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 malicum 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_WJBE0100000149048640532,947RefSeq:NZ_WJBE01000001
NZ_WJBE0100000233632448368,117RefSeq:NZ_WJBE01000002
NZ_WJBE0100000325825215292,727RefSeq:NZ_WJBE01000003
NZ_WJBE0100000427126443292,390RefSeq:NZ_WJBE01000004
NZ_WJBE0100000524324111267,504RefSeq:NZ_WJBE01000005
NZ_WJBE0100000623623042227,113RefSeq:NZ_WJBE01000006
NZ_WJBE0100000720119731224,498RefSeq:NZ_WJBE01000007
NZ_WJBE0100000820119722218,310RefSeq:NZ_WJBE01000008
NZ_WJBE0100000911311201108,537RefSeq:NZ_WJBE01000009
NZ_WJBE01000010757401103,779RefSeq:NZ_WJBE01000010
NZ_WJBE01000011898621100,256RefSeq:NZ_WJBE01000011
NZ_WJBE010000121031012097,030RefSeq:NZ_WJBE01000012
NZ_WJBE0100001388835095,787RefSeq:NZ_WJBE01000013
NZ_WJBE0100001485840191,329RefSeq:NZ_WJBE01000014
NZ_WJBE0100001575740183,126RefSeq:NZ_WJBE01000015
NZ_WJBE0100001668626078,341RefSeq:NZ_WJBE01000016
NZ_WJBE0100001767660176,793RefSeq:NZ_WJBE01000017
NZ_WJBE0100001858580074,629RefSeq:NZ_WJBE01000018
NZ_WJBE0100001968661173,471RefSeq:NZ_WJBE01000019
NZ_WJBE0100002058570166,358RefSeq:NZ_WJBE01000020
NZ_WJBE0100002165595166,063RefSeq:NZ_WJBE01000021
NZ_WJBE0100002262590359,763RefSeq:NZ_WJBE01000022
NZ_WJBE0100002350500056,131RefSeq:NZ_WJBE01000023
NZ_WJBE0100002469626152,168RefSeq:NZ_WJBE01000024
NZ_WJBE0100002542357039,636RefSeq:NZ_WJBE01000025
NZ_WJBE0100002653530033,764RefSeq:NZ_WJBE01000026
NZ_WJBE0100002727260131,721RefSeq:NZ_WJBE01000027
NZ_WJBE0100002824240027,548RefSeq:NZ_WJBE01000028
NZ_WJBE0100002921180320,869RefSeq:NZ_WJBE01000029
NZ_WJBE0100003037360120,612RefSeq:NZ_WJBE01000030
NZ_WJBE0100003139380120,418RefSeq:NZ_WJBE01000031
NZ_WJBE0100003317152017,507RefSeq:NZ_WJBE01000033
NZ_WJBE0100003415141016,916RefSeq:NZ_WJBE01000034
NZ_WJBE0100003511110015,119RefSeq:NZ_WJBE01000035
NZ_WJBE01000040126605,763RefSeq:NZ_WJBE01000040
36 Undisplayed Contigs/Replicons959289120,187
Total:3,8363,71274504,077,227
Ortholog data available?No
Database Contents
Genes3,826
Pathways193
Enzymatic Reactions982
Transport Reactions64
Polypeptides3,735
Protein Complexes37
Enzymes723
Transporters300
Compounds744
Transcription Units2,383
tRNAs54
Protein Features4,911
Database Version29.0
Sequence SourceGCF_014284495.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Clostridia
Eubacteriales
Eubacteriaceae
Acetobacterium
Acetobacterium malicum
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN13171306
NCBI BioProjectPRJNA224116
NCBI-Taxonomy52692
Environmentditch sediment
Geographic LocationGermany
Collection Date1987-06-4
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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