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

Accession NumberNC_008048.1

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
nucleotide exchange factor grpeSALA_RS01255Q2G6M5-255275 - 25582920113.7
heat-inducible transcriptional repressor hrcaSALA_RS01260Q1GWJ6-255834 - 25687736937.4
ribonuclease phSALA_RS01265Q1GWJ5+256982 - 25769825510.6
hypothetical proteinSALA_RS01270Not Available+257743 - 25819216908.6
hypothetical proteinSALA_RS01275Not Available+258189 - 25866817325.1
rdgb/ham1 family non-canonical purine ntp pyrophosphataseSALA_RS01280Q2RN61+258677 - 25930922209.3
radical sam family heme chaperone hemwSALA_RS01285Q5SUV1+259318 - 26046340932.4
tyrosine recombinase xercSALA_RS01290B0UNY7+260564 - 26145731909.7
deda family proteinSALA_RS01295Q9CHL6-261537 - 26214523162.6
glutathione synthaseSALA_RS01300P61396-262302 - 26325534562.5

Displaying genes 271 – 280 of 3320 in total

Pathways

0 pathways

No pathways found

No metabolic pathways have been associated with this bacterium yet.

Metabolites

295 records
Metabolite IDMetabolite nameStructureCAS number
BASm0000237(R)-4'-phosphopantothenateC9H18NO8PChemical structure of (R)-4'-phosphopantothenateNot available
Average299.2149Da
Monoisotopic299.0770031Da
BASm00002512-dehydropantoateC6H9O4Chemical structure of 2-dehydropantoateNot available
Average145.1333Da
Monoisotopic145.050083776Da
BASm00002543-hydroxy-2-methylpropanoateC4H7O3Chemical structure of 3-hydroxy-2-methylpropanoateNot available
Average103.098Da
Monoisotopic103.0400677Da
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
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
BASm0000403(S)-acetoinC4H8O2Chemical structure of (S)-acetoinNot available
Average88.1051Da
Monoisotopic88.0524295Da

Displaying 1–10 of 295 metabolites