MiMeDB: Rhodobacter capsulatus SB1003 (MMDBm0002141)

Microbe Identification

Microbe name

Rhodobacter capsulatus SB1003

NCBI Taxonomy ID

272942

Microbe Taxonomy

Superkingdom

Bacteria

Kingdom

Eubacteria

Phylum

Proteobacteria

Class

Alphaproteobacteria

Order

Rhodobacterales

Family

Rhodobacteraceae

Genus

Rhodobacter

Species

capsulatus

Strain

Not Available

Microbe Properties

Gram staining properties

Positive

Shape

Bacilli

Mobility

Flagellar presence

Yes

Number of membranes

Oxygen preference

Aerobe; anaerobe

Optimal temperature

Temperature range

Mesophilic

Habitat

Multiple

Biotic relationship

Free living

Cell arrangement

Not Available

Sporulation

Nonsporulating

Metabolism

Not Available

Energy source

Phototroph

Host and Biospecimens

Host	Body site	Biospecimen	Details	Data Source	Reference
Human	Gut	Feces	Expected but not quantified

Health Effects

Host	Related Health Condition	Biospecimen	Microbal response/effect	Data Source	Reference

Related Metabolites

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0012903	Taurine	L-Alanine	Hypotaurine/taurine--pyruvate aminotransferase	Amine group addition	RHEA	34755880
MMDBr0012916	D-Glyceraldehyde 3-phosphate	aldehydo-D-ribose 5-phosphate	Transketolase	Transfer of ketol group	RHEA	34755880
MMDBr0012971	beta-D-Fructose 1,6-bisphosphate	beta-D-Fructose 6-phosphate	Fructose-1,6-bisphosphatase/inositol-1-monophosphatase	Aldol addition (or reverse); Dephosphorylation	RHEA	34755880
MMDBr0012988	5,6-Dimethylbenzimidazole	N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole	Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase	Transfer of a ribosyl group	RHEA	34755880
MMDBr0012996	(S)-Ureidoglycolic acid	glyoxylate	Ureidoglycolate lyase	Non-hydrolytic bond cleavage (or its reversal)	RHEA	34755880
MMDBr0013163	Glycine	5-Aminolevulinic acid	5-aminolevulinate synthase, mitochondrial	Synthesis	RHEA	34755880
MMDBr0013207	Sarcosine	Formaldehyde	Monomeric sarcosine oxidase	Oxidation	RHEA	34755880
MMDBr0013213	2-C-methyl-D-erythritol 4-phosphate	4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	Transfer of a cytidylyl group	RHEA	34755880
MMDBr0013269	Magnesium	Mg-protoporphyrin IX	Magnesium-chelatase 60 kDa subunit	Chelation	RHEA	34755880
MMDBr0013431	1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide	5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase	Isomerization	RHEA	34755880
MMDBr0013550	(S)-malyl-CoA	glyoxylate	Apparent malate synthase	Non-hydrolytic bond cleavage (or its reversal); Synthesis	RHEA	34755880
MMDBr0013672	Farnesyl pyrophosphate	(2E,6E,10E)-geranylgeranyl diphosphate	Variediene synthase	Synthesis; Reverse C-prenylation of phenalenone; Transfer of a prenyl group	RHEA	34755880
MMDBr0013708	Inosinic acid	Phosphoribosyl pyrophosphate	Hypoxanthine-guanine phosphoribosyltransferase	Transfer of phosphoribosyl group; Synthesis	RHEA	34755880
MMDBr0013709	Phosphoribosyl pyrophosphate	Inosinic acid	Hypoxanthine-guanine phosphoribosyltransferase	Transfer of a ribosyl group	RHEA	34755880
