Saccharophagus degradans 2-40

Gram-negativeRodMotileAerobe

Kingdom

Pseudomonadati

Phylum

Pseudomonadota

Class

Gammaproteobacteria

Order

Cellvibrionales

Family

Cellvibrionaceae

Genus

Saccharophagus

Description

Saccharophagus degradans (strain 2-40), formerly known as Microbulbifer degradans, is a Gram-negative, pleomorphic, aerobic, rod shaped, and motile bacterium. It belongs to a recently discovered group of marine bacteria that degrade and recycle complex carbohydrates. It was originally isolated from the salt marsh cord grass, Spartina alterniflora, in the Chesapeake Bay watershed. Saccharophagus degradans contains degradative surface protuberances, containing what is collectively termed hydrolosomes. The chitinase, agarase and alginase produced by S.degradans are not exported into the extracellular medium but are localized in these surface protuberances. Thanks to these protuberances, it is able to recycle a multitude of ICP (insoluble complex polysaccharides) including agar, chitin, alginic acid, carrageenan, cellulose, B-glucan, laminarin, pectin, pullulan, starch, and xylan. Agricultural, aquacultural, and algalcultural wastes threaten to become an increasingly serious problem. The wastes are mostly recalcitrant complex carbohydrates, namely cellulose, chitin and agar. The degradative protuberances of S.degradans may become important bioremediation tools, using them as concentrated, organized, protective enzyme packets. (EBI Integr8)

Taxonomy

KingdomPseudomonadati
PhylumPseudomonadota
ClassGammaproteobacteria
OrderCellvibrionales
FamilyCellvibrionaceae
GenusSaccharophagus
SpeciesSaccharophagus degradans
Strain2-40

Profile

Physiology
Gram staining propertiesNegative
ShapeRod
MobilityYes
Flagellar presenceYes
Number of membranes2
Image of Saccharophagus degradans 2-40
Ecology, Host, and Life Cycle
Oxygen requirementsAerobe
Optimal temperature4
Temperature rangeMesophilic
HabitatAquatic
Biotic relationshipFree living
Host(s)Not Available
Cell arrangementNot Available
SporulationNot Available
Energy sourceheterotroph
PathogenicityNo

Genome Summary

Saccharophagus degradans 2-40

Accession NumberNC_007912.1

Gene Summary

Adenine Count

1369925 bp

Thymine Count

1369938 bp

Guanine Count

1157231 bp

Cytosine Count

1160437 bp

Genome Length

5057531 bp

Protein-coding Genes

4086 genes

Non-Coding Genes

57 genes

# of Chromosomes/Plasmids

1

Genes

NameLocus TagUniProtStrandCoordinatesMolecular Weight
dna-processing protein dpraSDE_RS00125Not Available+26731 - 2787340995.4
l-threonylcarbamoyladenylate synthaseSDE_RS00130Not Available+28140 - 2871520882.5
oxygen-dependent coproporphyrinogen oxidaseSDE_RS00135Not Available+28757 - 2966834619.3
shikimate dehydrogenaseSDE_RS00140Not Available+29694 - 3053029276.9
retropepsin-like aspartic proteaseSDE_RS00145Not Available+30470 - 3179849011.1
ceramidase domain-containing proteinSDE_RS00150Not Available+31895 - 3253924059.1
simpl domain-containing proteinSDE_RS00155Not Available-32579 - 3334928201.6
gamma carbonic anhydrase family proteinSDE_RS00160Not Available-33407 - 3395219205.0
m3 family metallopeptidaseSDE_RS00165Not Available+34108 - 3616576798.6
yhev family putative zinc ribbon proteinSDE_RS00170Not Available+36171 - 363988666.64

Displaying genes 31 – 40 of 4143 in total

Pathways

0 pathways

No pathways found

No metabolic pathways have been associated with this bacterium yet.

Metabolites

81 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
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
BASm0001717fumarateC4H2O4Chemical structure of fumarateNot available
Average114.0563Da
Monoisotopic113.9953086Da
BASm0001779orotateC5H3N2O4Chemical structure of orotateNot available
Average155.09Da
Monoisotopic155.0098302Da
BASm0001865diphosphateHO7P2Chemical structure of diphosphateNot available
Average174.95Da
Monoisotopic174.9213971Da
BASm0001921(S)-3-methyl-2-oxopentanoateC6H9O3Chemical structure of (S)-3-methyl-2-oxopentanoate1460-34-0
Average129.1339Da
Monoisotopic129.0551692Da
BASm00021577-cyano-7-deazaguanineC7H5N5OChemical structure of 7-cyano-7-deazaguanineNot available
Average175.1475Da
Monoisotopic175.0494098Da
BASm0002243S-methyl-5'-thioinosineC11H14N4O4SChemical structure of S-methyl-5'-thioinosineNot available
Average298.32Da
Monoisotopic298.0735761Da

Displaying 1–10 of 81 metabolites