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 sp. HMSC08A01 HMSC08A01, 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_KV78906539538474416,774RefSeq:NZ_KV789065
NZ_KV789061318305103349,681RefSeq:NZ_KV789061
NZ_KV789063329316103341,732RefSeq:NZ_KV789063
NZ_KV789067304291121333,971RefSeq:NZ_KV789067
NZ_KV78905622822233262,076RefSeq:NZ_KV789056
NZ_KV78905713112812136,980RefSeq:NZ_KV789057
NZ_KV78906912712142134,333RefSeq:NZ_KV789069
NZ_KV78906858544064,611RefSeq:NZ_KV789068
NZ_KV78907228280030,572RefSeq:NZ_KV789072
NZ_KV78906417170028,637RefSeq:NZ_KV789064
NZ_KV78907016160019,680RefSeq:NZ_KV789070
NZ_KV78906013130015,422RefSeq:NZ_KV789060
NZ_KV78906211100111,946RefSeq:NZ_KV789062
NZ_KV789059990010,928RefSeq:NZ_KV789059
NZ_KV78907130305,439RefSeq:NZ_KV789071
NZ_KV78905844004,326RefSeq:NZ_KV789058
NZ_KV78906600001,814RefSeq:NZ_KV789066
Total:1,9911,91854192,168,922
Ortholog data available?No
Database Contents
Genes1,991
Pathways173
Enzymatic Reactions871
Transport Reactions43
Polypeptides1,931
Protein Complexes3
Enzymes494
Transporters252
Compounds630
Transcription Units1,140
tRNAs48
Protein Features2,381
GO Terms181
Database Version29.0
Sequence SourceGCF_001807435.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. HMSC08A01
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03434237
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1581131
EnvironmentUrinary Tract
HostHomo sapiens
Human Microbiome Body Siteurogenital-tract
Annotation ProviderNCBI RefSeq
Annotation Date2021-07-13
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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