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 Acidimicrobium ferrooxidans DSM 10331, 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_0131242,0962,01055312,158,157RefSeq:NC_013124
Ortholog data available?Yes
Database Contents
Genes2,096
Pathways174
Enzymatic Reactions922
Transport Reactions31
Polypeptides2,010
Protein Complexes29
Enzymes544
Transporters145
Compounds757
Transcription Units1,091
tRNAs46
Protein Features2,501
Database Version29.0
Sequence SourceGCF_000023265.1
Synonyms Acidimicrobium ferrooxidans ICP
Acidimicrobium ferrooxidans str. DSM 10331
Acidimicrobium ferrooxidans strain DSM 10331
Acidimicrobium ferrooxidans DSM 10331
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Acidimicrobiia
Acidimicrobiales
Acidimicrobiaceae
Acidimicrobium
Acidimicrobium ferrooxidans
Acidimicrobium ferrooxidans DSM 10331
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02598466
NCBI BioProjectPRJNA224116
NCBI-Taxonomy525909
EnvironmentHot spring run-off in Iceland
Geographic LocationIceland
Latitude/Longitude63.93 N 22.1 W
Temperature Rangethermophile
Biotic Relationshipfree-living
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-26
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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