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 Acetobacter orientalis 21F-2, 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_BAMX0100001424423644268,874RefSeq:NZ_BAMX01000014
NZ_BAMX0100002423222921254,243RefSeq:NZ_BAMX01000024
NZ_BAMX0100001021220831239,100RefSeq:NZ_BAMX01000010
NZ_BAMX0100000621120362232,297RefSeq:NZ_BAMX01000006
NZ_BAMX0100001315114182166,702RefSeq:NZ_BAMX01000013
NZ_BAMX0100002211611402162,000RefSeq:NZ_BAMX01000022
NZ_BAMX0100001714614501159,374RefSeq:NZ_BAMX01000017
NZ_BAMX0100000710610411136,857RefSeq:NZ_BAMX01000007
NZ_BAMX0100000210910621128,822RefSeq:NZ_BAMX01000002
NZ_BAMX0100000110410112127,470RefSeq:NZ_BAMX01000001
NZ_BAMX01000055959032108,404RefSeq:NZ_BAMX01000055
NZ_BAMX010000031079944106,418RefSeq:NZ_BAMX01000003
NZ_BAMX0100003577770084,970RefSeq:NZ_BAMX01000035
NZ_BAMX0100002061601077,481RefSeq:NZ_BAMX01000020
NZ_BAMX0100003193920176,813RefSeq:NZ_BAMX01000031
NZ_BAMX0100003957551162,342RefSeq:NZ_BAMX01000039
NZ_BAMX0100000941410049,134RefSeq:NZ_BAMX01000009
NZ_BAMX0100000838350347,597RefSeq:NZ_BAMX01000008
NZ_BAMX0100003734331044,485RefSeq:NZ_BAMX01000037
NZ_BAMX0100001540380240,621RefSeq:NZ_BAMX01000015
NZ_BAMX0100001941410040,413RefSeq:NZ_BAMX01000019
NZ_BAMX0100001625230233,342RefSeq:NZ_BAMX01000016
NZ_BAMX0100003830290132,134RefSeq:NZ_BAMX01000038
NZ_BAMX0100001232302030,595RefSeq:NZ_BAMX01000012
NZ_BAMX0100003328261129,812RefSeq:NZ_BAMX01000033
NZ_BAMX0100001827261029,715RefSeq:NZ_BAMX01000018
NZ_BAMX0100002625232026,083RefSeq:NZ_BAMX01000026
NZ_BAMX0100002314140014,955RefSeq:NZ_BAMX01000023
NZ_BAMX0100001113120114,355RefSeq:NZ_BAMX01000011
37 Undisplayed Contigs/Replicons63567985,281
Total:2,5812,48750442,910,689
Ortholog data available?No
Database Contents
Genes2,581
Pathways245
Enzymatic Reactions1,166
Transport Reactions49
Polypeptides2,502
Protein Complexes29
Enzymes631
Transporters246
Compounds868
Transcription Units1,731
tRNAs43
Protein Features3,139
GO Terms589
Database Version29.0
Sequence SourceGCF_000963965.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter orientalis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00036633
NCBI BioProjectPRJNA224116
NCBI-Taxonomy146474
EnvironmentG_DNA_L_Antecubital fossa
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+
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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