Database Authors
Pallavi Subhraveti1, Anamika Kothari1, Peter Midford1, Ron Caspi1, Lisa Moore1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 03-Nov-2025 from the annotated genome of Chlamydia trachomatis IU888, as obtained from RefSeq (annotation date: 16-MAR-2025). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 29.5) [Karp11, Karp16] using MetaCyc version 29.5 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_02051293689046141,043,022RefSeq:NC_020512
pIU88888007,502RefSeq:NC_020513
Total:95889846141,050,524
Ortholog data available?Yes
Database Contents
Genes944
Pathways82
Enzymatic Reactions662
Transport Reactions30
Polypeptides902
Protein Complexes29
Enzymes259
Transporters74
Compounds629
Transcription Units634
tRNAs37
GO Annotations1,377
Database Version29.6
Sequence SourceGCF_000348825.1
Synonyms Chlamydia trachomatis strain IU888
Chlamydia trachomatis str. IU888
Chlamydia trachomatis IU888
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
PVC group
Chlamydiota
Chlamydiia
Chlamydiales
Chlamydiaceae
Chlamydia/Chlamydophila group
Chlamydia
Chlamydia trachomatis
Chlamydia trachomatis IU888
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA2272485
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1260223
Annotation ProviderNCBI RefSeq
Annotation Date2025-03-16
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.9
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.5 (software by SRI International) on Sat Apr 4, 2026, BIOCYC17.