Database Authors
Pallavi Subhraveti1, Anamika Kothari1, Peter Midford1, Ron Caspi1, Lisa Moore1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 25-Oct-2024 from the annotated genome of Acidocella sp. MX-AZ02 MX-AZ02, as obtained from RefSeq (annotation date: 14-AUG-2023). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 28.5) [Karp11, Karp16] using MetaCyc version 28.1 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_JH9762071,6021,53930331,674,653RefSeq:NZ_JH976207
NZ_JH9762087557261316831,830RefSeq:NZ_JH976208
NZ_JH976209510489912522,749RefSeq:NZ_JH976209
NZ_JH976210310299011363,681RefSeq:NZ_JH976210
NZ_JH97621166620471,053RefSeq:NZ_JH976211
NZ_JH97621235340133,212RefSeq:NZ_JH976212
NZ_JH97621324220225,669RefSeq:NZ_JH976213
NZ_JH97621419180117,484RefSeq:NZ_JH976214
76 Undisplayed Contigs/Replicons505001684,526
Total:3,3873,23952963,624,857
Ortholog data available?No
Database Contents
Genes3,387
Pathways294
Enzymatic Reactions1,634
Transport Reactions62
Polypeptides3,502
Protein Complexes101
Enzymes799
Transporters302
Compounds1,479
Transcription Units2,277
tRNAs45
Protein Features4,134
GO Terms4,494
Database Version29.0
Sequence SourceGCF_000306035.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acidocella
unclassified Acidocella
Acidocella sp. MX-AZ02
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02469423
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1214225
Environmentgeothermal lake
Geographic LocationMexico
Collection Date2010-03-10
Annotation ProviderNCBI RefSeq
Annotation Date2023-08-12
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.5
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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