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 Naval-13, 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_AMDR0100003638037055385,479RefSeq:NZ_AMDR01000036
NZ_AMDR0100006230129083319,368RefSeq:NZ_AMDR01000062
NZ_AMDR0100002230229318308,659RefSeq:NZ_AMDR01000022
NZ_AMDR0100000226525636279,897RefSeq:NZ_AMDR01000002
NZ_AMDR0100006325524915252,806RefSeq:NZ_AMDR01000063
NZ_AMDR0100004623423202249,112RefSeq:NZ_AMDR01000046
NZ_AMDR0100000123623303242,845RefSeq:NZ_AMDR01000001
NZ_AMDR01000049246233121240,600RefSeq:NZ_AMDR01000049
NZ_AMDR0100004412712160143,867RefSeq:NZ_AMDR01000044
NZ_AMDR0100001813112272134,843RefSeq:NZ_AMDR01000018
NZ_AMDR0100001513713106122,566RefSeq:NZ_AMDR01000015
NZ_AMDR0100002812511591116,227RefSeq:NZ_AMDR01000028
NZ_AMDR01000003979241110,054RefSeq:NZ_AMDR01000003
NZ_AMDR0100005488844089,927RefSeq:NZ_AMDR01000054
NZ_AMDR0100004068660273,540RefSeq:NZ_AMDR01000040
NZ_AMDR0100000766559270,503RefSeq:NZ_AMDR01000007
NZ_AMDR0100006185840162,713RefSeq:NZ_AMDR01000061
NZ_AMDR0100003861580362,611RefSeq:NZ_AMDR01000038
NZ_AMDR0100002056511458,009RefSeq:NZ_AMDR01000020
NZ_AMDR0100002761527256,861RefSeq:NZ_AMDR01000027
NZ_AMDR0100000451490256,641RefSeq:NZ_AMDR01000004
NZ_AMDR0100005953465256,309RefSeq:NZ_AMDR01000059
NZ_AMDR0100005150443356,273RefSeq:NZ_AMDR01000051
NZ_AMDR0100004750490156,221RefSeq:NZ_AMDR01000047
NZ_AMDR0100002356505156,082RefSeq:NZ_AMDR01000023
NZ_AMDR0100003044430150,734RefSeq:NZ_AMDR01000030
NZ_AMDR0100001737350239,862RefSeq:NZ_AMDR01000017
NZ_AMDR0100006431290239,325RefSeq:NZ_AMDR01000064
NZ_AMDR0100001230255034,858RefSeq:NZ_AMDR01000012
NZ_AMDR0100000933293134,385RefSeq:NZ_AMDR01000009
NZ_AMDR0100005834295032,266RefSeq:NZ_AMDR01000058
NZ_AMDR0100000832320031,859RefSeq:NZ_AMDR01000008
NZ_AMDR0100005735301430,133RefSeq:NZ_AMDR01000057
NZ_AMDR0100004826220426,441RefSeq:NZ_AMDR01000048
NZ_AMDR0100004226240225,595RefSeq:NZ_AMDR01000042
NZ_AMDR0100005016140220,448RefSeq:NZ_AMDR01000050
NZ_AMDR0100000626240218,632RefSeq:NZ_AMDR01000006
NZ_AMDR0100006019151314,335RefSeq:NZ_AMDR01000060
NZ_AMDR010000391311029,902RefSeq:NZ_AMDR01000039
25 Undisplayed Contigs/Replicons222201736,949
Total:4,0223,8091051084,107,737
Ortholog data available?Yes
Database Contents
Genes4,022
Pathways258
Enzymatic Reactions1,279
Transport Reactions111
Polypeptides3,835
Protein Complexes52
Enzymes781
Transporters368
Compounds1,041
Transcription Units2,786
tRNAs77
GO Terms1,414
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii Naval-13
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761220
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903904
Environmentwound
Geographic LocationUSA
Collection Date2006-05-27
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-05-16
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.2
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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