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 Aciduliprofundum boonei T469, 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_0139261,5861,52451111,486,778RefSeq:NC_013926
Ortholog data available?Yes
Database Contents
Genes1,586
Pathways74
Enzymatic Reactions495
Transport Reactions23
Polypeptides1,524
Protein Complexes13
Enzymes313
Transporters131
Compounds432
Transcription Units792
tRNAs46
Protein Features1,855
Database Version29.0
Sequence SourceGCF_000025665.1
Synonyms Aciduliprofundum boonei DSM 19572
Aciduliprofundum boonei str. T469
Aciduliprofundum boonei strain T469
Aciduliprofundum boonei T469
Taxonomic Lineage cellular organisms
Archaea
Candidatus Thermoplasmatota
DHVE2 group
Candidatus Aciduliprofundum
Candidatus Aciduliprofundum boonei
Aciduliprofundum boonei T469
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02598523
NCBI BioProjectPRJNA224116
NCBI-Taxonomy439481
EnvironmentHydrothermally heated black smoker wall at the TAG site at the Mid Atlantic Ridge depth 3650m
Latitude/Longitude22.16889 S 176.60028 W
Depth (m)-1920.0
Temperature Rangethermophile
Biotic Relationshipfree-living
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-7
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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