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 Acidaminococcus fermentans DSM 20731, 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
NC_0137402,1742,03882542,329,769RefSeq:NC_013740
Ortholog data available?Yes
Database Contents
Genes2,174
Pathways149
Enzymatic Reactions872
Transport Reactions55
Polypeptides2,039
Protein Complexes25
Enzymes491
Transporters246
Compounds666
Transcription Units1,240
tRNAs60
Protein Features2,785
Database Version29.0
Sequence SourceGCF_000025305.1
Synonyms Acidaminococcus fermentans str. DSM 20731
Acidaminococcus fermentans strain DSM 20731
Acidaminococcus fermentans DSM 20731
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Negativicutes
Acidaminococcales
Acidaminococcaceae
Acidaminococcus
Acidaminococcus fermentans
Acidaminococcus fermentans DSM 20731
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02598507
NCBI BioProjectPRJNA224116
NCBI-Taxonomy591001
EnvironmentPig gut
Temperature Rangemesophile
Biotic Relationshipfree-living
HostSus scrofa
Annotation ProviderNCBI RefSeq
Annotation Date2019-08-25
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.9
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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