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 Actinomyces sp. HMSC065F11 HMSC065F11, 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_KV811470605582176678,921RefSeq:NZ_KV811470
NZ_KV811484389366167437,612RefSeq:NZ_KV811484
NZ_KV81146528126588302,449RefSeq:NZ_KV811465
NZ_KV81146213713511167,632RefSeq:NZ_KV811462
NZ_KV81148213212723153,462RefSeq:NZ_KV811482
NZ_KV81147215514960153,140RefSeq:NZ_KV811472
NZ_KV81145844422052,766RefSeq:NZ_KV811458
NZ_KV81148340380249,688RefSeq:NZ_KV811483
NZ_KV81147123230031,713RefSeq:NZ_KV811471
NZ_KV81146810100010,863RefSeq:NZ_KV811468
17 Undisplayed Contigs/Replicons15154226,082
Total:1,8371,75256292,064,328
Ortholog data available?No
Database Contents
Genes1,833
Pathways170
Enzymatic Reactions888
Transport Reactions35
Polypeptides1,790
Protein Complexes75
Enzymes446
Transporters143
Compounds604
Transcription Units1,136
tRNAs48
Protein Features2,291
GO Terms152
Database Version29.0
Sequence SourceGCF_001813085.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. HMSC065F11
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04480058
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1739395
Environmentbone misc
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-09-1
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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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