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 gerencseriae DSM 6844, 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_KE386871416389423507,851RefSeq:NZ_KE386871
NZ_AUBN0100000329628628348,302RefSeq:NZ_AUBN01000003
NZ_KE386872257242312321,621RefSeq:NZ_KE386872
NZ_AUBN01000006301284215317,986RefSeq:NZ_AUBN01000006
NZ_KE386873278254915303,046RefSeq:NZ_KE386873
NZ_AUBN01000009222205125260,424RefSeq:NZ_AUBN01000009
NZ_AUBN0100001020619277249,415RefSeq:NZ_AUBN01000010
NZ_AUBN0100001113512348161,355RefSeq:NZ_AUBN01000011
NZ_AUBN0100001211598116153,715RefSeq:NZ_AUBN01000012
NZ_AUBN010000131059627137,165RefSeq:NZ_AUBN01000013
NZ_AUBN01000014959005136,673RefSeq:NZ_AUBN01000014
NZ_AUBN0100001510810332123,096RefSeq:NZ_AUBN01000015
NZ_AUBN0100001664591484,548RefSeq:NZ_AUBN01000016
NZ_AUBN0100001748460268,451RefSeq:NZ_AUBN01000017
NZ_AUBN0100001858552168,038RefSeq:NZ_AUBN01000018
NZ_AUBN0100001938333245,973RefSeq:NZ_AUBN01000019
NZ_AUBN0100002020190131,034RefSeq:NZ_AUBN01000020
NZ_AUBN0100002126241127,821RefSeq:NZ_AUBN01000021
NZ_AUBN0100002219190023,460RefSeq:NZ_AUBN01000022
NZ_AUBN0100002313120120,157RefSeq:NZ_AUBN01000023
8 Undisplayed Contigs/Replicons21193229,888
Total:2,8442,648591373,420,019
Ortholog data available?Yes
Database Contents
Genes2,840
Pathways204
Enzymatic Reactions943
Transport Reactions60
Polypeptides2,659
Protein Complexes32
Enzymes551
Transporters311
Compounds733
Transcription Units2,034
tRNAs50
Protein Features3,082
Database Version29.0
Sequence SourceGCF_000429265.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces gerencseriae
Actinomyces gerencseriae DSM 6844
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02441199
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120943
EnvironmentGingival crevices; Host
Geographic LocationUSA
Latitude/Longitude44.028866 N 92.46855 W
Relationship to Oxygenobligate-anaerobe
Temperature Rangemesophile
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.