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-57, 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_AMFP01000093427413113450,965RefSeq:NZ_AMFP01000093
NZ_AMFP01000085376361510389,977RefSeq:NZ_AMFP01000085
NZ_AMFP01000033257244112270,960RefSeq:NZ_AMFP01000033
NZ_AMFP0100013223722683248,873RefSeq:NZ_AMFP01000132
NZ_AMFP0100008920520122222,236RefSeq:NZ_AMFP01000089
NZ_AMFP0100007518817882196,877RefSeq:NZ_AMFP01000075
NZ_AMFP0100003616515834178,414RefSeq:NZ_AMFP01000036
NZ_AMFP0100003413413301145,479RefSeq:NZ_AMFP01000034
NZ_AMFP0100003511611042116,352RefSeq:NZ_AMFP01000035
NZ_AMFP0100001112411752114,168RefSeq:NZ_AMFP01000011
NZ_AMFP0100010093891398,074RefSeq:NZ_AMFP01000100
NZ_AMFP0100010284791495,532RefSeq:NZ_AMFP01000102
NZ_AMFP0100000590836190,001RefSeq:NZ_AMFP01000005
NZ_AMFP0100009974684280,002RefSeq:NZ_AMFP01000099
NZ_AMFP0100004983774277,976RefSeq:NZ_AMFP01000049
NZ_AMFP0100004756504273,409RefSeq:NZ_AMFP01000047
NZ_AMFP0100012265610471,621RefSeq:NZ_AMFP01000122
NZ_AMFP0100000761572270,944RefSeq:NZ_AMFP01000007
NZ_AMFP0100007258560263,283RefSeq:NZ_AMFP01000072
NZ_AMFP0100009754530160,152RefSeq:NZ_AMFP01000097
NZ_AMFP0100005057552058,155RefSeq:NZ_AMFP01000050
NZ_AMFP0100007843430054,282RefSeq:NZ_AMFP01000078
NZ_AMFP0100009651472253,086RefSeq:NZ_AMFP01000096
NZ_AMFP0100001257513350,620RefSeq:NZ_AMFP01000012
NZ_AMFP0100009841390244,592RefSeq:NZ_AMFP01000098
NZ_AMFP0100009141371339,003RefSeq:NZ_AMFP01000091
NZ_AMFP0100008332320037,980RefSeq:NZ_AMFP01000083
NZ_AMFP0100012543391337,465RefSeq:NZ_AMFP01000125
NZ_AMFP0100005635330236,795RefSeq:NZ_AMFP01000056
NZ_AMFP0100011028260232,607RefSeq:NZ_AMFP01000110
NZ_AMFP0100003737305232,522RefSeq:NZ_AMFP01000037
NZ_AMFP0100006832273232,179RefSeq:NZ_AMFP01000068
NZ_AMFP0100006530270331,829RefSeq:NZ_AMFP01000065
NZ_AMFP0100011430282028,247RefSeq:NZ_AMFP01000114
NZ_AMFP0100009042400223,899RefSeq:NZ_AMFP01000090
NZ_AMFP0100012324210322,906RefSeq:NZ_AMFP01000123
NZ_AMFP0100000916150116,736RefSeq:NZ_AMFP01000009
NZ_AMFP010000161690712,984RefSeq:NZ_AMFP01000016
NZ_AMFP010000451480612,564RefSeq:NZ_AMFP01000045
NZ_AMFP010000271816027,670RefSeq:NZ_AMFP01000027
98 Undisplayed Contigs/Replicons148147299172,180
Total:3,8823,584802183,953,596
Ortholog data available?Yes
Database Contents
Genes3,873
Pathways271
Enzymatic Reactions1,334
Transport Reactions36
Polypeptides3,622
Protein Complexes42
Enzymes778
Transporters376
Compounds1,063
Transcription Units2,751
tRNAs61
GO Terms1,256
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii Naval-57
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761216
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903927
Environmentwound
Geographic LocationUSA
Collection Date2006-07-23
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-11-24
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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