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 Novosphingobium sp. FSY-9 FSY-9, 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_SACO0100000147447223538,333RefSeq:NZ_SACO01000001
NZ_SACO0100000241140743459,226RefSeq:NZ_SACO01000002
NZ_SACO01000003411401102436,475RefSeq:NZ_SACO01000003
NZ_SACO0100000433133102432,683RefSeq:NZ_SACO01000004
NZ_SACO0100000522822080257,316RefSeq:NZ_SACO01000005
NZ_SACO0100000621721520220,890RefSeq:NZ_SACO01000006
NZ_SACO0100000719519413197,842RefSeq:NZ_SACO01000007
NZ_SACO0100000812612330165,543RefSeq:NZ_SACO01000008
NZ_SACO0100000913112743160,409RefSeq:NZ_SACO01000009
NZ_SACO0100001012712441149,031RefSeq:NZ_SACO01000010
NZ_SACO0100001114914631132,432RefSeq:NZ_SACO01000011
NZ_SACO0100001212512230131,002RefSeq:NZ_SACO01000012
NZ_SACO0100001311811710102,518RefSeq:NZ_SACO01000013
NZ_SACO0100001482820192,391RefSeq:NZ_SACO01000014
NZ_SACO0100001577770284,489RefSeq:NZ_SACO01000015
NZ_SACO0100001652520179,559RefSeq:NZ_SACO01000016
NZ_SACO0100001752520463,265RefSeq:NZ_SACO01000017
NZ_SACO0100001843421152,512RefSeq:NZ_SACO01000018
NZ_SACO0100001934340247,226RefSeq:NZ_SACO01000019
NZ_SACO0100002037325038,278RefSeq:NZ_SACO01000020
NZ_SACO0100002124240036,510RefSeq:NZ_SACO01000021
NZ_SACO0100002225250032,614RefSeq:NZ_SACO01000022
NZ_SACO0100002321210225,329RefSeq:NZ_SACO01000023
NZ_SACO0100002424240023,285RefSeq:NZ_SACO01000024
NZ_SACO0100002518180220,025RefSeq:NZ_SACO01000025
NZ_SACO0100002611110014,588RefSeq:NZ_SACO01000026
NZ_SACO0100002711110314,540RefSeq:NZ_SACO01000027
64 Undisplayed Contigs/Replicons6047191780,191
Total:3,6673,55170534,088,502
Ortholog data available?No
Database Contents
Genes3,614
Pathways254
Enzymatic Reactions1,296
Transport Reactions56
Polypeptides3,586
Protein Complexes37
Enzymes751
Transporters285
Compounds981
Transcription Units2,308
tRNAs59
Protein Features4,533
GO Annotations14,881
Database Version29.6
Sequence SourceGCF_004005905.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae
Novosphingobium
unclassified Novosphingobium
Novosphingobium sp. FSY-9
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN10685039
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1908524
Environmentwater
Geographic LocationTaiwan
Collection Date2017-03-15
Annotation ProviderNCBI RefSeq
Annotation Date2020-08-9
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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