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 Photorhabdus luminescens DSM 3368, 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_JXSK0100000196194417411,199,632RefSeq:NZ_JXSK01000001
NZ_JXSK01000002630622822736,256RefSeq:NZ_JXSK01000002
NZ_JXSK010000035585421623628,123RefSeq:NZ_JXSK01000003
NZ_JXSK010000044223932916530,955RefSeq:NZ_JXSK01000004
NZ_JXSK01000005299294616374,921RefSeq:NZ_JXSK01000005
NZ_JXSK01000008251248325362,969RefSeq:NZ_JXSK01000008
NZ_JXSK01000006192191115314,884RefSeq:NZ_JXSK01000006
NZ_JXSK01000007210206424306,351RefSeq:NZ_JXSK01000007
NZ_JXSK010000092622481612267,191RefSeq:NZ_JXSK01000009
NZ_JXSK01000011170169110220,732RefSeq:NZ_JXSK01000011
NZ_JXSK0100001015414969180,906RefSeq:NZ_JXSK01000010
NZ_JXSK0100001210391132112,335RefSeq:NZ_JXSK01000012
NZ_JXSK0100001310310132105,084RefSeq:NZ_JXSK01000013
NZ_JXSK0100001475724388,892RefSeq:NZ_JXSK01000014
NZ_JXSK0100001621210124,244RefSeq:NZ_JXSK01000016
NZ_JXSK01000015990711,495RefSeq:NZ_JXSK01000015
Total:4,6484,3001272285,464,970
Ortholog data available?No
Database Contents
Genes4,420
Pathways365
Enzymatic Reactions1,786
Transport Reactions144
Polypeptides4,306
Protein Complexes12
Enzymes1,022
Transporters445
Compounds1,259
Transcription Units2,896
tRNAs90
Protein Features5,816
GO Annotations325
Database Version29.6
Sequence SourceGCF_001083805.1
Synonyms Photorhabdus luminescens subsp. luminescens
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Morganellaceae
Photorhabdus
Photorhabdus luminescens
Photorhabdus luminescens luminescens
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03292525
NCBI BioProjectPRJNA224116
NCBI-Taxonomy171439
Geographic LocationAustralia
Collection Date1979
HostHeterorhabditis bacteriophora
Annotation ProviderNCBI RefSeq
Annotation Date2021-03-31
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.1
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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