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 Acetobacterium fimetarium DER-2019, 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_WJBC0100000126225813304,900RefSeq:NZ_WJBC01000001
NZ_WJBC0100000227226309293,651RefSeq:NZ_WJBC01000002
NZ_WJBC0100000321320625211,338RefSeq:NZ_WJBC01000003
NZ_WJBC0100000419118272210,431RefSeq:NZ_WJBC01000004
NZ_WJBC0100000518918711199,189RefSeq:NZ_WJBC01000005
NZ_WJBC0100000614113704144,802RefSeq:NZ_WJBC01000006
NZ_WJBC0100000712011532135,296RefSeq:NZ_WJBC01000007
NZ_WJBC01000008989413118,001RefSeq:NZ_WJBC01000008
NZ_WJBC0100000911911405117,876RefSeq:NZ_WJBC01000009
NZ_WJBC0100001011010712117,721RefSeq:NZ_WJBC01000010
NZ_WJBC0100001111310841110,257RefSeq:NZ_WJBC01000011
NZ_WJBC01000012928930109,032RefSeq:NZ_WJBC01000012
NZ_WJBC0100001389872094,020RefSeq:NZ_WJBC01000013
NZ_WJBC0100001463630074,813RefSeq:NZ_WJBC01000014
NZ_WJBC0100001577761070,962RefSeq:NZ_WJBC01000015
NZ_WJBC0100001651501067,904RefSeq:NZ_WJBC01000016
NZ_WJBC0100001761610063,729RefSeq:NZ_WJBC01000017
NZ_WJBC0100001847440362,149RefSeq:NZ_WJBC01000018
NZ_WJBC0100001951465056,557RefSeq:NZ_WJBC01000019
NZ_WJBC0100002053466155,701RefSeq:NZ_WJBC01000020
NZ_WJBC0100002146451050,976RefSeq:NZ_WJBC01000021
NZ_WJBC0100002246440245,411RefSeq:NZ_WJBC01000022
NZ_WJBC0100002346442044,498RefSeq:NZ_WJBC01000023
NZ_WJBC0100002435330241,594RefSeq:NZ_WJBC01000024
NZ_WJBC0100002531310037,368RefSeq:NZ_WJBC01000025
NZ_WJBC0100002632320031,734RefSeq:NZ_WJBC01000026
NZ_WJBC0100002723221027,614RefSeq:NZ_WJBC01000027
NZ_WJBC0100002827225025,572RefSeq:NZ_WJBC01000028
NZ_WJBC0100002919181022,731RefSeq:NZ_WJBC01000029
NZ_WJBC0100003016160022,112RefSeq:NZ_WJBC01000030
NZ_WJBC0100003120200021,789RefSeq:NZ_WJBC01000031
NZ_WJBC0100003216160021,441RefSeq:NZ_WJBC01000032
NZ_WJBC0100003322220019,353RefSeq:NZ_WJBC01000033
NZ_WJBC0100003423210216,975RefSeq:NZ_WJBC01000034
NZ_WJBC0100003518180016,743RefSeq:NZ_WJBC01000035
NZ_WJBC0100003624177016,345RefSeq:NZ_WJBC01000036
NZ_WJBC0100003713120112,879RefSeq:NZ_WJBC01000037
41 Undisplayed Contigs/Replicons1141031212144,023
Total:2,9962,86967603,237,487
Ortholog data available?No
Database Contents
Genes2,994
Pathways176
Enzymatic Reactions920
Transport Reactions54
Polypeptides2,903
Protein Complexes33
Enzymes652
Transporters209
Compounds691
Transcription Units1,900
tRNAs54
Protein Features3,875
GO Terms13
Database Version29.0
Sequence SourceGCF_014284475.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Clostridia
Eubacteriales
Eubacteriaceae
Acetobacterium
Acetobacterium fimetarium
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN13171308
NCBI BioProjectPRJNA224116
NCBI-Taxonomy52691
Environmentcattle manure
Geographic LocationRussia
Collection Date1993-04-27
Annotation ProviderNCBI RefSeq
Annotation Date2020-08-27
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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