Paracoccus denitrificans

BacilliNon-motilefacultative anaerobe

Kingdom

Pseudomonadati

Phylum

Pseudomonadota

Class

Alphaproteobacteria

Order

Rhodobacterales

Family

Paracoccaceae

Genus

Paracoccus

Description

Paracoccus denitrificans is a Gram-negative, bacilli-shaped bacterium that is characterized by its ability to form singles, pairs, and clusters. This organism is non-motile and possesses flagella, though its mobility is not active. It thrives in mesophilic conditions, with an optimal growth temperature of 25°C. The genome of Paracoccus denitrificans contains three replicons, a trait that is indicative of its genetic complexity and adaptability. As a free-living bacterium, it occupies diverse ecological niches and plays a significant role in nitrogen cycling processes, particularly denitrification. This metabolic pathway is crucial for the conversion of nitrates to nitrogen gas, contributing to the regulation of nitrogen levels in various environments. The genetic accessions for Paracoccus denitrificans, CP035090.1, CP035091.1, and CP035092.1, provide insight into its genomic structure and potential functionalities, further emphasizing its ecological importance. Understanding the traits of Paracoccus denitrificans helps elucidate its role in biogeochemical cycles, particularly in soil and aquatic systems where it may contribute to nutrient cycling and ecosystem health.

Taxonomy

KingdomPseudomonadati
PhylumPseudomonadota
ClassAlphaproteobacteria
OrderRhodobacterales
FamilyParacoccaceae
GenusParacoccus
SpeciesParacoccus denitrificans
StrainNo strain

Profile

Physiology
Gram staining propertiesNegative
ShapeBacilli
MobilityNo
Flagellar presenceYes
Number of membranesNot Available
Image of Paracoccus denitrificans
AI-generated image based on bacteria physiology
Ecology, Host, and Life Cycle
Oxygen requirementsfacultative anaerobe
Optimal temperature25
Temperature rangeMesophilic
Habitatmangrove soil; Sundarbans mangrove
Biotic relationshipFree living
Host(s)Not Available
Cell arrangementSingles- Pairs- Clusters
SporulationNot Available
Energy sourceNot Available
PathogenicityNot Available

Genome Summary

MAG: Paracoccus denitrificans isolate S2_018_000_R3_116

Gene Summary

Adenine Count

567522 bp

Thymine Count

565294 bp

Guanine Count

984848 bp

Cytosine Count

978486 bp

Genome Length

3096150 bp

Protein-coding Genes

2923 genes

Non-Coding Genes

131 genes

# of Chromosomes/Plasmids

1

Genes

NameLocus TagUniProt IDStrand OrientationGene Start/EndProtein Molecular Weight
fe3+/spermidine/putrescine abc transporter atp-binding proteinDI498_11385Not AvailablePositive2320956 - 232203539158.4
trimeric intracellular cation channel family proteinDI498_11390Not AvailableNegative2322040 - 232268722570.3
ribonuclease hiDI498_11395Not AvailableNegative2322684 - 232313316383.3
glutathione s-transferaseDI498_11400Not AvailableNegative2323197 - 232380221966.4
4-hydroxy-3-methylbut-2-enyl diphosphate reductaseDI498_11405Not AvailableNegative2323811 - 232476134245.2
nyn domain-containing proteinDI498_11410Not AvailableNegative2324803 - 232535721117.3
2-amino-4-hydroxy-6- hydroxymethyldihydropteridine diphosphokinaseDI498_11415Not AvailablePositive2325408 - 232598620246.3
dna-directed rna polymerase subunit omegaDI498_11420Not AvailablePositive2326054 - 232641013272.8
bifunctional (p)ppgpp synthetase/guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolaseDI498_11425Not AvailablePositive2326438 - 232858880538.7
hypothetical proteinDI498_11430Not AvailablePositive2328745 - 232936122183.4

Displaying genes 2301 – 2310 of 3054 in total

Pathways

0 pathways

No pathways found

No metabolic pathways have been associated with this bacterium yet.

Metabolites

98 records
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Result columns

Structure search compares stored SMILES, InChI, and InChIKey text. Exact mass must match the stored database value.

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Metabolite IDMetabolite nameStructureCAS number
Average massMonoisotopic mass
BASm0001661Cu(2+)CuChemical structure of Cu(2+)7440-50-8
Average63.546Da
Monoisotopic62.929601079Da
BASm0001865diphosphateHO7P2Chemical structure of diphosphateNot available
Average174.95Da
Monoisotopic174.9213971Da
BASm0002002glyoxylateC2HO3Chemical structure of glyoxylateNot available
Average73.0275Da
Monoisotopic72.9925689Da
BASm0002529(3S)-3-hydroxy-L-aspartateC4H6NO5Chemical structure of (3S)-3-hydroxy-L-aspartateNot available
Average148.095Da
Monoisotopic148.0251459Da
BASm0003389NADP(+)C21H25N7O17P3Chemical structure of NADP(+)Not available
Average740.386Da
Monoisotopic740.053624107Da
BASm0003997Fe(II)-heme oC49H56FeN4O5Chemical structure of Fe(II)-heme oNot available
Average836.856Da
Monoisotopic836.361104Da
BASm0004030(3S)-3-hydroxy-D-aspartateC4H6NO5Chemical structure of (3S)-3-hydroxy-D-aspartateNot available
Average148.095Da
Monoisotopic148.025145877Da
BASm00055001-octadecanoyl-sn-glycero-3-phosphateC21H41O7PChemical structure of 1-octadecanoyl-sn-glycero-3-phosphateNot available
Average436.5198Da
Monoisotopic436.2589902Da
BASm0012554N-acetyl-beta-D-glucosaminyl-(1->4)-1,6-anhydro-N-acetyl-beta-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-diaminoheptanedioate-D-alanineC37H57N7O20Not availableNot available
Average919.893Da
Monoisotopic919.366934423Da
BASm0014032Acetic acidC2H4O2Chemical structure of Acetic acid64-19-7
Average60.052Da
Monoisotopic60.021129372Da

Displaying 1–10 of 98 metabolites

Health Effects

No health effects information available for this bacterium.