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 Actinobaculum sp. oral taxon 183 F0552, 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_KE95140513412635162,904RefSeq:NZ_KE951405
NZ_KE951406979250135,637RefSeq:NZ_KE951406
NZ_KE95141710610123131,498RefSeq:NZ_KE951417
NZ_KE95142810110001125,388RefSeq:NZ_KE951428
NZ_KE951439979412109,436RefSeq:NZ_KE951439
NZ_KE9514501029543106,471RefSeq:NZ_KE951450
NZ_KE9514611061024099,913RefSeq:NZ_KE951461
NZ_KE95147277734082,004RefSeq:NZ_KE951472
NZ_KE95147669681080,189RefSeq:NZ_KE951476
NZ_KE95147768644075,431RefSeq:NZ_KE951477
NZ_KE95140760571273,454RefSeq:NZ_KE951407
NZ_KE95140853520166,150RefSeq:NZ_KE951408
NZ_KE95140951473162,108RefSeq:NZ_KE951409
NZ_KE95141047470060,428RefSeq:NZ_KE951410
NZ_KE95141142410158,781RefSeq:NZ_KE951411
NZ_KE95141235310449,328RefSeq:NZ_KE951412
NZ_KE95141343430048,896RefSeq:NZ_KE951413
NZ_KE95141440390145,310RefSeq:NZ_KE951414
NZ_KE95141541381244,741RefSeq:NZ_KE951415
NZ_KE95141633320144,523RefSeq:NZ_KE951416
NZ_KE95141834340041,867RefSeq:NZ_KE951418
NZ_KE95141933321036,855RefSeq:NZ_KE951419
NZ_KE95142023211134,737RefSeq:NZ_KE951420
NZ_KE95142130280232,670RefSeq:NZ_KE951421
NZ_KE95142227232230,690RefSeq:NZ_KE951422
NZ_KE95142327224129,564RefSeq:NZ_KE951423
NZ_KE95142428243128,213RefSeq:NZ_KE951424
NZ_KE95142524220228,023RefSeq:NZ_KE951425
NZ_KE95142624230128,006RefSeq:NZ_KE951426
NZ_KE95142725250024,348RefSeq:NZ_KE951427
NZ_KE95142913111124,228RefSeq:NZ_KE951429
NZ_KE95143018180022,790RefSeq:NZ_KE951430
NZ_KE95143116160022,058RefSeq:NZ_KE951431
NZ_KE95143215141020,047RefSeq:NZ_KE951432
NZ_KE95143412102019,014RefSeq:NZ_KE951434
NZ_KE95143312110118,923RefSeq:NZ_KE951433
NZ_KE95143512120015,582RefSeq:NZ_KE951435
NZ_KE95143711110013,917RefSeq:NZ_KE951437
NZ_KE95143811110013,402RefSeq:NZ_KE951438
NZ_KE95144014130113,204RefSeq:NZ_KE951440
NZ_KE95144111100112,785RefSeq:NZ_KE951441
32 Undisplayed Contigs/Replicons124122215192,502
Total:1,9611,85550562,366,015
Ortholog data available?No
Database Contents
Genes1,961
Pathways170
Enzymatic Reactions880
Transport Reactions33
Polypeptides1,953
Protein Complexes76
Enzymes447
Transporters160
Compounds645
Transcription Units1,382
tRNAs45
Protein Features2,295
GO Terms152
Database Version29.0
Sequence SourceGCF_000466165.1
Synonyms Actinobaculum sp. oral taxon 183 str. F0552
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinobaculum
unclassified Actinobaculum
Actinobaculum sp. oral taxon 183
Actinobaculum sp. oral taxon 183 F0552
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02436889
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1227261
Environmentsubgingival plaque biofilm of oral cavity
Geographic LocationUnited Kingdom
Collection Date1999
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-18
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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