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 Rhodobacter sphaeroides 2.4.1; ATCC BAA-808, 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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome 13,0893,04049553,188,524RefSeq:NC_007493
Chromosome 28638451838943,018RefSeq:NC_007494
B10310302114,179RefSeq:NC_007488
A878703114,045RefSeq:NC_009007
C828208105,284RefSeq:NC_007489
D9494018100,827RefSeq:NC_007490
E29290337,100RefSeq:NC_009008
Total:4,4744,280671274,602,977
Ortholog data available?Yes
Database Contents
Genes4,347
Pathways374
Enzymatic Reactions1,706
Transport Reactions127
Polypeptides4,282
Protein Complexes108
Enzymes1,142
Transporters428
Compounds1,285
Transcription Units2,621
tRNAs54
Protein Features7,199
GO Annotations3,107
Database Version29.6
Sequence SourceGCF_000012905.2
Synonyms Rhodobacter sphaeroides ATCC 17023
Rhodobacter sphaeroides ATH 2.4.1
Rhodobacter sphaeroides str. 2.4.1
Rhodobacter sphaeroides strain 2.4.1
Rhodobacter sphaeroides 2.4.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Alphaproteobacteria
Rhodobacterales
Paracoccaceae
Cereibacter
Cereibacter sphaeroides
Cereibacter sphaeroides 2.4.1
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI BioProjectPRJNA57653
NCBI-Taxonomy272943
NCBI Genome Typereference

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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