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 Dielma fastidiosa type strain: JC13, 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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_HE578923580567138608,951RefSeq:NZ_HE578923
NZ_HE57892444544327456,888RefSeq:NZ_HE578924
NZ_HE578925438424142434,182RefSeq:NZ_HE578925
NZ_HE57892637436953410,413RefSeq:NZ_HE578926
NZ_HE57892738938456408,047RefSeq:NZ_HE578927
NZ_HE57892830230202341,115RefSeq:NZ_HE578928
NZ_HE57892924023555242,904RefSeq:NZ_HE578929
NZ_HE57893021921812208,175RefSeq:NZ_HE578930
NZ_HE57893111711613143,563RefSeq:NZ_HE578931
NZ_HE57893213212753136,227RefSeq:NZ_HE578932
NZ_HE57893313613600119,425RefSeq:NZ_HE578933
84 Undisplayed Contigs/Replicons4035512105,144
Total:3,4653,35656533,615,034
Ortholog data available?Yes
Database Contents
Genes3,412
Pathways139
Enzymatic Reactions666
Transport Reactions107
Polypeptides3,387
Protein Complexes65
Enzymes459
Transporters382
Compounds514
Transcription Units2,006
tRNAs49
Protein Features4,083
GO Annotations1
Database Version29.6
Sequence SourceGCF_000313565.1
Synonyms Clostridiaceae bacterium JC13
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Bacillati
Bacillota
Erysipelotrichia
Erysipelotrichales
Erysipelotrichaceae
Dielma
Dielma fastidiosa
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA2272058
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1034346
Environmenthost stool sample
Geographic LocationSenegal
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2019-11-25
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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