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 Acidaminococcus sp. BV3L6 BV3L6, 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_AWUR01000008174159141183,839RefSeq:NZ_AWUR01000008
NZ_AWUR0100000711711322121,013RefSeq:NZ_AWUR01000007
NZ_AWUR01000038827741107,859RefSeq:NZ_AWUR01000038
NZ_AWUR0100004810910810107,626RefSeq:NZ_AWUR01000048
NZ_AWUR01000055868510104,617RefSeq:NZ_AWUR01000055
NZ_AWUR010000341029912102,399RefSeq:NZ_AWUR01000034
NZ_AWUR0100000486811498,466RefSeq:NZ_AWUR01000004
NZ_AWUR0100004779763091,095RefSeq:NZ_AWUR01000047
NZ_AWUR0100004064593280,499RefSeq:NZ_AWUR01000040
NZ_AWUR0100002267641278,619RefSeq:NZ_AWUR01000022
NZ_AWUR0100002578780072,684RefSeq:NZ_AWUR01000025
NZ_AWUR0100004270644272,052RefSeq:NZ_AWUR01000042
NZ_AWUR0100003171691171,214RefSeq:NZ_AWUR01000031
NZ_AWUR0100001966660066,913RefSeq:NZ_AWUR01000019
NZ_AWUR0100004458571065,894RefSeq:NZ_AWUR01000044
NZ_AWUR0100001158561164,559RefSeq:NZ_AWUR01000011
NZ_AWUR0100000643421052,809RefSeq:NZ_AWUR01000006
NZ_AWUR0100000948480049,599RefSeq:NZ_AWUR01000009
NZ_AWUR0100005347470048,948RefSeq:NZ_AWUR01000053
NZ_AWUR0100001839380143,814RefSeq:NZ_AWUR01000018
NZ_AWUR0100000336350142,873RefSeq:NZ_AWUR01000003
NZ_AWUR0100002936351039,577RefSeq:NZ_AWUR01000029
NZ_AWUR0100003239325236,324RefSeq:NZ_AWUR01000032
NZ_AWUR0100002133260736,232RefSeq:NZ_AWUR01000021
NZ_AWUR0100001536351034,435RefSeq:NZ_AWUR01000015
NZ_AWUR0100000533321034,029RefSeq:NZ_AWUR01000005
NZ_AWUR0100001434340033,960RefSeq:NZ_AWUR01000014
NZ_AWUR0100001627260132,545RefSeq:NZ_AWUR01000016
NZ_AWUR0100003325240123,488RefSeq:NZ_AWUR01000033
NZ_AWUR0100001019180120,677RefSeq:NZ_AWUR01000010
NZ_AWUR0100002316160020,479RefSeq:NZ_AWUR01000023
NZ_AWUR0100000218170114,879RefSeq:NZ_AWUR01000002
NZ_AWUR0100004915150013,286RefSeq:NZ_AWUR01000049
NZ_AWUR0100002412111012,558RefSeq:NZ_AWUR01000024
NZ_AWUR01000017116506,555RefSeq:NZ_AWUR01000017
20 Undisplayed Contigs/Replicons66633084,849
Total:2,0001,91156332,171,264
Ortholog data available?No
Database Contents
Genes2,000
Pathways156
Enzymatic Reactions898
Transport Reactions37
Polypeptides1,933
Protein Complexes48
Enzymes487
Transporters231
Compounds677
Transcription Units1,109
tRNAs49
Protein Features2,658
GO Terms200
Database Version29.0
Sequence SourceGCF_000468835.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Negativicutes
Acidaminococcales
Acidaminococcaceae
Acidaminococcus
unclassified Acidaminococcus
Acidaminococcus sp. BV3L6
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00829141
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1111120
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-9
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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