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 1 str. 4074, as obtained from RefSeq (annotation date: 03-MAR-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_AACK010000011079854104,676RefSeq:NZ_AACK01000001
NZ_AACK0100000292882298,272RefSeq:NZ_AACK01000002
NZ_AACK0100000386761996,588RefSeq:NZ_AACK01000003
NZ_AACK0100000475701493,964RefSeq:NZ_AACK01000004
NZ_AACK0100000582810191,321RefSeq:NZ_AACK01000005
NZ_AACK0100000681760586,486RefSeq:NZ_AACK01000006
NZ_AACK0100000761540777,521RefSeq:NZ_AACK01000007
NZ_AACK0100000881752469,352RefSeq:NZ_AACK01000008
NZ_AACK0100000959523466,421RefSeq:NZ_AACK01000009
NZ_AACK0100001071609266,203RefSeq:NZ_AACK01000010
NZ_AACK0100001163552664,130RefSeq:NZ_AACK01000011
NZ_AACK0100001254530159,714RefSeq:NZ_AACK01000012
NZ_AACK0100001340390159,048RefSeq:NZ_AACK01000013
NZ_AACK0100001455520357,807RefSeq:NZ_AACK01000014
NZ_AACK0100001540380248,003RefSeq:NZ_AACK01000015
NZ_AACK0100001643430047,478RefSeq:NZ_AACK01000016
NZ_AACK0100001741371346,953RefSeq:NZ_AACK01000017
NZ_AACK0100001848421541,944RefSeq:NZ_AACK01000018
NZ_AACK0100001948442239,063RefSeq:NZ_AACK01000019
NZ_AACK0100002032300237,032RefSeq:NZ_AACK01000020
NZ_AACK0100002132300235,737RefSeq:NZ_AACK01000021
NZ_AACK0100002226240231,786RefSeq:NZ_AACK01000022
NZ_AACK0100002330290131,527RefSeq:NZ_AACK01000023
NZ_AACK0100002430291031,502RefSeq:NZ_AACK01000024
NZ_AACK0100002528240430,655RefSeq:NZ_AACK01000025
NZ_AACK0100002637315129,485RefSeq:NZ_AACK01000026
NZ_AACK0100002720180228,847RefSeq:NZ_AACK01000027
NZ_AACK0100002826250127,958RefSeq:NZ_AACK01000028
NZ_AACK0100002922191226,934RefSeq:NZ_AACK01000029
NZ_AACK0100003036267326,418RefSeq:NZ_AACK01000030
NZ_AACK0100003138370125,184RefSeq:NZ_AACK01000031
NZ_AACK0100003229244125,126RefSeq:NZ_AACK01000032
NZ_AACK0100003323201224,824RefSeq:NZ_AACK01000033
NZ_AACK0100003420190124,417RefSeq:NZ_AACK01000034
NZ_AACK0100003523202121,538RefSeq:NZ_AACK01000035
NZ_AACK0100003620180221,192RefSeq:NZ_AACK01000036
NZ_AACK0100003713120120,980RefSeq:NZ_AACK01000037
NZ_AACK0100003818170119,198RefSeq:NZ_AACK01000038
NZ_AACK0100003916140218,064RefSeq:NZ_AACK01000039
NZ_AACK0100004014130117,400RefSeq:NZ_AACK01000040
NZ_AACK0100004214130116,627RefSeq:NZ_AACK01000042
NZ_AACK0100004314120216,436RefSeq:NZ_AACK01000043
NZ_AACK0100004419170216,289RefSeq:NZ_AACK01000044
NZ_AACK0100004517105215,684RefSeq:NZ_AACK01000045
NZ_AACK0100004617170015,187RefSeq:NZ_AACK01000046
NZ_AACK0100004717150215,063RefSeq:NZ_AACK01000047
NZ_AACK0100004814110314,457RefSeq:NZ_AACK01000048
NZ_AACK0100004914130113,922RefSeq:NZ_AACK01000049
NZ_AACK0100005017140313,808RefSeq:NZ_AACK01000050
NZ_AACK0100005316130313,194RefSeq:NZ_AACK01000053
NZ_AACK0100005412120012,835RefSeq:NZ_AACK01000054
NZ_AACK0100005518170112,472RefSeq:NZ_AACK01000055
NZ_AACK0100005614140012,369RefSeq:NZ_AACK01000056
NZ_AACK010000601060411,100RefSeq:NZ_AACK01000060
NZ_AACK010000641514017,874RefSeq:NZ_AACK01000064
85 Undisplayed Contigs/Replicons1361261153214,283
Total:2,1781,936661762,292,348
Ortholog data available?No
Database Contents
Genes2,170
Pathways260
Enzymatic Reactions1,455
Transport Reactions104
Polypeptides1,998
Protein Complexes77
Enzymes675
Transporters232
Compounds1,296
Transcription Units1,583
tRNAs45
Protein Features2,829
GO Terms3,383
Database Version29.0
Sequence SourceGCF_000167095.1
Synonyms Actinobacillus pleuropneumoniae 4074
Actinobacillus pleuropneumoniae serovar 1 strain 4074
Actinobacillus pleuropneumoniae serovar 1 str. 4074
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Pasteurellales
Pasteurellaceae
Actinobacillus
Actinobacillus pleuropneumoniae
Actinobacillus pleuropneumoniae serovar 1
Actinobacillus pleuropneumoniae serovar 1 str. 4074
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471910
NCBI BioProjectPRJNA224116
NCBI-Taxonomy228399
Annotation ProviderNCBI RefSeq
Annotation Date2024-04-3
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.7
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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