Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Acetomicrobium hydrogeniformans OS1, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_ACJX030000012,0952,01758202,103,414RefSeq:NZ_ACJX03000001
7 Undisplayed Contigs/Replicons17170220,511
Ortholog data available?No
Database Contents
Genes2,114
Pathways185
Enzymatic Reactions975
Transport Reactions42
Polypeptides2,040
Protein Complexes66
Enzymes507
Transporters194
Compounds759
Transcription Units963
tRNAs48
Protein Features2,744
GO Terms170
Database Version29.0
Sequence SourceGCF_000160455.2
Synonyms Anaerobaculum hydrogeniforman DSM 22491
Anaerobaculum hydrogeniforman OS1
Anaerobaculum hydrogeniformans ATCC BAA-1850
Anaerobaculum sp. OS1
Acetomicrobium hydrogeniformans ATCC BAA-1850
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Synergistota
Synergistia
Synergistales
Synergistaceae
Acetomicrobium
Acetomicrobium hydrogeniformans
Acetomicrobium hydrogeniformans ATCC BAA-1850
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00009040
NCBI BioProjectPRJNA224116
NCBI-Taxonomy592015
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2022-03-29
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.1
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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