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 AB900, 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_ABXK0100000133031569349,398RefSeq:NZ_ABXK01000001
NZ_ABXK0100000220019622223,041RefSeq:NZ_ABXK01000002
NZ_ABXK01000003212197114222,045RefSeq:NZ_ABXK01000003
NZ_ABXK0100000414714304160,003RefSeq:NZ_ABXK01000004
NZ_ABXK0100000513112713139,199RefSeq:NZ_ABXK01000005
NZ_ABXK0100000612011820130,480RefSeq:NZ_ABXK01000006
NZ_ABXK0100000712612204128,708RefSeq:NZ_ABXK01000007
NZ_ABXK0100000812511960127,545RefSeq:NZ_ABXK01000008
NZ_ABXK0100000912211642126,573RefSeq:NZ_ABXK01000009
NZ_ABXK0100001012612114126,434RefSeq:NZ_ABXK01000010
NZ_ABXK0100001111110713119,705RefSeq:NZ_ABXK01000011
NZ_ABXK0100001213112245118,544RefSeq:NZ_ABXK01000012
NZ_ABXK0100001310410103117,281RefSeq:NZ_ABXK01000013
NZ_ABXK0100001412811918114,849RefSeq:NZ_ABXK01000014
NZ_ABXK0100001510410301110,638RefSeq:NZ_ABXK01000015
NZ_ABXK01000016968556108,680RefSeq:NZ_ABXK01000016
NZ_ABXK0100001791870499,256RefSeq:NZ_ABXK01000017
NZ_ABXK0100001889862193,219RefSeq:NZ_ABXK01000018
NZ_ABXK0100001983811188,829RefSeq:NZ_ABXK01000019
NZ_ABXK0100002093921086,698RefSeq:NZ_ABXK01000020
NZ_ABXK0100002179763085,643RefSeq:NZ_ABXK01000021
NZ_ABXK0100002274684284,649RefSeq:NZ_ABXK01000022
NZ_ABXK0100002374720283,245RefSeq:NZ_ABXK01000023
NZ_ABXK0100002483800379,841RefSeq:NZ_ABXK01000024
NZ_ABXK0100002567650274,755RefSeq:NZ_ABXK01000025
NZ_ABXK0100002681772274,188RefSeq:NZ_ABXK01000026
NZ_ABXK0100002758570160,648RefSeq:NZ_ABXK01000027
NZ_ABXK0100002849490052,746RefSeq:NZ_ABXK01000028
NZ_ABXK0100002945441051,676RefSeq:NZ_ABXK01000029
NZ_ABXK0100003048460250,466RefSeq:NZ_ABXK01000030
NZ_ABXK0100003146460046,409RefSeq:NZ_ABXK01000031
NZ_ABXK0100003235340136,110RefSeq:NZ_ABXK01000032
NZ_ABXK0100003331290233,490RefSeq:NZ_ABXK01000033
NZ_ABXK0100003431300128,868RefSeq:NZ_ABXK01000034
NZ_ABXK0100003521210027,215RefSeq:NZ_ABXK01000035
NZ_ABXK0100003628270126,571RefSeq:NZ_ABXK01000036
NZ_ABXK0100003743420126,491RefSeq:NZ_ABXK01000037
NZ_ABXK0100003826230323,479RefSeq:NZ_ABXK01000038
NZ_ABXK0100003923230021,537RefSeq:NZ_ABXK01000039
NZ_ABXK0100004019180119,352RefSeq:NZ_ABXK01000040
NZ_ABXK0100004120190116,606RefSeq:NZ_ABXK01000041
NZ_ABXK0100004214120216,509RefSeq:NZ_ABXK01000042
NZ_ABXK0100004312120012,350RefSeq:NZ_ABXK01000043
NZ_ABXK0100004515141010,544RefSeq:NZ_ABXK01000045
NZ_ABXK010000471514017,379RefSeq:NZ_ABXK01000047
23 Undisplayed Contigs/Replicons494541568,985
Total:3,7703,600631073,910,877
Ortholog data available?Yes
Database Contents
Genes3,770
Pathways258
Enzymatic Reactions1,285
Transport Reactions109
Polypeptides3,615
Protein Complexes53
Enzymes773
Transporters359
Compounds1,054
Transcription Units2,644
tRNAs57
GO Terms1,266
Database Version29.0
Synonyms Acinetobacter baumannii str. AB900
Acinetobacter baumannii strain AB900
Acinetobacter baumannii AB900
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB900
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471436
NCBI BioProjectPRJNA224116
NCBI-Taxonomy557601
Environmentperineal isolate
Geographic LocationUSA
Collection Date2003
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-11-15
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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