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 13-Mar-2021 from the annotated genome of Actinobacillus pleuropneumoniae serovar "5b" str. L20, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [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
NC_0090532,1652,02485562,274,482RefSeq:NC_009053
Ortholog data available?Yes
Database Contents
Genes2,165
Pathways251
Enzymatic Reactions1,250
Transport Reactions117
Polypeptides2,024
Protein Complexes41
Enzymes688
Transporters268
Compounds893
Transcription Units1,403
tRNAs62
Protein Features4,558
GO Terms69
Database Version29.0
Sequence SourceGCF_000015885.1
Synonyms Actinobacillus pleuropneumoniae L20
Actinobacillus pleuropneumoniae serovar 5b strain L20
Actinobacillus pleuropneumoniae serovar 5b str. L20
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Pasteurellales
Pasteurellaceae
Actinobacillus
Actinobacillus pleuropneumoniae
Actinobacillus pleuropneumoniae serovar 5
Actinobacillus pleuropneumoniae serovar 5b str. L20
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603665
NCBI BioProjectPRJNA224116
NCBI-Taxonomy416269
Annotation ProviderNCBI RefSeq
Annotation Date2021-01-31
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

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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