Database Authors
Pallavi Subhraveti1, Anamika Kothari1, Peter Midford1, Ron Caspi1, Lisa Moore1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 30-Oct-2024 from the annotated genome of Actinobacillus pleuropneumoniae serovar 11 str. 56153, as obtained from RefSeq (annotation date: 07-SEP-2023). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 28.5) [Karp11, Karp16] using MetaCyc version 28.1 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_ADOK0100001922721656233,007RefSeq:NZ_ADOK01000019
NZ_ADOK0100001422320788231,044RefSeq:NZ_ADOK01000014
NZ_ADOK0100001218717737188,625RefSeq:NZ_ADOK01000012
NZ_ADOK0100001313212723150,740RefSeq:NZ_ADOK01000013
NZ_ADOK0100003712612420121,053RefSeq:NZ_ADOK01000037
NZ_ADOK0100000310410211109,156RefSeq:NZ_ADOK01000003
NZ_ADOK0100003110610042105,722RefSeq:NZ_ADOK01000031
NZ_ADOK01000009959113105,322RefSeq:NZ_ADOK01000009
NZ_ADOK0100001572680490,014RefSeq:NZ_ADOK01000015
NZ_ADOK0100000177760182,910RefSeq:NZ_ADOK01000001
NZ_ADOK0100003281770478,985RefSeq:NZ_ADOK01000032
NZ_ADOK0100000773691378,948RefSeq:NZ_ADOK01000007
NZ_ADOK0100002072665168,348RefSeq:NZ_ADOK01000020
NZ_ADOK0100003664640067,899RefSeq:NZ_ADOK01000036
NZ_ADOK0100001749450456,439RefSeq:NZ_ADOK01000017
NZ_ADOK0100003468680055,508RefSeq:NZ_ADOK01000034
NZ_ADOK0100002440380247,856RefSeq:NZ_ADOK01000024
NZ_ADOK0100000241410045,053RefSeq:NZ_ADOK01000002
NZ_ADOK0100000834330137,892RefSeq:NZ_ADOK01000008
NZ_ADOK0100002333330035,778RefSeq:NZ_ADOK01000023
NZ_ADOK0100002634340035,600RefSeq:NZ_ADOK01000026
NZ_ADOK0100002140364035,295RefSeq:NZ_ADOK01000021
NZ_ADOK0100003534313030,724RefSeq:NZ_ADOK01000035
NZ_ADOK0100000628261130,357RefSeq:NZ_ADOK01000006
NZ_ADOK0100003040328029,085RefSeq:NZ_ADOK01000030
NZ_ADOK0100003317142120,565RefSeq:NZ_ADOK01000033
NZ_ADOK0100002716151016,550RefSeq:NZ_ADOK01000027
20 Undisplayed Contigs/Replicons46442878,148
Total:2,1672,05453602,266,623
Ortholog data available?No
Database Contents
Genes2,167
Pathways280
Enzymatic Reactions1,520
Transport Reactions106
Polypeptides2,072
Protein Complexes81
Enzymes704
Transporters242
Compounds1,333
Transcription Units1,489
tRNAs45
Protein Features2,929
GO Terms3,478
Database Version29.0
Sequence SourceGCF_000178615.1
Synonyms Actinobacillus pleuropneumoniae 56153
Actinobacillus pleuropneumoniae serovar 11 strain 56153
Actinobacillus pleuropneumoniae serovar 11 str. 56153
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Pasteurellales
Pasteurellaceae
Actinobacillus
Actinobacillus pleuropneumoniae
Actinobacillus pleuropneumoniae serovar 11
Actinobacillus pleuropneumoniae serovar 11 str. 56153
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02469624
NCBI BioProjectPRJNA224116
NCBI-Taxonomy754260
Annotation ProviderNCBI RefSeq
Annotation Date2023-09-6
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.6
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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