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_2008-15-71, 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_AMHP0100003224923964270,770RefSeq:NZ_AMHP01000032
NZ_AMHP0100001822021028220,333RefSeq:NZ_AMHP01000018
NZ_AMHP0100006320920063217,502RefSeq:NZ_AMHP01000063
NZ_AMHP0100002017817413195,076RefSeq:NZ_AMHP01000020
NZ_AMHP0100000317516285182,658RefSeq:NZ_AMHP01000003
NZ_AMHP0100009016315904170,688RefSeq:NZ_AMHP01000090
NZ_AMHP0100006814113236161,856RefSeq:NZ_AMHP01000068
NZ_AMHP0100001015314814150,691RefSeq:NZ_AMHP01000010
NZ_AMHP0100001614613871147,984RefSeq:NZ_AMHP01000016
NZ_AMHP0100004913813611146,754RefSeq:NZ_AMHP01000049
NZ_AMHP0100006612812305140,379RefSeq:NZ_AMHP01000066
NZ_AMHP0100008913613312135,102RefSeq:NZ_AMHP01000089
NZ_AMHP01000051989611119,999RefSeq:NZ_AMHP01000051
NZ_AMHP0100008610910504116,140RefSeq:NZ_AMHP01000086
NZ_AMHP01000019989602111,281RefSeq:NZ_AMHP01000019
NZ_AMHP0100004010410211110,235RefSeq:NZ_AMHP01000040
NZ_AMHP0100006084794187,730RefSeq:NZ_AMHP01000060
NZ_AMHP0100008075750077,235RefSeq:NZ_AMHP01000080
NZ_AMHP0100002371680375,515RefSeq:NZ_AMHP01000023
NZ_AMHP0100005769680166,683RefSeq:NZ_AMHP01000057
NZ_AMHP0100003666624063,544RefSeq:NZ_AMHP01000036
NZ_AMHP0100005576704261,169RefSeq:NZ_AMHP01000055
NZ_AMHP0100007355520358,640RefSeq:NZ_AMHP01000073
NZ_AMHP0100003052511056,014RefSeq:NZ_AMHP01000030
NZ_AMHP0100002537343052,821RefSeq:NZ_AMHP01000025
NZ_AMHP0100003347460151,914RefSeq:NZ_AMHP01000033
NZ_AMHP0100004449460350,375RefSeq:NZ_AMHP01000044
NZ_AMHP0100008455522147,360RefSeq:NZ_AMHP01000084
NZ_AMHP0100003752510147,151RefSeq:NZ_AMHP01000037
NZ_AMHP0100004836340237,021RefSeq:NZ_AMHP01000048
NZ_AMHP0100000730290136,883RefSeq:NZ_AMHP01000007
NZ_AMHP0100000527260135,003RefSeq:NZ_AMHP01000005
NZ_AMHP0100003824220231,978RefSeq:NZ_AMHP01000038
NZ_AMHP0100005328280026,407RefSeq:NZ_AMHP01000053
NZ_AMHP0100003423210226,000RefSeq:NZ_AMHP01000034
NZ_AMHP0100003922220023,205RefSeq:NZ_AMHP01000039
NZ_AMHP0100004726260020,448RefSeq:NZ_AMHP01000047
NZ_AMHP0100002716151018,365RefSeq:NZ_AMHP01000027
NZ_AMHP0100005917170018,271RefSeq:NZ_AMHP01000059
NZ_AMHP0100007615150017,700RefSeq:NZ_AMHP01000076
NZ_AMHP0100005418151217,366RefSeq:NZ_AMHP01000054
NZ_AMHP0100006715150016,271RefSeq:NZ_AMHP01000067
NZ_AMHP0100002913120114,088RefSeq:NZ_AMHP01000029
NZ_AMHP0100001113120113,759RefSeq:NZ_AMHP01000011
NZ_AMHP0100007518170112,888RefSeq:NZ_AMHP01000075
NZ_AMHP0100001721200111,036RefSeq:NZ_AMHP01000017
44 Undisplayed Contigs/Replicons9993628115,813
Total:3,7223,546641123,886,101
Ortholog data available?Yes
Database Contents
Genes3,722
Pathways269
Enzymatic Reactions1,309
Transport Reactions100
Polypeptides3,577
Protein Complexes54
Enzymes773
Transporters355
Compounds1,067
Transcription Units2,619
tRNAs56
GO Terms1,290
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_2008-15-71
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471278
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221260
Environmentsputum
HostHomo sapiens
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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