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 25-Oct-2020 from the annotated genome of Actinobacteria bacterium IMCC26207 IMCC26207, 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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_LCZK01000010727714103836,048RefSeq:NZ_LCZK01000010
NZ_LCZK0100000967466365718,897RefSeq:NZ_LCZK01000009
NZ_LCZK0100000829829026344,959RefSeq:NZ_LCZK01000008
NZ_LCZK0100000722121362258,227RefSeq:NZ_LCZK01000007
NZ_LCZK0100000625925261254,168RefSeq:NZ_LCZK01000006
NZ_LCZK0100000522221291247,305RefSeq:NZ_LCZK01000005
NZ_LCZK0100000418618150203,690RefSeq:NZ_LCZK01000004
NZ_LCZK0100000317416932201,503RefSeq:NZ_LCZK01000003
NZ_LCZK0100000215414833162,019RefSeq:NZ_LCZK01000002
NZ_LCZK0100000176751089,983RefSeq:NZ_LCZK01000001
Total:2,9912,91751233,316,799
Ortholog data available?Yes
Database Contents
Genes2,991
Pathways175
Enzymatic Reactions948
Transport Reactions39
Polypeptides2,924
Protein Complexes32
Enzymes565
Transporters147
Compounds772
Transcription Units1,967
tRNAs45
Protein Features3,557
GO Terms10,015
Database Version29.0
Sequence SourceGCF_001025035.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
unclassified Actinobacteria (class)
unclassified Actinobacteria (class) (miscellaneous)
Actinobacteria bacterium IMCC26207
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03480620
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1641811
Environmentfreshwater
Geographic LocationSouth Korea
Collection Date2014-04-14
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-10
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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