Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Plasmodium berghei ANKA, 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
Replicon/ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome 142061861192,549,703RefSeq:NC_036172
Chromosome 131781571472,521,873RefSeq:NC_036171
Chromosome 12126109891,807,262RefSeq:NC_036170
Chromosome 1115212313161,762,642RefSeq:NC_036169
Chromosome 10125981981,640,193RefSeq:NC_036168
Chromosome 9106931031,633,586RefSeq:NC_036167
Chromosome 8120107851,420,537RefSeq:NC_036166
Chromosome 6604965984,266RefSeq:NC_036164
Chromosome 5776935931,174RefSeq:NC_036163
Chromosome 7584747846,620RefSeq:NC_036165
Chromosome 4524255712,327RefSeq:NC_036162
Chromosome 35339410659,512RefSeq:NC_036161
Chromosome 24831215622,508RefSeq:NC_036160
Chromosome 1332904515,659RefSeq:NC_036159
Chromosome Unknown200256,810RefSeq:NW_023259977
Chromosome Unknown10001034,265RefSeq:NW_023259978
NC_030892522229130,861RefSeq:NC_030892
Chromosome Unknown300324,479RefSeq:NW_023259979
Chromosome Unknown500510,286RefSeq:NW_023259980
Chromosome Unknown30036,544RefSeq:NW_023259981
NC_0153031721505,957RefSeq:NC_015303
Total:1,4861,20315113218,777,064
Ortholog data available?Yes
Database Contents
Genes1,486
Pathways97
Enzymatic Reactions733
Transport Reactions11
Polypeptides4,943
Protein Complexes7
Enzymes608
Transporters173
Compounds471
tRNAs70
Protein Features1,232
Database Version29.0
Sequence SourceGCF_900002375.2
Synonyms Plasmodium berghei (strain ANKA)
Plasmodium berghei strain ANKA
Plasmodium berghei str. ANKA
Plasmodium berghei ANKA
Taxonomic Lineage cellular organisms
Eukaryota
Sar
Alveolata
Apicomplexa
Aconoidasida
Haemosporida
Plasmodiidae
Plasmodium <Plasmodium>
Plasmodium (Vinckeia)
Plasmodium berghei
Plasmodium berghei ANKA
Genetic Code Number 1 -- Standard
BIOSAMPLESAMEA1323892, SAMEA736069
NCBI BioProjectPRJNA317456, PRJNA64941
NCBI-Taxonomy5823
Annotation ProviderINSDC submitter
Annotation PipelineEukaryotic Annotation Propagation Pipeline

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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