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 13-Mar-2021 from the annotated genome of Acetobacter indonesiensis 5H-1, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [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_BAMW0100000630129632360,736RefSeq:NZ_BAMW01000006
NZ_BAMW0100001528127533320,734RefSeq:NZ_BAMW01000015
NZ_BAMW0100004528227741309,652RefSeq:NZ_BAMW01000045
NZ_BAMW0100003020219750230,542RefSeq:NZ_BAMW01000030
NZ_BAMW0100005718217480204,155RefSeq:NZ_BAMW01000057
NZ_BAMW0100000718618033203,514RefSeq:NZ_BAMW01000007
NZ_BAMW0100000214013541139,519RefSeq:NZ_BAMW01000002
NZ_BAMW0100005011611600126,937RefSeq:NZ_BAMW01000050
NZ_BAMW0100002412311706119,478RefSeq:NZ_BAMW01000024
NZ_BAMW0100002610810350111,366RefSeq:NZ_BAMW01000026
NZ_BAMW01000082807703101,352RefSeq:NZ_BAMW01000082
NZ_BAMW0100000958580079,017RefSeq:NZ_BAMW01000009
NZ_BAMW0100002275730278,700RefSeq:NZ_BAMW01000022
NZ_BAMW0100007868680077,400RefSeq:NZ_BAMW01000078
NZ_BAMW0100001668632372,708RefSeq:NZ_BAMW01000016
NZ_BAMW0100001167622369,259RefSeq:NZ_BAMW01000011
NZ_BAMW0100002154521165,469RefSeq:NZ_BAMW01000021
NZ_BAMW0100009264630159,312RefSeq:NZ_BAMW01000092
NZ_BAMW0100005945450058,219RefSeq:NZ_BAMW01000059
NZ_BAMW0100000445440151,492RefSeq:NZ_BAMW01000004
NZ_BAMW0100003841391150,903RefSeq:NZ_BAMW01000038
NZ_BAMW0100000346380843,458RefSeq:NZ_BAMW01000003
NZ_BAMW0100006335331142,738RefSeq:NZ_BAMW01000063
NZ_BAMW0100001240380242,166RefSeq:NZ_BAMW01000012
NZ_BAMW0100000833310240,757RefSeq:NZ_BAMW01000008
NZ_BAMW0100000533330032,603RefSeq:NZ_BAMW01000005
NZ_BAMW0100004025221228,272RefSeq:NZ_BAMW01000040
NZ_BAMW0100006121210024,163RefSeq:NZ_BAMW01000061
NZ_BAMW0100001919190021,067RefSeq:NZ_BAMW01000019
NZ_BAMW0100001417160120,979RefSeq:NZ_BAMW01000014
NZ_BAMW010000831070312,339RefSeq:NZ_BAMW01000083
NZ_BAMW0100010211100110,479RefSeq:NZ_BAMW01000102
NZ_BAMW010000251514018,600RefSeq:NZ_BAMW01000025
148 Undisplayed Contigs/Replicons120114642198,683
Total:3,0532,91049943,416,768
Ortholog data available?Yes
Database Contents
Genes3,053
Pathways263
Enzymatic Reactions1,253
Transport Reactions55
Polypeptides2,965
Protein Complexes33
Enzymes702
Transporters278
Compounds911
Transcription Units2,125
tRNAs42
Protein Features3,543
GO Terms3
Database Version29.0
Sequence SourceGCF_000963945.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter indonesiensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00036632
NCBI BioProjectPRJNA224116
NCBI-Taxonomy104101
Annotation ProviderNCBI RefSeq
Annotation Date2020-07-26
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.12
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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