Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 13-Mar-2021 from the annotated genome of Neisseria gonorrhoeae 32867, as obtained from RefSeq (see the RefSeq entry for the authors of the original genome sequence). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [Caspi20]. It has not undergone any manual curation or review, and may contain errors. Development of this PGDB was supported by grant GM080746 from the National Institutes of Health.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0160152,3262,051712042,218,818RefSeq:NZ_CP016015
Ortholog data available?Yes
Database Contents
Genes2,326
Pathways192
Enzymatic Reactions1,050
Transport Reactions47
Polypeptides2,051
Protein Complexes23
Enzymes593
Transporters138
Compounds749
Transcription Units1,564
tRNAs55
Protein Features2,423
GO Terms1,037
Database Version29.0
Sequence SourceGCF_001661085.1
Synonyms Diplococcus gonorrhoeae
Gonococcus neisseri
Merismopedia gonorrhoeae
Micrococcus der gonorrhoe
Micrococcus gonococcus
Micrococcus gonorrhoeae
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Neisseriales
Neisseriaceae
Neisseria
Neisseria gonorrhoeae
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04233132
NCBI BioProjectPRJNA224116
NCBI-Taxonomy485
Geographic LocationCanada
Latitude/Longitude43.655067 N 79.388885 W
Collection Date2010-01-27
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2020-11-27
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.13
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

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