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 83 KBS 83, 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_KB9067338618388151,015,184RefSeq:NZ_KB906733
NZ_KB906734806785813933,261RefSeq:NZ_KB906734
NZ_KB9067357166721331849,966RefSeq:NZ_KB906735
NZ_KB906736647626219826,801RefSeq:NZ_KB906736
NZ_KB90673754153047671,818RefSeq:NZ_KB906737
NZ_KB906738430414511504,707RefSeq:NZ_KB906738
NZ_KB90673934834305441,401RefSeq:NZ_KB906739
NZ_KB906740310296311373,762RefSeq:NZ_KB906740
NZ_KB90674126625574307,927RefSeq:NZ_KB906741
NZ_KB90674214713728169,102RefSeq:NZ_KB906742
NZ_KB90674335290640,955RefSeq:NZ_KB906743
NZ_KB90674415130226,972RefSeq:NZ_KB906744
NZ_KB90674518180021,727RefSeq:NZ_KB906745
NZ_KB90674617140320,920RefSeq:NZ_KB906746
NZ_KB90674719160320,730RefSeq:NZ_KB906747
6 Undisplayed Contigs/Replicons15150225,581
Total:5,1935,001521406,250,814
Ortholog data available?No
Database Contents
Genes5,193
Pathways199
Enzymatic Reactions1,161
Transport Reactions51
Polypeptides5,016
Protein Complexes31
Enzymes702
Transporters348
Compounds876
Transcription Units3,916
tRNAs46
Protein Features5,963
Database Version29.0
Sequence SourceGCF_000381585.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Acidobacteriota
Acidobacteriia
Acidobacteriales
Acidobacteriaceae
unclassified Acidobacteriaceae
Acidobacteriaceae bacterium KBS 83
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02440487
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1267533
EnvironmentYellowstone National Park
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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.