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 Acetobacter nitrogenifigens DSM 23921, 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_AUBI01000001542526106609,938RefSeq:NZ_AUBI01000001
NZ_AUBI0100000237736746423,545RefSeq:NZ_AUBI01000002
NZ_AUBI01000003385372310418,109RefSeq:NZ_AUBI01000003
NZ_AUBI0100000433432167377,264RefSeq:NZ_AUBI01000004
NZ_AUBI0100000523823314293,892RefSeq:NZ_AUBI01000005
NZ_AUBI0100000624523744275,560RefSeq:NZ_AUBI01000006
NZ_KE38685321120335240,512RefSeq:NZ_KE386853
NZ_AUBI0100000913612925170,990RefSeq:NZ_AUBI01000009
NZ_AUBI0100001014513753163,835RefSeq:NZ_AUBI01000010
NZ_AUBI010000111029732133,089RefSeq:NZ_AUBI01000011
NZ_AUBI0100001212011523118,738RefSeq:NZ_AUBI01000012
NZ_AUBI010000131019326110,887RefSeq:NZ_AUBI01000013
NZ_AUBI0100001480790193,909RefSeq:NZ_AUBI01000014
NZ_AUBI0100001576750192,856RefSeq:NZ_AUBI01000015
NZ_AUBI0100001653530076,587RefSeq:NZ_AUBI01000016
NZ_AUBI0100001761592068,811RefSeq:NZ_AUBI01000017
NZ_AUBI0100001848451254,526RefSeq:NZ_AUBI01000018
NZ_AUBI0100001952511053,605RefSeq:NZ_AUBI01000019
NZ_AUBI0100002046431252,771RefSeq:NZ_AUBI01000020
NZ_AUBI0100002141400148,370RefSeq:NZ_AUBI01000021
NZ_AUBI0100002242380444,445RefSeq:NZ_AUBI01000022
NZ_AUBI0100002329280134,642RefSeq:NZ_AUBI01000023
NZ_AUBI0100002448460233,998RefSeq:NZ_AUBI01000024
NZ_AUBI0100002532300227,826RefSeq:NZ_AUBI01000025
NZ_AUBI0100002631290223,364RefSeq:NZ_AUBI01000026
NZ_AUBI0100002726200623,269RefSeq:NZ_AUBI01000027
NZ_AUBI0100002823190421,591RefSeq:NZ_AUBI01000028
NZ_AUBI0100002912120014,955RefSeq:NZ_AUBI01000029
NZ_AUBI0100003111100114,096RefSeq:NZ_AUBI01000031
NZ_AUBI0100003217120513,914RefSeq:NZ_AUBI01000032
NZ_AUBI0100003313100313,661RefSeq:NZ_AUBI01000033
NZ_AUBI0100003413130013,201RefSeq:NZ_AUBI01000034
NZ_AUBI01000040139047,650RefSeq:NZ_AUBI01000040
18 Undisplayed Contigs/Replicons837679106,110
Total:3,7953,627571114,270,516
Ortholog data available?Yes
Database Contents
Genes3,794
Pathways249
Enzymatic Reactions1,238
Transport Reactions68
Polypeptides3,664
Protein Complexes39
Enzymes757
Transporters303
Compounds962
Transcription Units2,706
tRNAs47
Protein Features4,251
GO Terms1
Database Version29.0
Sequence SourceGCF_000429165.1
Synonyms Acetobacter nitrogenifigens BCRC 80095
Acetobacter nitrogenifigens DSM 23921
Acetobacter nitrogenifigens LMG 23498
Acetobacter nitrogenifigens LMG 23498 = DSM 23921
Acetobacter nitrogenifigens NBRC 105050
Acetobacter nitrogenifigens RG1
Acetobacter sp. RG1
Acetobacter nitrogenifigens DSM 23921 = LMG 23498
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter nitrogenifigens
Acetobacter nitrogenifigens DSM 23921 = LMG 23498
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02441211
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120919
EnvironmentKombucha tea
Geographic LocationIndia
Annotation ProviderNCBI RefSeq
Annotation Date2019-11-25
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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