Database Authors
Ingrid Keseler1, Anamika Kothari1, Ron Caspi1
1SRI International
Summary This Pathway/Genome Database (PGDB) for Sinorhizobium meliloti 1021 was created on 18-Feb-2020 using the PathoLogic component of the Pathway Tools software version 24.0 [Karp11, Karp19] and the MetaCyc reference database version 24.0 [Caspi20].

The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation.

Development of this PGDB was supported by BioCyc subscription revenues and by grant GM080746 from the National Institute of Health.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_0030473,5273,43167293,654,135RefSeq:NC_003047
pSymB1,6701,6401291,683,333RefSeq:NC_003078
pSymA1,4321,3693601,354,226RefSeq:NC_003037
Total:6,6296,440711186,691,694
Ortholog data available?Yes
Database Contents
Genes6,629
Pathways370
Enzymatic Reactions1,407
Transport Reactions93
Polypeptides6,450
Protein Complexes99
Enzymes1,126
Transporters934
Compounds1,021
Transcription Units4,195
tRNAs55
Transcriptional Regulation1
Protein Features25,261
GO Terms26,429
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Hyphomicrobiales
Rhizobiaceae
Sinorhizobium/Ensifer group
Sinorhizobium
Sinorhizobium meliloti
Sinorhizobium meliloti 1021
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI BioProjectPRJNA57603
Biotic Relationshipsymbiont
Pathogenicityplant
NCBI Genome Typereference
Copyright © SRI International 2020. All Rights Reserved.

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

Karp19: Karp PD, Midford PE, Billington R, Kothari A, Krummenacker M, Latendresse M, Ong WK, Subhraveti P, Caspi R, Fulcher C, Keseler IM, Paley SM (2019). "Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform. PMID: 31813964

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