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 TAA166 TAA 166, 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_ATWD010000014,0013,844381194,712,210RefSeq:NZ_ATWD01000001
NZ_ATWD0100000292990013161,108,612RefSeq:NZ_ATWD01000002
NZ_ATWD0100000324223921316,111RefSeq:NZ_ATWD01000003
Total:5,1724,983531366,136,933
Ortholog data available?No
Database Contents
Genes5,172
Pathways223
Enzymatic Reactions1,203
Transport Reactions48
Polypeptides4,984
Protein Complexes25
Enzymes768
Transporters329
Compounds919
Transcription Units3,920
tRNAs47
Protein Features5,675
Database Version29.0
Sequence SourceGCF_000421065.1
Synonyms Acidobacteriaceae bacterium TAA 166
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Acidobacteriota
Acidobacteriia
Acidobacteriales
Acidobacteriaceae
unclassified Acidobacteriaceae
Acidobacteriaceae bacterium TAA166
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02440899
NCBI BioProjectPRJNA224116
NCBI-Taxonomy278963
EnvironmentFresh water; Aquatic
Annotation ProviderNCBI RefSeq
Annotation Date2020-02-5
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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