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 Absiella argi N6H1-5, 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_AP0196953,0382,88887632,991,568RefSeq:NZ_AP019695
pABar166004,730RefSeq:NZ_AP019696
Total:3,0442,89487632,996,298
Ortholog data available?Yes
Database Contents
Genes3,044
Pathways127
Enzymatic Reactions711
Transport Reactions79
Polypeptides2,894
Protein Complexes30
Enzymes472
Transporters269
Compounds597
Transcription Units1,783
tRNAs66
Protein Features3,417
GO Terms39
Database Version29.0
Sequence SourceGCF_010537155.1
Synonyms Eubacterium sp. 1-3
Eubacterium sp. 1-5
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Erysipelotrichia
Erysipelotrichales
Erysipelotrichaceae
Absiella
Absiella argi
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00172297
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1671597
EnvironmentIntestinal
Geographic LocationSouth Korea
Collection Date2014-04-15
HostCanis lupus
Annotation ProviderNCBI RefSeq
Annotation Date2020-04-17
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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