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 Streptomyces sp. NRRL F-5053 NRRL F-5053, 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_JOHT01000009627624322810,721RefSeq:NZ_JOHT01000009
NZ_JOHT010000036636422135808,383RefSeq:NZ_JOHT01000003
NZ_JOHT01000004401399218498,941RefSeq:NZ_JOHT01000004
NZ_JOHT01000012375372315461,662RefSeq:NZ_JOHT01000012
NZ_JOHT01000002380380019458,722RefSeq:NZ_JOHT01000002
NZ_JOHT01000001317317012437,620RefSeq:NZ_JOHT01000001
NZ_JOHT01000014290286413346,157RefSeq:NZ_JOHT01000014
NZ_JOHT01000006250249110335,322RefSeq:NZ_JOHT01000006
NZ_JOHT01000007282278413323,733RefSeq:NZ_JOHT01000007
NZ_JOHT01000008244239513318,582RefSeq:NZ_JOHT01000008
NZ_JOHT01000005232232010299,377RefSeq:NZ_JOHT01000005
NZ_JOHT0100001020720527267,748RefSeq:NZ_JOHT01000010
NZ_JOHT01000022160160011222,147RefSeq:NZ_JOHT01000022
NZ_JOHT0100001817016736212,142RefSeq:NZ_JOHT01000018
NZ_JOHT0100001518217576204,709RefSeq:NZ_JOHT01000015
NZ_JOHT0100001116516425203,217RefSeq:NZ_JOHT01000011
NZ_JOHT01000019144144011201,416RefSeq:NZ_JOHT01000019
NZ_JOHT0100001717217202199,503RefSeq:NZ_JOHT01000017
NZ_JOHT0100001614514238198,783RefSeq:NZ_JOHT01000016
NZ_JOHT0100001316316129197,087RefSeq:NZ_JOHT01000013
NZ_JOHT0100002514214205164,033RefSeq:NZ_JOHT01000025
NZ_JOHT0100002010110107129,568RefSeq:NZ_JOHT01000020
NZ_JOHT0100002111511503123,330RefSeq:NZ_JOHT01000021
NZ_JOHT01000023848313110,235RefSeq:NZ_JOHT01000023
NZ_JOHT01000024444402107,119RefSeq:NZ_JOHT01000024
NZ_JOHT01000031232303100,013RefSeq:NZ_JOHT01000031
NZ_JOHT0100002670700293,901RefSeq:NZ_JOHT01000026
NZ_JOHT0100002773730587,898RefSeq:NZ_JOHT01000027
NZ_JOHT0100002869690481,242RefSeq:NZ_JOHT01000028
NZ_JOHT0100003053530774,403RefSeq:NZ_JOHT01000030
NZ_JOHT0100002959590766,606RefSeq:NZ_JOHT01000029
NZ_JOHT0100003243430660,655RefSeq:NZ_JOHT01000032
NZ_JOHT0100004142420253,578RefSeq:NZ_JOHT01000041
NZ_JOHT0100003352520353,544RefSeq:NZ_JOHT01000033
NZ_JOHT0100003445450445,298RefSeq:NZ_JOHT01000034
NZ_JOHT0100003531310141,626RefSeq:NZ_JOHT01000035
NZ_JOHT0100004027252239,687RefSeq:NZ_JOHT01000040
NZ_JOHT0100003726260433,913RefSeq:NZ_JOHT01000037
NZ_JOHT0100003619190231,733RefSeq:NZ_JOHT01000036
NZ_JOHT0100003822220625,584RefSeq:NZ_JOHT01000038
NZ_JOHT0100003920201125,385RefSeq:NZ_JOHT01000039
NZ_JOHT0100004413130221,343RefSeq:NZ_JOHT01000044
NZ_JOHT0100004311110118,625RefSeq:NZ_JOHT01000043
124 Undisplayed Contigs/Replicons79771351230,376
Total:7,2106,766793788,825,667
Ortholog data available?Yes
Database Contents
Genes6,832
Pathways307
Enzymatic Reactions1,466
Transport Reactions87
Polypeptides6,830
Protein Complexes64
Enzymes1,074
Transporters586
Compounds1,126
Transcription Units5,688
tRNAs61
Protein Features8,187
GO Annotations5
Database Version29.6
Sequence SourceGCF_000721445.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Bacillati
Actinomycetota
Actinomycetes
Kitasatosporales
Streptomycetaceae
Streptomyces
unclassified Streptomyces
Streptomyces sp. NRRL F-5053
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02645488
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1463854
Collection Date2010-12-31/2010-01-1
Annotation ProviderNCBI RefSeq
Annotation Date2020-01-16
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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