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 25-Oct-2020 from the annotated genome of Actinobaculum suis U311, 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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_LFUS01000018176159512205,384RefSeq:NZ_LFUS01000018
NZ_LFUS0100000211410923159,967RefSeq:NZ_LFUS01000002
NZ_LFUS010000251009046134,668RefSeq:NZ_LFUS01000025
NZ_LFUS01000032918461112,095RefSeq:NZ_LFUS01000032
NZ_LFUS0100001173691393,736RefSeq:NZ_LFUS01000011
NZ_LFUS0100002389880192,616RefSeq:NZ_LFUS01000023
NZ_LFUS0100002768640491,506RefSeq:NZ_LFUS01000027
NZ_LFUS0100001272702087,129RefSeq:NZ_LFUS01000012
NZ_LFUS0100003065641084,547RefSeq:NZ_LFUS01000030
NZ_LFUS0100004170672180,703RefSeq:NZ_LFUS01000041
NZ_LFUS0100003162591275,465RefSeq:NZ_LFUS01000031
NZ_LFUS0100001772641769,766RefSeq:NZ_LFUS01000017
NZ_LFUS0100002844393262,957RefSeq:NZ_LFUS01000028
NZ_LFUS0100002948443162,606RefSeq:NZ_LFUS01000029
NZ_LFUS0100000745450061,730RefSeq:NZ_LFUS01000007
NZ_LFUS0100000163621059,306RefSeq:NZ_LFUS01000001
NZ_LFUS0100001446433058,869RefSeq:NZ_LFUS01000014
NZ_LFUS0100001543421057,906RefSeq:NZ_LFUS01000015
NZ_LFUS0100003949444157,616RefSeq:NZ_LFUS01000039
NZ_LFUS0100003447441257,600RefSeq:NZ_LFUS01000034
NZ_LFUS0100001936341149,661RefSeq:NZ_LFUS01000019
NZ_LFUS0100002135311346,259RefSeq:NZ_LFUS01000021
NZ_LFUS0100002033330041,673RefSeq:NZ_LFUS01000020
NZ_LFUS0100004532320039,536RefSeq:NZ_LFUS01000045
NZ_LFUS0100002430291036,828RefSeq:NZ_LFUS01000024
NZ_LFUS0100002223230034,978RefSeq:NZ_LFUS01000022
NZ_LFUS0100001328270133,411RefSeq:NZ_LFUS01000013
NZ_LFUS0100001023190429,993RefSeq:NZ_LFUS01000010
NZ_LFUS0100002620173028,182RefSeq:NZ_LFUS01000026
NZ_LFUS0100000818161124,229RefSeq:NZ_LFUS01000008
NZ_LFUS0100003311110020,631RefSeq:NZ_LFUS01000033
NZ_LFUS0100004813130019,947RefSeq:NZ_LFUS01000048
NZ_LFUS0100003515120319,577RefSeq:NZ_LFUS01000035
NZ_LFUS0100004013120117,863RefSeq:NZ_LFUS01000040
NZ_LFUS0100004916160017,076RefSeq:NZ_LFUS01000049
NZ_LFUS0100004416140213,799RefSeq:NZ_LFUS01000044
NZ_LFUS010000431211019,454RefSeq:NZ_LFUS01000043
22 Undisplayed Contigs/Replicons838127109,389
Total:1,9011,78150702,358,658
Ortholog data available?Yes
Database Contents
Genes1,901
Pathways151
Enzymatic Reactions753
Transport Reactions46
Polypeptides1,800
Protein Complexes22
Enzymes419
Transporters205
Compounds587
Transcription Units1,402
tRNAs44
Protein Features2,158
GO Terms6,979
Database Version29.0
Sequence SourceGCF_001183565.1
Synonyms Actinomyces suis
Corynebacterium suis
Eubacterium suis
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinobaculum
Actinobaculum suis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03783260
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1657
Environmenturine
Geographic LocationBrazil
Collection Date2011
HostSus scrofa
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-10
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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