Paracoccus denitrificans PD1222

Gram-negativeBacilliNon-motileAerobic

Kingdom

Pseudomonadati

Phylum

Pseudomonadota

Class

Alphaproteobacteria

Order

Rhodobacterales

Family

Paracoccaceae

Genus

Paracoccus

Description

Paracoccus denitrificans PD1222 is a Gram-negative, aerobic bacterium characterized by its bacilli shape and the presence of flagella, although it is non-motile. This organism typically exists in various habitats, indicating its adaptability to different environmental conditions. It can be found as singles, pairs, or clusters, demonstrating a versatile cell arrangement. P. denitrificans PD1222 is a mesophilic organism, with an optimal growth temperature of 25°C, and it operates effectively within a temperature range that accommodates typical mesophilic conditions. The bacterium possesses three replicons and has a double-membrane structure, which is a common feature among Gram-negative bacteria. As a free-living organism, P. denitrificans PD1222 does not exhibit pathogenicity nor does it undergo sporulation. Its ecological role may be significant in biogeochemical cycles, particularly in the nitrogen cycle, where denitrification processes are critical for converting nitrates to nitrogen gas, thus reducing nutrient loading in various environments. This trait underscores the potential of P. denitrificans PD1222 in environmental biotechnology applications, particularly in bioremediation and nutrient management in agricultural systems. The specific accession numbers for genetic studies of this strain are NC_008686.1, NC_008687.1, and NC_008688.1, which facilitate further research into its genomic characteristics and functionalities.

Taxonomy

KingdomPseudomonadati
PhylumPseudomonadota
ClassAlphaproteobacteria
OrderRhodobacterales
FamilyParacoccaceae
GenusParacoccus
SpeciesParacoccus denitrificans
StrainPD1222

Profile

Physiology
Gram staining propertiesNegative
ShapeBacilli
MobilityNo
Flagellar presenceYes
Number of membranes2
Image of Paracoccus denitrificans PD1222
AI-generated image based on bacteria physiology
Ecology, Host, and Life Cycle
Oxygen requirementsAerobic
Optimal temperature25
Temperature rangeMesophilic
HabitatMultiple
Biotic relationshipFree living
Host(s)Not Available
Cell arrangementSingles- Pairs- Clusters
SporulationNonsporulating
Energy sourceNot Available
PathogenicityNo

Genome Summary

Paracoccus denitrificans PD1222 chromosome 2, complete sequence.

Gene Summary

Adenine Count

Not Available

Thymine Count

Not Available

Guanine Count

Not Available

Cytosine Count

Not Available

Genome Length

Not Available

Protein-coding Genes

1657 genes

Non-Coding Genes

68 genes

# of Chromosomes/Plasmids

3

Genes

NameLocus TagUniProt IDStrand OrientationGene Start/EndProtein Molecular Weight
iron-sulfur cluster repair di-iron proteinPDEN_RS15090Not AvailablePositive201003 - 20167424855.9
hexameric tyrosine-coordinated heme proteinPDEN_RS15095Not AvailablePositive201788 - 20211111369.5
carboxymuconolactone decarboxylase family proteinPDEN_RS15100Not AvailablePositive202131 - 20246911735.2
cytochrome c oxidase subunit 1PDEN_RS15105Not AvailablePositive202683 - 20435362278.4
tonb-dependent siderophore receptorPDEN_RS15110Not AvailablePositive204599 - 20693284132.3
class i sam-dependent methyltransferasePDEN_RS15115Not AvailablePositive206944 - 20776830183.1
feccd family abc transporter permeasePDEN_RS15120Not AvailablePositive207773 - 20878635200.5
abc transporter atp-binding proteinPDEN_RS15125Not AvailablePositive208783 - 20955327474.9
abc transporter substrate-binding proteinPDEN_RS15130Not AvailablePositive209564 - 21060138692.4
butyrate--acetoacetate coa-transferasePDEN_RS27025Not AvailableNegative211066 - 2112215358.54

Displaying genes 271 – 280 of 5238 in total

Metabolites

1787 records
Metabolite IDMetabolite nameStructureCAS number
BASm0000237(R)-4'-phosphopantothenateC9H18NO8PChemical structure of (R)-4'-phosphopantothenateNot available
Average299.2149Da
Monoisotopic299.0770031Da
BASm00002502,5-didehydro-D-gluconateC6H7O7Chemical structure of 2,5-didehydro-D-gluconate53736-12-2
Average191.1156Da
Monoisotopic191.019177578Da
BASm00002512-dehydropantoateC6H9O4Chemical structure of 2-dehydropantoateNot available
Average145.1333Da
Monoisotopic145.050083776Da
BASm00002532-oxopent-4-enoateC5H5O3Chemical structure of 2-oxopent-4-enoateNot available
Average113.093Da
Monoisotopic113.024417601Da
BASm00002603alpha,7alpha-dihydroxy-12-oxo-5beta-cholanateC24H37O5Chemical structure of 3alpha,7alpha-dihydroxy-12-oxo-5beta-cholanateNot available
Average405.556Da
Monoisotopic405.264647871Da
BASm0000274aldehydo-D-galacturonateC6H9O7Chemical structure of aldehydo-D-galacturonateNot available
Average193.132Da
Monoisotopic193.0353762Da
BASm0000387(6R)-5,10-methylene-5,6,7,8-tetrahydrofolateC20H21N7O6Chemical structure of (6R)-5,10-methylene-5,6,7,8-tetrahydrofolateNot available
Average455.432Da
Monoisotopic455.1564286Da
BASm0000401(S)-2-succinylamino-6-oxoheptanedioateC11H12NO8Chemical structure of (S)-2-succinylamino-6-oxoheptanedioateNot available
Average286.218Da
Monoisotopic286.0579371Da
BASm00004283-oxoadipateC6H6O5Chemical structure of 3-oxoadipateNot available
Average158.11Da
Monoisotopic158.022620453Da
BASm00005166-deoxyerythronolide BC21H38O6Chemical structure of 6-deoxyerythronolide BNot available
Average386.5228Da
Monoisotopic386.2668389Da

Displaying 1–10 of 1787 metabolites

Health Effects

No health effects information available for this bacterium.