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-83, 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_AMFK01000068302281174299,322RefSeq:NZ_AMFK01000068
NZ_AMFK0100006324723863270,979RefSeq:NZ_AMFK01000063
NZ_AMFK0100005126726313257,579RefSeq:NZ_AMFK01000051
NZ_AMFK0100005322221318221,295RefSeq:NZ_AMFK01000053
NZ_AMFK01000058201179166203,313RefSeq:NZ_AMFK01000058
NZ_AMFK0100009518818404196,580RefSeq:NZ_AMFK01000095
NZ_AMFK0100010217316823188,859RefSeq:NZ_AMFK01000102
NZ_AMFK0100007614614501157,255RefSeq:NZ_AMFK01000076
NZ_AMFK0100003814414301153,182RefSeq:NZ_AMFK01000038
NZ_AMFK0100006612511762138,386RefSeq:NZ_AMFK01000066
NZ_AMFK0100008414013343134,119RefSeq:NZ_AMFK01000084
NZ_AMFK01000011929002105,449RefSeq:NZ_AMFK01000011
NZ_AMFK010000361009451104,459RefSeq:NZ_AMFK01000036
NZ_AMFK0100010390860497,377RefSeq:NZ_AMFK01000103
NZ_AMFK0100003790827194,000RefSeq:NZ_AMFK01000037
NZ_AMFK0100005088860287,536RefSeq:NZ_AMFK01000050
NZ_AMFK0100003494842878,725RefSeq:NZ_AMFK01000034
NZ_AMFK0100000375675378,204RefSeq:NZ_AMFK01000003
NZ_AMFK0100005569640576,224RefSeq:NZ_AMFK01000055
NZ_AMFK0100001055484366,154RefSeq:NZ_AMFK01000010
NZ_AMFK0100003962547160,017RefSeq:NZ_AMFK01000039
NZ_AMFK0100001853490457,827RefSeq:NZ_AMFK01000018
NZ_AMFK0100004947450254,465RefSeq:NZ_AMFK01000049
NZ_AMFK0100005748415249,786RefSeq:NZ_AMFK01000057
NZ_AMFK0100009445403249,412RefSeq:NZ_AMFK01000094
NZ_AMFK0100009947415148,581RefSeq:NZ_AMFK01000099
NZ_AMFK0100001350464046,746RefSeq:NZ_AMFK01000013
NZ_AMFK0100008238380044,046RefSeq:NZ_AMFK01000082
NZ_AMFK0100006144394142,704RefSeq:NZ_AMFK01000061
NZ_AMFK0100007949490038,372RefSeq:NZ_AMFK01000079
NZ_AMFK0100003038360237,991RefSeq:NZ_AMFK01000030
NZ_AMFK0100007129280137,199RefSeq:NZ_AMFK01000071
NZ_AMFK0100000935321233,570RefSeq:NZ_AMFK01000009
NZ_AMFK0100009334275231,718RefSeq:NZ_AMFK01000093
NZ_AMFK0100009630300030,309RefSeq:NZ_AMFK01000096
NZ_AMFK0100002230300029,102RefSeq:NZ_AMFK01000022
NZ_AMFK0100002825210428,974RefSeq:NZ_AMFK01000028
NZ_AMFK0100001522190319,068RefSeq:NZ_AMFK01000015
NZ_AMFK0100009718115218,483RefSeq:NZ_AMFK01000097
NZ_AMFK0100005614120217,935RefSeq:NZ_AMFK01000056
NZ_AMFK0100002718160217,736RefSeq:NZ_AMFK01000027
NZ_AMFK0100001919180117,126RefSeq:NZ_AMFK01000019
NZ_AMFK0100006016140216,315RefSeq:NZ_AMFK01000060
NZ_AMFK0100004019180115,309RefSeq:NZ_AMFK01000040
NZ_AMFK0100010018140414,089RefSeq:NZ_AMFK01000100
NZ_AMFK0100008611110014,077RefSeq:NZ_AMFK01000086
NZ_AMFK0100007218170112,184RefSeq:NZ_AMFK01000072
NZ_AMFK010000691515008,940RefSeq:NZ_AMFK01000069
NZ_AMFK010000021511048,322RefSeq:NZ_AMFK01000002
NZ_AMFK01000044128047,112RefSeq:NZ_AMFK01000044
53 Undisplayed Contigs/Replicons152152055190,091
Total:4,0343,7471151724,106,603
Ortholog data available?Yes
Database Contents
Genes4,030
Pathways267
Enzymatic Reactions1,297
Transport Reactions110
Polypeptides3,805
Protein Complexes52
Enzymes792
Transporters352
Compounds1,047
Transcription Units2,830
tRNAs81
GO Terms2,329
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii Naval-83
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761238
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903909
Environmentwound
Geographic LocationUSA
Collection Date2006-10-16
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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