MMDBr0013717	alpha-Ketoglutarate	L-Glutamic acid	Acetylornithine aminotransferase	Amine group addition	RHEA	34755880
MMDBr0013851	heme b	heme b	Cytochrome c biogenesis ATP-binding export protein CcmA	Transport	RHEA	34755880
MMDBr0013905	(E)-4-coumarate	(E)-4-coumaroyl-CoA	4-coumarate--CoA ligase	Ligation	RHEA	34755880
MMDBr0014117	N-Acetyl-L-glutamate 5-semialdehyde	N-Acetyl-L-glutamyl 5-phosphate	Protein ARG5,6, mitochondrial	Reduction	RHEA	34755880
MMDBr0014135	S-Adenosylhomocysteine	Deoxyadenosine	Adenosylhomocysteinase	Reversible hydrolysis	RHEA	34755880
MMDBr0014165	Precorrin 4	Precorrin 5	Precorrin-4 C(11)-methyltransferase	Methylation	RHEA	34755880
MMDBr0014251	(6R)-5,10-methylene-5,6,7,8-tetrahydrofolic acid	5,10-Methenyltetrahydrofolate	C-1-tetrahydrofolate synthase, cytoplasmic	Synthesis	RHEA	34755880
MMDBr0014256	1-(5-phosphoribosyl)-ATP	1-(5-phosphoribosyl)-5'-AMP	Phosphoribosyl-ATP pyrophosphatase	Dephosphorylation; Synthesis	RHEA	34755880
MMDBr0014295	(2R)-3-phosphoglyceric acid	D-Ribulose 1,5-bisphosphate	Ribulose bisphosphate carboxylase large chain	Carboxylation	RHEA	34755880
MMDBr0014311	Isopentenyl pyrophosphate	Dimethylallylpyrophosphate	Isopentenyl-diphosphate Delta-isomerase	Isomerization	RHEA	34755880
MMDBr0014328	precorrin-6B	precorrin-6A	Precorrin-6A reductase	Reduction	RHEA	34755880
MMDBr0014340	1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate	(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate	Indole-3-glycerol phosphate synthase	Synthesis	RHEA	34755880
MMDBr0014369	5,10-Methenyltetrahydrofolate	(6S)-10-formyltetrahydrofolic acid	C-1-tetrahydrofolate synthase, cytoplasmic	Reversible cyclization	RHEA	34755880
MMDBr0014392	2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol	2-C-Methyl-D-erythritol-2,4-cyclodiphosphate	Bifunctional enzyme IspD/IspF	Synthesis	RHEA	34755880
MMDBr0014423	Acetyl phosphate	Sulfoacetaldehyde	Sulfoacetaldehyde acetyltransferase	N-Acetylation	RHEA	34755880
MMDBr0014556	GMP	Phosphoribosyl pyrophosphate	Hypoxanthine-guanine phosphoribosyltransferase	Transfer of a ribosyl group	RHEA	34755880
MMDBr0014557	Phosphoribosyl pyrophosphate	GMP	Hypoxanthine-guanine phosphoribosyltransferase	Transfer of a ribosyl group	RHEA	34755880
MMDBr0014629	Phytyl diphosphate	2-trans,6-trans,10-trans-Geranylgeranyl diphosphate	Geranylgeranyl diphosphate reductase	Reduction	RHEA	34755880
MMDBr0014669	FMNH2	5,6-Dimethylbenzimidazole	5,6-dimethylbenzimidazole synthase	Synthesis	RHEA	34755880
MMDBr0014768	propanoyl-CoA	Propanoyl phosphate	Phosphate propanoyltransferase	N-Acetylation	RHEA	34755880
MMDBr0015020	demethylspheroidene	S-Adenosylhomocysteine	Demethylspheroidene O-methyltransferase	Methylation	RHEA	34755880
MMDBr0015058	rhodopin	Lycopene	Acyclic carotenoid 1,2-hydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0015059	1,1'-dihydroxy-1,1',2,2'-tetrahydrolycopene	rhodopin	Acyclic carotenoid 1,2-hydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0015120	(6R)-NADHX	(6S)-NADHX	Bifunctional NAD(P)H-hydrate repair enzyme Nnr	Epimerization	RHEA	34755880
