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 Nonomuraea cavernae CGMCC 4.7368, 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_BMNH010000017977651418847,481RefSeq:NZ_BMNH01000001
NZ_BMNH01000002562549013542,892RefSeq:NZ_BMNH01000002
NZ_BMNH01000003488471107514,887RefSeq:NZ_BMNH01000003
NZ_BMNH0100000437837224404,231RefSeq:NZ_BMNH01000004
NZ_BMNH0100000529328544300,322RefSeq:NZ_BMNH01000005
NZ_BMNH0100000631430167280,231RefSeq:NZ_BMNH01000006
NZ_BMNH0100000724423428276,806RefSeq:NZ_BMNH01000007
NZ_BMNH0100000827326526273,714RefSeq:NZ_BMNH01000008
NZ_BMNH0100000921320517240,431RefSeq:NZ_BMNH01000009
NZ_BMNH0100001019819503217,887RefSeq:NZ_BMNH01000010
NZ_BMNH01000011221211010217,202RefSeq:NZ_BMNH01000011
NZ_BMNH0100001219719205213,264RefSeq:NZ_BMNH01000012
NZ_BMNH0100001320319715205,469RefSeq:NZ_BMNH01000013
NZ_BMNH0100001417717511194,092RefSeq:NZ_BMNH01000014
NZ_BMNH0100001517817701185,430RefSeq:NZ_BMNH01000015
NZ_BMNH01000016158147011178,822RefSeq:NZ_BMNH01000016
NZ_BMNH0100001714314012161,214RefSeq:NZ_BMNH01000017
NZ_BMNH0100001812512203154,891RefSeq:NZ_BMNH01000018
NZ_BMNH0100001914514122145,320RefSeq:NZ_BMNH01000019
NZ_BMNH0100002012011604143,547RefSeq:NZ_BMNH01000020
NZ_BMNH0100002112612321137,088RefSeq:NZ_BMNH01000021
NZ_BMNH0100002210610213134,767RefSeq:NZ_BMNH01000022
NZ_BMNH0100002315715142130,936RefSeq:NZ_BMNH01000023
NZ_BMNH01000024848301115,031RefSeq:NZ_BMNH01000024
NZ_BMNH0100002510810701111,294RefSeq:NZ_BMNH01000025
NZ_BMNH0100002610410220111,029RefSeq:NZ_BMNH01000026
NZ_BMNH01000027989305107,910RefSeq:NZ_BMNH01000027
NZ_BMNH010000281019902105,296RefSeq:NZ_BMNH01000028
NZ_BMNH01000029102934594,513RefSeq:NZ_BMNH01000029
NZ_BMNH0100003090850594,112RefSeq:NZ_BMNH01000030
NZ_BMNH0100003183801288,419RefSeq:NZ_BMNH01000031
NZ_BMNH0100003290788484,560RefSeq:NZ_BMNH01000032
NZ_BMNH0100003383821081,990RefSeq:NZ_BMNH01000033
NZ_BMNH0100003461600170,210RefSeq:NZ_BMNH01000034
NZ_BMNH0100003567640367,346RefSeq:NZ_BMNH01000035
NZ_BMNH0100003652500265,946RefSeq:NZ_BMNH01000036
NZ_BMNH0100003754520265,133RefSeq:NZ_BMNH01000037
NZ_BMNH0100003869680163,866RefSeq:NZ_BMNH01000038
NZ_BMNH0100003959570258,425RefSeq:NZ_BMNH01000039
NZ_BMNH0100004054521156,093RefSeq:NZ_BMNH01000040
NZ_BMNH0100004155520354,386RefSeq:NZ_BMNH01000041
NZ_BMNH0100004239370249,041RefSeq:NZ_BMNH01000042
NZ_BMNH0100004343420146,936RefSeq:NZ_BMNH01000043
NZ_BMNH0100004448452146,464RefSeq:NZ_BMNH01000044
NZ_BMNH0100004539390045,302RefSeq:NZ_BMNH01000045
NZ_BMNH0100004644420242,925RefSeq:NZ_BMNH01000046
NZ_BMNH0100004732310137,055RefSeq:NZ_BMNH01000047
NZ_BMNH0100004829270236,594RefSeq:NZ_BMNH01000048
NZ_BMNH0100004930291030,273RefSeq:NZ_BMNH01000049
NZ_BMNH0100005017150224,904RefSeq:NZ_BMNH01000050
NZ_BMNH0100005119180124,618RefSeq:NZ_BMNH01000051
NZ_BMNH0100005219181022,874RefSeq:NZ_BMNH01000052
NZ_BMNH0100005327250222,197RefSeq:NZ_BMNH01000053
NZ_BMNH0100005419180118,752RefSeq:NZ_BMNH01000054
NZ_BMNH0100005515150018,030RefSeq:NZ_BMNH01000055
NZ_BMNH0100005612120010,421RefSeq:NZ_BMNH01000056
26 Undisplayed Contigs/Replicons36352751,051
Total:7,7067,441761898,123,920
Ortholog data available?No
Database Contents
Genes7,703
Pathways266
Enzymatic Reactions1,373
Transport Reactions65
Polypeptides7,492
Protein Complexes67
Enzymes1,031
Transporters540
Compounds1,065
Transcription Units5,246
tRNAs64
Protein Features8,489
GO Terms1
Database Version29.0
Sequence SourceGCF_014646355.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Streptosporangiales
Streptosporangiaceae
Nonomuraea
Nonomuraea cavernae
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00245206
NCBI BioProjectPRJNA224116
NCBI-Taxonomy2045107
Annotation ProviderNCBI RefSeq
Annotation Date2020-11-23
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.13
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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