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. HMSC08A09 HMSC08A09, 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_KV78913317817314211,957RefSeq:NZ_KV789133
NZ_KV78909612612420164,115RefSeq:NZ_KV789096
NZ_KV78909311010523146,414RefSeq:NZ_KV789093
NZ_KV78911812711674145,838RefSeq:NZ_KV789118
NZ_KV78912211611204121,965RefSeq:NZ_KV789122
NZ_KV7891511029813108,149RefSeq:NZ_KV789151
NZ_KV7890749484100106,704RefSeq:NZ_KV789074
NZ_KV789089848301100,087RefSeq:NZ_KV789089
NZ_KV78912586830395,399RefSeq:NZ_KV789125
NZ_KV78908477713395,118RefSeq:NZ_KV789084
NZ_KV78915978771094,690RefSeq:NZ_KV789159
NZ_KV78909469622590,073RefSeq:NZ_KV789094
NZ_KV78914783755388,623RefSeq:NZ_KV789147
NZ_KV78912083830085,414RefSeq:NZ_KV789120
NZ_KV78909058560280,899RefSeq:NZ_KV789090
NZ_KV78910763610272,376RefSeq:NZ_KV789107
NZ_KV78912465591572,154RefSeq:NZ_KV789124
NZ_KV78907750482068,908RefSeq:NZ_KV789077
NZ_KV78908863611167,386RefSeq:NZ_KV789088
NZ_KV78915752482262,714RefSeq:NZ_KV789157
NZ_KV78913852510162,639RefSeq:NZ_KV789138
NZ_KV78911148411659,105RefSeq:NZ_KV789111
NZ_KV78915344440055,779RefSeq:NZ_KV789153
NZ_KV78913545383445,786RefSeq:NZ_KV789135
NZ_KV78913937340341,681RefSeq:NZ_KV789139
NZ_KV78909132281340,299RefSeq:NZ_KV789091
NZ_KV78909718180032,383RefSeq:NZ_KV789097
NZ_KV78913224230130,309RefSeq:NZ_KV789132
NZ_KV78912632273230,283RefSeq:NZ_KV789126
NZ_KV78914221201029,285RefSeq:NZ_KV789142
NZ_KV78910823230028,439RefSeq:NZ_KV789108
NZ_KV78915521200127,971RefSeq:NZ_KV789155
NZ_KV78908620200027,086RefSeq:NZ_KV789086
NZ_KV78908321210026,758RefSeq:NZ_KV789083
NZ_KV78907623192226,354RefSeq:NZ_KV789076
NZ_KV78913718170125,387RefSeq:NZ_KV789137
NZ_KV78910022220025,151RefSeq:NZ_KV789100
NZ_KV78911620200024,407RefSeq:NZ_KV789116
NZ_KV78915818180023,311RefSeq:NZ_KV789158
NZ_KV78913621201023,174RefSeq:NZ_KV789136
NZ_KV78914417170021,275RefSeq:NZ_KV789144
NZ_KV78910218170121,141RefSeq:NZ_KV789102
NZ_KV78915215150016,320RefSeq:NZ_KV789152
NZ_KV78914812120015,026RefSeq:NZ_KV789148
NZ_KV78907313120113,899RefSeq:NZ_KV789073
NZ_KV7891041412029,225RefSeq:NZ_KV789104
41 Undisplayed Contigs/Replicons103101322185,286
Total:2,5392,38955953,046,742
Ortholog data available?No
Database Contents
Genes2,538
Pathways192
Enzymatic Reactions949
Transport Reactions52
Polypeptides2,430
Protein Complexes94
Enzymes542
Transporters206
Compounds712
Transcription Units1,838
tRNAs49
Protein Features2,892
GO Terms188
Database Version29.0
Sequence SourceGCF_001807465.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. HMSC08A09
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03434240
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1581133
HostHomo sapiens
Human Microbiome Body Sitenot-specified
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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