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 johnsonii F0510, 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_KE951826898621109,553RefSeq:NZ_KE951826
NZ_KE95176582736387,920RefSeq:NZ_KE951765
NZ_KE95165775686185,896RefSeq:NZ_KE951657
NZ_KE95161464640075,546RefSeq:NZ_KE951614
NZ_KE95182172710168,650RefSeq:NZ_KE951821
NZ_KE95158460543361,522RefSeq:NZ_KE951584
NZ_KE95178951462359,596RefSeq:NZ_KE951789
NZ_KE95180443420158,422RefSeq:NZ_KE951804
NZ_KE95170656532155,877RefSeq:NZ_KE951706
NZ_KE95175345450049,957RefSeq:NZ_KE951753
NZ_KE95155843421044,868RefSeq:NZ_KE951558
NZ_KE95158044403143,665RefSeq:NZ_KE951580
NZ_KE95173232310143,158RefSeq:NZ_KE951732
NZ_KE95172142400243,115RefSeq:NZ_KE951721
NZ_KE95158937360140,006RefSeq:NZ_KE951589
NZ_KE95154633312039,356RefSeq:NZ_KE951546
NZ_KE95172630240638,990RefSeq:NZ_KE951726
NZ_KE95165323230037,443RefSeq:NZ_KE951653
NZ_KE95177828270136,810RefSeq:NZ_KE951778
NZ_KE95151734313035,393RefSeq:NZ_KE951517
NZ_KE95156233310234,492RefSeq:NZ_KE951562
NZ_KE95178028230534,449RefSeq:NZ_KE951780
NZ_KE95178731310033,962RefSeq:NZ_KE951787
NZ_KE95165824230133,850RefSeq:NZ_KE951658
NZ_KE95159428280033,012RefSeq:NZ_KE951594
NZ_KE95161130300031,791RefSeq:NZ_KE951611
NZ_KE95163821191130,553RefSeq:NZ_KE951638
NZ_KE95166324240029,510RefSeq:NZ_KE951663
NZ_KE95155119190028,419RefSeq:NZ_KE951551
NZ_KE95173119180128,198RefSeq:NZ_KE951731
NZ_KE95152423210228,026RefSeq:NZ_KE951524
NZ_KE95157731273126,989RefSeq:NZ_KE951577
NZ_KE95156022220026,480RefSeq:NZ_KE951560
NZ_KE95150822191226,148RefSeq:NZ_KE951508
NZ_KE95172527261025,828RefSeq:NZ_KE951725
NZ_KE95174320191025,139RefSeq:NZ_KE951743
NZ_KE95170332320024,973RefSeq:NZ_KE951703
NZ_KE95168514140024,906RefSeq:NZ_KE951685
NZ_KE95181219170224,873RefSeq:NZ_KE951812
NZ_KE95177222220024,454RefSeq:NZ_KE951772
NZ_KE95159921200123,787RefSeq:NZ_KE951599
NZ_KE95151417160123,098RefSeq:NZ_KE951514
NZ_KE95177321191123,070RefSeq:NZ_KE951773
NZ_KE95166016150122,700RefSeq:NZ_KE951660
NZ_KE95155319190021,586RefSeq:NZ_KE951553
NZ_KE95176618170120,958RefSeq:NZ_KE951766
NZ_KE95181016150120,886RefSeq:NZ_KE951810
NZ_KE95166912110120,780RefSeq:NZ_KE951669
NZ_KE95167517170020,495RefSeq:NZ_KE951675
NZ_KE95156919180120,295RefSeq:NZ_KE951569
NZ_KE95160713130019,807RefSeq:NZ_KE951607
NZ_KE95169516160018,183RefSeq:NZ_KE951695
NZ_KE95160311110017,752RefSeq:NZ_KE951603
NZ_KE95175413110217,601RefSeq:NZ_KE951754
NZ_KE95177016141117,518RefSeq:NZ_KE951770
NZ_KE95170515130217,041RefSeq:NZ_KE951705
NZ_KE95152612110116,589RefSeq:NZ_KE951526
NZ_KE95157112110116,574RefSeq:NZ_KE951571
NZ_KE951813760115,974RefSeq:NZ_KE951813
NZ_KE95161312110115,578RefSeq:NZ_KE951613
NZ_KE95157612120015,121RefSeq:NZ_KE951576
NZ_KE95162411110014,483RefSeq:NZ_KE951624
NZ_KE95163913111114,409RefSeq:NZ_KE951639
NZ_KE95160410100014,290RefSeq:NZ_KE951604
NZ_KE95166214131013,968RefSeq:NZ_KE951662
NZ_KE95165913130013,862RefSeq:NZ_KE951659
NZ_KE95173011110013,828RefSeq:NZ_KE951730
NZ_KE95160912101113,667RefSeq:NZ_KE951609
NZ_KE95159613120113,583RefSeq:NZ_KE951596
NZ_KE95155912120013,110RefSeq:NZ_KE951559
NZ_KE95182414120213,005RefSeq:NZ_KE951824
NZ_KE95161512110112,850RefSeq:NZ_KE951615
NZ_KE9517041190212,217RefSeq:NZ_KE951704
NZ_KE95163611110011,991RefSeq:NZ_KE951636
NZ_KE951764961211,977RefSeq:NZ_KE951764
NZ_KE95167411110010,980RefSeq:NZ_KE951674
NZ_KE95163411110010,367RefSeq:NZ_KE951634
NZ_KE9515751010009,631RefSeq:NZ_KE951575
NZ_KE9516891211018,736RefSeq:NZ_KE951689
245 Undisplayed Contigs/Replicons604592161271,058,921
Total:2,7322,475591983,383,063
Ortholog data available?No
Database Contents
Genes2,728
Pathways181
Enzymatic Reactions913
Transport Reactions55
Polypeptides2,784
Protein Complexes95
Enzymes514
Transporters227
Compounds691
Transcription Units2,277
tRNAs50
Protein Features2,757
GO Terms199
Database Version29.0
Sequence SourceGCF_000466205.2
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces johnsonii
Actinomyces johnsonii F0510
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02436754
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1227262
Environmentsupragingival plaque biofilm of a molar
Geographic LocationUSA
Collection Date2008
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-12
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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