Database Authors
Pallavi Subhraveti1, Peter Midford, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2019 from the annotated genome of Acinetobacter baumannii OIFC047, 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 23.0) [Karp16, Karp11] using MetaCyc version 23.0 [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_AMFW010000256986641420760,154RefSeq:NZ_AMFW01000025
NZ_AMFW0100001730229714308,900RefSeq:NZ_AMFW01000017
NZ_AMFW0100001327326067288,973RefSeq:NZ_AMFW01000013
NZ_AMFW0100003322421833243,035RefSeq:NZ_AMFW01000033
NZ_AMFW0100000719117795200,035RefSeq:NZ_AMFW01000007
NZ_AMFW01000011197179135198,634RefSeq:NZ_AMFW01000011
NZ_AMFW0100000919918928196,894RefSeq:NZ_AMFW01000009
NZ_AMFW0100000415915135169,758RefSeq:NZ_AMFW01000004
NZ_AMFW0100002913012073139,721RefSeq:NZ_AMFW01000029
NZ_AMFW0100000610910702116,660RefSeq:NZ_AMFW01000006
NZ_AMFW010000121039805114,400RefSeq:NZ_AMFW01000012
NZ_AMFW0100000312211651111,796RefSeq:NZ_AMFW01000003
NZ_AMFW0100003110610411105,856RefSeq:NZ_AMFW01000031
NZ_AMFW0100003490836190,228RefSeq:NZ_AMFW01000034
NZ_AMFW0100002387843089,836RefSeq:NZ_AMFW01000023
NZ_AMFW0100002482790384,250RefSeq:NZ_AMFW01000024
NZ_AMFW0100000574721181,788RefSeq:NZ_AMFW01000005
NZ_AMFW0100003972682274,614RefSeq:NZ_AMFW01000039
NZ_AMFW0100003845420352,633RefSeq:NZ_AMFW01000038
NZ_AMFW0100000850472151,392RefSeq:NZ_AMFW01000008
NZ_AMFW0100002139390041,668RefSeq:NZ_AMFW01000021
NZ_AMFW0100001641390240,450RefSeq:NZ_AMFW01000016
NZ_AMFW0100002737350235,800RefSeq:NZ_AMFW01000027
NZ_AMFW0100002028280034,277RefSeq:NZ_AMFW01000020
NZ_AMFW0100001031283029,942RefSeq:NZ_AMFW01000010
NZ_AMFW0100002632320027,575RefSeq:NZ_AMFW01000026
NZ_AMFW0100000218160221,563RefSeq:NZ_AMFW01000002
12 Undisplayed Contigs/Replicons262601229,852
Total:3,5773,39881983,740,684
Ortholog data available?Yes
Database Contents
Genes3,567
Pathways263
Enzymatic Reactions1,272
Transport Reactions35
Polypeptides3,411
Protein Complexes41
Enzymes758
Transporters352
Compounds1,013
Transcription Units2,529
tRNAs61
GO Terms1,285
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii OIFC047
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761250
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903933
Environmentperineum
Geographic LocationUSA
Collection Date2003-08-13
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-11-23
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.3
Annotation CommentBest-placed reference protein set; GeneMarkS+

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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.