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 13-Mar-2021 from the annotated genome of Acinetobacter indicus CIP 110367, 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 24.5 [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_KI5307459198652628949,323RefSeq:NZ_KI530745
NZ_KI5307547657222914800,571RefSeq:NZ_KI530754
NZ_KI5307555455092115560,030RefSeq:NZ_KI530755
NZ_KI530756333312165356,705RefSeq:NZ_KI530756
NZ_KI530757165142716182,761RefSeq:NZ_KI530757
NZ_KI530758129114015144,426RefSeq:NZ_KI530758
NZ_KI53075910594101111,614RefSeq:NZ_KI530759
NZ_KI53076062555262,250RefSeq:NZ_KI530760
NZ_KI53076112110112,013RefSeq:NZ_KI530761
8 Undisplayed Contigs/Replicons29290131,946
Total:3,0652,853114983,211,639
Ortholog data available?Yes
Database Contents
Genes3,056
Pathways232
Enzymatic Reactions1,175
Transport Reactions72
Polypeptides2,859
Protein Complexes39
Enzymes696
Transporters251
Compounds875
Transcription Units2,186
tRNAs82
Protein Features3,636
GO Terms23
Database Version29.0
Sequence SourceGCF_000488255.1
Synonyms Acinetobacter indicus A648
Acinetobacter indicus DSM 25388
Acinetobacter sp. A648
Acinetobacter indicus CIP 110367
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter indicus
Acinetobacter indicus CIP 110367
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02335352
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1341679
Collection Date2012
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+

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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