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 13-Mar-2021 from the annotated genome of Acetomicrobium mobile DSM 13181, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [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_0180242,0962,01657232,160,700RefSeq:NC_018024
Ortholog data available?Yes
Database Contents
Genes2,096
Pathways165
Enzymatic Reactions936
Transport Reactions66
Polypeptides2,016
Protein Complexes33
Enzymes522
Transporters260
Compounds730
Transcription Units948
tRNAs48
Protein Features2,734
Database Version29.0
Sequence SourceGCF_000266925.1
Synonyms Acetomicrobium mobile ATCC BAA-54
Anaerobaculum mobile ATCC BAA-54
Anaerobaculum mobile DSM 13181
Anaerobaculum mobile NGA
Acetomicrobium mobile DSM 13181
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Synergistota
Synergistia
Synergistales
Synergistaceae
Acetomicrobium
Acetomicrobium mobile
Acetomicrobium mobile DSM 13181
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02261375
NCBI BioProjectPRJNA224116
NCBI-Taxonomy891968
Environmentanaerobic wool-scouring wastewater treatment lagoon
Geographic LocationUruguay
Latitude/Longitude33.51 S 56.89 W
Relationship to Oxygenobligate-anaerobe
Trophic Levelchemoorganotroph
Temperature Rangethermophile
Biotic Relationshipfree-living
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-3
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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17.