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 lutulentus DSM 45883, 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_JACHWI0100000011,7141,6907171,960,616RefSeq:NZ_JACHWI010000001
NZ_JACHWI0100000021,4651,42816211,642,164RefSeq:NZ_JACHWI010000002
NZ_JACHWI0100000031,0401,0254111,208,547RefSeq:NZ_JACHWI010000003
NZ_JACHWI0100000041,0501,01224141,141,432RefSeq:NZ_JACHWI010000004
NZ_JACHWI010000006607587020713,263RefSeq:NZ_JACHWI010000006
NZ_JACHWI010000005672657105711,589RefSeq:NZ_JACHWI010000005
NZ_JACHWI010000007525506316547,665RefSeq:NZ_JACHWI010000007
NZ_JACHWI01000000841340805465,771RefSeq:NZ_JACHWI010000008
NZ_JACHWI010000009286274120309,629RefSeq:NZ_JACHWI010000009
NZ_JACHWI01000001120019604209,719RefSeq:NZ_JACHWI010000011
NZ_JACHWI01000001022021604207,449RefSeq:NZ_JACHWI010000010
NZ_JACHWI01000001216615934187,244RefSeq:NZ_JACHWI010000012
NZ_JACHWI01000001314914108148,649RefSeq:NZ_JACHWI010000013
NZ_JACHWI010000014150130191135,627RefSeq:NZ_JACHWI010000014
NZ_JACHWI01000001512512500113,026RefSeq:NZ_JACHWI010000015
NZ_JACHWI01000001654530173,762RefSeq:NZ_JACHWI010000016
NZ_JACHWI01000001738380044,778RefSeq:NZ_JACHWI010000017
NZ_JACHWI01000001816141116,228RefSeq:NZ_JACHWI010000018
Total:8,8908,659991329,837,158
Ortholog data available?No
Database Contents
Genes8,890
Pathways294
Enzymatic Reactions1,480
Transport Reactions69
Polypeptides8,680
Protein Complexes68
Enzymes1,183
Transporters798
Compounds1,139
Transcription Units5,895
tRNAs78
Protein Features9,974
Database Version29.0
Sequence SourceGCF_014191235.1
Synonyms Actinoplanes sp. NEAU-GRX6
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Micromonosporales
Micromonosporaceae
Actinoplanes
Actinoplanes lutulentus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN11512348
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1287878
Annotation ProviderNCBI RefSeq
Annotation Date2020-08-16
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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