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 OIFC0162, 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_AMFH0100002644943298476,465RefSeq:NZ_AMFH01000026
NZ_AMFH0100004534133614344,127RefSeq:NZ_AMFH01000045
NZ_AMFH0100002127026064289,004RefSeq:NZ_AMFH01000021
NZ_AMFH0100001625924766269,886RefSeq:NZ_AMFH01000016
NZ_AMFH0100000221821422241,848RefSeq:NZ_AMFH01000002
NZ_AMFH01000020197179135197,499RefSeq:NZ_AMFH01000020
NZ_AMFH0100001119919072196,367RefSeq:NZ_AMFH01000011
NZ_AMFH0100002417917216184,868RefSeq:NZ_AMFH01000024
NZ_AMFH0100001915915432163,790RefSeq:NZ_AMFH01000019
NZ_AMFH0100002812912513135,236RefSeq:NZ_AMFH01000028
NZ_AMFH0100003410910900127,850RefSeq:NZ_AMFH01000034
NZ_AMFH0100002311911630125,480RefSeq:NZ_AMFH01000023
NZ_AMFH0100001210510104119,693RefSeq:NZ_AMFH01000012
NZ_AMFH0100001711210705115,618RefSeq:NZ_AMFH01000017
NZ_AMFH010000371059807108,605RefSeq:NZ_AMFH01000037
NZ_AMFH0100005411411004104,583RefSeq:NZ_AMFH01000054
NZ_AMFH0100001090836189,154RefSeq:NZ_AMFH01000010
NZ_AMFH0100005273700380,491RefSeq:NZ_AMFH01000052
NZ_AMFH0100003578760277,216RefSeq:NZ_AMFH01000035
NZ_AMFH0100003078722471,811RefSeq:NZ_AMFH01000030
NZ_AMFH0100001368607168,971RefSeq:NZ_AMFH01000013
NZ_AMFH0100003363600365,886RefSeq:NZ_AMFH01000033
NZ_AMFH0100004452464263,677RefSeq:NZ_AMFH01000044
NZ_AMFH0100002974720255,567RefSeq:NZ_AMFH01000029
NZ_AMFH0100004749471151,500RefSeq:NZ_AMFH01000047
NZ_AMFH0100002238323340,128RefSeq:NZ_AMFH01000022
NZ_AMFH0100000333321029,664RefSeq:NZ_AMFH01000003
NZ_AMFH0100003229281027,803RefSeq:NZ_AMFH01000032
NZ_AMFH0100000926251026,014RefSeq:NZ_AMFH01000009
NZ_AMFH0100003814120220,059RefSeq:NZ_AMFH01000038
NZ_AMFH0100005320200020,046RefSeq:NZ_AMFH01000053
NZ_AMFH0100000516130315,953RefSeq:NZ_AMFH01000005
NZ_AMFH0100004817150210,497RefSeq:NZ_AMFH01000048
NZ_AMFH010000421211016,945RefSeq:NZ_AMFH01000042
21 Undisplayed Contigs/Replicons303002256,098
Total:3,9463,754781144,078,399
Ortholog data available?Yes
Database Contents
Genes3,939
Pathways273
Enzymatic Reactions1,305
Transport Reactions107
Polypeptides3,758
Protein Complexes54
Enzymes806
Transporters378
Compounds1,062
Transcription Units2,740
tRNAs62
GO Terms1,459
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii OIFC0162
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761223
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903907
Environmenttrachea
Geographic LocationUSA
Collection Date2003-04-24
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

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