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 13-Mar-2021 from the annotated genome of Acetobacter cibinongensis 4H-1, 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 24.5 [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_BAMV01000017323310112360,009RefSeq:NZ_BAMV01000017
NZ_BAMV0100000727325968279,941RefSeq:NZ_BAMV01000007
NZ_BAMV0100001125124731279,492RefSeq:NZ_BAMV01000011
NZ_BAMV0100001825625132273,734RefSeq:NZ_BAMV01000018
NZ_BAMV0100000823022640252,068RefSeq:NZ_BAMV01000008
NZ_BAMV0100001616416031180,216RefSeq:NZ_BAMV01000016
NZ_BAMV0100000113513401177,492RefSeq:NZ_BAMV01000001
NZ_BAMV0100001013713502166,647RefSeq:NZ_BAMV01000010
NZ_BAMV0100000313513311163,603RefSeq:NZ_BAMV01000003
NZ_BAMV0100000511911342131,299RefSeq:NZ_BAMV01000005
NZ_BAMV0100000211210804122,479RefSeq:NZ_BAMV01000002
NZ_BAMV0100000679763087,931RefSeq:NZ_BAMV01000006
NZ_BAMV0100002546450155,987RefSeq:NZ_BAMV01000025
NZ_BAMV0100001447470054,429RefSeq:NZ_BAMV01000014
NZ_BAMV0100001247461053,418RefSeq:NZ_BAMV01000012
NZ_BAMV0100000432300245,483RefSeq:NZ_BAMV01000004
NZ_BAMV0100005136351041,380RefSeq:NZ_BAMV01000051
NZ_BAMV0100004453500340,769RefSeq:NZ_BAMV01000044
NZ_BAMV0100001932310136,350RefSeq:NZ_BAMV01000019
NZ_BAMV0100005729260335,961RefSeq:NZ_BAMV01000057
NZ_BAMV0100000939380129,529RefSeq:NZ_BAMV01000009
NZ_BAMV0100002422200225,095RefSeq:NZ_BAMV01000024
NZ_BAMV0100003622192123,479RefSeq:NZ_BAMV01000036
NZ_BAMV0100001517170021,198RefSeq:NZ_BAMV01000015
NZ_BAMV0100004922220017,614RefSeq:NZ_BAMV01000049
NZ_BAMV0100001315130213,013RefSeq:NZ_BAMV01000013
94 Undisplayed Contigs/Replicons7366724136,471
Total:2,7702,65749643,105,087
Ortholog data available?Yes
Database Contents
Genes2,770
Pathways232
Enzymatic Reactions1,152
Transport Reactions52
Polypeptides2,684
Protein Complexes34
Enzymes668
Transporters248
Compounds855
Transcription Units1,854
tRNAs42
Protein Features3,314
GO Terms4
Database Version29.0
Sequence SourceGCF_000963925.1
Synonyms Acetobacter sp. DsW_47
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter cibinongensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00036631
NCBI BioProjectPRJNA224116
NCBI-Taxonomy146475
Annotation ProviderNCBI RefSeq
Annotation Date2020-07-26
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.12
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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