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 12-July-2021 from the annotated genome of Actinobacteria bacterium 15TR583 15TR583, 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 25.0) [Karp16, Karp11] using MetaCyc version 25.0 [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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_RPFW010000011,7401,6637701,889,528RefSeq:NZ_RPFW01000001
NZ_RPFW010000021,2351,1951391,327,398RefSeq:NZ_RPFW01000002
NZ_RPFW010000031,0441,0117261,129,685RefSeq:NZ_RPFW01000003
NZ_RPFW010000041,0049709251,103,890RefSeq:NZ_RPFW01000004
NZ_RPFW01000005727695032733,295RefSeq:NZ_RPFW01000005
NZ_RPFW010000066786421224708,174RefSeq:NZ_RPFW01000006
NZ_RPFW01000007555536712586,150RefSeq:NZ_RPFW01000007
NZ_RPFW01000008420408111448,547RefSeq:NZ_RPFW01000008
NZ_RPFW01000009348338010373,870RefSeq:NZ_RPFW01000009
NZ_RPFW01000010260242612294,650RefSeq:NZ_RPFW01000010
NZ_RPFW0100001119318418203,777RefSeq:NZ_RPFW01000011
NZ_RPFW01000012178157183184,672RefSeq:NZ_RPFW01000012
NZ_RPFW0100001370661382,918RefSeq:NZ_RPFW01000013
NZ_RPFW0100001460570348,372RefSeq:NZ_RPFW01000014
NZ_RPFW0100001532241733,505RefSeq:NZ_RPFW01000015
NZ_RPFW0100001626250127,177RefSeq:NZ_RPFW01000016
NZ_RPFW0100001726210527,032RefSeq:NZ_RPFW01000017
76 Undisplayed Contigs/Replicons212182852,006
Total:8,6538,255793199,254,646
Ortholog data available?Yes
Database Contents
Genes8,645
Pathways274
Enzymatic Reactions1,486
Transport Reactions50
Polypeptides8,281
Protein Complexes59
Enzymes1,128
Transporters622
Compounds1,088
Transcription Units6,271
tRNAs64
Protein Features9,293
Database Version29.0
Sequence SourceGCF_007827045.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
unclassified Actinobacteria
Actinobacteria bacterium 15TR583
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN10256292
NCBI BioProjectPRJNA224116
NCBI-Taxonomy2480626
Environmentsoil
Geographic LocationCzech Republic
Latitude/Longitude48.97422 N 14.76985 E
Altitude (m)440.0
Collection Date2015
Annotation ProviderNCBI RefSeq
Annotation Date2020-08-31
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.12
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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