Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Actinomyces massiliensis 4401292, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_JH7114811,6321,56322471,978,101RefSeq:NZ_JH711481
NZ_JH711482639607248748,168RefSeq:NZ_JH711482
NZ_JH711483522502614629,909RefSeq:NZ_JH711483
10 Undisplayed Contigs/Replicons633414,856
Total:2,8032,67555733,371,034
Ortholog data available?Yes
Database Contents
Genes2,803
Pathways183
Enzymatic Reactions885
Transport Reactions69
Polypeptides2,680
Protein Complexes30
Enzymes534
Transporters284
Compounds691
Transcription Units2,024
tRNAs49
Protein Features3,107
Database Version29.0
Sequence SourceGCF_000269805.1
Synonyms Actinomyces massiliensis JCM 16130
Actinomyces massiliensis str. 4401292
Actinomyces massiliensis strain 4401292
Actinomyces massiliensis 4401292
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces massiliensis
Actinomyces massiliensis 4401292
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02469892
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1167628
Environmentpatient blood culture
Geographic LocationFrance
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2019-11-25
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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