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 12-July-2021 from the annotated genome of Acinetobacter sp. Ac_1271 WCHAc060096, 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 25.0 [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_RAXU0100000134633385377,956RefSeq:NZ_RAXU01000001
NZ_RAXU0100000226726430282,037RefSeq:NZ_RAXU01000002
NZ_RAXU0100000323323012255,631RefSeq:NZ_RAXU01000003
NZ_RAXU0100000421720845223,123RefSeq:NZ_RAXU01000004
NZ_RAXU0100000516816260185,234RefSeq:NZ_RAXU01000005
NZ_RAXU0100000616415761172,997RefSeq:NZ_RAXU01000006
NZ_RAXU0100000714714601157,460RefSeq:NZ_RAXU01000007
NZ_RAXU0100000814113704149,878RefSeq:NZ_RAXU01000008
NZ_RAXU0100000911510663130,856RefSeq:NZ_RAXU01000009
NZ_RAXU0100001013913135123,713RefSeq:NZ_RAXU01000010
NZ_RAXU0100001110710601116,446RefSeq:NZ_RAXU01000011
NZ_RAXU0100001211110641100,309RefSeq:NZ_RAXU01000012
NZ_RAXU0100001394891494,397RefSeq:NZ_RAXU01000013
NZ_RAXU0100001478744092,700RefSeq:NZ_RAXU01000014
NZ_RAXU0100001577743091,009RefSeq:NZ_RAXU01000015
NZ_RAXU0100001691856086,132RefSeq:NZ_RAXU01000016
NZ_RAXU0100001776741185,875RefSeq:NZ_RAXU01000017
NZ_RAXU0100001880800083,472RefSeq:NZ_RAXU01000018
NZ_RAXU0100001957561074,832RefSeq:NZ_RAXU01000019
NZ_RAXU0100002063593165,411RefSeq:NZ_RAXU01000020
NZ_RAXU0100002160571261,262RefSeq:NZ_RAXU01000021
NZ_RAXU0100002244430146,547RefSeq:NZ_RAXU01000022
NZ_RAXU0100002347460144,114RefSeq:NZ_RAXU01000023
NZ_RAXU0100002431310042,046RefSeq:NZ_RAXU01000024
NZ_RAXU0100002528280036,718RefSeq:NZ_RAXU01000025
NZ_RAXU0100002632320034,831RefSeq:NZ_RAXU01000026
NZ_RAXU0100002727260129,447RefSeq:NZ_RAXU01000027
NZ_RAXU0100002826250128,754RefSeq:NZ_RAXU01000028
NZ_RAXU0100002924240022,824RefSeq:NZ_RAXU01000029
NZ_RAXU0100003021200120,044RefSeq:NZ_RAXU01000030
NZ_RAXU0100003116120419,373RefSeq:NZ_RAXU01000031
NZ_RAXU0100003221180318,341RefSeq:NZ_RAXU01000032
NZ_RAXU0100003319190016,729RefSeq:NZ_RAXU01000033
NZ_RAXU0100003413130014,096RefSeq:NZ_RAXU01000034
NZ_RAXU0100003514140013,434RefSeq:NZ_RAXU01000035
NZ_RAXU0100003617160113,263RefSeq:NZ_RAXU01000036
NZ_RAXU0100003715150012,030RefSeq:NZ_RAXU01000037
NZ_RAXU0100003815150010,955RefSeq:NZ_RAXU01000038
NZ_RAXU010000401311208,220RefSeq:NZ_RAXU01000040
NZ_RAXU010000411615106,557RefSeq:NZ_RAXU01000041
54 Undisplayed Contigs/Replicons605831992,189
Total:3,3503,21567683,541,242
Ortholog data available?Yes
Database Contents
Genes3,349
Pathways262
Enzymatic Reactions1,301
Transport Reactions85
Polypeptides3,275
Protein Complexes46
Enzymes745
Transporters333
Compounds972
Transcription Units2,313
tRNAs59
Protein Features3,993
GO Terms11
Database Version29.0
Sequence SourceGCF_003611455.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
unclassified Acinetobacter
Acinetobacter sp. Ac_1271
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN09842374
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1843371
EnvironmentSewage
Geographic LocationChina
Collection Date2018
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-20
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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