Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Escherichia coli O104:H4 2011C-3493, 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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_0186585,1234,8061231945,273,097RefSeq:NC_018658
pESBL-EA1197940388,544RefSeq:NC_018659
pAA-EA11915603574,217RefSeq:NC_018666
pG-EA1122001,549RefSeq:NC_018660
Total:5,3134,9581232325,437,407
Ortholog data available?Yes
Database Contents
Genes5,313
Pathways513
Enzymatic Reactions2,101
Transport Reactions424
Polypeptides4,964
Protein Complexes288
Enzymes1,402
Transporters527
Compounds1,429
Transcription Units3,189
tRNAs92
Protein Features6,794
GO Terms22,225
Database Version29.0
Sequence SourceGCF_000299455.1
Synonyms Escherichia coli O104:H4 strain 2011C-3493
Escherichia coli O104:H4 str. 2011C-3493
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Escherichia
Escherichia coli
Escherichia coli O104:H4
Escherichia coli O104:H4 2011C-3493
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01831188
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1133852
Collection Date2011
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2021-05-6
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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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