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 slackii ATCC 49928, 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_AUAK0100000131129966379,852RefSeq:NZ_AUAK01000001
NZ_KE386778248233105304,282RefSeq:NZ_KE386778
NZ_KE38677924924243297,149RefSeq:NZ_KE386779
NZ_AUAK0100000718417932221,996RefSeq:NZ_AUAK01000007
NZ_KE38678016916126197,536RefSeq:NZ_KE386780
NZ_AUAK0100001012311904139,487RefSeq:NZ_AUAK01000010
NZ_KE3867811049734127,029RefSeq:NZ_KE386781
NZ_KE3867821009901108,798RefSeq:NZ_KE386782
NZ_AUAK01000015787503107,388RefSeq:NZ_AUAK01000015
NZ_AUAK0100001688815294,955RefSeq:NZ_AUAK01000016
NZ_AUAK0100001791900194,626RefSeq:NZ_AUAK01000017
NZ_AUAK0100001876731286,610RefSeq:NZ_AUAK01000018
NZ_KE38678368616180,514RefSeq:NZ_KE386783
NZ_AUAK0100002157551177,084RefSeq:NZ_AUAK01000021
NZ_AUAK0100002257541266,013RefSeq:NZ_AUAK01000022
NZ_AUAK0100002314140063,593RefSeq:NZ_AUAK01000023
NZ_AUAK0100002442390362,602RefSeq:NZ_AUAK01000024
NZ_AUAK0100002549461250,709RefSeq:NZ_AUAK01000025
NZ_AUAK0100002643362548,382RefSeq:NZ_AUAK01000026
NZ_AUAK0100002741382147,913RefSeq:NZ_AUAK01000027
NZ_AUAK0100002843394046,579RefSeq:NZ_AUAK01000028
NZ_AUAK0100002935323041,776RefSeq:NZ_AUAK01000029
NZ_AUAK0100003033320141,766RefSeq:NZ_AUAK01000030
NZ_KE38678427250241,551RefSeq:NZ_KE386784
NZ_KE38678534313040,607RefSeq:NZ_KE386785
NZ_KE38678628270140,076RefSeq:NZ_KE386786
NZ_AUAK0100003923210231,422RefSeq:NZ_AUAK01000039
NZ_AUAK0100004027260130,842RefSeq:NZ_AUAK01000040
NZ_AUAK0100004129281029,379RefSeq:NZ_AUAK01000041
NZ_AUAK0100004223220129,112RefSeq:NZ_AUAK01000042
NZ_AUAK0100004323210227,555RefSeq:NZ_AUAK01000043
NZ_KE38678718171027,068RefSeq:NZ_KE386787
NZ_AUAK0100004815140117,557RefSeq:NZ_AUAK01000048
NZ_AUAK0100004917170016,497RefSeq:NZ_AUAK01000049
12 Undisplayed Contigs/Replicons39390352,787
Total:2,6092,48259683,171,092
Ortholog data available?Yes
Database Contents
Genes2,604
Pathways200
Enzymatic Reactions894
Transport Reactions59
Polypeptides2,510
Protein Complexes43
Enzymes532
Transporters268
Compounds670
Transcription Units1,853
tRNAs49
Protein Features3,074
Database Version29.0
Sequence SourceGCF_000428685.1
Synonyms Actinomyces slackii Sh13/4563
Actinomyces slackii ATCC 49928
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces slackii
Actinomyces slackii ATCC 49928
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02441219
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1278298
EnvironmentHost
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+

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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