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 25-Oct-2020 from the annotated genome of Acetobacterium bakii DSM 8239, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_LGYO0100002227326544290,121RefSeq:NZ_LGYO01000022
NZ_LGYO0100000825925270276,986RefSeq:NZ_LGYO01000008
NZ_LGYO0100000720519663228,119RefSeq:NZ_LGYO01000007
NZ_LGYO0100001115815800175,563RefSeq:NZ_LGYO01000011
NZ_LGYO0100003315215110175,298RefSeq:NZ_LGYO01000033
NZ_LGYO0100002715015000158,648RefSeq:NZ_LGYO01000027
NZ_LGYO0100003410210101126,959RefSeq:NZ_LGYO01000034
NZ_LGYO0100000412412211122,089RefSeq:NZ_LGYO01000004
NZ_LGYO0100001911110920115,974RefSeq:NZ_LGYO01000019
NZ_LGYO0100003112912720112,968RefSeq:NZ_LGYO01000031
NZ_LGYO0100000611811251112,537RefSeq:NZ_LGYO01000006
NZ_LGYO01000012959500107,463RefSeq:NZ_LGYO01000012
NZ_LGYO01000044928822103,215RefSeq:NZ_LGYO01000044
NZ_LGYO0100004093930096,718RefSeq:NZ_LGYO01000040
NZ_LGYO0100001774730192,431RefSeq:NZ_LGYO01000017
NZ_LGYO0100000391861488,578RefSeq:NZ_LGYO01000003
NZ_LGYO0100001377760182,080RefSeq:NZ_LGYO01000013
NZ_LGYO0100006763630077,411RefSeq:NZ_LGYO01000067
NZ_LGYO0100002666651077,088RefSeq:NZ_LGYO01000026
NZ_LGYO0100004268640476,220RefSeq:NZ_LGYO01000042
NZ_LGYO0100000962610168,165RefSeq:NZ_LGYO01000009
NZ_LGYO0100001669650468,149RefSeq:NZ_LGYO01000016
NZ_LGYO0100000263580565,632RefSeq:NZ_LGYO01000002
NZ_LGYO0100000163591364,997RefSeq:NZ_LGYO01000001
NZ_LGYO0100002160573061,390RefSeq:NZ_LGYO01000021
NZ_LGYO0100001567652060,366RefSeq:NZ_LGYO01000015
NZ_LGYO0100005149480151,008RefSeq:NZ_LGYO01000051
NZ_LGYO0100005251490246,246RefSeq:NZ_LGYO01000052
NZ_LGYO0100003941360545,181RefSeq:NZ_LGYO01000039
NZ_LGYO0100004640390143,818RefSeq:NZ_LGYO01000046
NZ_LGYO0100004148460241,031RefSeq:NZ_LGYO01000041
NZ_LGYO0100001041391140,989RefSeq:NZ_LGYO01000010
NZ_LGYO0100002039390039,732RefSeq:NZ_LGYO01000020
NZ_LGYO0100002529272034,048RefSeq:NZ_LGYO01000025
NZ_LGYO0100004538380033,951RefSeq:NZ_LGYO01000045
NZ_LGYO0100006131310033,371RefSeq:NZ_LGYO01000061
NZ_LGYO0100006526260030,410RefSeq:NZ_LGYO01000065
NZ_LGYO0100006926260030,338RefSeq:NZ_LGYO01000069
NZ_LGYO0100004924231029,567RefSeq:NZ_LGYO01000049
NZ_LGYO0100007017170027,569RefSeq:NZ_LGYO01000070
NZ_LGYO0100002831280326,467RefSeq:NZ_LGYO01000028
NZ_LGYO0100006225250026,369RefSeq:NZ_LGYO01000062
NZ_LGYO0100005820200024,417RefSeq:NZ_LGYO01000058
NZ_LGYO0100001818180023,137RefSeq:NZ_LGYO01000018
NZ_LGYO0100007220190122,553RefSeq:NZ_LGYO01000072
NZ_LGYO0100007720190122,207RefSeq:NZ_LGYO01000077
NZ_LGYO0100003821210021,990RefSeq:NZ_LGYO01000038
NZ_LGYO0100003226230321,893RefSeq:NZ_LGYO01000032
NZ_LGYO0100006025200521,746RefSeq:NZ_LGYO01000060
NZ_LGYO0100002931310020,974RefSeq:NZ_LGYO01000029
NZ_LGYO0100002419180120,673RefSeq:NZ_LGYO01000024
NZ_LGYO0100004718180019,044RefSeq:NZ_LGYO01000047
NZ_LGYO0100005514140016,960RefSeq:NZ_LGYO01000055
NZ_LGYO0100003617170016,125RefSeq:NZ_LGYO01000036
NZ_LGYO0100002312120015,872RefSeq:NZ_LGYO01000023
NZ_LGYO0100000514140015,733RefSeq:NZ_LGYO01000005
NZ_LGYO0100003715105014,541RefSeq:NZ_LGYO01000037
NZ_LGYO0100005312120012,599RefSeq:NZ_LGYO01000053
NZ_LGYO0100008013121012,427RefSeq:NZ_LGYO01000080
NZ_LGYO0100006813110212,228RefSeq:NZ_LGYO01000068
NZ_LGYO0100006316151010,767RefSeq:NZ_LGYO01000063
29 Undisplayed Contigs/Replicons93831012124,489
Total:3,8893,75559754,135,635
Ortholog data available?No
Database Contents
Genes3,889
Pathways200
Enzymatic Reactions1,017
Transport Reactions65
Polypeptides3,785
Protein Complexes42
Enzymes686
Transporters435
Compounds796
Transcription Units2,421
tRNAs49
Protein Features4,874
GO Terms14,046
Database Version29.0
Sequence SourceGCF_001263355.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Clostridia
Eubacteriales
Eubacteriaceae
Acetobacterium
Acetobacterium bakii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03892803
NCBI BioProjectPRJNA224116
NCBI-Taxonomy52689
Environmenta paper mill waste water polluted pond
Geographic LocationRussia
Collection Date1995
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-8
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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