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 OV320 OV320, 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_LJCX01000029864846315965,522RefSeq:NZ_LJCX01000029
NZ_LJCX010000308197831026922,110RefSeq:NZ_LJCX01000030
NZ_LJCX01000027790752632886,187RefSeq:NZ_LJCX01000027
NZ_LJCX010000287877412323863,542RefSeq:NZ_LJCX01000028
NZ_LJCX01000026760723136825,853RefSeq:NZ_LJCX01000026
NZ_LJCX01000031571547816627,481RefSeq:NZ_LJCX01000031
NZ_LJCX01000024464448610523,183RefSeq:NZ_LJCX01000024
NZ_LJCX01000025407388910459,148RefSeq:NZ_LJCX01000025
NZ_LJCX0100002341339887450,682RefSeq:NZ_LJCX01000023
NZ_LJCX01000001367347119439,232RefSeq:NZ_LJCX01000001
NZ_LJCX01000019376361510392,581RefSeq:NZ_LJCX01000019
NZ_LJCX01000005344332210386,242RefSeq:NZ_LJCX01000005
NZ_LJCX01000032327283044350,470RefSeq:NZ_LJCX01000032
NZ_LJCX0100003427025677311,655RefSeq:NZ_LJCX01000034
NZ_LJCX01000021213192021256,226RefSeq:NZ_LJCX01000021
NZ_LJCX01000010226208216237,884RefSeq:NZ_LJCX01000010
NZ_LJCX01000033216204012235,551RefSeq:NZ_LJCX01000033
NZ_LJCX0100003719919108228,362RefSeq:NZ_LJCX01000037
NZ_LJCX0100002219118641203,093RefSeq:NZ_LJCX01000022
NZ_LJCX010000369984015101,797RefSeq:NZ_LJCX01000036
NZ_LJCX010000351027203094,259RefSeq:NZ_LJCX01000035
NZ_LJCX010000181281270193,135RefSeq:NZ_LJCX01000018
NZ_LJCX0100003863570692,646RefSeq:NZ_LJCX01000038
NZ_LJCX0100000450480258,495RefSeq:NZ_LJCX01000004
NZ_LJCX0100002046420452,423RefSeq:NZ_LJCX01000020
NZ_LJCX0100000215130226,380RefSeq:NZ_LJCX01000002
NZ_LJCX0100000323220126,135RefSeq:NZ_LJCX01000003
NZ_LJCX01000006128049,292RefSeq:NZ_LJCX01000006
10 Undisplayed Contigs/Replicons14131519,033
Total:9,1618,6729639310,138,599
Ortholog data available?Yes
Database Contents
Genes9,161
Pathways319
Enzymatic Reactions1,649
Transport Reactions78
Polypeptides8,684
Protein Complexes82
Enzymes1,256
Transporters739
Compounds1,208
Transcription Units6,869
tRNAs83
Protein Features9,960
GO Terms25,067
Database Version29.0
Sequence SourceGCF_001298545.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
unclassified Actinobacteria (class)
unclassified Actinobacteria (class) (miscellaneous)
Actinobacteria bacterium OV320
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03275776
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1592329
EnvironmentEndosphere of plant Populus trichocarpa BESC137
Geographic LocationUSA
Collection Date2012-05-31/2012-05-1
HostPopulus trichocarpa
Annotation ProviderNCBI RefSeq
Annotation Date2020-01-12
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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