Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Priestia aryabhattai K13, 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_CP0240355,1815,024157435,035,815RefSeq:NZ_CP024035
unnamed114714613139,863RefSeq:NZ_CP024036
unnamed2826220278,572RefSeq:NZ_CP024037
Total:5,4585,232178485,254,250
Ortholog data available?Yes
Database Contents
Genes5,458
Pathways318
Enzymatic Reactions1,458
Transport Reactions46
Polypeptides5,235
Protein Complexes116
Enzymes974
Transporters551
Compounds1,103
Transcription Units3,931
tRNAs130
Protein Features6,284
GO Terms1,721
Database Version29.1
Sequence SourceGCF_002688605.1
Synonyms Arthrobacter sp. BDR3P1B1-M
Arthrobacter sp. CHR1P1B3-M
Arthrobacter sp. CHR3P2B1-M
Bacillus aryabhattai
Bacillus sp. BHR2P1B1-M
Bacillus sp. JP44SK11
Bacillus sp. JP44SK38
Bacillus sp. KU2
Bacillus sp. LK25
Bacillus sp. T61
Microbacterium sp. CHR3P2B2
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Bacillales
Bacillaceae
Priestia
Priestia aryabhattai
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN07785025
NCBI BioProjectPRJNA224116
NCBI-Taxonomy412384
Environmentenriched culture of compost
Geographic LocationSouth Korea
Collection Date2015-01-14
Annotation ProviderNCBI RefSeq
Annotation Date2022-02-27
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.0
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

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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