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 colistiniresistens NIPH 2036, 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_KE3403809639346231,019,064RefSeq:NZ_KE340380
NZ_KE3403796476071525720,953RefSeq:NZ_KE340379
NZ_KE3403784113861312435,584RefSeq:NZ_KE340378
NZ_KE3403813893471329412,938RefSeq:NZ_KE340381
NZ_KE340376325307126351,710RefSeq:NZ_KE340376
NZ_KE340383331314134344,903RefSeq:NZ_KE340383
NZ_KE340382220209110239,759RefSeq:NZ_KE340382
NZ_KE34038418217435187,637RefSeq:NZ_KE340384
NZ_KE340377959212101,526RefSeq:NZ_KE340377
NZ_KE34037465574473,431RefSeq:NZ_KE340374
NZ_KE34037517170010,179RefSeq:NZ_KE340375
Total:3,6453,444811203,897,684
Ortholog data available?Yes
Database Contents
Genes3,641
Pathways257
Enzymatic Reactions1,266
Transport Reactions77
Polypeptides3,451
Protein Complexes42
Enzymes751
Transporters349
Compounds942
Transcription Units2,548
tRNAs63
Protein Features4,302
GO Terms12
Database Version29.0
Sequence SourceGCF_000413935.1
Synonyms Acinetobacter genomosp. 13BJ
Acinetobacter genomosp. 14
Acinetobacter genomosp. 14TU
Acinetobacter genomosp. BJ13
Acinetobacter genomosp. TU14
Acinetobacter genomospecies 14
Acinetobacter sp. group 14
Acinetobacter sp. NIPH 1859
Acinetobacter sp. NIPH 2036
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter colistiniresistens
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01087860
NCBI BioProjectPRJNA224116
NCBI-Taxonomy280145
EnvironmentCatheter
Geographic LocationBelgium
Collection Date1990
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-16
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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