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 25-Oct-2020 from the annotated genome of bacterium endosymbiont of Mortierella elongata FMR23-6 , 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_DF8505212,3272,124411622,763,170RefSeq:NZ_DF850521
11 Undisplayed Contigs/Replicons23185932,211
Ortholog data available?No
Database Contents
Genes2,359
Pathways173
Enzymatic Reactions929
Transport Reactions38
Polypeptides2,149
Protein Complexes29
Enzymes513
Transporters160
Compounds678
Transcription Units1,505
tRNAs39
Protein Features3,214
GO Terms7
Database Version29.0
Sequence SourceGCF_000775775.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Burkholderiaceae
unclassified Burkholderiaceae
bacterium endosymbiont of Mortierella elongata FMR23-6
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00020951
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1562701
Environmentenvironmental material
Geographic LocationJapan
Latitude/Longitude36.03 N 140.21 E
Collection Date2014-07-1
HostFungi
Annotation ProviderNCBI
Annotation Date2017-04-9
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+

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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