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 tropicalis LMG 1663, 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_LHZT0100013241440743471,083RefSeq:NZ_LHZT01000132
NZ_LHZT0100013115514717185,287RefSeq:NZ_LHZT01000131
NZ_LHZT0100013014813927174,786RefSeq:NZ_LHZT01000130
NZ_LHZT0100012914213831170,151RefSeq:NZ_LHZT01000129
NZ_LHZT0100012811310706145,606RefSeq:NZ_LHZT01000128
NZ_LHZT0100012713012910141,949RefSeq:NZ_LHZT01000127
NZ_LHZT0100012610210020110,745RefSeq:NZ_LHZT01000126
NZ_LHZT01000125878304107,426RefSeq:NZ_LHZT01000125
NZ_LHZT010001241059744105,959RefSeq:NZ_LHZT01000124
NZ_LHZT01000123949112103,241RefSeq:NZ_LHZT01000123
NZ_LHZT0100012280782099,520RefSeq:NZ_LHZT01000122
NZ_LHZT0100012194834798,274RefSeq:NZ_LHZT01000121
NZ_LHZT0100012079763089,286RefSeq:NZ_LHZT01000120
NZ_LHZT0100011976741187,355RefSeq:NZ_LHZT01000119
NZ_LHZT0100011872682285,419RefSeq:NZ_LHZT01000118
NZ_LHZT0100011788870182,296RefSeq:NZ_LHZT01000117
NZ_LHZT0100011661600182,071RefSeq:NZ_LHZT01000116
NZ_LHZT0100011575704180,361RefSeq:NZ_LHZT01000115
NZ_LHZT0100011458560273,009RefSeq:NZ_LHZT01000114
NZ_LHZT0100011356542067,724RefSeq:NZ_LHZT01000113
NZ_LHZT0100011265641066,255RefSeq:NZ_LHZT01000112
NZ_LHZT0100011164620264,663RefSeq:NZ_LHZT01000111
NZ_LHZT0100011038380048,888RefSeq:NZ_LHZT01000110
NZ_LHZT0100010943411147,213RefSeq:NZ_LHZT01000109
NZ_LHZT0100010846450144,660RefSeq:NZ_LHZT01000108
NZ_LHZT0100010738362041,703RefSeq:NZ_LHZT01000107
NZ_LHZT0100010629290040,236RefSeq:NZ_LHZT01000106
NZ_LHZT0100010526230340,048RefSeq:NZ_LHZT01000105
NZ_LHZT0100010443420139,960RefSeq:NZ_LHZT01000104
NZ_LHZT0100010332320036,034RefSeq:NZ_LHZT01000103
NZ_LHZT0100010230291033,087RefSeq:NZ_LHZT01000102
NZ_LHZT0100010131282131,722RefSeq:NZ_LHZT01000101
NZ_LHZT0100010018140428,344RefSeq:NZ_LHZT01000100
NZ_LHZT0100009921210026,945RefSeq:NZ_LHZT01000099
NZ_LHZT0100009828260224,979RefSeq:NZ_LHZT01000098
NZ_LHZT0100009721191124,748RefSeq:NZ_LHZT01000097
NZ_LHZT0100009625230223,368RefSeq:NZ_LHZT01000096
NZ_LHZT0100009522210122,234RefSeq:NZ_LHZT01000095
NZ_LHZT0100009422200221,078RefSeq:NZ_LHZT01000094
NZ_LHZT0100009316150119,299RefSeq:NZ_LHZT01000093
NZ_LHZT0100009220190119,239RefSeq:NZ_LHZT01000092
NZ_LHZT0100009115150019,179RefSeq:NZ_LHZT01000091
NZ_LHZT0100009030290117,845RefSeq:NZ_LHZT01000090
NZ_LHZT0100008916150117,538RefSeq:NZ_LHZT01000089
NZ_LHZT0100008716150116,432RefSeq:NZ_LHZT01000087
NZ_LHZT0100008613110216,256RefSeq:NZ_LHZT01000086
NZ_LHZT0100008514120216,088RefSeq:NZ_LHZT01000085
NZ_LHZT0100008419160313,474RefSeq:NZ_LHZT01000084
NZ_LHZT0100008215120313,045RefSeq:NZ_LHZT01000082
NZ_LHZT010000671211017,798RefSeq:NZ_LHZT01000067
82 Undisplayed Contigs/Replicons248241735325,725
Total:3,3403,168511213,769,631
Ortholog data available?Yes
Database Contents
Genes3,340
Pathways262
Enzymatic Reactions1,282
Transport Reactions57
Polypeptides3,229
Protein Complexes45
Enzymes755
Transporters305
Compounds956
Transcription Units2,260
tRNAs44
Protein Features3,819
GO Terms2
Database Version29.0
Sequence SourceGCF_001580945.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter tropicalis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03799291
NCBI BioProjectPRJNA224116
NCBI-Taxonomy104102
EnvironmentFermenting putrified meat sample
Geographic LocationBelgium
Collection Date2014
Annotation ProviderNCBI RefSeq
Annotation Date2020-12-13
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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