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 Metabacillus halosaccharovorans DSM 25387, 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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_KV9173712,8652,77590272,975,153RefSeq:NZ_KV917371
NZ_KV9173722,0071,96344342,157,347RefSeq:NZ_KV917372
NZ_KV91737325124740257,646RefSeq:NZ_KV917373
NZ_MTIR0100000899009,221RefSeq:NZ_MTIR01000008
Total:5,1934,994138615,399,367
Ortholog data available?Yes
Database Contents
Genes5,193
Pathways287
Enzymatic Reactions1,441
Transport Reactions84
Polypeptides4,995
Protein Complexes159
Enzymes901
Transporters521
Compounds1,070
Transcription Units3,644
tRNAs98
Protein Features6,421
GO Terms483
Database Version29.1
Sequence SourceGCF_002019635.1
Synonyms Bacillus halosaccharovorans
Bacillus sp. E33(2010)
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Bacillales
Bacillaceae
Metabacillus
Metabacillus halosaccharovorans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05934487
NCBI BioProjectPRJNA224116
NCBI-Taxonomy930124
Geographic LocationChina
Collection Date2015-12-12
Annotation ProviderNCBI RefSeq
Annotation Date2022-04-18
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.1
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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