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 Kurthia senegalensis JC8E, 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_HE61106498692710491,016,226RefSeq:NZ_HE611064
NZ_HE611065426405219435,210RefSeq:NZ_HE611065
NZ_HE611066429405024434,399RefSeq:NZ_HE611066
NZ_HE61106736435419354,481RefSeq:NZ_HE611067
NZ_HE611068204176199185,434RefSeq:NZ_HE611068
NZ_HE6110691581291514148,440RefSeq:NZ_HE611069
NZ_HE61107015114704141,179RefSeq:NZ_HE611070
NZ_HE61107173651773,642RefSeq:NZ_HE611071
NZ_HE61107256522257,822RefSeq:NZ_HE611072
NZ_HE61107341381246,788RefSeq:NZ_HE611073
NZ_HE61107450432544,957RefSeq:NZ_HE611074
NZ_HE61107514121113,679RefSeq:NZ_HE611075
NZ_HE61107616160013,453RefSeq:NZ_HE611076
30 Undisplayed Contigs/Replicons40244621,059
Total:3,0202,771981512,986,769
Ortholog data available?Yes
Database Contents
Genes3,013
Pathways203
Enzymatic Reactions1,063
Transport Reactions60
Polypeptides2,795
Protein Complexes84
Enzymes572
Transporters223
Compounds762
Transcription Units2,020
tRNAs81
Protein Features3,392
GO Terms222
Database Version29.0
Sequence SourceGCF_000285595.1
Synonyms Kurthia sp. JC8E
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Bacillales
Planococcaceae
Kurthia
Kurthia senegalensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA2272665
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1033740
Environmenthost stool sample
Geographic LocationSenegal
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2022-01-25
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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