Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Pseudothermotoga elfii NBRC 107921, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_0227922,1192,06752192,169,860RefSeq:NC_022792
Ortholog data available?Yes
Database Contents
Genes2,119
Pathways151
Enzymatic Reactions858
Transport Reactions44
Polypeptides2,068
Protein Complexes44
Enzymes471
Transporters340
Compounds639
Transcription Units803
tRNAs46
Protein Features2,732
GO Annotations1,493
Database Version29.6
Sequence SourceGCF_000504085.1
Synonyms Pseudothermotoga elfii DSM 9442
Pseudothermotoga elfii NBRC 107921
Pseudothermotoga elfii NBRC 107921 = DSM 9442
Thermotoga elfii DSM 9442
Thermotoga elfii DSM 9442 = NBRC 107921
Thermotoga elfii NBRC 107921
Pseudothermotoga elfii DSM 9442 = NBRC 107921
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Thermotogati
Thermotogota
Thermotogae <Thermotogae>
Thermotogales
Thermotogaceae
Pseudothermotoga
Pseudothermotoga elfii
Pseudothermotoga elfii DSM 9442 = NBRC 107921
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00061030
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1123383
Annotation ProviderNCBI
Annotation Date2017-04-9
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+
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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