Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Actinomyces vulturis VUL7, 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_KV700385684661212811,449RefSeq:NZ_KV700385
NZ_LZRK01000003431414116489,560RefSeq:NZ_LZRK01000003
NZ_LZRK01000004354340113420,311RefSeq:NZ_LZRK01000004
NZ_KV700386281263117352,708RefSeq:NZ_KV700386
NZ_LZRK0100000747470049,023RefSeq:NZ_LZRK01000007
NZ_LZRK0100000859563045,677RefSeq:NZ_LZRK01000008
NZ_LZRK0100000939345025,368RefSeq:NZ_LZRK01000009
NZ_LZRK0100001030305,539RefSeq:NZ_LZRK01000010
NZ_LZRK0100001111002,459RefSeq:NZ_LZRK01000011
NZ_LZRK010000120000572RefSeq:NZ_LZRK01000012
Total:1,8991,81665182,202,666
Ortholog data available?Yes
Database Contents
Genes1,899
Pathways159
Enzymatic Reactions770
Transport Reactions37
Polypeptides1,820
Protein Complexes3
Enzymes449
Transporters212
Compounds553
Transcription Units1,238
tRNAs59
Protein Features2,200
GO Terms138
Database Version29.0
Sequence SourceGCF_001687305.1
Synonyms Actinomyces sp. VUL7
Actinomyces sp. VUL8
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces vulturis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05226836
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1857645
Environmentfeces of vulture
Geographic LocationChina
Collection Date2013
Annotation ProviderNCBI RefSeq
Annotation Date2021-07-12
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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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