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 tropicalis NBRC 16470, 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_DF85010133932649394,032RefSeq:NZ_DF850101
NZ_DF85010920319823242,412RefSeq:NZ_DF850109
NZ_DF85008219118722202,859RefSeq:NZ_DF850082
NZ_DF85007616715791186,730RefSeq:NZ_DF850076
NZ_DF85007315814747183,770RefSeq:NZ_DF850073
NZ_DF85010313713340163,301RefSeq:NZ_DF850103
NZ_DF850036978629138,455RefSeq:NZ_DF850036
NZ_DF85010211610844114,140RefSeq:NZ_DF850102
NZ_DF850107818001106,917RefSeq:NZ_DF850107
NZ_DF850090939120100,279RefSeq:NZ_DF850090
NZ_DF85048777760197,875RefSeq:NZ_DF850487
NZ_DF85010587823297,379RefSeq:NZ_DF850105
NZ_DF85009881772288,813RefSeq:NZ_DF850098
NZ_DF85005267620584,087RefSeq:NZ_DF850052
NZ_DF85010480770377,140RefSeq:NZ_DF850104
NZ_DF85007446430366,980RefSeq:NZ_DF850074
NZ_DF85048650500064,543RefSeq:NZ_DF850486
NZ_DF85005141341649,270RefSeq:NZ_DF850051
NZ_DF85048539360348,575RefSeq:NZ_DF850485
NZ_DF85010643401245,122RefSeq:NZ_DF850106
NZ_DF85010834310339,745RefSeq:NZ_DF850108
NZ_DF85009532320037,153RefSeq:NZ_DF850095
NZ_DF85009228271033,835RefSeq:NZ_DF850092
NZ_DF85048427270032,600RefSeq:NZ_DF850484
NZ_DF85010026260032,218RefSeq:NZ_DF850100
NZ_DF85048329280132,139RefSeq:NZ_DF850483
NZ_DF85004631280330,148RefSeq:NZ_DF850046
NZ_DF85048224230130,111RefSeq:NZ_DF850482
NZ_DF85048132320029,855RefSeq:NZ_DF850481
NZ_DF85048027252028,806RefSeq:NZ_DF850480
NZ_DF85047921210028,267RefSeq:NZ_DF850479
NZ_DF85006524220227,774RefSeq:NZ_DF850065
NZ_DF85047821190224,069RefSeq:NZ_DF850478
NZ_DF85047719130621,598RefSeq:NZ_DF850477
NZ_DF85047618180020,716RefSeq:NZ_DF850476
NZ_DF85008617170020,386RefSeq:NZ_DF850086
NZ_DF85047522220018,913RefSeq:NZ_DF850475
NZ_DF85005314140018,322RefSeq:NZ_DF850053
NZ_DF85047420180217,374RefSeq:NZ_DF850474
NZ_DF85047323220117,289RefSeq:NZ_DF850473
NZ_DF85003714130116,242RefSeq:NZ_DF850037
NZ_DF8500911090115,006RefSeq:NZ_DF850091
NZ_DF8504711290314,631RefSeq:NZ_DF850471
NZ_DF85047013130013,991RefSeq:NZ_DF850470
NZ_DF85005714110313,168RefSeq:NZ_DF850057
NZ_DF850043880011,345RefSeq:NZ_DF850043
NZ_DF8500841170410,276RefSeq:NZ_DF850084
406 Undisplayed Contigs/Replicons2802746102487,071
Total:3,1462,899491983,675,727
Ortholog data available?Yes
Database Contents
Genes3,146
Pathways255
Enzymatic Reactions1,232
Transport Reactions51
Polypeptides3,065
Protein Complexes33
Enzymes758
Transporters283
Compounds911
Transcription Units2,305
tRNAs42
Protein Features3,593
GO Terms1
Database Version29.0
Sequence SourceGCF_000787635.2
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter tropicalis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00019861
NCBI BioProjectPRJNA224116
NCBI-Taxonomy104102
Annotation ProviderNCBI RefSeq
Annotation Date2021-01-24
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
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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