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 Actinomycetospora chiangmaiensis DSM 45062, 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_KB9032179148851514924,042RefSeq:NZ_KB903217
NZ_KB90321856155218605,725RefSeq:NZ_KB903218
NZ_KB90322948847468496,619RefSeq:NZ_KB903229
NZ_KB90324046045028482,162RefSeq:NZ_KB903240
NZ_KB903243453439311462,485RefSeq:NZ_KB903243
NZ_KB903244439426013445,577RefSeq:NZ_KB903244
NZ_KB90324530429338309,071RefSeq:NZ_KB903245
NZ_KB90324625324454265,889RefSeq:NZ_KB903246
NZ_KB90324725324634260,285RefSeq:NZ_KB903247
NZ_KB90324821521023216,827RefSeq:NZ_KB903248
NZ_KB90321918718232200,391RefSeq:NZ_KB903219
NZ_KB90322015915423164,614RefSeq:NZ_KB903220
NZ_KB90322114814602158,126RefSeq:NZ_KB903221
NZ_KB903222978935116,426RefSeq:NZ_KB903222
NZ_KB90322311210804107,196RefSeq:NZ_KB903223
NZ_KB90322410410103106,974RefSeq:NZ_KB903224
NZ_KB9032251011001097,290RefSeq:NZ_KB903225
NZ_KB90322692870585,757RefSeq:NZ_KB903226
NZ_KB90322776750174,132RefSeq:NZ_KB903227
NZ_KB90322852455252,026RefSeq:NZ_KB903228
NZ_KB90323045400545,294RefSeq:NZ_KB903230
NZ_KB90323143390443,702RefSeq:NZ_KB903231
NZ_KB90323247440341,737RefSeq:NZ_KB903232
NZ_KB90323330250523,437RefSeq:NZ_KB903233
NZ_KB90323417150221,430RefSeq:NZ_KB903234
NZ_KB9032371310039,920RefSeq:NZ_KB903237
6 Undisplayed Contigs/Replicons24215543,945
Total:5,6945,500591355,861,079
Ortholog data available?Yes
Database Contents
Genes5,689
Pathways247
Enzymatic Reactions1,310
Transport Reactions51
Polypeptides5,505
Protein Complexes37
Enzymes844
Transporters269
Compounds997
Transcription Units3,847
tRNAs47
Protein Features6,295
Database Version29.0
Sequence SourceGCF_000379625.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Pseudonocardiales
Pseudonocardiaceae
Actinomycetospora
Actinomycetospora chiangmaiensis
Actinomycetospora chiangmaiensis DSM 45062
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02256421
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120948
EnvironmentSoil
Geographic LocationThailand
Latitude/Longitude18.79 N 98.66 E
Relationship to Oxygenaerobe
Temperature Rangemesophile
Biotic Relationshipfree-living
Annotation ProviderNCBI
Annotation Date2017-05-17
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.2
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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.