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 modestus CCM 8639, 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_BMDV010000018227821624895,613RefSeq:NZ_BMDV01000001
NZ_BMDV01000002798777714820,794RefSeq:NZ_BMDV01000002
NZ_BMDV01000003412395116406,095RefSeq:NZ_BMDV01000003
NZ_BMDV0100000430629484319,026RefSeq:NZ_BMDV01000004
NZ_BMDV0100000526025064277,187RefSeq:NZ_BMDV01000005
NZ_BMDV01000006228211116238,764RefSeq:NZ_BMDV01000006
NZ_BMDV0100000713613321136,533RefSeq:NZ_BMDV01000007
NZ_BMDV0100000899970299,339RefSeq:NZ_BMDV01000008
NZ_BMDV0100000996924095,599RefSeq:NZ_BMDV01000009
NZ_BMDV0100001057560164,317RefSeq:NZ_BMDV01000010
NZ_BMDV0100001153511157,318RefSeq:NZ_BMDV01000011
NZ_BMDV0100001240380240,414RefSeq:NZ_BMDV01000012
NZ_BMDV0100001323210223,988RefSeq:NZ_BMDV01000013
NZ_BMDV0100001414120214,415RefSeq:NZ_BMDV01000014
NZ_BMDV0100001512120011,225RefSeq:NZ_BMDV01000015
NZ_BMDV010000161211019,414RefSeq:NZ_BMDV01000016
NZ_BMDV010000171212009,234RefSeq:NZ_BMDV01000017
12 Undisplayed Contigs/Replicons24195326,809
Total:3,4073,26371733,546,084
Ortholog data available?Yes
Database Contents
Genes3,407
Pathways242
Enzymatic Reactions1,207
Transport Reactions67
Polypeptides3,274
Protein Complexes41
Enzymes705
Transporters283
Compounds878
Transcription Units2,339
tRNAs64
Protein Features3,865
GO Terms17
Database Version29.0
Sequence SourceGCF_014636095.1
Synonyms Acinetobacter genomosp. 18
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter modestus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00244890
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1776740
Annotation ProviderNCBI RefSeq
Annotation Date2020-11-22
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.13
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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