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_2007-16-25-01-7, 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_AMHI0100007833332319353,194RefSeq:NZ_AMHI01000078
NZ_AMHI0100001829828963336,363RefSeq:NZ_AMHI01000018
NZ_AMHI0100002526225156282,670RefSeq:NZ_AMHI01000025
NZ_AMHI0100006319719403212,758RefSeq:NZ_AMHI01000063
NZ_AMHI0100003118417185186,384RefSeq:NZ_AMHI01000031
NZ_AMHI0100004116816701179,000RefSeq:NZ_AMHI01000041
NZ_AMHI0100007313512951147,142RefSeq:NZ_AMHI01000073
NZ_AMHI0100001413112704141,677RefSeq:NZ_AMHI01000014
NZ_AMHI0100002413713106135,995RefSeq:NZ_AMHI01000024
NZ_AMHI0100002613412752135,573RefSeq:NZ_AMHI01000026
NZ_AMHI0100005612912612129,544RefSeq:NZ_AMHI01000056
NZ_AMHI0100007112211741112,537RefSeq:NZ_AMHI01000071
NZ_AMHI01000040989404112,427RefSeq:NZ_AMHI01000040
NZ_AMHI01000047948806102,238RefSeq:NZ_AMHI01000047
NZ_AMHI0100005777750291,957RefSeq:NZ_AMHI01000057
NZ_AMHI0100000487834088,720RefSeq:NZ_AMHI01000004
NZ_AMHI0100002989822585,287RefSeq:NZ_AMHI01000029
NZ_AMHI0100000883793181,532RefSeq:NZ_AMHI01000008
NZ_AMHI0100001775685274,294RefSeq:NZ_AMHI01000017
NZ_AMHI0100001167630472,362RefSeq:NZ_AMHI01000011
NZ_AMHI0100003366630367,875RefSeq:NZ_AMHI01000033
NZ_AMHI0100002257551159,139RefSeq:NZ_AMHI01000022
NZ_AMHI0100002851491158,589RefSeq:NZ_AMHI01000028
NZ_AMHI0100001648460253,324RefSeq:NZ_AMHI01000016
NZ_AMHI0100005945413150,546RefSeq:NZ_AMHI01000059
NZ_AMHI0100004842410141,456RefSeq:NZ_AMHI01000048
NZ_AMHI0100003844394140,940RefSeq:NZ_AMHI01000038
NZ_AMHI0100003644390540,937RefSeq:NZ_AMHI01000036
NZ_AMHI0100007248470138,571RefSeq:NZ_AMHI01000072
NZ_AMHI0100003527270029,600RefSeq:NZ_AMHI01000035
NZ_AMHI0100008127260128,237RefSeq:NZ_AMHI01000081
NZ_AMHI0100002322200227,207RefSeq:NZ_AMHI01000023
NZ_AMHI0100003229280126,850RefSeq:NZ_AMHI01000032
NZ_AMHI0100004628280026,661RefSeq:NZ_AMHI01000046
NZ_AMHI0100003435350025,452RefSeq:NZ_AMHI01000034
NZ_AMHI0100005132260624,631RefSeq:NZ_AMHI01000051
NZ_AMHI0100005026251023,270RefSeq:NZ_AMHI01000050
NZ_AMHI0100002036360022,007RefSeq:NZ_AMHI01000020
NZ_AMHI0100003923230021,380RefSeq:NZ_AMHI01000039
NZ_AMHI0100004529280121,050RefSeq:NZ_AMHI01000045
NZ_AMHI0100006520180220,163RefSeq:NZ_AMHI01000065
NZ_AMHI0100005512110112,677RefSeq:NZ_AMHI01000055
NZ_AMHI0100000512110112,251RefSeq:NZ_AMHI01000005
NZ_AMHI0100006727270011,932RefSeq:NZ_AMHI01000067
NZ_AMHI010000091919009,813RefSeq:NZ_AMHI01000009
NZ_AMHI010000431414007,338RefSeq:NZ_AMHI01000043
35 Undisplayed Contigs/Replicons686352197,886
Total:3,8523,669641193,961,436
Ortholog data available?Yes
Database Contents
Genes3,852
Pathways268
Enzymatic Reactions1,290
Transport Reactions96
Polypeptides3,685
Protein Complexes53
Enzymes776
Transporters354
Compounds1,053
Transcription Units2,693
tRNAs57
GO Terms1,278
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_2007-16-25-01-7
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471225
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221253
Environmenthospital surface
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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