Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2020 from the annotated genome of Streptococcus dysgalactiae subsp. equisimilis AC-2713, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_0190422,0141,938761172,179,445RefSeq:NC_019042
Ortholog data available?Yes
Database Contents
Genes2,014
Pathways162
Enzymatic Reactions835
Transport Reactions82
Polypeptides1,939
Protein Complexes32
Enzymes451
Transporters240
Compounds625
Transcription Units1,279
tRNAs57
Protein Features2,601
GO Annotations113
Database Version29.6
Sequence SourceGCF_000317855.1
Synonyms Streptococcus dysgalactiae subsp. equisimilis str. AC-2713
Streptococcus dysgalactiae subsp. equisimilis strain AC-2713
Streptococcus dysgalactiae subsp. equisimilis AC-2713
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Bacillati
Bacillota
Bacilli
Lactobacillales
Streptococcaceae
Streptococcus
Streptococcus dysgalactiae group
Streptococcus dysgalactiae
Streptococcus dysgalactiae equisimilis
Streptococcus dysgalactiae equisimilis AC-2713
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA3138428
NCBI BioProjectPRJNA224116
NCBI-Taxonomy759913
Annotation ProviderNCBI RefSeq
Annotation Date2020-06-2
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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