Pedobacter heparinus DSM 2366

Gram-negativeBacilliNon-motileAerobic

Kingdom

Pseudomonadati

Phylum

Bacteroidota

Class

Sphingobacteriia

Order

Sphingobacteriales

Family

Sphingobacteriaceae

Genus

Pedobacter

Description

Pedobacter heparinus DSM 2366, (also known as ATCC 13125, IFO 12017 and LMG 10399 among others) is a heparinase producing bacterium isolated from dry soil which prefers carbohydrates and sugars as carbon sources. It grows as Gram-negative rods ranging in size from 0.7 to 6 um long. It is obligately aerobic, does not sporulate and has gliding motility. It is interesting due to its ability to degrade acidic sulfated mucoheteropolysaccharides, like heparin and chondroitin that are formed in various animal tissues. It contains menaquinone MK-7 (adapted from PMID 9542086 and http://standardsingenomics.org/index.php/sigen/article/view/sigs22138/sig22138.pdf). (EBI Integr8)

Taxonomy

Kingdom	Pseudomonadati
Phylum	Bacteroidota
Class	Sphingobacteriia
Order	Sphingobacteriales
Family	Sphingobacteriaceae
Genus	Pedobacter
Species	Pedobacter heparinus
Strain	DSM 2366

Profile

Physiology
Gram staining properties	Negative
Shape	Bacilli
Mobility	No
Flagellar presence	Yes
Number of membranes	2

AI-generated image based on bacteria physiology

Ecology, Host, and Life Cycle
Oxygen requirements	Aerobic
Optimal temperature	Not Available
Temperature range	Mesophilic
Habitat	Terrestrial
Biotic relationship	Free living
Host(s)	Not Available
Cell arrangement	Not Available
Sporulation	Nonsporulating
Energy source	Chemoorganotroph
Pathogenicity	No

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

Name	Locus Tag	UniProt	Strand	Coordinates	Molecular Weight
aspartyl protease family protein	PHEP_RS00005	Not Available	+	19 - 1260	45935.4
phosphodiester glycosidase family protein	PHEP_RS00010	Not Available	+	1284 - 2153	31550.9
hypothetical protein	PHEP_RS00015	Not Available	+	2155 - 3102	36234.5
cold-shock protein	PHEP_RS00020	Not Available	+	3200 - 3391	6960.28
glycerophosphodiester phosphodiesterase	PHEP_RS00025	Not Available	-	3460 - 4257	29956.4
duf4175 family protein	PHEP_RS00030	Not Available	+	4414 - 7722	125551.0
rrna maturation rnase ybey	PHEP_RS00035	Not Available	+	7733 - 8161	16434.7
abc-f family atp-binding cassette domain-containing protein	PHEP_RS00040	Not Available	+	8282 - 10144	70814.7
trna uridine-5-carboxymethylaminomethyl(34) synthesis enzyme mnmg	PHEP_RS00045	Not Available	+	10253 - 12115	69300.2
ig-like domain-containing protein	PHEP_RS00050	Not Available	+	12319 - 13887	59412.1

Displaying genes 1 – 10 of 4285 in total

Pathways

0 pathways

No pathways found

No metabolic pathways have been associated with this bacterium yet.

Metabolite ID	Metabolite name	Structure	CAS number	Average mass Monoisotopic mass
BASm0000250	2,5-didehydro-D-gluconateC6H7O7		`53736-12-2`	Average191.1156Da Monoisotopic191.019177578Da
BASm0000253	2-oxopent-4-enoateC5H5O3		Not available	Average113.093Da Monoisotopic113.024417601Da
BASm0000260	3alpha,7alpha-dihydroxy-12-oxo-5beta-cholanateC24H37O5		Not available	Average405.556Da Monoisotopic405.264647871Da
BASm0000274	aldehydo-D-galacturonateC6H9O7		Not available	Average193.132Da Monoisotopic193.0353762Da
BASm0000428	3-oxoadipateC6H6O5		Not available	Average158.11Da Monoisotopic158.022620453Da
BASm0000516	6-deoxyerythronolide BC21H38O6		Not available	Average386.5228Da Monoisotopic386.2668389Da
BASm0000553	biphenyl-2,3-diolC12H10O2		Not available	Average186.2066Da Monoisotopic186.0680796Da
BASm0000592	(S)-1-phenylethanolC8H10O		Not available	Average122.1644Da Monoisotopic122.0731649Da
BASm0000893	crotonobetaineC7H13NO2		`927-89-9`	Average143.1836Da Monoisotopic143.0946287Da
BASm0001225	dodecanoateC12H23O2		Not available	Average199.3098Da Monoisotopic199.169805Da

Displaying 1–10 of 224 metabolites