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 12-July-2021 from the annotated genome of Actinoplanes lobatus DSM 43150, 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 25.0 [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_JACHNC0100000019,3869,11010417210,370,198RefSeq:NZ_JACHNC010000001
NZ_JACHNC01000000263630035,535RefSeq:NZ_JACHNC010000002
Total:9,4499,17310417210,405,733
Ortholog data available?No
Database Contents
Genes9,449
Pathways285
Enzymatic Reactions1,456
Transport Reactions76
Polypeptides9,174
Protein Complexes77
Enzymes1,207
Transporters772
Compounds1,101
Transcription Units6,305
tRNAs83
Protein Features10,360
Database Version29.0
Sequence SourceGCF_014205215.1
Synonyms Ampullaria lobata
Ampullariella lobata
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Micromonosporales
Micromonosporaceae
Actinoplanes
Actinoplanes lobatus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05878390
NCBI BioProjectPRJNA224116
NCBI-Taxonomy113568
Annotation ProviderNCBI RefSeq
Annotation Date2020-09-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.12
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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