Sphingopyxis alaskensis RB2256

Gram-negativeNon-motileAerobe

Kingdom

Pseudomonadati

Phylum

Pseudomonadota

Class

Alphaproteobacteria

Order

Sphingomonadales

Family

Sphingopyxidaceae

Genus

Sphingopyxis

Description

S. alaskensis is an obligate aerobe isolated as one of the most numerically abundant bacteria from Alaskan waters over a period spanning ten years, demonstrating it is one of the most common culturable inhabitants from these environments. Its capacity to thrive in oligotrophic environments at 4-10 degrees Celsius is linked to unique genetic and physiological properties which are fundamentally different from those of the well studied bacteria such as Escherichia coli. It has a constant ultramicro-size (its volume is 0.1 um 3), irrespective of whether it is growing or starved, that provides it with a mechanism for avoiding predation, and a high surface to volume ratio to enhance nutrient uptake. This is coupled with the ability to utilize low concentrations of nutrients using high affinity, broad specificity uptake systems ( e.g. highest reported rates of alanine transport for any bacterium) and the ability to simultaneously take up mixed substrates. It is likely to be an important contributor in terms of biomass and nutrient cycling in marine environments. Ultramicrobacteria (nanobacteria), such as S. alaskensis, have been reported in a range of aquatic, terrestrial and clinical samples, and in fossils; many of which are controversial. The reports have raised questions about the minimum size of a free-living cell. The astrobiology community has been particularly interested, as the minimum cell-size has important implications for cellular evolution and for the search for extraterrestrial life. S. alaskensis is a useful model for these purposes, as it has been shown, for example, to achieve maximum rates of growth with 200 ribosomes per cell. (EBI Integr8)

Taxonomy

KingdomPseudomonadati
PhylumPseudomonadota
ClassAlphaproteobacteria
OrderSphingomonadales
FamilySphingopyxidaceae
GenusSphingopyxis
SpeciesSphingopyxis alaskensis
StrainRB2256

Profile

Physiology
Gram staining propertiesNegative
ShapeNot Available
MobilityNo
Flagellar presenceNot Available
Number of membranes2
Ecology, Host, and Life Cycle
Oxygen requirementsAerobe
Optimal temperatureNot Available
Temperature rangeMesophilic
HabitatAquatic
Biotic relationshipFree living
Host(s)Not Available
Cell arrangementNot Available
SporulationNonsporulating
Energy sourceOligotroph - Heterotroph
PathogenicityNo

Genome Summary

Sphingopyxis alaskensis RB2256


Gene Summary

Adenine Count

579938 bp

Thymine Count

574094 bp

Guanine Count

1094262 bp

Cytosine Count

1096876 bp

Genome Length

3345170 bp

Protein-coding Genes

3231 genes

Non-Coding Genes

58 genes

# of Chromosomes/Plasmids

2

Genes

NameLocus TagUniProtStrandCoordinatesMolecular Weight
phage tail assembly chaperoneSALA_RS10135Not Available-2104697 - 21049007091.4
gene transfer agent family proteinSALA_RS10140Not Available-2104902 - 210521010642.0
Gene transfer aget (gta) orfg9-like phage major tail proteinSALA_RS10145Not Available-2105225 - 210563214232.6
hypothetical proteinSALA_RS10150Not Available+2105680 - 210601512419.6
duf3168 domain-containing proteinSALA_RS10155Not Available-2106033 - 210642513654.6
hypothetical proteinSALA_RS10160Not Available-2106422 - 210697018836.8
hypothetical proteinSALA_RS10165Not Available-2106967 - 210724810056.9
hypothetical proteinSALA_RS17135Not Available-2107272 - 21074275317.4
Putative tail fiber proteinSALA_RS10170P13390-2107424 - 210891751736.4
Major capsid protein precursorSALA_RS10175Not Available-2109026 - 211016839868.0

Displaying genes 1 – 10 of 3320 in total

Pathways

0 pathways

No pathways found

No metabolic pathways have been associated with this bacterium yet.

Metabolites

1889 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
BASm00002543-hydroxy-2-methylpropanoateC4H7O3Chemical structure of 3-hydroxy-2-methylpropanoateNot available
Average103.098Da
Monoisotopic103.0400677Da
BASm00002603alpha,7alpha-dihydroxy-12-oxo-5beta-cholanateC24H37O5Chemical structure of 3alpha,7alpha-dihydroxy-12-oxo-5beta-cholanateNot available
Average405.556Da
Monoisotopic405.264647871Da
BASm0000272(E)-4-coumarateC9H7O3Chemical structure of (E)-4-coumarateNot available
Average163.1501Da
Monoisotopic163.0395191Da
BASm0000274aldehydo-D-galacturonateC6H9O7Chemical structure of aldehydo-D-galacturonateNot available
Average193.132Da
Monoisotopic193.0353762Da
BASm0000338(1R,4R,5R)-5-hydroxycamphorC10H16O2Chemical structure of (1R,4R,5R)-5-hydroxycamphorNot available
Average168.2328Da
Monoisotopic168.115029756Da
BASm0000377(S)-malateC4H4O5Chemical structure of (S)-malateNot available
Average132.0716Da
Monoisotopic132.005873238Da

Displaying 1–10 of 1889 metabolites