Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Acetobacter papayae JCM 25143, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_BAIN01000001171101367175,293RefSeq:NZ_BAIN01000001
NZ_BAIN0100000210279023118,879RefSeq:NZ_BAIN01000002
NZ_BAIN01000003835722498,850RefSeq:NZ_BAIN01000003
NZ_BAIN01000004896502497,494RefSeq:NZ_BAIN01000004
NZ_BAIN01000005815722290,957RefSeq:NZ_BAIN01000005
NZ_BAIN01000006885413387,116RefSeq:NZ_BAIN01000006
NZ_BAIN01000007664102573,799RefSeq:NZ_BAIN01000007
NZ_BAIN01000008644022272,813RefSeq:NZ_BAIN01000008
NZ_BAIN01000009795632071,425RefSeq:NZ_BAIN01000009
NZ_BAIN01000010705211770,252RefSeq:NZ_BAIN01000010
NZ_BAIN01000011654901668,457RefSeq:NZ_BAIN01000011
NZ_BAIN01000012604011967,581RefSeq:NZ_BAIN01000012
NZ_BAIN01000013533431661,096RefSeq:NZ_BAIN01000013
NZ_BAIN01000014544201254,262RefSeq:NZ_BAIN01000014
NZ_BAIN01000015372501250,640RefSeq:NZ_BAIN01000015
NZ_BAIN01000016432601749,732RefSeq:NZ_BAIN01000016
NZ_BAIN01000017412311747,909RefSeq:NZ_BAIN01000017
NZ_BAIN01000018372511142,303RefSeq:NZ_BAIN01000018
NZ_BAIN01000019372611041,042RefSeq:NZ_BAIN01000019
NZ_BAIN0100002051430839,757RefSeq:NZ_BAIN01000020
NZ_BAIN0100002132232739,377RefSeq:NZ_BAIN01000021
NZ_BAIN01000022452831438,686RefSeq:NZ_BAIN01000022
NZ_BAIN0100002326190738,048RefSeq:NZ_BAIN01000023
NZ_BAIN0100002435290637,634RefSeq:NZ_BAIN01000024
NZ_BAIN0100002526191634,416RefSeq:NZ_BAIN01000025
NZ_BAIN0100002631260533,376RefSeq:NZ_BAIN01000026
NZ_BAIN01000027271501231,725RefSeq:NZ_BAIN01000027
NZ_BAIN01000028362501131,681RefSeq:NZ_BAIN01000028
NZ_BAIN0100002939370231,573RefSeq:NZ_BAIN01000029
NZ_BAIN0100003023180531,376RefSeq:NZ_BAIN01000030
NZ_BAIN01000031241301130,917RefSeq:NZ_BAIN01000031
NZ_BAIN0100003233231930,805RefSeq:NZ_BAIN01000032
NZ_BAIN0100003330221729,001RefSeq:NZ_BAIN01000033
NZ_BAIN0100003431220928,558RefSeq:NZ_BAIN01000034
NZ_BAIN0100003525200527,498RefSeq:NZ_BAIN01000035
NZ_BAIN0100003628240427,466RefSeq:NZ_BAIN01000036
NZ_BAIN0100003725161826,809RefSeq:NZ_BAIN01000037
NZ_BAIN0100003826171825,864RefSeq:NZ_BAIN01000038
NZ_BAIN0100003919100925,097RefSeq:NZ_BAIN01000039
NZ_BAIN0100004019130623,578RefSeq:NZ_BAIN01000040
NZ_BAIN0100004123150823,561RefSeq:NZ_BAIN01000041
NZ_BAIN0100004220150523,499RefSeq:NZ_BAIN01000042
NZ_BAIN0100004323131922,256RefSeq:NZ_BAIN01000043
NZ_BAIN0100004422171422,224RefSeq:NZ_BAIN01000044
NZ_BAIN0100004522170520,973RefSeq:NZ_BAIN01000045
NZ_BAIN0100004621130820,829RefSeq:NZ_BAIN01000046
NZ_BAIN0100004716110519,693RefSeq:NZ_BAIN01000047
NZ_BAIN0100004823170619,473RefSeq:NZ_BAIN01000048
NZ_BAIN0100004920151417,738RefSeq:NZ_BAIN01000049
NZ_BAIN0100005023191317,689RefSeq:NZ_BAIN01000050
NZ_BAIN0100005117110616,789RefSeq:NZ_BAIN01000051
NZ_BAIN0100005216130316,426RefSeq:NZ_BAIN01000052
NZ_BAIN0100005315100516,310RefSeq:NZ_BAIN01000053
NZ_BAIN010000541280415,455RefSeq:NZ_BAIN01000054
NZ_BAIN0100005521161414,718RefSeq:NZ_BAIN01000055
NZ_BAIN0100005713110214,498RefSeq:NZ_BAIN01000057
NZ_BAIN0100005813110213,839RefSeq:NZ_BAIN01000058
NZ_BAIN010000591281313,605RefSeq:NZ_BAIN01000059
NZ_BAIN0100006016112313,264RefSeq:NZ_BAIN01000060
NZ_BAIN0100006111100113,159RefSeq:NZ_BAIN01000061
NZ_BAIN010000621380512,714RefSeq:NZ_BAIN01000062
NZ_BAIN0100006416150112,641RefSeq:NZ_BAIN01000064
NZ_BAIN010000651370612,297RefSeq:NZ_BAIN01000065
NZ_BAIN0100006614102212,254RefSeq:NZ_BAIN01000066
NZ_BAIN010000701231811,849RefSeq:NZ_BAIN01000070
NZ_BAIN010000711180311,442RefSeq:NZ_BAIN01000071
NZ_BAIN010000721390411,315RefSeq:NZ_BAIN01000072
NZ_BAIN010000731090111,234RefSeq:NZ_BAIN01000073
NZ_BAIN010000751280410,796RefSeq:NZ_BAIN01000075
NZ_BAIN010000761160510,772RefSeq:NZ_BAIN01000076
NZ_BAIN010000931210027,262RefSeq:NZ_BAIN01000093
NZ_BAIN01000095129036,907RefSeq:NZ_BAIN01000095
105 Undisplayed Contigs/Replicons2272198182450,457
Total:2,8681,936508823,041,080
Ortholog data available?Yes
Database Contents
Genes2,868
Pathways162
Enzymatic Reactions893
Transport Reactions33
Polypeptides2,032
Protein Complexes18
Enzymes406
Transporters151
Compounds752
Transcription Units1,962
tRNAs43
Protein Features2,136
GO Terms1
Database Version29.0
Sequence SourceGCF_000613285.1
Synonyms Acetobacter papayae 1-25
Acetobacter papayae LMG 26456
Acetobacter sp. 1-25
Acetobacter sp. JCM 25143
Acetobacter papayae JCM 25143
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter papayae
Acetobacter papayae JCM 25143
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00008625
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1234671
Annotation ProviderNCBI RefSeq
Annotation Date2019-08-27
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.9
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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