Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Abiotrophia defectiva ATCC 49176, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_KI5353401,4721,44314151,587,476RefSeq:NZ_KI535340
NZ_KI535341281235406284,983RefSeq:NZ_KI535341
NZ_KI53534213813044169,911RefSeq:NZ_KI535342
NZ_KI53534321011,069RefSeq:NZ_KI535343
Total:1,8931,80958262,043,439
Ortholog data available?No
Database Contents
Genes1,892
Pathways143
Enzymatic Reactions803
Transport Reactions58
Polypeptides1,825
Protein Complexes74
Enzymes406
Transporters150
Compounds599
Transcription Units1,043
tRNAs47
Protein Features2,487
GO Terms143
Database Version29.0
Sequence SourceGCF_000160075.2
Synonyms Abiotrophia defectiva strain ATCC 49176
Abiotrophia defectiva str. ATCC 49176
Abiotrophia defectiva ATCC 49176
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Lactobacillales
Aerococcaceae
Abiotrophia
Abiotrophia defectiva
Abiotrophia defectiva ATCC 49176
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02436801
NCBI BioProjectPRJNA224116
NCBI-Taxonomy592010
Environmentblood
HostHomo sapiens
Human Microbiome Body Siteblood
Annotation ProviderNCBI RefSeq
Annotation Date2022-05-5
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.1
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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17.