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 OIFC099, 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_AMFT0100004736635079386,254RefSeq:NZ_AMFT01000047
NZ_AMFT0100005925324751282,426RefSeq:NZ_AMFT01000059
NZ_AMFT01000074252238104265,047RefSeq:NZ_AMFT01000074
NZ_AMFT0100002020219921221,663RefSeq:NZ_AMFT01000020
NZ_AMFT01000001223211102214,327RefSeq:NZ_AMFT01000001
NZ_AMFT0100007219519104200,124RefSeq:NZ_AMFT01000072
NZ_AMFT0100005618818404198,578RefSeq:NZ_AMFT01000056
NZ_AMFT01000031177161115178,525RefSeq:NZ_AMFT01000031
NZ_AMFT0100001016916630168,336RefSeq:NZ_AMFT01000010
NZ_AMFT0100006215614943162,648RefSeq:NZ_AMFT01000062
NZ_AMFT01000016138128010141,511RefSeq:NZ_AMFT01000016
NZ_AMFT0100000213212543130,935RefSeq:NZ_AMFT01000002
NZ_AMFT0100004110810512108,420RefSeq:NZ_AMFT01000041
NZ_AMFT01000053949202105,652RefSeq:NZ_AMFT01000053
NZ_AMFT010000051059915104,436RefSeq:NZ_AMFT01000005
NZ_AMFT0100001886811486,409RefSeq:NZ_AMFT01000018
NZ_AMFT0100007592832783,460RefSeq:NZ_AMFT01000075
NZ_AMFT0100006165650069,140RefSeq:NZ_AMFT01000061
NZ_AMFT0100006668634168,870RefSeq:NZ_AMFT01000066
NZ_AMFT0100004564621167,742RefSeq:NZ_AMFT01000045
NZ_AMFT0100006352490357,059RefSeq:NZ_AMFT01000063
NZ_AMFT0100006751480355,774RefSeq:NZ_AMFT01000067
NZ_AMFT0100000749461251,540RefSeq:NZ_AMFT01000007
NZ_AMFT0100001140380240,324RefSeq:NZ_AMFT01000011
NZ_AMFT0100002734283338,721RefSeq:NZ_AMFT01000027
NZ_AMFT0100007331290235,436RefSeq:NZ_AMFT01000073
NZ_AMFT0100003733302134,697RefSeq:NZ_AMFT01000037
NZ_AMFT0100002432310133,552RefSeq:NZ_AMFT01000024
NZ_AMFT0100002836323131,209RefSeq:NZ_AMFT01000028
NZ_AMFT01000035372301430,935RefSeq:NZ_AMFT01000035
NZ_AMFT0100002128260226,018RefSeq:NZ_AMFT01000021
NZ_AMFT0100005824181526,001RefSeq:NZ_AMFT01000058
NZ_AMFT0100004925231123,749RefSeq:NZ_AMFT01000049
NZ_AMFT0100007117140320,083RefSeq:NZ_AMFT01000071
NZ_AMFT0100001418170119,533RefSeq:NZ_AMFT01000014
NZ_AMFT0100004617142119,039RefSeq:NZ_AMFT01000046
NZ_AMFT0100000916130317,677RefSeq:NZ_AMFT01000009
NZ_AMFT0100004412100215,054RefSeq:NZ_AMFT01000044
NZ_AMFT0100006919190012,633RefSeq:NZ_AMFT01000069
NZ_AMFT0100003317130412,078RefSeq:NZ_AMFT01000033
NZ_AMFT010000321212007,232RefSeq:NZ_AMFT01000032
34 Undisplayed Contigs/Replicons555252265,330
Total:3,8123,584841443,918,177
Ortholog data available?Yes
Database Contents
Genes3,802
Pathways265
Enzymatic Reactions1,313
Transport Reactions112
Polypeptides3,610
Protein Complexes53
Enzymes807
Transporters359
Compounds1,072
Transcription Units2,688
tRNAs64
GO Terms1,460
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii OIFC099
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761236
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903930
Geographic LocationUSA
Collection Date2003
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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