Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Acetobacterium wieringae DSM 1911, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_LKEU0100002737336346407,530RefSeq:NZ_LKEU01000027
NZ_LKEU0100003325824693278,574RefSeq:NZ_LKEU01000033
NZ_LKEU0100001023422572246,124RefSeq:NZ_LKEU01000010
NZ_LKEU0100003518718043212,275RefSeq:NZ_LKEU01000035
NZ_LKEU0100003718318111207,145RefSeq:NZ_LKEU01000037
NZ_LKEU0100003117116812180,404RefSeq:NZ_LKEU01000031
NZ_LKEU01000014176160151160,752RefSeq:NZ_LKEU01000014
NZ_LKEU0100003012812602156,997RefSeq:NZ_LKEU01000030
NZ_LKEU0100005012412022142,882RefSeq:NZ_LKEU01000050
NZ_LKEU0100003913713304140,547RefSeq:NZ_LKEU01000039
NZ_LKEU0100002913513122139,361RefSeq:NZ_LKEU01000029
NZ_LKEU0100001811311300134,932RefSeq:NZ_LKEU01000018
NZ_LKEU0100001311110902124,888RefSeq:NZ_LKEU01000013
NZ_LKEU0100002411211110121,289RefSeq:NZ_LKEU01000024
NZ_LKEU010000421141122097,755RefSeq:NZ_LKEU01000042
NZ_LKEU010000121101091094,751RefSeq:NZ_LKEU01000012
NZ_LKEU0100002697941293,454RefSeq:NZ_LKEU01000026
NZ_LKEU0100000978771091,735RefSeq:NZ_LKEU01000009
NZ_LKEU0100002375731179,511RefSeq:NZ_LKEU01000023
NZ_LKEU0100001770627179,202RefSeq:NZ_LKEU01000017
NZ_LKEU0100002079780177,343RefSeq:NZ_LKEU01000020
NZ_LKEU0100003665640174,010RefSeq:NZ_LKEU01000036
NZ_LKEU0100004057570071,183RefSeq:NZ_LKEU01000040
NZ_LKEU0100004377740370,668RefSeq:NZ_LKEU01000043
NZ_LKEU0100001563630070,581RefSeq:NZ_LKEU01000015
NZ_LKEU0100004475701467,093RefSeq:NZ_LKEU01000044
NZ_LKEU0100002857560154,967RefSeq:NZ_LKEU01000028
NZ_LKEU0100004641390247,409RefSeq:NZ_LKEU01000046
NZ_LKEU0100002140360440,063RefSeq:NZ_LKEU01000021
NZ_LKEU0100004122210118,587RefSeq:NZ_LKEU01000041
NZ_LKEU0100004715141017,222RefSeq:NZ_LKEU01000047
NZ_LKEU0100004915150013,358RefSeq:NZ_LKEU01000049
NZ_LKEU0100005128270113,063RefSeq:NZ_LKEU01000051
29 Undisplayed Contigs/Replicons565112870,173
Total:3,6913,55873603,895,828
Ortholog data available?Yes
Database Contents
Genes3,679
Pathways183
Enzymatic Reactions973
Transport Reactions51
Polypeptides3,590
Protein Complexes107
Enzymes700
Transporters263
Compounds769
Transcription Units2,254
tRNAs52
Protein Features4,729
GO Terms230
Database Version29.0
Sequence SourceGCF_001766835.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Clostridia
Eubacteriales
Eubacteriaceae
Acetobacterium
Acetobacterium wieringae
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04121044
NCBI BioProjectPRJNA224116
NCBI-Taxonomy52694
Environmentsewage digester
Geographic LocationGermany
Collection Date1982
Annotation ProviderNCBI RefSeq
Annotation Date2022-03-31
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.1
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

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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