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 Acinetobacter tandoii CIP 107469, 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_KE007367789760821811,934RefSeq:NZ_KE007367
NZ_KE007366588557238573,052RefSeq:NZ_KE007366
NZ_KE007365507487218512,466RefSeq:NZ_KE007365
NZ_KE007368462444162469,791RefSeq:NZ_KE007368
NZ_KE007371461438158469,151RefSeq:NZ_KE007371
NZ_KE00736026625376281,238RefSeq:NZ_KE007360
NZ_KE00735917016082191,884RefSeq:NZ_KE007359
NZ_KE00736115014406186,962RefSeq:NZ_KE007361
NZ_KE00736216816143186,275RefSeq:NZ_KE007362
NZ_KE00737513212822137,139RefSeq:NZ_KE007375
NZ_KE007376120100020111,892RefSeq:NZ_KE007376
NZ_KE00737750410958,402RefSeq:NZ_KE007377
NZ_KE00737840350552,090RefSeq:NZ_KE007378
NZ_KE0073521212008,179RefSeq:NZ_KE007352
14 Undisplayed Contigs/Replicons23230528,467
Total:3,9433,743851154,078,922
Ortholog data available?Yes
Database Contents
Genes3,940
Pathways265
Enzymatic Reactions1,307
Transport Reactions73
Polypeptides3,765
Protein Complexes41
Enzymes798
Transporters338
Compounds992
Transcription Units2,636
tRNAs67
Protein Features4,353
GO Terms18
Database Version29.0
Sequence SourceGCF_000400735.1
Synonyms Acinetobacter tandoii CIP 107469
Acinetobacter tandoii CIP 107469 = DSM 14970
Acinetobacter tandoii DSM 14970
Acinetobacter tandoii DSM 14970 = CIP 107469
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter tandoii
Acinetobacter tandoii DSM 14970 = CIP 107469
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01087852
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120927
Environmentactivated sludge plant
Geographic LocationAustralia
Collection Date1991
Annotation ProviderNCBI RefSeq
Annotation Date2019-11-25
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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