Treponema pallidum subsp. pallidum str. Nichols

Gram-negativeSpirillaNon-motileAnaerobe

Kingdom

Pseudomonadati

Phylum

Spirochaetota

Class

Spirochaetia

Order

Spirochaetales

Family

Treponemataceae

Genus

Treponema

Description

Treponema pallidum, is a helical to sinusoidal spirochaete with 2 membranes, a thin peptidoglycan layer and flagella that lie in the periplasmic space. It is the causative agent of syphilis, plays a role in the transmission and acquisition of HIV, and is a major cause of stillbirth and perinatal morbidity in the developing world. Even if the primary infection is localized, bacteria rapidly disseminate and cause manifestations in the cardiovascular and nervous systems. It is an obligate human parasite.The first T.pallidum strain to be sequenced was strain Nichols, which was isolated in 1912 from the cerebrospinal fluid of patient with secondary syphilis. It has since been passed in rabbits for nearly a century. This Chicago strain was isolated in 1951, has not been passed continually in rabbits and has had an important role in research on antigenic variation, immune escape and pathogen persistence. There are 44 nucleotide substitutions, 21 deletions and 75 insertions compared to the Nichols genome (adapted from PMID). (EBI Integr8)

Taxonomy

KingdomPseudomonadati
PhylumSpirochaetota
ClassSpirochaetia
OrderSpirochaetales
FamilyTreponemataceae
GenusTreponema
SpeciesTreponema pallidum
StrainNichols

Profile

Physiology
Gram staining propertiesNegative
ShapeSpirilla
MobilityNo
Flagellar presenceYes
Number of membranes2
Ecology, Host, and Life Cycle
Oxygen requirementsAnaerobe
Optimal temperatureNot Available
Temperature rangeMesophilic
HabitatHostAssociated
Biotic relationshipFree living
Host(s)Homo sapiens
Cell arrangementSingles
SporulationNonsporulating
Energy sourceNot Available
PathogenicityYes

Genome Summary

Treponema pallidum subsp. pallidum str. Nichols

Accession NumberNC_021490.2

Gene Summary

Adenine Count

Not Available

Thymine Count

Not Available

Guanine Count

Not Available

Cytosine Count

Not Available

Genome Length

Not Available

Protein-coding Genes

984 genes

Non-Coding Genes

54 genes

# of Chromosomes/Plasmids

1

Genes

NameLocus TagUniProtStrandCoordinatesMolecular Weight
chromosomal replication initiator protein dnaaTPANIC_RS00005Not Available+4 - 139852968.4
dna polymerase iii subunit betaTPANIC_RS00010Not Available+1641 - 275641292.8
dna replication/repair protein recfTPANIC_RS00015Not Available+2701 - 383444064.4
duf721 domain-containing proteinTPANIC_RS00020Not Available+3827 - 426416338.6
dna topoisomerase (atp-hydrolyzing) subunit aTPANIC_RS00025Not Available+4391 - 683289931.9
30s ribosomal protein s16TPANIC_RS00035Not Available+7203 - 826139368.2
major outer sheath c-terminal domain-containing proteinTPANIC_RS05525Not Available-8341 - 926133587.1
30s ribosomal protein s16TPANIC_RS05530Not Available-9274 - 94476250.57
major outer sheath n-terminal domain-containing proteinTPANIC_RS05535Not Available-9374 - 995221325.1
major outer sheath c-terminal domain-containing proteinTPANIC_RS00045Not Available+10397 - 1237971110.1

Displaying genes 1 – 10 of 1038 in total

Pathways

0 pathways

No pathways found

No metabolic pathways have been associated with this bacterium yet.

Metabolites

36 records
Metabolite IDMetabolite nameStructureCAS number
BASm0004172(R)-4'-phosphopantetheineC11H21N2O7PSChemical structure of (R)-4'-phosphopantetheineNot available
Average356.33Da
Monoisotopic356.081806356Da
BASm0004232(4R)-4-hydroxy-2-oxoglutarateC5H4O6Chemical structure of (4R)-4-hydroxy-2-oxoglutarateNot available
Average160.082Da
Monoisotopic160.001885009Da
BASm0004925UDP-N-acetyl-alpha-D-muramateC20H28N3O19P2Chemical structure of UDP-N-acetyl-alpha-D-muramateNot available
Average676.395Da
Monoisotopic676.080870429Da
BASm0005091(4S)-4-hydroxy-2-oxoglutarateC5H4O6Chemical structure of (4S)-4-hydroxy-2-oxoglutarateNot available
Average160.082Da
Monoisotopic160.001885009Da
BASm0007001UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamateC28H39N5O23P2Chemical structure of UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamateNot available
Average875.582Da
Monoisotopic875.1533009Da
BASm0007003UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioateC35H51N7O26P2Chemical structure of UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioateNot available
Average1047.7583Da
Monoisotopic1047.235898Da
BASm0008099(2E)-4-hydroxy-3-methylbut-2-enyl diphosphateC5H9O8P2Chemical structure of (2E)-4-hydroxy-3-methylbut-2-enyl diphosphateNot available
Average259.0677Da
Monoisotopic258.9772653Da
BASm0014032Acetic acidC2H4O2Chemical structure of Acetic acid64-19-7
Average60.052Da
Monoisotopic60.021129372Da
BASm0016958Desferrioxamine EC27H48N6O9Chemical structure of Desferrioxamine ENULL
Average600.714Da
Monoisotopic600.34827715Da
BASm0017265Uridine diphosphate-N-acetylglucosamineC17H27N3O17P2Chemical structure of Uridine diphosphate-N-acetylglucosamine528-04-1
Average607.3537Da
Monoisotopic607.081569477Da

Displaying 21–30 of 36 metabolites