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 Acaryochloris marina MBIC11017, 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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_0099255,8235,619831216,503,724RefSeq:NC_009925
pREB1323298025374,161RefSeq:NC_009926
pREB2345319026356,087RefSeq:NC_009927
pREB3290249041273,121RefSeq:NC_009928
pREB4227211115226,680RefSeq:NC_009929
pREB517917504177,162RefSeq:NC_009930
pREB6166147019172,728RefSeq:NC_009931
pREB713312805155,110RefSeq:NC_009932
pREB81049905120,693RefSeq:NC_009933
pREB921012,133RefSeq:NC_009934
Total:7,5927,246842628,361,599
Ortholog data available?Yes
Database Contents
Genes7,592
Pathways258
Enzymatic Reactions1,416
Transport Reactions47
Polypeptides7,246
Protein Complexes76
Enzymes980
Transporters370
Compounds1,048
Transcription Units6,045
tRNAs74
Protein Features9,809
GO Terms270
Database Version29.0
Sequence SourceGCF_000018105.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Cyanobacteriota/Melainabacteria group
Cyanobacteriota
Cyanophyceae
Acaryochloridales
Acaryochloridaceae
Acaryochloris
Acaryochloris marina
Acaryochloris marina MBIC11017
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02604308
NCBI BioProjectPRJNA224116
NCBI-Taxonomy329726
Annotation ProviderNCBI RefSeq
Annotation Date2022-02-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.0
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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