Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 27-Feb-2018 from the annotated genome of Acinetobacter apis ANC 5114, 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 22.0) [Karp16, Karp11] using MetaCyc version 21.5 [Caspi18]. 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 Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_FZLN010000011,2891,2473571,380,796RefSeq:NZ_FZLN01000001
NZ_FZLN0100000234032893338,539RefSeq:NZ_FZLN01000002
NZ_FZLN01000003257240134304,364RefSeq:NZ_FZLN01000003
NZ_FZLN0100000414614051156,573RefSeq:NZ_FZLN01000004
NZ_FZLN0100000558571073,135RefSeq:NZ_FZLN01000005
NZ_FZLN0100000644440045,576RefSeq:NZ_FZLN01000006
NZ_FZLN0100000737360141,292RefSeq:NZ_FZLN01000007
NZ_FZLN0100000835350035,211RefSeq:NZ_FZLN01000008
NZ_FZLN0100000912120017,203RefSeq:NZ_FZLN01000009
NZ_FZLN0100001017170014,371RefSeq:NZ_FZLN01000010
NZ_FZLN0100001150505,578RefSeq:NZ_FZLN01000011
NZ_FZLN0100001200001,144RefSeq:NZ_FZLN01000012
Total:2,2402,15668162,413,782
Ortholog data available?Yes
Database Contents
Genes2,238
Pathways189
Enzymatic Reactions1,144
Transport Reactions78
Polypeptides2,159
Protein Complexes11
Enzymes612
Transporters214
Compounds935
Transcription Units1,504
tRNAs59
Protein Features2,803
GO Terms11,829
Database Version29.0
Synonyms JCM 18575
KACC 16906
strain HYN18
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter apis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05444584
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1229165
NCBI Genome Typerepresentative

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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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