Shimia sp. SK013

Kingdom

Pseudomonadati

Phylum

Pseudomonadota

Class

Alphaproteobacteria

Order

Rhodobacterales

Family

Roseobacteraceae

Genus

Shimia

Description

Shimia sp. SK013 is a Gram-negative bacterium characterized by possessing a single replicon. This classification as a Gram-negative organism is significant as it indicates the presence of an outer membrane that can influence various biological processes, including pathogenicity and antibiotic resistance. The genomic data for Shimia sp. SK013 is cataloged under the accession LAJH00000000.1, which provides a reference for further studies and analyses. The single replicon suggests a streamlined genetic structure, which is often associated with certain ecological niches and metabolic efficiencies. The traits of Shimia sp. SK013 underline its potential ecological roles and interactions within its environment. Gram-negative bacteria are often involved in nutrient cycling, degradation of organic matter, and can play a role in symbiotic relationships with other organisms. Understanding the specific traits of Shimia sp. SK013 can contribute to insights into its ecological significance, particularly in its native habitat. The presence of a single replicon may also indicate a capacity for rapid adaptation to environmental changes, enhancing its survival and ecological impact.

Taxonomy

KingdomPseudomonadati
PhylumPseudomonadota
ClassAlphaproteobacteria
OrderRhodobacterales
FamilyRoseobacteraceae
GenusShimia
SpeciesShimia sp. SK013
StrainNo strain

Profile

Physiology
Gram staining propertiesGram-negative
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
HabitatNot Available
Biotic relationshipNot Available
Host(s)Not Available
Cell arrangementNot Available
SporulationNot Available
Energy sourceNot Available
PathogenicityNot Available

Genome Summary

Shimia sp. SK013 shim_contig000028, whole genome shotgun sequence.

Gene Summary

Adenine Count

863690 bp

Thymine Count

868777 bp

Guanine Count

1170566 bp

Cytosine Count

1146775 bp

Genome Length

4049808 bp

Protein-coding Genes

3968 genes

Non-Coding Genes

59 genes

# of Chromosomes/Plasmids

1

Genes

NameLocus TagUniProt IDStrand OrientationGene Start/EndProtein Molecular Weight
3-oxoacyl-(acyl-carrier-protein) reductase fabgshim_29310P73574Positive2933175 - 293399928202.9
succinyl-coa:(r)-benzylsuccinate coa-transferase subunit bbseshim_29320O06543Positive2934055 - 293513438123.4
uroporphyrinogen decarboxylaseshim_29330Q16AR3Negative2935324 - 293635837631.0
porphobilinogen deaminaseshim_29340A1B853Positive2936565 - 293752433784.4
hypothetical proteinshim_29350Not AvailablePositive2937628 - 293819720948.3
coproporphyrinogen-iii oxidase, aerobicshim_29360Q89SC2Negative2938246 - 293913933060.8
3-oxoacyl-(acyl-carrier-protein) reductase fabgshim_29370A5W4G5Negative2939215 - 294001528234.7
ribosomal rna large subunit methyltransferase gshim_29380Not AvailableNegative2940064 - 294104735834.5
atp-dependent clp protease adapter protein clpsshim_29390Q16AR8Negative2941073 - 294141112811.6
dump phosphataseshim_29400Not AvailablePositive2941506 - 294220725837.9

Displaying genes 2931 – 2940 of 4027 in total

Pathways

0 pathways

No pathways found

No metabolic pathways have been associated with this bacterium yet.

Metabolites

309 records
Metabolite IDMetabolite nameStructureCAS number
BASm0000217alpha-ribazoleC14H18N2O4Chemical structure of alpha-ribazoleNot available
Average278.3037Da
Monoisotopic278.126657074Da
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
BASm00002583-(carbamoylamino)propanoateC4H7N2O3Chemical structure of 3-(carbamoylamino)propanoateNot available
Average131.112Da
Monoisotopic131.046215673Da
BASm00002593alpha,12alpha-dihydroxy-7-oxo-5beta-cholanateC24H37O5Chemical structure of 3alpha,12alpha-dihydroxy-7-oxo-5beta-cholanateNot available
Average405.556Da
Monoisotopic405.264647871Da
BASm00002654-formylbenzenesulfonateC7H5O4SChemical structure of 4-formylbenzenesulfonateNot available
Average185.17Da
Monoisotopic184.991403395Da
BASm0000274aldehydo-D-galacturonateC6H9O7Chemical structure of aldehydo-D-galacturonateNot available
Average193.132Da
Monoisotopic193.0353762Da
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

Displaying 1–10 of 309 metabolites

Health Effects

No health effects information available for this bacterium.