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 Actibacterium atlanticum 22II-S11-z10, 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_AQQY01000001775758116785,574RefSeq:NZ_AQQY01000001
NZ_AQQY0100000238638321368,092RefSeq:NZ_AQQY01000002
NZ_AQQY0100000328327832292,416RefSeq:NZ_AQQY01000003
NZ_AQQY0100000427226633279,242RefSeq:NZ_AQQY01000004
NZ_AQQY0100000527926964275,793RefSeq:NZ_AQQY01000005
NZ_AQQY0100000623422671243,669RefSeq:NZ_AQQY01000006
NZ_AQQY0100000721220561199,981RefSeq:NZ_AQQY01000007
NZ_AQQY01000008979700114,145RefSeq:NZ_AQQY01000008
NZ_AQQY0100000910710403113,538RefSeq:NZ_AQQY01000009
NZ_AQQY0100001011811710112,431RefSeq:NZ_AQQY01000010
NZ_AQQY0100001189880182,782RefSeq:NZ_AQQY01000011
NZ_AQQY0100001280781176,398RefSeq:NZ_AQQY01000012
NZ_AQQY0100001372693069,242RefSeq:NZ_AQQY01000013
NZ_AQQY0100001460600055,188RefSeq:NZ_AQQY01000014
NZ_AQQY0100001538360236,320RefSeq:NZ_AQQY01000015
NZ_AQQY0100001621201027,591RefSeq:NZ_AQQY01000016
NZ_AQQY0100001724240019,846RefSeq:NZ_AQQY01000017
7 Undisplayed Contigs/Replicons17116024,135
Total:3,1643,08950253,176,383
Ortholog data available?Yes
Database Contents
Genes3,164
Pathways279
Enzymatic Reactions1,322
Transport Reactions72
Polypeptides3,096
Protein Complexes47
Enzymes745
Transporters318
Compounds986
Transcription Units1,937
tRNAs44
Protein Features4,023
Database Version29.0
Sequence SourceGCF_000671395.1
Synonyms Actibacterium sp. 22II-S11-z10
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodobacterales
Paracoccaceae
Actibacterium
Actibacterium atlanticum
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02742681
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1461693
Environmentdeep sea sediment from the Atlantic Ocean
Collection Date2012-11-15
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-9
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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