Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 12-July-2021 from the annotated genome of Acidocella aromatica DSM 27026, 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 25.0) [Karp16, Karp11] using MetaCyc version 25.0 [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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_JACHFJ010000001500481127503,554RefSeq:NZ_JACHFJ010000001
NZ_JACHFJ010000002421406132428,052RefSeq:NZ_JACHFJ010000002
NZ_JACHFJ01000000332631673340,243RefSeq:NZ_JACHFJ010000003
NZ_JACHFJ01000000416716412176,884RefSeq:NZ_JACHFJ010000004
NZ_JACHFJ01000000514113812148,965RefSeq:NZ_JACHFJ010000005
NZ_JACHFJ01000000613513203147,261RefSeq:NZ_JACHFJ010000006
NZ_JACHFJ01000000712111542127,167RefSeq:NZ_JACHFJ010000007
NZ_JACHFJ01000000813012910124,896RefSeq:NZ_JACHFJ010000008
NZ_JACHFJ01000000912912621124,336RefSeq:NZ_JACHFJ010000009
NZ_JACHFJ01000001011711601120,831RefSeq:NZ_JACHFJ010000010
NZ_JACHFJ01000001110910522118,029RefSeq:NZ_JACHFJ010000011
NZ_JACHFJ01000001211711412115,250RefSeq:NZ_JACHFJ010000012
NZ_JACHFJ01000001385841088,521RefSeq:NZ_JACHFJ010000013
NZ_JACHFJ01000001459590060,849RefSeq:NZ_JACHFJ010000014
NZ_JACHFJ01000001547452044,188RefSeq:NZ_JACHFJ010000015
NZ_JACHFJ01000001644430141,795RefSeq:NZ_JACHFJ010000016
NZ_JACHFJ01000001733320140,349RefSeq:NZ_JACHFJ010000017
NZ_JACHFJ01000001840370339,737RefSeq:NZ_JACHFJ010000018
NZ_JACHFJ01000001921191123,525RefSeq:NZ_JACHFJ010000019
NZ_JACHFJ01000002019180122,094RefSeq:NZ_JACHFJ010000020
NZ_JACHFJ01000002119190018,309RefSeq:NZ_JACHFJ010000021
8 Undisplayed Contigs/Replicons18117222,516
Total:2,8002,70955362,877,351
Ortholog data available?No
Database Contents
Genes2,800
Pathways246
Enzymatic Reactions1,237
Transport Reactions47
Polypeptides2,717
Protein Complexes47
Enzymes710
Transporters226
Compounds923
Transcription Units1,496
tRNAs48
Protein Features3,484
Database Version29.0
Sequence SourceGCF_014201825.1
Synonyms Acidocella sp. LGS-3
Acidocella sp. PFBC
Acidocella sp. WJB-3
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acidocella
Acidocella aromatica
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN14908346
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1303579
Annotation ProviderNCBI RefSeq
Annotation Date2020-08-16
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.12
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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