Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2020 from the annotated genome of Acinetobacter nosocomialis 6411, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [Caspi20]. 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 Institutes of Health.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0103683,6423,46794813,858,956RefSeq:NZ_CP010368
p6411-89.111kb856502089,111RefSeq:NZ_CP010369
p6411-66.409kb69660366,409RefSeq:NZ_CP010903
p6411-9.012kb51500147,274RefSeq:NZ_CP010370
Total:3,8473,648941054,061,750
Ortholog data available?Yes
Database Contents
Genes3,847
Pathways273
Enzymatic Reactions1,312
Transport Reactions91
Polypeptides3,650
Protein Complexes45
Enzymes795
Transporters409
Compounds975
Transcription Units2,677
tRNAs72
Protein Features4,535
GO Terms2,402
Database Version29.0
Sequence SourceGCF_000814165.3
Synonyms Acinetobacter genomosp. 13TU
Acinetobacter genosp. 13TU
Acinetobacter sp. NF108071
Acinetobacter sp. WC-487
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter nosocomialis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03263968
NCBI BioProjectPRJNA224116
NCBI-Taxonomy106654
Environmentexcreted bodily substance
Geographic LocationColombia
Latitude/Longitude1.12 N 77.16 W
Collection Date2012
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-17
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

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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