Database Authors
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Actinomyces sp. HMSC065F12 HMSC065F12, 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_KV81703024023631273,083RefSeq:NZ_KV817030
NZ_KV81698319418671214,065RefSeq:NZ_KV816983
NZ_KV81704118617565205,257RefSeq:NZ_KV817041
NZ_KV81696814914621177,511RefSeq:NZ_KV816968
NZ_KV81697613313012170,048RefSeq:NZ_KV816976
NZ_KV81704213112533161,741RefSeq:NZ_KV817042
NZ_KV81696713513410151,433RefSeq:NZ_KV816967
NZ_KV816945918641111,889RefSeq:NZ_KV816945
NZ_KV816946948932111,170RefSeq:NZ_KV816946
NZ_KV816938949031109,233RefSeq:NZ_KV816938
NZ_KV81703377733187,568RefSeq:NZ_KV817033
NZ_KV81695474721186,553RefSeq:NZ_KV816954
NZ_KV81694373694079,135RefSeq:NZ_KV816943
NZ_KV81695372702078,198RefSeq:NZ_KV816953
NZ_KV81700667650270,326RefSeq:NZ_KV817006
NZ_KV81695541401046,064RefSeq:NZ_KV816955
NZ_KV81694040373045,971RefSeq:NZ_KV816940
NZ_KV81699127270037,745RefSeq:NZ_KV816991
NZ_KV81693524230132,910RefSeq:NZ_KV816935
NZ_KV81700334330131,436RefSeq:NZ_KV817003
NZ_KV81699333330030,980RefSeq:NZ_KV816993
NZ_KV81698135320328,809RefSeq:NZ_KV816981
NZ_KV81697122220027,644RefSeq:NZ_KV816971
NZ_KV81702825241027,230RefSeq:NZ_KV817028
NZ_KV81696226260025,594RefSeq:NZ_KV816962
NZ_KV81693621210019,829RefSeq:NZ_KV816936
NZ_KV81695211110015,871RefSeq:NZ_KV816952
NZ_KV81696126260014,131RefSeq:NZ_KV816961
87 Undisplayed Contigs/Replicons9893522156,694
Total:2,2952,19453482,628,118
Ortholog data available?No
Database Contents
Genes2,295
Pathways174
Enzymatic Reactions851
Transport Reactions37
Polypeptides2,300
Protein Complexes84
Enzymes487
Transporters168
Compounds646
Transcription Units1,466
tRNAs47
Protein Features2,624
GO Terms192
Database Version29.0
Sequence SourceGCF_001814535.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. HMSC065F12
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04480398
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1739479
Environmentbone r great toe
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-10-30
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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