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 Actinomadura cremea JCM 3308, 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_BMRF010000011,0661,02312311,107,176RefSeq:NZ_BMRF01000001
NZ_BMRF01000002826805615880,391RefSeq:NZ_BMRF01000002
NZ_BMRF0100000363762485655,484RefSeq:NZ_BMRF01000003
NZ_BMRF0100000452150957582,097RefSeq:NZ_BMRF01000004
NZ_BMRF0100000542240679437,516RefSeq:NZ_BMRF01000005
NZ_BMRF0100000632832125344,948RefSeq:NZ_BMRF01000006
NZ_BMRF0100000726925928314,518RefSeq:NZ_BMRF01000007
NZ_BMRF0100000828127308293,593RefSeq:NZ_BMRF01000008
NZ_BMRF0100000925324607277,280RefSeq:NZ_BMRF01000009
NZ_BMRF0100001023422923254,760RefSeq:NZ_BMRF01000010
NZ_BMRF0100001121320715225,981RefSeq:NZ_BMRF01000011
NZ_BMRF0100001220820224215,729RefSeq:NZ_BMRF01000012
NZ_BMRF0100001314714205214,211RefSeq:NZ_BMRF01000013
NZ_BMRF0100001419418851201,300RefSeq:NZ_BMRF01000014
NZ_BMRF0100001517717124200,219RefSeq:NZ_BMRF01000015
NZ_BMRF0100001616615943192,191RefSeq:NZ_BMRF01000016
NZ_BMRF0100001715314904174,729RefSeq:NZ_BMRF01000017
NZ_BMRF0100001815315003169,987RefSeq:NZ_BMRF01000018
NZ_BMRF01000019151139012156,092RefSeq:NZ_BMRF01000019
NZ_BMRF0100002013512906155,078RefSeq:NZ_BMRF01000020
NZ_BMRF0100002112412103133,045RefSeq:NZ_BMRF01000021
NZ_BMRF0100002214313742130,006RefSeq:NZ_BMRF01000022
NZ_BMRF0100002311211101128,932RefSeq:NZ_BMRF01000023
NZ_BMRF0100002411411202120,887RefSeq:NZ_BMRF01000024
NZ_BMRF01000025746905109,546RefSeq:NZ_BMRF01000025
NZ_BMRF01000026979304101,830RefSeq:NZ_BMRF01000026
NZ_BMRF01000027929200100,265RefSeq:NZ_BMRF01000027
NZ_BMRF01000028100913697,107RefSeq:NZ_BMRF01000028
NZ_BMRF0100002990853288,219RefSeq:NZ_BMRF01000029
NZ_BMRF0100003070690173,445RefSeq:NZ_BMRF01000030
NZ_BMRF0100003164604070,970RefSeq:NZ_BMRF01000031
NZ_BMRF0100003264630170,054RefSeq:NZ_BMRF01000032
NZ_BMRF0100003361590265,947RefSeq:NZ_BMRF01000033
NZ_BMRF0100003455520359,605RefSeq:NZ_BMRF01000034
NZ_BMRF0100003562610157,035RefSeq:NZ_BMRF01000035
NZ_BMRF0100003631310039,405RefSeq:NZ_BMRF01000036
NZ_BMRF0100003734310332,472RefSeq:NZ_BMRF01000037
NZ_BMRF0100003821190232,098RefSeq:NZ_BMRF01000038
NZ_BMRF0100003918170131,180RefSeq:NZ_BMRF01000039
NZ_BMRF0100004031291128,161RefSeq:NZ_BMRF01000040
NZ_BMRF0100004121200128,117RefSeq:NZ_BMRF01000041
NZ_BMRF0100004221190227,969RefSeq:NZ_BMRF01000042
NZ_BMRF0100004415150026,282RefSeq:NZ_BMRF01000044
NZ_BMRF0100004517160125,392RefSeq:NZ_BMRF01000045
NZ_BMRF0100004622210123,824RefSeq:NZ_BMRF01000046
NZ_BMRF0100004718171020,542RefSeq:NZ_BMRF01000047
NZ_BMRF0100004822210120,247RefSeq:NZ_BMRF01000048
NZ_BMRF0100005016100614,270RefSeq:NZ_BMRF01000050
NZ_BMRF01000063139135,854RefSeq:NZ_BMRF01000063
287 Undisplayed Contigs/Replicons1221132071449,624
Total:8,3607,994952719,265,610
Ortholog data available?Yes
Database Contents
Genes8,348
Pathways275
Enzymatic Reactions1,452
Transport Reactions63
Polypeptides8,106
Protein Complexes62
Enzymes990
Transporters605
Compounds1,130
Transcription Units5,872
tRNAs77
Protein Features9,158
Database Version29.0
Sequence SourceGCF_014648495.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Streptosporangiales
Thermomonosporaceae
Actinomadura
Actinomadura cremea
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00245351
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1991
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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