Pedobacter heparinus DSM 2366

Gram-negativeBacilliNon-motileAerobic

Kingdom

Pseudomonadati

Phylum

Bacteroidota

Class

Sphingobacteriia

Order

Sphingobacteriales

Family

Sphingobacteriaceae

Genus

Pedobacter

Description

Pedobacter heparinus DSM 2366 is a Gram-negative, mesophilic bacterium characterized by its bacilli shape and aerobic metabolism, functioning as a chemoorganotroph. This organism is notable for its free-living lifestyle, indicating that it does not form symbiotic or pathogenic relationships with other organisms. One significant feature of P. heparinus is its non-motility, despite possessing flagella, suggesting that these structures may not be used for movement but could have other roles, such as adherence or environmental sensing. With a single replicon and a double membrane structure, Pedobacter heparinus is adapted to its terrestrial habitat. The bacterium thrives in environments with moderate temperatures, aligning with its mesophilic classification. Its aerobic nature indicates a reliance on oxygen for energy production, which is typical for many bacteria in terrestrial ecosystems. The absence of pathogenicity suggests that P. heparinus may play a role in nutrient cycling or the decomposition of organic matter in soil environments, contributing to ecosystem processes. Its ability to utilize organic compounds for energy positions it as an important player in the microbial community, likely aiding in the breakdown of complex organic materials and enhancing soil health. The accession number NC_013061.1 provides a reference for further genomic studies, which could elucidate the specific metabolic pathways and ecological functions of this bacterium.

Taxonomy

KingdomPseudomonadati
PhylumBacteroidota
ClassSphingobacteriia
OrderSphingobacteriales
FamilySphingobacteriaceae
GenusPedobacter
SpeciesPedobacter heparinus
StrainDSM 2366

Profile

Physiology
Gram staining propertiesNegative
ShapeBacilli
MobilityNo
Flagellar presenceYes
Number of membranes2
Image of Pedobacter heparinus DSM 2366
AI-generated image based on bacteria physiology
Ecology, Host, and Life Cycle
Oxygen requirementsAerobic
Optimal temperatureNot Available
Temperature rangeMesophilic
HabitatTerrestrial
Biotic relationshipFree living
Host(s)Not Available
Cell arrangementNot Available
SporulationNonsporulating
Energy sourceChemoorganotroph
PathogenicityNo

Genome Summary

Pedobacter heparinus DSM 2366


Gene Summary

Adenine Count

1491779 bp

Thymine Count

1502777 bp

Guanine Count

1083931 bp

Cytosine Count

1088896 bp

Genome Length

5167383 bp

Protein-coding Genes

4228 genes

Non-Coding Genes

57 genes

# of Chromosomes/Plasmids

1

Genes

NameLocus TagUniProt IDStrand OrientationGene Start/EndProtein Molecular Weight
aspartyl protease family proteinPHEP_RS00005Not AvailablePositive19 - 126045935.4
phosphodiester glycosidase family proteinPHEP_RS00010Not AvailablePositive1284 - 215331550.9
hypothetical proteinPHEP_RS00015Not AvailablePositive2155 - 310236234.5
cold-shock proteinPHEP_RS00020Not AvailablePositive3200 - 33916960.28
glycerophosphodiester phosphodiesterasePHEP_RS00025Not AvailableNegative3460 - 425729956.4
duf4175 family proteinPHEP_RS00030Not AvailablePositive4414 - 7722125551.0
rrna maturation rnase ybeyPHEP_RS00035Not AvailablePositive7733 - 816116434.7
abc-f family atp-binding cassette domain-containing proteinPHEP_RS00040Not AvailablePositive8282 - 1014470814.7
trna uridine-5-carboxymethylaminomethyl(34) synthesis enzyme mnmgPHEP_RS00045Not AvailablePositive10253 - 1211569300.2
ig-like domain-containing proteinPHEP_RS00050Not AvailablePositive12319 - 1388759412.1

Displaying genes 1 – 10 of 4285 in total

Metabolites

224 records
Metabolite IDMetabolite nameStructureCAS number
BASm00002502,5-didehydro-D-gluconateC6H7O7Chemical structure of 2,5-didehydro-D-gluconate53736-12-2
Average191.1156Da
Monoisotopic191.019177578Da
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
BASm00004283-oxoadipateC6H6O5Chemical structure of 3-oxoadipateNot available
Average158.11Da
Monoisotopic158.022620453Da
BASm00005166-deoxyerythronolide BC21H38O6Chemical structure of 6-deoxyerythronolide BNot available
Average386.5228Da
Monoisotopic386.2668389Da
BASm0000553biphenyl-2,3-diolC12H10O2Chemical structure of biphenyl-2,3-diolNot available
Average186.2066Da
Monoisotopic186.0680796Da
BASm0000592(S)-1-phenylethanolC8H10OChemical structure of (S)-1-phenylethanolNot available
Average122.1644Da
Monoisotopic122.0731649Da
BASm0000893crotonobetaineC7H13NO2Chemical structure of crotonobetaine927-89-9
Average143.1836Da
Monoisotopic143.0946287Da
BASm0001225dodecanoateC12H23O2Chemical structure of dodecanoateNot available
Average199.3098Da
Monoisotopic199.169805Da

Displaying 1–10 of 224 metabolites

Health Effects

No health effects information available for this bacterium.