MMDBr0015125	(6R)-NADPHX	(6S)-NADPHX	Bifunctional NAD(P)H-hydrate repair enzyme Nnr	Epimerization	RHEA	34755880
MMDBr0015518	D-Ribulose 1,5-bisphosphate	(2R)-3-phosphoglyceric acid	Ribulose bisphosphate carboxylase large chain	Carboxylation	RHEA	34755880
MMDBr0015625	(2R,3S)-beta-methylmalyl-CoA	glyoxylate	L-malyl-CoA/beta-methylmalyl-CoA lyase	Non-hydrolytic bond cleavage (or its reversal)	RHEA	34755880
MMDBr0017979	Mg-protoporphyrin IX 13-monomethyl ester	3,8-divinyl protochlorophyllide a	Anaerobic magnesium-protoporphyrin IX monomethyl ester cyclase	Cycle formation	RHEA	34755880
MMDBr0017849	Hydrogenobyrinate	hydrogenobyrinate a,c-diamide	Hydrogenobyrinate a,c-diamide synthase	Synthesis	RHEA	34755880
MMDBr0017916	5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide	AICAR	Imidazole glycerol phosphate synthase subunit HisH	Synthesis	RHEA	34755880
MMDBr0024380	Iron(3+)	Hydrogen Ion	Ubiquinol-cytochrome c reductase iron-sulfur subunit	Reduction	RHEA	34755880
MMDBr0024546	(6R)-5,10-methylene-5,6,7,8-tetrahydrofolic acid	(6S)-5,6,7,8-tetrahydrofolic acid	Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO	Methylation	RHEA	34755880
MMDBr0024686	Nitrogen	Hydrogen	Nitrogenase iron protein	Nitrogen fixation	RHEA	34755880
MMDBr0024747	NADP(+)	Uridine 5'-monophosphate	Probable tRNA-dihydrouridine synthase	Synthesis	RHEA	34755880
MMDBr0024833	Tetra-mu3-sulfido-tetrairon(2+)	Tetra-mu3-sulfido-tetrairon(1+)	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein	Reduction	RHEA	34755880
MMDBr0024862	15-cis-phytoene	all-trans-neurosporene	Phytoene desaturase (neurosporene-forming)	Desaturation	RHEA	34755880
MMDBr0024867	rhodopin	(3E)-3,4-didehydrorhodopin	1-hydroxycarotenoid 3,4-desaturase	Desaturation	RHEA	34755880
MMDBr0024901	di-mu-Sulfido-diiron(1+)	di-mu-Sulfido-diiron(2+)	Spheroidene monooxygenase	Oxygenation	RHEA	34755880
MMDBr0024902	di-mu-Sulfido-diiron(1+)	di-mu-Sulfido-diiron(2+)	Spheroidene monooxygenase	Oxygenation	RHEA	34755880
MMDBr0024903	di-mu-Sulfido-diiron(1+)	di-mu-Sulfido-diiron(2+)	Spheroidene monooxygenase	Oxygenation	RHEA	34755880
MMDBr0024970	di-mu-Sulfido-diiron(2+)	di-mu-Sulfido-diiron(1+)	Chlorophyllide reductase subunit Z	Reduction	RHEA	34755880
MMDBr0025309	di-mu-Sulfido-diiron(2+)	di-mu-Sulfido-diiron(1+)	Chlorophyllide reductase subunit Z	Reduction	RHEA	34755880
MMDBr0025310	di-mu-Sulfido-diiron(2+)	di-mu-Sulfido-diiron(1+)	Chlorophyllide reductase subunit Z	Reduction	RHEA	34755880
MMDBr0025505	NAD	Uridine 5'-monophosphate	Probable tRNA-dihydrouridine synthase	Synthesis	RHEA	34755880
MMDBr0025777	(6R)-5,10-methylene-5,6,7,8-tetrahydrofolic acid	(6S)-5,6,7,8-tetrahydrofolic acid	Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO	Methylation	RHEA	34755880

Genome Data

Genome Link

Not Available

Genome Length

Not Available

# Predicted Proteins

GenBank Sequence Modification Date

17-FEB-2022

MiMeDB Deposition Date

Reference

PMID: 17704766

Source Links

GenBank