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 Acetobacter malorum DmCS_005, 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_JOJU010000671,0271,0088111,153,578RefSeq:NZ_JOJU01000067
NZ_JOJU0100003622721962260,587RefSeq:NZ_JOJU01000036
NZ_JOJU0100000821320922234,711RefSeq:NZ_JOJU01000008
NZ_JOJU0100007116615862174,493RefSeq:NZ_JOJU01000071
NZ_JOJU0100000514513870169,488RefSeq:NZ_JOJU01000005
NZ_JOJU0100006115915252162,051RefSeq:NZ_JOJU01000061
NZ_JOJU0100003514413572154,732RefSeq:NZ_JOJU01000035
NZ_JOJU0100004710810701146,890RefSeq:NZ_JOJU01000047
NZ_JOJU01000063777700102,505RefSeq:NZ_JOJU01000063
NZ_JOJU01000004858320101,241RefSeq:NZ_JOJU01000004
NZ_JOJU0100004081752495,900RefSeq:NZ_JOJU01000040
NZ_JOJU0100005271710091,326RefSeq:NZ_JOJU01000052
NZ_JOJU0100002690882085,627RefSeq:NZ_JOJU01000026
NZ_JOJU0100001451492061,952RefSeq:NZ_JOJU01000014
NZ_JOJU0100000947440356,950RefSeq:NZ_JOJU01000009
NZ_JOJU0100001944421154,160RefSeq:NZ_JOJU01000019
NZ_JOJU0100007647460148,398RefSeq:NZ_JOJU01000076
NZ_JOJU0100003345450048,085RefSeq:NZ_JOJU01000033
NZ_JOJU0100000140340645,577RefSeq:NZ_JOJU01000001
NZ_JOJU0100004125240122,318RefSeq:NZ_JOJU01000041
NZ_JOJU0100007313130016,686RefSeq:NZ_JOJU01000073
NZ_JOJU0100001313120116,151RefSeq:NZ_JOJU01000013
NZ_JOJU0100002114140011,729RefSeq:NZ_JOJU01000021
NZ_JOJU0100001811110010,807RefSeq:NZ_JOJU01000018
52 Undisplayed Contigs/Replicons9391321187,488
Total:3,0582,94553603,513,430
Ortholog data available?No
Database Contents
Genes3,056
Pathways265
Enzymatic Reactions1,347
Transport Reactions50
Polypeptides2,965
Protein Complexes4
Enzymes730
Transporters297
Compounds991
Transcription Units2,025
tRNAs45
Protein Features3,610
GO Terms218
Database Version29.0
Sequence SourceGCF_000743885.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter malorum
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02849420
NCBI BioProjectPRJNA224116
NCBI-Taxonomy178901
Environmentpure bacterial culture
Geographic LocationUSA
Collection Date2011-10-1
HostDrosophila melanogaster
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-11
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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