Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Acinetobacter schindleri CIP 107287, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_KB8495761,00496026181,065,534RefSeq:NZ_KB849576
NZ_KB8495758668262911912,463RefSeq:NZ_KB849575
NZ_KB849574598580126645,607RefSeq:NZ_KB849574
NZ_KB849580296277154284,621RefSeq:NZ_KB849580
NZ_KB84957911210129135,285RefSeq:NZ_KB849579
NZ_KB84957886860064,078RefSeq:NZ_KB849578
NZ_KB84957764622059,656RefSeq:NZ_KB849577
NZ_KB84958750463154,948RefSeq:NZ_KB849587
NZ_KB849586503901152,911RefSeq:NZ_KB849586
NZ_KB84958845370850,003RefSeq:NZ_KB849588
NZ_KB84957126220422,935RefSeq:NZ_KB849571
NZ_KB84957211110011,415RefSeq:NZ_KB849572
NZ_KB84957312120010,326RefSeq:NZ_KB849573
NZ_KB8495841313009,424RefSeq:NZ_KB849584
NZ_KB84958566004,659RefSeq:NZ_KB849585
NZ_KB84958366004,434RefSeq:NZ_KB849583
NZ_KB84958120203,187RefSeq:NZ_KB849581
NZ_KB84958222003,072RefSeq:NZ_KB849582
Total:3,2493,08691723,394,558
Ortholog data available?Yes
Database Contents
Genes3,243
Pathways256
Enzymatic Reactions1,285
Transport Reactions54
Polypeptides3,094
Protein Complexes6
Enzymes735
Transporters310
Compounds946
Transcription Units2,271
tRNAs69
Protein Features3,697
GO Terms228
Database Version29.0
Sequence SourceGCF_000368625.1
Synonyms Acinetobacter schindleri CCUG 45560
Acinetobacter schindleri DSM 16038
Acinetobacter schindleri LMG 19576
Acinetobacter schindleri NIPH 1034
Acinetobacter schindleri CIP 107287
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter schindleri
Acinetobacter schindleri CIP 107287
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01828163
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1217988
Environmenturine
Geographic LocationCzech Republic
Collection Date1998
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2021-11-7
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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