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 Erwinia amylovora ATCC 49946, 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_0139713,4563,257122773,805,874RefSeq:NC_013971
276760071,487RefSeq:NC_013973
129220728,243RefSeq:NC_013972
Total:3,5613,355122843,905,604
Ortholog data available?No
Database Contents
Genes3,561
Pathways336
Enzymatic Reactions1,642
Transport Reactions118
Polypeptides3,355
Protein Complexes112
Enzymes959
Transporters317
Compounds1,139
Transcription Units2,285
tRNAs78
Protein Features4,580
GO Terms2,485
Database Version29.0
Sequence SourceGCF_000027205.1
Synonyms Erwinia amylovora 27-3
Erwinia amylovora BC206
Erwinia amylovora Ea273
Erwinia amylovora strain ATCC 49946
Erwinia amylovora str. ATCC 49946
Erwinia amylovora ATCC 49946
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Erwiniaceae
Erwinia
Erwinia amylovora
Erwinia amylovora ATCC 49946
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA2272701
NCBI BioProjectPRJNA224116
NCBI-Taxonomy716540
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-14
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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