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 AB_TG19617, 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_AMID01000004948926715968,623RefSeq:NZ_AMID01000004
NZ_AMID01000014453434127463,022RefSeq:NZ_AMID01000014
NZ_AMID0100001637636367395,740RefSeq:NZ_AMID01000016
NZ_AMID0100001032531726335,015RefSeq:NZ_AMID01000010
NZ_AMID0100005024023064255,744RefSeq:NZ_AMID01000050
NZ_AMID0100005926025316255,372RefSeq:NZ_AMID01000059
NZ_AMID0100004519518654219,009RefSeq:NZ_AMID01000045
NZ_AMID01000033193179113191,990RefSeq:NZ_AMID01000033
NZ_AMID0100002716115623168,556RefSeq:NZ_AMID01000027
NZ_AMID0100004013513131162,871RefSeq:NZ_AMID01000040
NZ_AMID0100000913513140132,447RefSeq:NZ_AMID01000009
NZ_AMID0100000671690287,414RefSeq:NZ_AMID01000006
NZ_AMID0100003873683280,090RefSeq:NZ_AMID01000038
NZ_AMID0100002640390142,304RefSeq:NZ_AMID01000026
NZ_AMID0100001733321029,371RefSeq:NZ_AMID01000017
NZ_AMID0100002025230213,649RefSeq:NZ_AMID01000020
43 Undisplayed Contigs/Replicons999272289,368
Total:3,7843,62970853,890,585
Ortholog data available?Yes
Database Contents
Genes3,784
Pathways265
Enzymatic Reactions1,293
Transport Reactions102
Polypeptides3,634
Protein Complexes53
Enzymes779
Transporters346
Compounds1,056
Transcription Units2,604
tRNAs63
GO Terms1,322
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_TG19617
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471228
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221273
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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