Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Actinopolyspora erythraea YIM 90600, 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_KN2141741,2891,25024151,439,557RefSeq:NZ_KN214174
NZ_KN21417565564177765,801RefSeq:NZ_KN214175
NZ_KN21417664863819745,622RefSeq:NZ_KN214176
NZ_KN214177649632611742,036RefSeq:NZ_KN214177
NZ_KN21417852851738581,971RefSeq:NZ_KN214178
NZ_KN21417947746593522,681RefSeq:NZ_KN214179
NZ_KN21418036435158395,801RefSeq:NZ_KN214180
NZ_KN2141811081080099,599RefSeq:NZ_KN214181
NZ_KN214182980117,364RefSeq:NZ_KN214182
28 Undisplayed Contigs/Replicons22213449,467
Total:4,7554,63158665,359,899
Ortholog data available?Yes
Database Contents
Genes4,753
Pathways268
Enzymatic Reactions1,392
Transport Reactions39
Polypeptides4,695
Protein Complexes3
Enzymes877
Transporters342
Compounds1,072
Transcription Units3,563
tRNAs51
Protein Features5,261
GO Terms236
Database Version29.0
Sequence SourceGCF_000763095.1
Synonyms Actinopolyspora sp. YIM 90600
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinopolysporales
Actinopolysporaceae
Actinopolyspora
Actinopolyspora erythraea
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02911260
NCBI BioProjectPRJNA224116
NCBI-Taxonomy414996
Environmentsoil sample
Geographic LocationChina
Collection Date2011-01
Annotation ProviderNCBI RefSeq
Annotation Date2022-01-23
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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