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 sp. LMG 1627 LMG 1627, 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_WOSY01000001413394415484,470RefSeq:NZ_WOSY01000001
NZ_WOSY01000002284267710311,033RefSeq:NZ_WOSY01000002
NZ_WOSY0100000329628655306,351RefSeq:NZ_WOSY01000003
NZ_WOSY0100000427326175299,726RefSeq:NZ_WOSY01000004
NZ_WOSY0100000524423833288,417RefSeq:NZ_WOSY01000005
NZ_WOSY0100000618618123234,700RefSeq:NZ_WOSY01000006
NZ_WOSY0100000719018523230,861RefSeq:NZ_WOSY01000007
NZ_WOSY0100000817216633205,029RefSeq:NZ_WOSY01000008
NZ_WOSY0100000915614745177,901RefSeq:NZ_WOSY01000009
NZ_WOSY0100001015014136161,485RefSeq:NZ_WOSY01000010
NZ_WOSY0100001110310021124,665RefSeq:NZ_WOSY01000011
NZ_WOSY0100001294870794,754RefSeq:NZ_WOSY01000012
NZ_WOSY0100001375710486,295RefSeq:NZ_WOSY01000013
NZ_WOSY0100001448450363,015RefSeq:NZ_WOSY01000014
NZ_WOSY0100001551491155,433RefSeq:NZ_WOSY01000015
NZ_WOSY0100001644421151,459RefSeq:NZ_WOSY01000016
NZ_WOSY0100001747441251,423RefSeq:NZ_WOSY01000017
NZ_WOSY0100001843380544,858RefSeq:NZ_WOSY01000018
NZ_WOSY0100001941361443,207RefSeq:NZ_WOSY01000019
NZ_WOSY0100002049470243,031RefSeq:NZ_WOSY01000020
NZ_WOSY0100002140390140,060RefSeq:NZ_WOSY01000021
NZ_WOSY0100002233290432,756RefSeq:NZ_WOSY01000022
NZ_WOSY0100002327250232,133RefSeq:NZ_WOSY01000023
NZ_WOSY0100002427270031,463RefSeq:NZ_WOSY01000024
NZ_WOSY0100002531290228,388RefSeq:NZ_WOSY01000025
NZ_WOSY0100002624220225,668RefSeq:NZ_WOSY01000026
NZ_WOSY0100002715150024,221RefSeq:NZ_WOSY01000027
NZ_WOSY0100002814130121,538RefSeq:NZ_WOSY01000028
NZ_WOSY0100002917160120,469RefSeq:NZ_WOSY01000029
NZ_WOSY0100003016110519,526RefSeq:NZ_WOSY01000030
NZ_WOSY0100003123220119,252RefSeq:NZ_WOSY01000031
NZ_WOSY0100003217170018,476RefSeq:NZ_WOSY01000032
NZ_WOSY010000331190212,853RefSeq:NZ_WOSY01000033
NZ_WOSY0100003417160112,535RefSeq:NZ_WOSY01000034
NZ_WOSY010000391212009,861RefSeq:NZ_WOSY01000039
NZ_WOSY010000401615019,278RefSeq:NZ_WOSY01000040
52 Undisplayed Contigs/Replicons118111726167,541
Total:3,4433,253531373,884,131
Ortholog data available?No
Database Contents
Genes3,443
Pathways230
Enzymatic Reactions1,190
Transport Reactions56
Polypeptides3,309
Protein Complexes49
Enzymes719
Transporters293
Compounds922
Transcription Units2,332
tRNAs46
Protein Features3,974
GO Terms3
Database Version29.0
Sequence SourceGCF_011516755.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
unclassified Acetobacter
Acetobacter sp. LMG 1627
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN13343656
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1737472
EnvironmentCider fermentation
Geographic LocationUnited Kingdom
Collection Date1900
Annotation ProviderNCBI RefSeq
Annotation Date2020-12-29
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
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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