Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Rhizobium selenitireducens ATCC BAA-1503, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_JAEG01000001861850118901,216RefSeq:NZ_JAEG01000001
NZ_JAEG01000002573561126585,619RefSeq:NZ_JAEG01000002
NZ_KI91249551350679535,257RefSeq:NZ_KI912495
NZ_JAEG0100000646245843500,130RefSeq:NZ_JAEG01000006
NZ_JAEG0100000738438134372,796RefSeq:NZ_JAEG01000007
NZ_JAEG0100000831030826355,640RefSeq:NZ_JAEG01000008
NZ_JAEG0100000929229027314,374RefSeq:NZ_JAEG01000009
NZ_JAEG01000010184184011213,805RefSeq:NZ_JAEG01000010
NZ_JAEG0100001115215110166,466RefSeq:NZ_JAEG01000011
NZ_JAEG0100001214414411157,196RefSeq:NZ_JAEG01000012
NZ_KI91249613013004139,001RefSeq:NZ_KI912496
NZ_JAEG0100001510910902128,310RefSeq:NZ_JAEG01000015
NZ_JAEG0100001610610607125,287RefSeq:NZ_JAEG01000016
NZ_JAEG0100001778771280,177RefSeq:NZ_JAEG01000017
NZ_JAEG0100001883830176,380RefSeq:NZ_JAEG01000018
NZ_JAEG0100001969681071,059RefSeq:NZ_JAEG01000019
NZ_JAEG0100002051492766,026RefSeq:NZ_JAEG01000020
NZ_JAEG0100002158580362,277RefSeq:NZ_JAEG01000021
NZ_JAEG0100002233330341,992RefSeq:NZ_JAEG01000022
NZ_JAEG0100002336360533,176RefSeq:NZ_JAEG01000023
NZ_JAEG0100002414131119,738RefSeq:NZ_JAEG01000024
8 Undisplayed Contigs/Replicons25207330,765
Total:4,7604,61555934,976,687
Ortholog data available?Yes
Database Contents
Genes4,667
Pathways324
Enzymatic Reactions1,524
Transport Reactions83
Polypeptides4,634
Protein Complexes61
Enzymes907
Transporters615
Compounds1,037
Transcription Units3,185
tRNAs45
Protein Features5,968
GO Annotations3
Database Version29.6
Sequence SourceGCF_000518785.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Alphaproteobacteria
Hyphomicrobiales
Rhizobiaceae
Rhizobium/Agrobacterium group
Rhizobium
Rhizobium selenitireducens
Rhizobium selenitireducens ATCC BAA-1503
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02584964
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1336235
EnvironmentBioreactor used to remove selenate from water isolation date: 2004
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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