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 IS-143, 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_AMGE01000070347332105369,162RefSeq:NZ_AMGE01000070
NZ_AMGE0100001532931487347,050RefSeq:NZ_AMGE01000015
NZ_AMGE0100006724824701259,333RefSeq:NZ_AMGE01000067
NZ_AMGE0100004123022604245,660RefSeq:NZ_AMGE01000041
NZ_AMGE01000011186175101197,982RefSeq:NZ_AMGE01000011
NZ_AMGE0100009018017523193,473RefSeq:NZ_AMGE01000090
NZ_AMGE0100007218117281192,952RefSeq:NZ_AMGE01000072
NZ_AMGE0100008615915711176,683RefSeq:NZ_AMGE01000086
NZ_AMGE0100000417716782167,576RefSeq:NZ_AMGE01000004
NZ_AMGE0100008415414932161,939RefSeq:NZ_AMGE01000084
NZ_AMGE0100002613612772142,917RefSeq:NZ_AMGE01000026
NZ_AMGE010000811009541127,992RefSeq:NZ_AMGE01000081
NZ_AMGE0100006410510221112,738RefSeq:NZ_AMGE01000064
NZ_AMGE0100008712311418111,138RefSeq:NZ_AMGE01000087
NZ_AMGE010000231061041194,642RefSeq:NZ_AMGE01000023
NZ_AMGE0100005090836190,360RefSeq:NZ_AMGE01000050
NZ_AMGE0100004380716385,172RefSeq:NZ_AMGE01000043
NZ_AMGE0100004879770282,846RefSeq:NZ_AMGE01000048
NZ_AMGE0100003480742476,019RefSeq:NZ_AMGE01000034
NZ_AMGE0100006171670472,515RefSeq:NZ_AMGE01000061
NZ_AMGE0100004966641168,410RefSeq:NZ_AMGE01000049
NZ_AMGE0100002456550167,743RefSeq:NZ_AMGE01000024
NZ_AMGE0100004459560364,727RefSeq:NZ_AMGE01000044
NZ_AMGE0100003363620160,730RefSeq:NZ_AMGE01000033
NZ_AMGE0100007552470555,790RefSeq:NZ_AMGE01000075
NZ_AMGE0100007452474154,689RefSeq:NZ_AMGE01000074
NZ_AMGE0100001842373247,055RefSeq:NZ_AMGE01000018
NZ_AMGE0100000224230133,001RefSeq:NZ_AMGE01000002
NZ_AMGE0100008530282028,546RefSeq:NZ_AMGE01000085
NZ_AMGE0100003925230227,868RefSeq:NZ_AMGE01000039
NZ_AMGE0100002020190117,297RefSeq:NZ_AMGE01000020
NZ_AMGE0100005818170117,036RefSeq:NZ_AMGE01000058
NZ_AMGE0100005713120113,524RefSeq:NZ_AMGE01000057
NZ_AMGE0100001715150013,207RefSeq:NZ_AMGE01000017
NZ_AMGE010000761313009,606RefSeq:NZ_AMGE01000076
NZ_AMGE010000381411038,568RefSeq:NZ_AMGE01000038
NZ_AMGE010000881110018,541RefSeq:NZ_AMGE01000088
NZ_AMGE010000141412026,689RefSeq:NZ_AMGE01000014
55 Undisplayed Contigs/Replicons105105043108,843
Total:3,8963,684891234,020,019
Ortholog data available?Yes
Database Contents
Genes3,888
Pathways260
Enzymatic Reactions1,286
Transport Reactions111
Polypeptides3,737
Protein Complexes53
Enzymes796
Transporters360
Compounds1,049
Transcription Units2,729
tRNAs68
GO Terms2,434
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii IS-143
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761239
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903911
Environmentwound
Geographic LocationIraq
Collection Date2008-06-6
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-03-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.