_annotation:	1
  multimedia content:	EM_DSM_12261_1.jpg
  multimedia.multimedia content:	EM_DSM_12261_1.jpg
  caption:	electron microscopic image
  intellectual property rights:	© HZI/Manfred Rohde

Culture medium

@ref	Name	Growth	Medium link	Composition
4661	AMINOMONAS MEDIUM (DSMZ Medium 846)		Medium recipe at MediaDive	Name: AMINOMONAS MEDIUM (DSMZ Medium 846) Composition: Yeast extract 1.99402 g/l Na2CO3 1.49551 g/l L-Serine 1.04686 g/l NaCl 0.997009 g/l Na2S x 9 H2O 0.498504 g/l KCl 0.498504 g/l L-Cysteine HCl x H2O 0.498504 g/l MgCl2 x 6 H2O 0.398804 g/l KH2PO4 0.299103 g/l NH4Cl 0.299103 g/l K2HPO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

Culture temp

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	threonine metabolism	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CMP-KDO biosynthesis	100	4 of 4
66794	palmitate biosynthesis	95.45	21 of 22
66794	lipid A biosynthesis	88.89	8 of 9
66794	peptidoglycan biosynthesis	80	12 of 15
66794	hydrogen production	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	citric acid cycle	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	d-mannose degradation	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	glutamate and glutamine metabolism	75	21 of 28
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	NAD metabolism	72.22	13 of 18
66794	photosynthesis	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	phenylalanine metabolism	69.23	9 of 13
66794	purine metabolism	67.02	63 of 94
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	alanine metabolism	65.52	19 of 29
66794	histidine metabolism	65.52	19 of 29
66794	glycolysis	64.71	11 of 17
66794	proline metabolism	63.64	7 of 11
66794	isoleucine metabolism	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	leucine metabolism	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	starch degradation	60	6 of 10
66794	Entner Doudoroff pathway	60	6 of 10
66794	methylglyoxal degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	methionine metabolism	57.69	15 of 26
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	oxidative phosphorylation	57.14	52 of 91
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	pentose phosphate pathway	54.55	6 of 11
66794	lysine metabolism	52.38	22 of 42
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	tetrahydrofolate metabolism	50	7 of 14
66794	non-pathway related	50	19 of 38
66794	ethanol fermentation	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	lactate fermentation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	glycine metabolism	50	5 of 10
66794	glutathione metabolism	50	7 of 14
66794	biotin biosynthesis	50	2 of 4
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	valine metabolism	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	allantoin degradation	44.44	4 of 9
66794	chorismate metabolism	44.44	4 of 9
66794	degradation of sugar acids	44	11 of 25
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	tryptophan metabolism	42.11	16 of 38
66794	arginine metabolism	41.67	10 of 24
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	gallate degradation	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	degradation of sugar alcohols	37.5	6 of 16
66794	ketogluconate metabolism	37.5	3 of 8
66794	tyrosine metabolism	35.71	5 of 14
66794	lipid metabolism	35.48	11 of 31
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	nitrate assimilation	33.33	3 of 9
66794	sulfate reduction	30.77	4 of 13
66794	polyamine pathway	26.09	6 of 23
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	degradation of pentoses	25	7 of 28
66794	ascorbate metabolism	22.73	5 of 22

Oxygen tolerance

Isolation source categories

Isolation

Taxonmaps

69479

Global distribution of 16S sequence AF069287 (>99% sequence identity) for Aminobacterium colombiense subclade from Microbeatlas

Aquatic Samples	111
Soil Samples	6
Animal Samples	1
Plant Samples	1
Total Samples	119

Risk assessment

GC content

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4661	Aminobacterium colombiense 16S ribosomal RNA gene, partial sequence	AF069287	1519		572547

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Aminobacterium colombiense DSM 12261	GCA_000025885	complete		572547
66792	Aminobacterium colombiense DSM 12261	572547.3	complete	PATRIC	572547
66792	Aminobacterium colombiense ALA-1, DSM 12261	646564503	complete	JGI IMG/M	572547

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete genome sequence of Aminobacterium colombiense type strain (ALA-1).	Chertkov O, Sikorski J, Brambilla E, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Spring S, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP	Stand Genomic Sci	10.4056/sigs.902116	2010
Phylogeny	Aminobacterium colombiensegen. nov. sp. nov., an amino acid-degrading anaerobe isolated from anaerobic sludge.	Baena S, Fardeau ML, Labat M, Ollivier B, Thomas P, Garcia JL, Patel BK	Anaerobe	10.1006/anae.1998.0170	1998

Straininfo Link

@ref	Straininfo	Culture collections
86758	49260	DSM 12261

Culture collection no.