Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Actinomyces dentalis DSM 19115, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_AUBL0100000114513870183,676RefSeq:NZ_AUBL01000001
NZ_AUBL0100000214514212173,387RefSeq:NZ_AUBL01000002
NZ_AUBL0100000311410833142,162RefSeq:NZ_AUBL01000003
NZ_AUBL0100000412012000124,751RefSeq:NZ_AUBL01000004
NZ_KE386864787215107,006RefSeq:NZ_KE386864
NZ_AUBL01000007948662103,344RefSeq:NZ_AUBL01000007
NZ_KE386865868411102,984RefSeq:NZ_KE386865
NZ_AUBL0100001086793498,231RefSeq:NZ_AUBL01000010
NZ_AUBL0100001164610377,195RefSeq:NZ_AUBL01000011
NZ_AUBL0100001269631577,083RefSeq:NZ_AUBL01000012
NZ_AUBL0100001362570576,978RefSeq:NZ_AUBL01000013
NZ_AUBL0100001465593376,609RefSeq:NZ_AUBL01000014
NZ_AUBL0100001563591374,621RefSeq:NZ_AUBL01000015
NZ_AUBL0100001668620670,739RefSeq:NZ_AUBL01000016
NZ_KE38686652500268,499RefSeq:NZ_KE386866
NZ_AUBL0100001955530266,494RefSeq:NZ_AUBL01000019
NZ_AUBL0100002055510465,248RefSeq:NZ_AUBL01000020
NZ_KE38686755530265,160RefSeq:NZ_KE386867
NZ_AUBL0100002350480262,692RefSeq:NZ_AUBL01000023
NZ_AUBL0100002449452262,455RefSeq:NZ_AUBL01000024
NZ_AUBL0100002557541261,866RefSeq:NZ_AUBL01000025
NZ_AUBL0100002644411257,724RefSeq:NZ_AUBL01000026
NZ_AUBL0100002750471257,222RefSeq:NZ_AUBL01000027
NZ_AUBL0100002846420456,743RefSeq:NZ_AUBL01000028
NZ_AUBL0100002944410356,134RefSeq:NZ_AUBL01000029
NZ_AUBL0100003043380554,867RefSeq:NZ_AUBL01000030
NZ_AUBL0100003143393151,879RefSeq:NZ_AUBL01000031
NZ_AUBL0100003232290350,925RefSeq:NZ_AUBL01000032
NZ_AUBL0100003328260250,444RefSeq:NZ_AUBL01000033
NZ_AUBL0100003445431149,868RefSeq:NZ_AUBL01000034
NZ_AUBL0100003540380248,018RefSeq:NZ_AUBL01000035
NZ_AUBL0100003635330245,614RefSeq:NZ_AUBL01000036
NZ_AUBL0100003733302143,684RefSeq:NZ_AUBL01000037
NZ_AUBL0100003828250341,892RefSeq:NZ_AUBL01000038
NZ_AUBL0100003930242438,383RefSeq:NZ_AUBL01000039
NZ_AUBL0100004030252338,237RefSeq:NZ_AUBL01000040
NZ_AUBL0100004130270337,997RefSeq:NZ_AUBL01000041
NZ_AUBL0100004231255137,181RefSeq:NZ_AUBL01000042
NZ_AUBL0100004331281235,880RefSeq:NZ_AUBL01000043
NZ_KE38686822190334,437RefSeq:NZ_KE386868
NZ_AUBL0100004631300134,147RefSeq:NZ_AUBL01000046
NZ_AUBL0100004730300032,355RefSeq:NZ_AUBL01000047
NZ_AUBL0100004832283132,162RefSeq:NZ_AUBL01000048
NZ_AUBL0100004926230329,930RefSeq:NZ_AUBL01000049
NZ_AUBL0100005025240129,242RefSeq:NZ_AUBL01000050
NZ_AUBL0100005126213228,524RefSeq:NZ_AUBL01000051
NZ_AUBL0100005222210127,708RefSeq:NZ_AUBL01000052
NZ_AUBL010000531390423,947RefSeq:NZ_AUBL01000053
NZ_AUBL0100005415150023,574RefSeq:NZ_AUBL01000054
NZ_AUBL0100005518170123,319RefSeq:NZ_AUBL01000055
NZ_AUBL0100005625250022,561RefSeq:NZ_AUBL01000056
NZ_AUBL0100005715120322,448RefSeq:NZ_AUBL01000057
NZ_AUBL0100005818171021,624RefSeq:NZ_AUBL01000058
NZ_AUBL0100005916150120,984RefSeq:NZ_AUBL01000059
NZ_AUBL0100006015141020,335RefSeq:NZ_AUBL01000060
NZ_AUBL0100006113120119,531RefSeq:NZ_AUBL01000061
NZ_AUBL0100006212120019,074RefSeq:NZ_AUBL01000062
NZ_AUBL0100006315140118,299RefSeq:NZ_AUBL01000063
NZ_AUBL0100006415140118,208RefSeq:NZ_AUBL01000064
NZ_AUBL0100006513130017,047RefSeq:NZ_AUBL01000065
NZ_AUBL0100006614112116,797RefSeq:NZ_AUBL01000066
NZ_AUBL0100006914130115,592RefSeq:NZ_AUBL01000069
NZ_AUBL0100007114110314,265RefSeq:NZ_AUBL01000071
NZ_AUBL0100007213130013,959RefSeq:NZ_AUBL01000072
NZ_AUBL0100007315140113,700RefSeq:NZ_AUBL01000073
NZ_AUBL010000761311029,956RefSeq:NZ_AUBL01000076
25 Undisplayed Contigs/Replicons8786218133,796
Total:2,9012,689601523,531,393
Ortholog data available?Yes
Database Contents
Genes2,897
Pathways160
Enzymatic Reactions821
Transport Reactions71
Polypeptides2,711
Protein Complexes31
Enzymes487
Transporters274
Compounds654
Transcription Units2,117
tRNAs50
Protein Features3,051
Database Version29.0
Sequence SourceGCF_000429225.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces dentalis
Actinomyces dentalis DSM 19115
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02440612
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120941
EnvironmentHost
Geographic LocationUnited Kingdom
Latitude/Longitude55.957848 N 3.187466 W
Collection Date2003-12-31/2002-12-31
Relationship to Oxygenanaerobe
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.