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 25-Oct-2020 from the annotated genome of Acidobacteriaceae bacterium KBS 89 KBS 89, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_KB9067541,3711,32215341,636,164RefSeq:NZ_KB906754
NZ_KB90675598494712251,164,827RefSeq:NZ_KB906755
NZ_KB906756711691614943,631RefSeq:NZ_KB906756
NZ_KB90675747446347586,549RefSeq:NZ_KB906757
NZ_KB90675846945838553,614RefSeq:NZ_KB906758
NZ_KB906759460442108541,582RefSeq:NZ_KB906759
NZ_KB906760394373516484,706RefSeq:NZ_KB906760
NZ_KB90676143411168,325RefSeq:NZ_KB906761
NZ_KB90676213130017,137RefSeq:NZ_KB906762
NZ_KB90676355008,593RefSeq:NZ_KB906763
NZ_KB90676400002,666RefSeq:NZ_KB906764
NZ_KB90676510011,099RefSeq:NZ_KB906765
NZ_KB90676610011,033RefSeq:NZ_KB906766
Total:4,9264,755561156,009,926
Ortholog data available?No
Database Contents
Genes4,926
Pathways219
Enzymatic Reactions1,191
Transport Reactions53
Polypeptides4,765
Protein Complexes26
Enzymes724
Transporters320
Compounds909
Transcription Units3,827
tRNAs50
Protein Features5,731
Database Version29.0
Sequence SourceGCF_000381605.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Acidobacteriota
Acidobacteriia
Acidobacteriales
Acidobacteriaceae
unclassified Acidobacteriaceae
Acidobacteriaceae bacterium KBS 89
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02441326
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1267534
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-8
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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