Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Escherichia coli BL21(DE3), 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_0129714,7004,3391162454,558,953RefSeq:NC_012971
Ortholog data available?Yes
Database Contents
Genes4,700
Pathways489
Enzymatic Reactions2,023
Transport Reactions422
Polypeptides4,347
Protein Complexes294
Enzymes1,366
Transporters485
Compounds1,351
Transcription Units2,945
tRNAs85
Protein Features61
GO Terms24,107
Database Version29.0
Sequence SourceGCF_000022665.1
Synonyms Escherichia coli str. BL21(DE3)
Escherichia coli strain BL21(DE3)
Escherichia coli BL21(DE3)
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Escherichia
Escherichia coli
Escherichia coli BL21(DE3)
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603478
NCBI BioProjectPRJNA224116
NCBI-Taxonomy469008
Annotation ProviderNCBI
Annotation Date2017-02-22
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+

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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