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 sp. LHW63021 LHW63021, 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_QLYX01000001732720102816,381RefSeq:NZ_QLYX01000001
NZ_QLYX01000002602576224684,335RefSeq:NZ_QLYX01000002
NZ_QLYX0100000356455545582,755RefSeq:NZ_QLYX01000003
NZ_QLYX0100000453552483537,560RefSeq:NZ_QLYX01000004
NZ_QLYX01000005467452114473,139RefSeq:NZ_QLYX01000005
NZ_QLYX0100000634834620398,508RefSeq:NZ_QLYX01000006
NZ_QLYX0100000734534023357,298RefSeq:NZ_QLYX01000007
NZ_QLYX0100000830730322310,454RefSeq:NZ_QLYX01000008
NZ_QLYX0100000930829927309,660RefSeq:NZ_QLYX01000009
NZ_QLYX0100001028828224293,461RefSeq:NZ_QLYX01000010
NZ_QLYX0100001121821503256,555RefSeq:NZ_QLYX01000011
NZ_QLYX0100001221021000255,108RefSeq:NZ_QLYX01000012
NZ_QLYX0100001324624051249,753RefSeq:NZ_QLYX01000013
NZ_QLYX0100001419218921222,141RefSeq:NZ_QLYX01000014
NZ_QLYX0100001520119911212,415RefSeq:NZ_QLYX01000015
NZ_QLYX0100001618518131209,549RefSeq:NZ_QLYX01000016
NZ_QLYX0100001718117722200,303RefSeq:NZ_QLYX01000017
NZ_QLYX0100001815415121158,868RefSeq:NZ_QLYX01000018
NZ_QLYX0100001914013712144,105RefSeq:NZ_QLYX01000019
NZ_QLYX0100002013713700143,782RefSeq:NZ_QLYX01000020
NZ_QLYX0100002111811611132,527RefSeq:NZ_QLYX01000021
NZ_QLYX01000022868402103,633RefSeq:NZ_QLYX01000022
NZ_QLYX0100002389862198,384RefSeq:NZ_QLYX01000023
NZ_QLYX0100002486860093,482RefSeq:NZ_QLYX01000024
NZ_QLYX0100002584830190,159RefSeq:NZ_QLYX01000025
NZ_QLYX0100002664593274,026RefSeq:NZ_QLYX01000026
NZ_QLYX0100002734312141,580RefSeq:NZ_QLYX01000027
14 Undisplayed Contigs/Replicons17153453,656
Total:6,9436,79392587,503,577
Ortholog data available?No
Database Contents
Genes6,937
Pathways271
Enzymatic Reactions1,394
Transport Reactions49
Polypeptides6,815
Protein Complexes58
Enzymes988
Transporters489
Compounds1,080
Transcription Units4,794
tRNAs79
Protein Features7,847
GO Terms19,698
Database Version29.0
Sequence SourceGCF_003289645.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Streptosporangiales
Thermomonosporaceae
Actinomadura
unclassified Actinomadura
Actinomadura sp. LHW63021
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN09453373
NCBI BioProjectPRJNA224116
NCBI-Taxonomy2231787
Geographic LocationChina
Latitude/Longitude16.75 N 112.35 E
Collection Date2015-04-30
Annotation ProviderNCBI RefSeq
Annotation Date2021-01-5
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
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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