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 Actinobacillus suis ATCC 33415, 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_CP0091592,3382,23286202,501,598RefSeq:NZ_CP009159
Ortholog data available?Yes
Database Contents
Genes2,338
Pathways258
Enzymatic Reactions1,268
Transport Reactions113
Polypeptides2,236
Protein Complexes46
Enzymes696
Transporters291
Compounds891
Transcription Units1,520
tRNAs63
Protein Features3,148
GO Terms1,701
Database Version29.0
Sequence SourceGCF_000739435.1
Synonyms Actinobacillus suis CCM 5586
Actinobacillus suis str. ATCC 33415
Actinobacillus suis strain ATCC 33415
Actinobacillus suis ATCC 33415
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Pasteurellales
Pasteurellaceae
Actinobacillus
Actinobacillus suis
Actinobacillus suis ATCC 33415
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01918029
NCBI BioProjectPRJNA224116
NCBI-Taxonomy743972
EnvironmentSepticemia in pig
Annotation ProviderNCBI RefSeq
Annotation Date2020-04-4
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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