Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Pseudomonas nitroreducens NBRC 12694, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_BDAI010000011,1761,1502661,231,025RefSeq:NZ_BDAI01000001
NZ_BDAI0100000262362307704,071RefSeq:NZ_BDAI01000002
NZ_BDAI0100000364163472684,969RefSeq:NZ_BDAI01000003
NZ_BDAI0100000450950721537,643RefSeq:NZ_BDAI01000004
NZ_BDAI0100000546846260515,737RefSeq:NZ_BDAI01000005
NZ_BDAI0100000626025731264,995RefSeq:NZ_BDAI01000006
NZ_BDAI0100000721421401229,400RefSeq:NZ_BDAI01000007
NZ_BDAI0100000818018001204,668RefSeq:NZ_BDAI01000008
NZ_BDAI0100000917417223199,856RefSeq:NZ_BDAI01000009
NZ_BDAI0100001018017732198,456RefSeq:NZ_BDAI01000010
NZ_BDAI0100001116816442169,396RefSeq:NZ_BDAI01000011
NZ_BDAI0100001214013911150,841RefSeq:NZ_BDAI01000012
NZ_BDAI0100001311911810141,473RefSeq:NZ_BDAI01000013
NZ_BDAI0100001411111101129,127RefSeq:NZ_BDAI01000014
NZ_BDAI0100001511311300126,760RefSeq:NZ_BDAI01000015
NZ_BDAI01000016707002110,787RefSeq:NZ_BDAI01000016
NZ_BDAI0100001771692085,115RefSeq:NZ_BDAI01000017
NZ_BDAI0100001867670073,417RefSeq:NZ_BDAI01000018
NZ_BDAI0100001952520265,772RefSeq:NZ_BDAI01000019
NZ_BDAI0100002061601063,122RefSeq:NZ_BDAI01000020
NZ_BDAI0100002147470158,126RefSeq:NZ_BDAI01000021
NZ_BDAI0100002237370142,859RefSeq:NZ_BDAI01000022
NZ_BDAI0100002330300037,334RefSeq:NZ_BDAI01000023
NZ_BDAI0100002420200021,038RefSeq:NZ_BDAI01000024
NZ_BDAI0100002512111015,416RefSeq:NZ_BDAI01000025
15 Undisplayed Contigs/Replicons292012243,734
Total:5,6085,50471366,105,137
Ortholog data available?Yes
Database Contents
Genes5,572
Pathways368
Enzymatic Reactions1,749
Transport Reactions113
Polypeptides5,536
Protein Complexes8
Enzymes1,187
Transporters760
Compounds1,230
Transcription Units3,775
tRNAs61
Protein Features7,540
GO Annotations563
Database Version29.6
Sequence SourceGCF_002091755.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae
Pseudomonas
Pseudomonas aeruginosa group
Pseudomonas nitroreducens/multiresinivorans group
Pseudomonas nitroreducens
Pseudomonas nitroreducens NBRC 12694
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00046934
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1215112
Annotation ProviderNCBI RefSeq
Annotation Date2021-07-16
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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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