Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Acinetobacter baumannii 6014059, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [Caspi20]. 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 Institutes of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_GL89183222121353237,284RefSeq:NZ_GL891832
NZ_GL89192418717674170,977RefSeq:NZ_GL891924
NZ_GL89187815214903160,739RefSeq:NZ_GL891878
NZ_GL89195714314003148,469RefSeq:NZ_GL891957
NZ_GL89190012712313146,014RefSeq:NZ_GL891900
NZ_GL89195114814512137,405RefSeq:NZ_GL891951
NZ_GL89193612712124136,614RefSeq:NZ_GL891936
NZ_GL89195411611312128,130RefSeq:NZ_GL891954
NZ_GL89185210910801113,211RefSeq:NZ_GL891852
NZ_GL8919121089846109,070RefSeq:NZ_GL891912
NZ_GL891821969411103,933RefSeq:NZ_GL891821
NZ_GL89184595894297,849RefSeq:NZ_GL891845
NZ_GL89183588880092,665RefSeq:NZ_GL891835
NZ_GL89184791881290,190RefSeq:NZ_GL891847
NZ_GL89195295913185,739RefSeq:NZ_GL891952
NZ_GL89182472700285,384RefSeq:NZ_GL891824
NZ_GL89182573730080,060RefSeq:NZ_GL891825
NZ_GL89192670700078,568RefSeq:NZ_GL891926
NZ_GL89184470670374,640RefSeq:NZ_GL891844
NZ_GL89195346423169,319RefSeq:NZ_GL891953
NZ_GL89182058560261,494RefSeq:NZ_GL891820
NZ_GL89181960591057,072RefSeq:NZ_GL891819
NZ_GL89182358570154,680RefSeq:NZ_GL891823
NZ_GL89194751444353,241RefSeq:NZ_GL891947
NZ_GL89187144430152,708RefSeq:NZ_GL891871
NZ_GL89186347461050,250RefSeq:NZ_GL891863
NZ_GL89183447470050,092RefSeq:NZ_GL891834
NZ_GL89184045450046,189RefSeq:NZ_GL891840
NZ_GL89192242383144,807RefSeq:NZ_GL891922
NZ_GL89188042410144,616RefSeq:NZ_GL891880
NZ_GL89193737370043,275RefSeq:NZ_GL891937
NZ_GL89184239390042,807RefSeq:NZ_GL891842
NZ_GL89182235340141,153RefSeq:NZ_GL891822
NZ_GL89194538320637,758RefSeq:NZ_GL891945
NZ_GL89194430280237,615RefSeq:NZ_GL891944
NZ_GL89183732320036,797RefSeq:NZ_GL891837
NZ_GL89186433321035,360RefSeq:NZ_GL891864
NZ_GL89195532293034,536RefSeq:NZ_GL891955
NZ_GL89192834321132,171RefSeq:NZ_GL891928
NZ_GL89186536333030,963RefSeq:NZ_GL891865
NZ_GL89182826250130,852RefSeq:NZ_GL891828
NZ_GL89182730290130,647RefSeq:NZ_GL891827
NZ_GL89193138320628,425RefSeq:NZ_GL891931
NZ_GL89183922210126,790RefSeq:NZ_GL891839
NZ_GL89183828280026,602RefSeq:NZ_GL891838
NZ_GL89184333330025,314RefSeq:NZ_GL891843
NZ_GL89192021210025,241RefSeq:NZ_GL891920
NZ_GL89186624231025,153RefSeq:NZ_GL891866
NZ_GL89184626241122,798RefSeq:NZ_GL891846
NZ_GL89183024221122,103RefSeq:NZ_GL891830
NZ_GL89183623220120,856RefSeq:NZ_GL891836
NZ_GL89181819180120,218RefSeq:NZ_GL891818
NZ_GL89185316150120,204RefSeq:NZ_GL891853
NZ_GL89192713130018,960RefSeq:NZ_GL891927
NZ_GL89183313110214,035RefSeq:NZ_GL891833
NZ_GL89187012101113,781RefSeq:NZ_GL891870
NZ_GL89184115131113,690RefSeq:NZ_GL891841
NZ_GL89194811110012,915RefSeq:NZ_GL891948
NZ_GL8919251814049,897RefSeq:NZ_GL891925
NZ_GL8918961412028,343RefSeq:NZ_GL891896
NZ_GL8918161212008,307RefSeq:NZ_GL891816
NZ_GL8919581210027,554RefSeq:NZ_GL891958
NZ_GL891908119027,380RefSeq:NZ_GL891908
80 Undisplayed Contigs/Replicons149147646204,904
Total:3,7343,537611363,878,813
Ortholog data available?Yes
Database Contents
Genes3,730
Pathways291
Enzymatic Reactions1,437
Transport Reactions83
Polypeptides3,646
Protein Complexes76
Enzymes806
Transporters348
Compounds1,084
Transcription Units2,610
tRNAs53
Protein Features4,340
GO Terms2,502
Database Version29.0
Sequence SourceGCF_000163395.2
Synonyms Acinetobacter sp. 6014059
Acinetobacter baumannii 6014059
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii 6014059
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00189092
NCBI BioProjectPRJNA224116
NCBI-Taxonomy525242
Environmentskin
HostHomo sapiens
Human Microbiome Body Siteskin
Annotation ProviderNCBI RefSeq
Annotation Date2021-11-7
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

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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