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 ZWS1122, 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_AMGR01000052389373133393,068RefSeq:NZ_AMGR01000052
NZ_AMGR0100004830229165353,582RefSeq:NZ_AMGR01000048
NZ_AMGR01000008325312103343,895RefSeq:NZ_AMGR01000008
NZ_AMGR0100001713713502153,367RefSeq:NZ_AMGR01000017
NZ_AMGR0100003612912801146,940RefSeq:NZ_AMGR01000036
NZ_AMGR0100004913612772146,430RefSeq:NZ_AMGR01000049
NZ_AMGR0100002613913324140,733RefSeq:NZ_AMGR01000026
NZ_AMGR0100004612312003133,538RefSeq:NZ_AMGR01000046
NZ_AMGR0100003112412301131,755RefSeq:NZ_AMGR01000031
NZ_AMGR0100001111510942129,488RefSeq:NZ_AMGR01000011
NZ_AMGR0100000412011721128,227RefSeq:NZ_AMGR01000004
NZ_AMGR0100004312311841126,049RefSeq:NZ_AMGR01000043
NZ_AMGR0100001312512311115,433RefSeq:NZ_AMGR01000013
NZ_AMGR0100003011411211112,420RefSeq:NZ_AMGR01000030
NZ_AMGR0100005010510311110,085RefSeq:NZ_AMGR01000050
NZ_AMGR01000027929002101,202RefSeq:NZ_AMGR01000027
NZ_AMGR0100005698934186,719RefSeq:NZ_AMGR01000056
NZ_AMGR0100002879780180,119RefSeq:NZ_AMGR01000028
NZ_AMGR0100003778751277,702RefSeq:NZ_AMGR01000037
NZ_AMGR0100000976731277,693RefSeq:NZ_AMGR01000009
NZ_AMGR0100000779717177,563RefSeq:NZ_AMGR01000007
NZ_AMGR0100002265613175,186RefSeq:NZ_AMGR01000022
NZ_AMGR0100005362620067,800RefSeq:NZ_AMGR01000053
NZ_AMGR0100001460590158,447RefSeq:NZ_AMGR01000014
NZ_AMGR0100000648470150,738RefSeq:NZ_AMGR01000006
NZ_AMGR0100004542420047,725RefSeq:NZ_AMGR01000045
NZ_AMGR0100003338380042,698RefSeq:NZ_AMGR01000033
NZ_AMGR0100000544420241,157RefSeq:NZ_AMGR01000005
NZ_AMGR0100002937370041,065RefSeq:NZ_AMGR01000029
NZ_AMGR0100000335350036,425RefSeq:NZ_AMGR01000003
NZ_AMGR0100005129281027,125RefSeq:NZ_AMGR01000051
NZ_AMGR0100000225250025,419RefSeq:NZ_AMGR01000002
NZ_AMGR0100000123230025,341RefSeq:NZ_AMGR01000001
NZ_AMGR0100002422210124,310RefSeq:NZ_AMGR01000024
NZ_AMGR0100001524210323,335RefSeq:NZ_AMGR01000015
NZ_AMGR0100006033330022,632RefSeq:NZ_AMGR01000060
NZ_AMGR0100002518180020,717RefSeq:NZ_AMGR01000025
NZ_AMGR0100001933320119,028RefSeq:NZ_AMGR01000019
NZ_AMGR0100001013130014,071RefSeq:NZ_AMGR01000010
NZ_AMGR0100005415130213,606RefSeq:NZ_AMGR01000054
NZ_AMGR0100002012110110,081RefSeq:NZ_AMGR01000020
NZ_AMGR010000231311028,194RefSeq:NZ_AMGR01000023
18 Undisplayed Contigs/Replicons71710776,150
Total:3,7773,64768623,937,258
Ortholog data available?Yes
Database Contents
Genes3,774
Pathways261
Enzymatic Reactions1,286
Transport Reactions112
Polypeptides3,668
Protein Complexes52
Enzymes794
Transporters360
Compounds1,044
Transcription Units2,603
tRNAs61
GO Terms2,500
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii ZWS1122
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02470994
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1223564
Environmentblood
Geographic LocationChina
Collection Date2011-11
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

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