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 IS-58, 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_AMGH01000013454434182467,575RefSeq:NZ_AMGH01000013
NZ_AMGH0100003833732548377,110RefSeq:NZ_AMGH01000038
NZ_AMGH0100001634633853356,008RefSeq:NZ_AMGH01000016
NZ_AMGH0100003131531113326,694RefSeq:NZ_AMGH01000031
NZ_AMGH0100001127827062303,933RefSeq:NZ_AMGH01000011
NZ_AMGH0100004224123533276,191RefSeq:NZ_AMGH01000042
NZ_AMGH01000020195177126197,460RefSeq:NZ_AMGH01000020
NZ_AMGH0100004516716304177,569RefSeq:NZ_AMGH01000045
NZ_AMGH0100005110810503114,020RefSeq:NZ_AMGH01000051
NZ_AMGH0100001010410031111,035RefSeq:NZ_AMGH01000010
NZ_AMGH01000056959104104,166RefSeq:NZ_AMGH01000056
NZ_AMGH01000041107972895,508RefSeq:NZ_AMGH01000041
NZ_AMGH0100004386806090,643RefSeq:NZ_AMGH01000043
NZ_AMGH0100003478761187,258RefSeq:NZ_AMGH01000034
NZ_AMGH0100004879736075,881RefSeq:NZ_AMGH01000048
NZ_AMGH0100000966642073,057RefSeq:NZ_AMGH01000009
NZ_AMGH0100004965630266,564RefSeq:NZ_AMGH01000049
NZ_AMGH0100003569624364,962RefSeq:NZ_AMGH01000035
NZ_AMGH0100004771671363,945RefSeq:NZ_AMGH01000047
NZ_AMGH0100001462620063,768RefSeq:NZ_AMGH01000014
NZ_AMGH0100002957540360,666RefSeq:NZ_AMGH01000029
NZ_AMGH0100001756488059,248RefSeq:NZ_AMGH01000017
NZ_AMGH0100003670700051,440RefSeq:NZ_AMGH01000036
NZ_AMGH0100002249462148,331RefSeq:NZ_AMGH01000022
NZ_AMGH0100002842390345,759RefSeq:NZ_AMGH01000028
NZ_AMGH0100003951473139,024RefSeq:NZ_AMGH01000039
NZ_AMGH0100001533293137,398RefSeq:NZ_AMGH01000015
NZ_AMGH0100005840400036,296RefSeq:NZ_AMGH01000058
NZ_AMGH0100000630282027,679RefSeq:NZ_AMGH01000006
NZ_AMGH0100004619180123,432RefSeq:NZ_AMGH01000046
NZ_AMGH0100001828270117,143RefSeq:NZ_AMGH01000018
NZ_AMGH0100002729271116,748RefSeq:NZ_AMGH01000027
NZ_AMGH0100002516160012,416RefSeq:NZ_AMGH01000025
NZ_AMGH0100000313130011,250RefSeq:NZ_AMGH01000003
NZ_AMGH010000082221019,700RefSeq:NZ_AMGH01000008
NZ_AMGH010000021615017,932RefSeq:NZ_AMGH01000002
25 Undisplayed Contigs/Replicons777702066,079
Total:3,9913,80893904,063,888
Ortholog data available?Yes
Database Contents
Genes3,982
Pathways271
Enzymatic Reactions1,362
Transport Reactions111
Polypeptides3,820
Protein Complexes52
Enzymes799
Transporters357
Compounds1,057
Transcription Units2,722
tRNAs70
GO Terms2,627
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii IS-58
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761215
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903914
Environmentrespiratory tract
Geographic LocationIraq
Collection Date2008-02
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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