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 oligospora ATCC 43269, 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_KI9124101,0481,01412221,148,980RefSeq:NZ_KI912410
NZ_JADG010000038738392321,096,711RefSeq:NZ_JADG01000003
NZ_JADG010000049479243201,044,562RefSeq:NZ_JADG01000004
NZ_KI912411613588223710,544RefSeq:NZ_KI912411
NZ_JADG01000008497480710533,483RefSeq:NZ_JADG01000008
NZ_JADG01000007491466817532,256RefSeq:NZ_JADG01000007
NZ_JADG01000009358343312457,291RefSeq:NZ_JADG01000009
NZ_JADG01000010412390517441,953RefSeq:NZ_JADG01000010
NZ_JADG01000011391377410439,683RefSeq:NZ_JADG01000011
NZ_JADG0100001236835837399,556RefSeq:NZ_JADG01000012
NZ_JADG0100001336935766387,927RefSeq:NZ_JADG01000013
NZ_KI91241231030334356,736RefSeq:NZ_KI912412
NZ_JADG0100001625024136278,732RefSeq:NZ_JADG01000016
NZ_JADG0100001718817936232,230RefSeq:NZ_JADG01000017
NZ_JADG0100001817416554185,051RefSeq:NZ_JADG01000018
NZ_JADG0100001917016712176,812RefSeq:NZ_JADG01000019
NZ_JADG0100002012712124170,311RefSeq:NZ_JADG01000020
NZ_JADG0100002113813512151,432RefSeq:NZ_JADG01000021
NZ_JADG0100002211010514126,748RefSeq:NZ_JADG01000022
NZ_JADG0100002310110100108,354RefSeq:NZ_JADG01000023
NZ_JADG0100002462610160,017RefSeq:NZ_JADG01000024
NZ_KI91241340370355,723RefSeq:NZ_KI912413
NZ_KI91241452492154,896RefSeq:NZ_KI912414
NZ_JADG0100002937361044,288RefSeq:NZ_JADG01000029
NZ_JADG0100003037311538,283RefSeq:NZ_JADG01000030
NZ_JADG0100003128280029,083RefSeq:NZ_JADG01000031
NZ_JADG0100003230263124,985RefSeq:NZ_JADG01000032
NZ_JADG0100003317140321,369RefSeq:NZ_JADG01000033
NZ_JADG0100003420200019,820RefSeq:NZ_JADG01000034
NZ_JADG0100003521210011,835RefSeq:NZ_JADG01000035
NZ_JADG010000361414008,723RefSeq:NZ_JADG01000036
NZ_JADG0100003744004,258RefSeq:NZ_JADG01000037
NZ_JADG0100003811001,033RefSeq:NZ_JADG01000038
Total:8,2987,995812229,353,665
Ortholog data available?Yes
Database Contents
Genes8,295
Pathways278
Enzymatic Reactions1,455
Transport Reactions62
Polypeptides8,001
Protein Complexes56
Enzymes1,109
Transporters652
Compounds1,198
Transcription Units6,233
tRNAs68
Protein Features9,097
Database Version29.0
Sequence SourceGCF_000518265.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Streptosporangiales
Thermomonosporaceae
Actinomadura
Actinomadura oligospora
Actinomadura oligospora ATCC 43269
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02584999
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1399798
Environmentsoil, India
Annotation ProviderNCBI
Annotation Date2017-04-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+
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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