Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Actinomadura flavalba DSM 45200, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_KB8940931,8651,80326362,052,655RefSeq:NZ_KB894093
NZ_KB894094726708513778,726RefSeq:NZ_KB894094
NZ_KB894095562542713603,710RefSeq:NZ_KB894095
NZ_KB894096541525214583,571RefSeq:NZ_KB894096
NZ_KB894097369353511414,752RefSeq:NZ_KB894097
NZ_KB89409836135155378,497RefSeq:NZ_KB894098
NZ_KB89409924924315238,962RefSeq:NZ_KB894099
NZ_KB89410017816909223,682RefSeq:NZ_KB894100
NZ_KB89410118417554221,622RefSeq:NZ_KB894101
NZ_KB89410216115515169,448RefSeq:NZ_KB894102
NZ_KB89410315815314157,832RefSeq:NZ_KB894103
NZ_KB89410413412950148,694RefSeq:NZ_KB894104
NZ_KB89410536350145,569RefSeq:NZ_KB894105
NZ_KB89410660570343,022RefSeq:NZ_KB894106
NZ_KB89410738360242,543RefSeq:NZ_KB894107
NZ_KB89410837370032,834RefSeq:NZ_KB894108
NZ_KB89410917161018,040RefSeq:NZ_KB894109
NZ_KB89411033004,001RefSeq:NZ_KB894110
NZ_KB89411100002,685RefSeq:NZ_KB894111
NZ_KB89411200002,645RefSeq:NZ_KB894112
NZ_KB89411300002,146RefSeq:NZ_KB894113
NZ_KB89411400002,146RefSeq:NZ_KB894114
Total:5,6795,490641256,167,782
Ortholog data available?Yes
Database Contents
Genes5,679
Pathways250
Enzymatic Reactions1,274
Transport Reactions52
Polypeptides5,498
Protein Complexes45
Enzymes879
Transporters405
Compounds1,007
Transcription Units3,931
tRNAs55
Protein Features6,347
Database Version29.0
Sequence SourceGCF_000374305.1
Synonyms Actinomadura flavalba YIM 61435
Actinomadura sp. YIM 61435
Actinomadura flavalba DSM 45200
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Streptosporangiales
Thermomonosporaceae
Actinomadura
Actinomadura flavalba
Actinomadura flavalba DSM 45200
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02441028
NCBI BioProjectPRJNA224116
NCBI-Taxonomy561175
EnvironmentPlants
Geographic LocationChina
Latitude/Longitude22.023 N 100.798 E
Collection Date2007-11-30/2007-11-1
Relationship to Oxygenaerobe
Temperature Rangemesophile
HostMaytenus austroyunnanensis
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-8
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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