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 campanulatus CECT 3287, 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_JACHXF0100000011,0871,0661381,244,668RefSeq:NZ_JACHXF010000001
NZ_JACHXF010000002641625214755,006RefSeq:NZ_JACHXF010000002
NZ_JACHXF0100000035064861010527,275RefSeq:NZ_JACHXF010000003
NZ_JACHXF01000000439638808460,807RefSeq:NZ_JACHXF010000004
NZ_JACHXF01000000542040776455,889RefSeq:NZ_JACHXF010000005
NZ_JACHXF01000000635935009443,940RefSeq:NZ_JACHXF010000006
NZ_JACHXF01000000740640006424,030RefSeq:NZ_JACHXF010000007
NZ_JACHXF01000000835434338422,896RefSeq:NZ_JACHXF010000008
NZ_JACHXF010000009363348114415,669RefSeq:NZ_JACHXF010000009
NZ_JACHXF01000001041240435406,883RefSeq:NZ_JACHXF010000010
NZ_JACHXF01000001130629556311,392RefSeq:NZ_JACHXF010000011
NZ_JACHXF01000001227026415304,883RefSeq:NZ_JACHXF010000012
NZ_JACHXF01000001325323698282,398RefSeq:NZ_JACHXF010000013
NZ_JACHXF01000001422221444249,002RefSeq:NZ_JACHXF010000014
NZ_JACHXF010000015270260010245,331RefSeq:NZ_JACHXF010000015
NZ_JACHXF01000001622721863235,417RefSeq:NZ_JACHXF010000016
NZ_JACHXF01000001727327003205,239RefSeq:NZ_JACHXF010000017
NZ_JACHXF01000001825024514200,034RefSeq:NZ_JACHXF010000018
NZ_JACHXF01000001916416022190,782RefSeq:NZ_JACHXF010000019
NZ_JACHXF01000002017616871182,997RefSeq:NZ_JACHXF010000020
NZ_JACHXF01000002116416112177,317RefSeq:NZ_JACHXF010000021
NZ_JACHXF01000002214714421163,047RefSeq:NZ_JACHXF010000022
NZ_JACHXF01000002314213624143,903RefSeq:NZ_JACHXF010000023
NZ_JACHXF01000002414213606139,361RefSeq:NZ_JACHXF010000024
NZ_JACHXF01000002513712737139,016RefSeq:NZ_JACHXF010000025
NZ_JACHXF010000026949400107,701RefSeq:NZ_JACHXF010000026
NZ_JACHXF0100000271009703105,586RefSeq:NZ_JACHXF010000027
NZ_JACHXF010000028676403100,605RefSeq:NZ_JACHXF010000028
NZ_JACHXF010000029797900100,189RefSeq:NZ_JACHXF010000029
NZ_JACHXF01000003078761196,800RefSeq:NZ_JACHXF010000030
NZ_JACHXF01000003183791383,546RefSeq:NZ_JACHXF010000031
NZ_JACHXF01000003259560381,898RefSeq:NZ_JACHXF010000032
NZ_JACHXF01000003367660178,925RefSeq:NZ_JACHXF010000033
NZ_JACHXF01000003483790474,859RefSeq:NZ_JACHXF010000034
NZ_JACHXF01000003565630264,530RefSeq:NZ_JACHXF010000035
NZ_JACHXF01000003665641061,483RefSeq:NZ_JACHXF010000036
NZ_JACHXF01000003751470458,552RefSeq:NZ_JACHXF010000037
NZ_JACHXF01000003851450647,792RefSeq:NZ_JACHXF010000038
NZ_JACHXF01000003952470547,708RefSeq:NZ_JACHXF010000039
NZ_JACHXF01000004045450039,685RefSeq:NZ_JACHXF010000040
NZ_JACHXF01000004120200022,729RefSeq:NZ_JACHXF010000041
NZ_JACHXF01000004219162122,694RefSeq:NZ_JACHXF010000042
NZ_JACHXF01000004314130116,302RefSeq:NZ_JACHXF010000043
10 Undisplayed Contigs/Replicons12112422,766
Total:9,1968,912891959,961,532
Ortholog data available?Yes
Database Contents
Genes9,194
Pathways296
Enzymatic Reactions1,500
Transport Reactions71
Polypeptides8,927
Protein Complexes73
Enzymes1,208
Transporters724
Compounds1,150
Transcription Units6,088
tRNAs81
Protein Features9,861
Database Version29.0
Sequence SourceGCF_014191935.1
Synonyms Ampullaria campanulata
Ampullariella campanulata
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Micromonosporales
Micromonosporaceae
Actinoplanes
Actinoplanes campanulatus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN12025112
NCBI BioProjectPRJNA224116
NCBI-Taxonomy113559
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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