Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 13-Mar-2021 from the annotated genome of Actinomyces neuii DSM 8576, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [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_ATUW0100000134333544388,766RefSeq:NZ_ATUW01000001
NZ_ATUW0100000231931054344,337RefSeq:NZ_ATUW01000002
NZ_ATUW0100000324923694283,356RefSeq:NZ_ATUW01000003
NZ_ATUW0100000421821161232,167RefSeq:NZ_ATUW01000004
NZ_ATUW0100000515514870184,621RefSeq:NZ_ATUW01000005
NZ_ATUW0100000615914982164,823RefSeq:NZ_ATUW01000006
NZ_ATUW0100000713613330153,380RefSeq:NZ_ATUW01000007
NZ_ATUW01000008999540100,422RefSeq:NZ_ATUW01000008
NZ_ATUW0100000952510173,520RefSeq:NZ_ATUW01000009
NZ_ATUW0100001044440050,980RefSeq:NZ_ATUW01000010
NZ_ATUW0100001150454149,294RefSeq:NZ_ATUW01000011
NZ_ATUW0100001236350138,796RefSeq:NZ_ATUW01000012
NZ_ATUW0100001329254035,124RefSeq:NZ_ATUW01000013
NZ_ATUW0100001429271131,998RefSeq:NZ_ATUW01000014
NZ_ATUW0100001517160130,188RefSeq:NZ_ATUW01000015
NZ_ATUW0100001623220125,063RefSeq:NZ_ATUW01000016
NZ_ATUW0100001711100117,199RefSeq:NZ_ATUW01000017
NZ_ATUW0100001912110114,463RefSeq:NZ_ATUW01000019
11 Undisplayed Contigs/Replicons41402051,796
Total:2,0231,94357232,270,293
Ortholog data available?Yes
Database Contents
Genes2,019
Pathways174
Enzymatic Reactions869
Transport Reactions55
Polypeptides1,956
Protein Complexes33
Enzymes467
Transporters242
Compounds661
Transcription Units1,161
tRNAs48
Protein Features2,443
Database Version29.0
Sequence SourceGCF_000420405.1
Synonyms Actinomyces neuii subsp. neuii DSM 8576
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces neuii
Actinomyces neuii neuii
Actinomyces neuii neuii DSM 8576
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02441245
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120945
EnvironmentHost
Geographic LocationSwitzerland
Latitude/Longitude47.373943 N 8.53941 E
Relationship to Oxygenfacultative
Temperature Rangemesophile
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2020-04-4
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.