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 Acetobacter malorum LMG 1746, 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_LHZC0100005734834026385,480RefSeq:NZ_LHZC01000057
NZ_LHZC0100005626926126322,741RefSeq:NZ_LHZC01000056
NZ_LHZC0100005526825936299,144RefSeq:NZ_LHZC01000055
NZ_LHZC01000054229212512248,207RefSeq:NZ_LHZC01000054
NZ_LHZC0100005320419365197,600RefSeq:NZ_LHZC01000053
NZ_LHZC0100005217316634186,250RefSeq:NZ_LHZC01000052
NZ_LHZC0100005112311139143,912RefSeq:NZ_LHZC01000051
NZ_LHZC0100005012512032137,929RefSeq:NZ_LHZC01000050
NZ_LHZC0100004910210101137,064RefSeq:NZ_LHZC01000049
NZ_LHZC0100004812912621134,335RefSeq:NZ_LHZC01000048
NZ_LHZC0100004711210633125,532RefSeq:NZ_LHZC01000047
NZ_LHZC0100004612011811115,955RefSeq:NZ_LHZC01000046
NZ_LHZC01000045938931110,651RefSeq:NZ_LHZC01000045
NZ_LHZC010000441049743100,025RefSeq:NZ_LHZC01000044
NZ_LHZC0100004377751189,926RefSeq:NZ_LHZC01000043
NZ_LHZC0100004273692288,702RefSeq:NZ_LHZC01000042
NZ_LHZC0100004173702188,522RefSeq:NZ_LHZC01000041
NZ_LHZC0100004054540082,029RefSeq:NZ_LHZC01000040
NZ_LHZC0100003974730169,991RefSeq:NZ_LHZC01000039
NZ_LHZC0100003865621267,072RefSeq:NZ_LHZC01000038
NZ_LHZC0100003753490461,484RefSeq:NZ_LHZC01000037
NZ_LHZC01000036534101258,471RefSeq:NZ_LHZC01000036
NZ_LHZC0100003546450156,465RefSeq:NZ_LHZC01000035
NZ_LHZC0100003446441152,607RefSeq:NZ_LHZC01000034
NZ_LHZC0100003342401152,473RefSeq:NZ_LHZC01000033
NZ_LHZC0100003254493249,827RefSeq:NZ_LHZC01000032
NZ_LHZC0100003148461148,678RefSeq:NZ_LHZC01000031
NZ_LHZC0100003033330042,806RefSeq:NZ_LHZC01000030
NZ_LHZC0100002938343137,065RefSeq:NZ_LHZC01000029
NZ_LHZC0100002830300033,006RefSeq:NZ_LHZC01000028
NZ_LHZC0100002728271032,440RefSeq:NZ_LHZC01000027
NZ_LHZC0100002632320029,762RefSeq:NZ_LHZC01000026
NZ_LHZC0100002516150123,223RefSeq:NZ_LHZC01000025
NZ_LHZC0100002411110020,391RefSeq:NZ_LHZC01000024
NZ_LHZC0100002316150117,317RefSeq:NZ_LHZC01000023
NZ_LHZC0100002214120216,031RefSeq:NZ_LHZC01000022
NZ_LHZC0100002110100011,804RefSeq:NZ_LHZC01000021
20 Undisplayed Contigs/Replicons413561058,559
Total:3,4363,270621043,833,476
Ortholog data available?Yes
Database Contents
Genes3,436
Pathways256
Enzymatic Reactions1,229
Transport Reactions55
Polypeptides3,304
Protein Complexes33
Enzymes716
Transporters283
Compounds909
Transcription Units2,313
tRNAs54
Protein Features3,697
GO Terms1
Database Version29.0
Sequence SourceGCF_001580615.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter malorum
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03799273
NCBI BioProjectPRJNA224116
NCBI-Taxonomy178901
EnvironmentRotting apple
Geographic LocationBelgium
Collection Date2014
Annotation ProviderNCBI RefSeq
Annotation Date2020-04-2
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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