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 01-June-2020 from the annotated genome of Acidobacterium capsulatum ATCC 51196, 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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_0124833,3983,30753384,127,356RefSeq:NC_012483
Ortholog data available?Yes
Database Contents
Genes3,398
Pathways218
Enzymatic Reactions1,139
Transport Reactions46
Polypeptides3,308
Protein Complexes29
Enzymes669
Transporters238
Compounds826
Transcription Units2,415
tRNAs46
Protein Features4,694
Database Version29.0
Sequence SourceGCF_000022565.1
Synonyms Acidobacterium capsulatum str. ATCC 51196
Acidobacterium capsulatum strain ATCC 51196
Acidobacterium capsulatum ATCC 51196
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Acidobacteriota
Acidobacteriia
Acidobacteriales
Acidobacteriaceae
Acidobacterium
Acidobacterium capsulatum
Acidobacterium capsulatum ATCC 51196
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603447
NCBI BioProjectPRJNA224116
NCBI-Taxonomy240015
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-3
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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