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 Acetilactobacillus jinshanensis HSLZ-75, 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_CP0347261,5901,49088121,616,430RefSeq:NZ_CP034726
Ortholog data available?Yes
Database Contents
Genes1,590
Pathways109
Enzymatic Reactions601
Transport Reactions18
Polypeptides1,490
Protein Complexes28
Enzymes330
Transporters144
Compounds420
Transcription Units1,042
tRNAs70
Protein Features1,682
GO Terms129
Database Version29.0
Sequence SourceGCF_004359375.1
Synonyms Lactobacillus jinshani
Lactobacillus sp. HSLZ-75
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Lactobacillales
Lactobacillaceae
Acetilactobacillus
Acetilactobacillus jinshanensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN10651137
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1720083
EnvironmentVinegar Pei
Geographic LocationChina
Collection Date2015-04
Annotation ProviderNCBI RefSeq
Annotation Date2022-06-20
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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