Paracoccus denitrificans

Kingdom

Pseudomonadati

Phylum

Pseudomonadota

Class

Alphaproteobacteria

Order

Rhodobacterales

Family

Paracoccaceae

Genus

Paracoccus

Description

Paracoccus denitrificans is a Gram-negative bacterium renowned for its versatile metabolic capabilities, particularly in the context of nitrogen cycling. This microbe is primarily characterized by its ability to perform denitrification, a process in which nitrate is reduced to nitrogen gas, thus playing a significant role in soil and aquatic ecosystems by contributing to the nitrogen cycle. P. denitrificans is typically found in various environments, including soil and water, where it participates actively in nutrient cycling. Its metabolic versatility allows it to thrive under both aerobic and anaerobic conditions, making it an important organism for studies related to environmental microbiology and biogeochemical cycles. The bacterium's cellular structure, typical of Gram-negative organisms, is defined by a thin peptidoglycan layer sandwiched between an inner and an outer membrane. This unique cell wall composition is crucial for its interaction with the environment and its ability to withstand various environmental stresses. Moreover, P. denitrificans serves as a model organism for understanding the biochemical pathways involved in denitrification and the broader implications of these processes on ecosystem functioning and nitrogen availability. Its metabolic flexibility not only enhances our understanding of microbial ecology but also presents potential applications in bioremediation and agricultural practices aimed at managing nitrogen levels in various habitats.

Taxonomy

KingdomPseudomonadati
PhylumPseudomonadota
ClassAlphaproteobacteria
OrderRhodobacterales
FamilyParacoccaceae
GenusParacoccus
SpeciesParacoccus denitrificans
StrainNo strain

Profile

Physiology
Gram staining propertiesNegative
ShapeNot Available
MobilityNot Available
Flagellar presenceNot Available
Number of membranesNot Available
Ecology, Host, and Life Cycle
Oxygen requirementsNot Available
Optimal temperatureNot Available
Temperature rangeNot Available
Habitatmangrove soil; Sundarbans mangrove
Biotic relationshipNot Available
Host(s)Not Available
Cell arrangementNot Available
SporulationNot Available
Energy sourceNot Available
PathogenicityNot Available

Genome Summary

Paracoccus denitrificans

Accession NumberQFMZ00000000.1

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 TagUniProtStrandCoordinatesMolecular Weight
Large packaging proteinDI498_09475Not Available+1943709 - 194500447243.3
Portal proteinDI498_09480Not Available+1945075 - 194628042982.2
hypothetical proteinDI498_09485Not Available+1946284 - 19465148931.93
Putative prohead proteaseDI498_09490Not Available+1946520 - 194705619038.1
Phage major capsid proteinDI498_09495Not Available+1947087 - 194825041038.7
Dna packaging/head-tail-connectorDI498_09500Not Available+1948402 - 194901021662.5
phage tail proteinDI498_09505Not Available+1949007 - 194934212088.5
duf3168 domain-containing proteinDI498_09510Not Available+1949339 - 194976714585.1
Gene transfer aget (gta) orfg9-like phage major tail proteinDI498_09515Not Available+1949780 - 195025016635.5
hypothetical proteinDI498_09520Not Available+1950247 - 195055510130.2

Displaying genes 1 – 10 of 3054 in total

Pathways

0 pathways

No pathways found

No metabolic pathways have been associated with this bacterium yet.

Metabolites

86 records
Metabolite IDMetabolite nameStructureCAS number
BASm0001865diphosphateHO7P2Chemical structure of diphosphateNot available
Average174.95Da
Monoisotopic174.9213971Da
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
BASm0014033AmmoniaH3NChemical structure of Ammonia7664-41-7
Average17.0305Da
Monoisotopic17.026549101Da
BASm0014041Oleic acidC18H34O2Chemical structure of Oleic acid112-80-1
Average282.4614Da
Monoisotopic282.255880332Da
BASm0014058Myristic acidC14H28O2Chemical structure of Myristic acid544-63-8
Average228.3709Da
Monoisotopic228.20893014Da
BASm0014182Vaccenic acidC18H34O2Chemical structure of Vaccenic acidNULL
Average282.468Da
Monoisotopic282.255880335Da
BASm0014219Palmitoleic acidC16H30O2Chemical structure of Palmitoleic acidNULL
Average254.4082Da
Monoisotopic254.224580204Da
BASm0014222DiethanolamineC4H11NO2Chemical structure of DiethanolamineNULL
Average105.1356Da
Monoisotopic105.078978601Da

Displaying 1–10 of 86 metabolites