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 13-Mar-2021 from the annotated genome of Pseudonocardia autotrophica DSM 43083, 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 24.5 [Caspi19]. 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_MIFY010000061,0149873241,198,703RefSeq:NZ_MIFY01000006
NZ_MIFY01000014707689513741,893RefSeq:NZ_MIFY01000014
NZ_MIFY0100000539037974430,669RefSeq:NZ_MIFY01000005
NZ_MIFY0100002839838936406,933RefSeq:NZ_MIFY01000028
NZ_MIFY0100002235634646345,677RefSeq:NZ_MIFY01000022
NZ_MIFY0100001134633394338,274RefSeq:NZ_MIFY01000011
NZ_MIFY0100000326325814282,049RefSeq:NZ_MIFY01000003
NZ_MIFY0100001725424842276,534RefSeq:NZ_MIFY01000017
NZ_MIFY0100003023222543255,175RefSeq:NZ_MIFY01000030
NZ_MIFY0100001223323021229,698RefSeq:NZ_MIFY01000012
NZ_MIFY0100000119919243208,047RefSeq:NZ_MIFY01000001
NZ_MIFY0100001317116713181,463RefSeq:NZ_MIFY01000013
NZ_MIFY0100000915314742169,463RefSeq:NZ_MIFY01000009
NZ_MIFY0100002116715917162,048RefSeq:NZ_MIFY01000021
NZ_MIFY0100001913312724144,301RefSeq:NZ_MIFY01000019
NZ_MIFY0100002413212831135,793RefSeq:NZ_MIFY01000024
NZ_MIFY010000291029840110,598RefSeq:NZ_MIFY01000029
NZ_MIFY0100001067602567,150RefSeq:NZ_MIFY01000010
NZ_MIFY0100001849463054,015RefSeq:NZ_MIFY01000018
NZ_MIFY0100002317161018,857RefSeq:NZ_MIFY01000023
NZ_MIFY0100002715140115,121RefSeq:NZ_MIFY01000027
NZ_MIFY010000151292113,733RefSeq:NZ_MIFY01000015
8 Undisplayed Contigs/Replicons27236943,902
Total:5,4485,270751035,830,096
Ortholog data available?Yes
Database Contents
Genes5,439
Pathways266
Enzymatic Reactions1,383
Transport Reactions77
Polypeptides5,286
Protein Complexes44
Enzymes961
Transporters460
Compounds1,083
Transcription Units3,666
tRNAs52
Protein Features6,386
GO Terms1
Database Version29.0
Sequence SourceGCF_001902615.1
Synonyms Amycolata autotrophica
Nocardia autotrophica
Streptomyces autotrophicus
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Pseudonocardiales
Pseudonocardiaceae
Pseudonocardia
Pseudonocardia autotrophica
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05718038
NCBI BioProjectPRJNA224116
NCBI-Taxonomy2074
Geographic LocationUSA
Collection Date1952
HostEmbryophyta
Annotation ProviderNCBI RefSeq
Annotation Date2020-06-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi19: 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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