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-2, 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_AMSX0100005426125056273,860RefSeq:NZ_AMSX01000054
NZ_AMSX0100003222422220229,512RefSeq:NZ_AMSX01000032
NZ_AMSX01000071204189114213,094RefSeq:NZ_AMSX01000071
NZ_AMSX0100005617216813185,637RefSeq:NZ_AMSX01000056
NZ_AMSX0100008219118713182,220RefSeq:NZ_AMSX01000082
NZ_AMSX0100009315715043165,136RefSeq:NZ_AMSX01000093
NZ_AMSX0100002116015631157,366RefSeq:NZ_AMSX01000021
NZ_AMSX0100010814313382143,294RefSeq:NZ_AMSX01000108
NZ_AMSX0100011114013514137,000RefSeq:NZ_AMSX01000111
NZ_AMSX0100003812712502132,903RefSeq:NZ_AMSX01000038
NZ_AMSX0100006410910405117,557RefSeq:NZ_AMSX01000064
NZ_AMSX0100004410610321114,631RefSeq:NZ_AMSX01000044
NZ_AMSX01000010939102106,007RefSeq:NZ_AMSX01000010
NZ_AMSX0100008412712601101,688RefSeq:NZ_AMSX01000084
NZ_AMSX0100010789870298,150RefSeq:NZ_AMSX01000107
NZ_AMSX0100010486820488,173RefSeq:NZ_AMSX01000104
NZ_AMSX0100003379760379,897RefSeq:NZ_AMSX01000033
NZ_AMSX0100003689808179,653RefSeq:NZ_AMSX01000036
NZ_AMSX0100009673700376,016RefSeq:NZ_AMSX01000096
NZ_AMSX0100004973680574,858RefSeq:NZ_AMSX01000049
NZ_AMSX0100005851434469,119RefSeq:NZ_AMSX01000058
NZ_AMSX0100010565594264,727RefSeq:NZ_AMSX01000105
NZ_AMSX0100006159570263,170RefSeq:NZ_AMSX01000061
NZ_AMSX0100008684830162,712RefSeq:NZ_AMSX01000086
NZ_AMSX0100001961562354,083RefSeq:NZ_AMSX01000019
NZ_AMSX0100001751463252,748RefSeq:NZ_AMSX01000017
NZ_AMSX0100008945450050,666RefSeq:NZ_AMSX01000089
NZ_AMSX0100002543421047,161RefSeq:NZ_AMSX01000025
NZ_AMSX0100000840390144,468RefSeq:NZ_AMSX01000008
NZ_AMSX0100001540390144,200RefSeq:NZ_AMSX01000015
NZ_AMSX0100005139371139,630RefSeq:NZ_AMSX01000051
NZ_AMSX0100002838343139,232RefSeq:NZ_AMSX01000028
NZ_AMSX0100005229280139,033RefSeq:NZ_AMSX01000052
NZ_AMSX0100010032290335,077RefSeq:NZ_AMSX01000100
NZ_AMSX0100003936360034,841RefSeq:NZ_AMSX01000039
NZ_AMSX0100005930290131,930RefSeq:NZ_AMSX01000059
NZ_AMSX0100000422192131,327RefSeq:NZ_AMSX01000004
NZ_AMSX0100003727242129,901RefSeq:NZ_AMSX01000037
NZ_AMSX0100000629272029,338RefSeq:NZ_AMSX01000006
NZ_AMSX0100011035350027,305RefSeq:NZ_AMSX01000110
NZ_AMSX0100009523220125,359RefSeq:NZ_AMSX01000095
NZ_AMSX0100009226176324,867RefSeq:NZ_AMSX01000092
NZ_AMSX0100005525231124,068RefSeq:NZ_AMSX01000055
NZ_AMSX0100008719170223,945RefSeq:NZ_AMSX01000087
NZ_AMSX0100006221190223,882RefSeq:NZ_AMSX01000062
NZ_AMSX0100004521200123,549RefSeq:NZ_AMSX01000045
NZ_AMSX0100004718160219,246RefSeq:NZ_AMSX01000047
NZ_AMSX0100007723191318,029RefSeq:NZ_AMSX01000077
NZ_AMSX0100005020180217,536RefSeq:NZ_AMSX01000050
NZ_AMSX0100000220190117,292RefSeq:NZ_AMSX01000002
NZ_AMSX0100006814120217,045RefSeq:NZ_AMSX01000068
NZ_AMSX0100001415130216,080RefSeq:NZ_AMSX01000014
NZ_AMSX0100002213112015,912RefSeq:NZ_AMSX01000022
NZ_AMSX010000601291215,214RefSeq:NZ_AMSX01000060
NZ_AMSX0100001216140215,064RefSeq:NZ_AMSX01000012
NZ_AMSX0100006313120113,920RefSeq:NZ_AMSX01000063
NZ_AMSX0100007914130113,303RefSeq:NZ_AMSX01000079
NZ_AMSX0100009911100110,955RefSeq:NZ_AMSX01000099
NZ_AMSX010000201010008,222RefSeq:NZ_AMSX01000020
55 Undisplayed Contigs/Replicons124124051135,742
Total:4,0683,827811604,126,550
Ortholog data available?Yes
Database Contents
Genes4,068
Pathways260
Enzymatic Reactions1,288
Transport Reactions111
Polypeptides3,879
Protein Complexes53
Enzymes802
Transporters358
Compounds1,040
Transcription Units2,827
tRNAs64
GO Terms2,189
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii Naval-2
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761227
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903922
Environmentblood
Geographic LocationUSA
Collection Date2006-05-22
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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