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 marinus ANC 3699, 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_FMYK0100000167666493773,491RefSeq:NZ_FMYK01000001
NZ_FMYK01000002502475243534,539RefSeq:NZ_FMYK01000002
NZ_FMYK01000003481462712495,358RefSeq:NZ_FMYK01000003
NZ_FMYK0100000428427653305,022RefSeq:NZ_FMYK01000004
NZ_FMYK0100000515915108168,760RefSeq:NZ_FMYK01000005
NZ_FMYK0100000613512672141,438RefSeq:NZ_FMYK01000006
NZ_FMYK0100000791882199,525RefSeq:NZ_FMYK01000007
NZ_FMYK0100000889871194,873RefSeq:NZ_FMYK01000008
NZ_FMYK0100000987816084,158RefSeq:NZ_FMYK01000009
NZ_FMYK0100001075730281,343RefSeq:NZ_FMYK01000010
NZ_FMYK0100001170690178,780RefSeq:NZ_FMYK01000011
NZ_FMYK0100001226260027,604RefSeq:NZ_FMYK01000012
NZ_FMYK0100001322170526,534RefSeq:NZ_FMYK01000013
NZ_FMYK0100001418170120,850RefSeq:NZ_FMYK01000014
NZ_FMYK0100001517170019,364RefSeq:NZ_FMYK01000015
NZ_FMYK0100001617130416,380RefSeq:NZ_FMYK01000016
6 Undisplayed Contigs/Replicons21165426,760
Total:2,7742,65866502,994,779
Ortholog data available?Yes
Database Contents
Genes2,770
Pathways245
Enzymatic Reactions1,261
Transport Reactions47
Polypeptides2,662
Protein Complexes4
Enzymes718
Transporters257
Compounds879
Transcription Units2,078
tRNAs55
Protein Features3,385
GO Terms173
Database Version29.0
Sequence SourceGCF_900096915.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter marinus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05421749
NCBI BioProjectPRJNA224116
NCBI-Taxonomy281375
Annotation ProviderNCBI RefSeq
Annotation Date2021-05-17
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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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