Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Prauserella marina DSM 45268, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0163536,3276,26859666,851,918RefSeq:NZ_CP016353
pPmarDSM4526816316301134,495RefSeq:NZ_CP016354
Total:6,5576,43159676,986,413
Ortholog data available?No
Database Contents
Genes6,490
Pathways301
Enzymatic Reactions1,543
Transport Reactions53
Polypeptides6,431
Protein Complexes4
Enzymes1,087
Transporters656
Compounds1,207
Transcription Units4,238
tRNAs47
Protein Features7,695
GO Annotations473
Database Version29.6
Sequence SourceGCF_002240355.1
Synonyms Prauserella sp. Ms498
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Bacillati
Actinomycetota
Actinomycetes
Pseudonocardiales
Pseudonocardiaceae
Prauserella
Prauserella marina
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05284052
NCBI BioProjectPRJNA224116
NCBI-Taxonomy530584
Environmentocean sediment
Geographic LocationChina
Collection Date2009
Annotation ProviderNCBI RefSeq
Annotation Date2021-07-29
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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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