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 15-Oct-2019 from the annotated genome of Lactobacillus helveticus IDCC3801, 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 23.0) [Karp16, Karp11] using MetaCyc version 23.1 [1]. 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_CP0353072,1851,828782792,133,343RefSeq:NZ_CP035307
pHel2391028230523,910RefSeq:NZ_CP035308
Total:2,2131,851782842,157,253
Ortholog data available?Yes
Database Contents
Genes2,213
Pathways112
Enzymatic Reactions711
Transport Reactions77
Polypeptides1,852
Protein Complexes28
Enzymes386
Transporters177
Compounds509
Transcription Units1,426
tRNAs63
Protein Features2,378
GO Terms101
Database Version29.0
Synonyms Bacillus casei e
Bacillus e
Caseobacterium e
Lactobacillus helveticum
Lactobacillus sp. JCM 1103
Lactobacillus sp. NCIM 2126
Lactobacillus sp. NCIM 2733
Lactobacillus suntoryeus
Lactobacterium helveticum
Plocamobacterium helveticum
Thermobacterium helveticum
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Lactobacillales
Lactobacillaceae
Lactobacillus
Lactobacillus helveticus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN10782597
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1587
Environmentinfant feces
Geographic LocationSouth Korea
Collection Date2018-11
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2019-01-30
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.7
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

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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