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
udp-n-acetylglucosamine 1-carboxyvinyltransferaseTPANIC_RS00145Not Available+36917 - 3819445544.7
chaperonin groelTPANIC_RS00150Not Available+38313 - 3994757983.9
hypothetical proteinTPANIC_RS00155Not Available+40011 - 4028910276.9
16s rrna (uracil(1498)-n(3))-methyltransferaseTPANIC_RS00160Not Available-40286 - 4108629380.9
duf1361 domain-containing proteinTPANIC_RS00165Not Available-41083 - 4175126100.8
metal abc transporter substrate-binding proteinTPANIC_RS00170Not Available-41795 - 4274535435.6
metal abc transporter atp-binding proteinTPANIC_RS00175Not Available+42943 - 4365926461.3
metal abc transporter permeaseTPANIC_RS00180Not Available+43659 - 4445928384.8
d-2-hydroxyacid dehydrogenaseTPANIC_RS00185Not Available-44568 - 4556336875.4
pts transporter subunit iicTPANIC_RS00190Not Available-45660 - 4671236925.3

Displaying genes 31 – 40 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
BASm0000237(R)-4'-phosphopantothenateC9H18NO8PChemical structure of (R)-4'-phosphopantothenateNot available
Average299.2149Da
Monoisotopic299.0770031Da
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
BASm0001865diphosphateHO7P2Chemical structure of diphosphateNot available
Average174.95Da
Monoisotopic174.9213971Da
BASm0002002glyoxylateC2HO3Chemical structure of glyoxylateNot available
Average73.0275Da
Monoisotopic72.9925689Da
BASm0002812aldehydo-D-glucose 6-phosphateC6H13O9PChemical structure of aldehydo-D-glucose 6-phosphateNot available
Average260.1358Da
Monoisotopic260.0297185Da
BASm0002826(2R)-3-phospho-glyceroyl phosphateC3H4O10P2Chemical structure of (2R)-3-phospho-glyceroyl phosphateNot available
Average262.005Da
Monoisotopic261.9301646Da
BASm0002833FMNH2C17H21N4O9PChemical structure of FMNH25666-16-0
Average456.3438Da
Monoisotopic456.1046148Da
BASm0002858all-trans-undecaprenyl phosphateC55H89O4PChemical structure of all-trans-undecaprenyl phosphateNot available
Average845.288Da
Monoisotopic844.6509455Da
BASm00029834-CDP-2-C-methyl-D-erythritolC14H23N3O14P2Chemical structure of 4-CDP-2-C-methyl-D-erythritolNot available
Average519.294Da
Monoisotopic519.0666236Da
BASm00030584-CDP-2-C-methyl-D-erythritol 2-phosphateC14H22N3O17P3Chemical structure of 4-CDP-2-C-methyl-D-erythritol 2-phosphateNot available
Average597.257Da
Monoisotopic597.0184016Da

Displaying 1–10 of 36 metabolites