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 intestini D21, 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_ACGB0100000114313841138,060RefSeq:NZ_ACGB01000001
NZ_ACGB0100000211911711111,847RefSeq:NZ_ACGB01000002
NZ_ACGB01000003968961106,444RefSeq:NZ_ACGB01000003
NZ_ACGB01000004999711100,348RefSeq:NZ_ACGB01000004
NZ_ACGB0100000575678090,089RefSeq:NZ_ACGB01000005
NZ_ACGB0100000676724079,129RefSeq:NZ_ACGB01000006
NZ_ACGB0100000766660076,863RefSeq:NZ_ACGB01000007
NZ_ACGB0100000846451057,176RefSeq:NZ_ACGB01000008
NZ_ACGB0100000947416056,438RefSeq:NZ_ACGB01000009
NZ_ACGB0100001048470153,541RefSeq:NZ_ACGB01000010
NZ_ACGB0100001150500050,780RefSeq:NZ_ACGB01000011
NZ_ACGB0100001241401048,819RefSeq:NZ_ACGB01000012
NZ_ACGB0100001355541047,085RefSeq:NZ_ACGB01000013
NZ_ACGB0100001440353245,876RefSeq:NZ_ACGB01000014
NZ_ACGB0100001540391045,451RefSeq:NZ_ACGB01000015
NZ_ACGB0100001642420043,082RefSeq:NZ_ACGB01000016
NZ_ACGB0100001739380142,363RefSeq:NZ_ACGB01000017
NZ_ACGB0100001845450042,133RefSeq:NZ_ACGB01000018
NZ_ACGB0100001938371041,862RefSeq:NZ_ACGB01000019
NZ_ACGB0100002035350039,720RefSeq:NZ_ACGB01000020
NZ_ACGB0100002130300037,472RefSeq:NZ_ACGB01000021
NZ_ACGB0100002233320136,858RefSeq:NZ_ACGB01000022
NZ_ACGB0100002342410136,746RefSeq:NZ_ACGB01000023
NZ_ACGB0100002437361035,945RefSeq:NZ_ACGB01000024
NZ_ACGB0100002532301133,224RefSeq:NZ_ACGB01000025
NZ_ACGB0100002626241131,763RefSeq:NZ_ACGB01000026
NZ_ACGB0100002736323130,925RefSeq:NZ_ACGB01000027
NZ_ACGB0100002826260029,441RefSeq:NZ_ACGB01000028
NZ_ACGB0100002928280029,289RefSeq:NZ_ACGB01000029
NZ_ACGB0100003027260128,654RefSeq:NZ_ACGB01000030
NZ_ACGB0100003123221028,136RefSeq:NZ_ACGB01000031
NZ_ACGB0100003224240028,068RefSeq:NZ_ACGB01000032
NZ_ACGB0100003328280027,194RefSeq:NZ_ACGB01000033
NZ_ACGB0100003424231026,353RefSeq:NZ_ACGB01000034
NZ_ACGB0100003522220026,105RefSeq:NZ_ACGB01000035
NZ_ACGB0100003622220024,163RefSeq:NZ_ACGB01000036
NZ_ACGB0100003724240023,675RefSeq:NZ_ACGB01000037
NZ_ACGB0100003819190022,062RefSeq:NZ_ACGB01000038
NZ_ACGB0100003915140122,031RefSeq:NZ_ACGB01000039
NZ_ACGB0100004017161020,036RefSeq:NZ_ACGB01000040
NZ_ACGB0100004116160019,903RefSeq:NZ_ACGB01000041
NZ_ACGB0100004220181119,538RefSeq:NZ_ACGB01000042
NZ_ACGB0100004319190019,147RefSeq:NZ_ACGB01000043
NZ_ACGB0100004413103018,276RefSeq:NZ_ACGB01000044
NZ_ACGB0100004517170016,771RefSeq:NZ_ACGB01000045
NZ_ACGB0100004612120016,101RefSeq:NZ_ACGB01000046
NZ_ACGB0100004716160015,907RefSeq:NZ_ACGB01000047
NZ_ACGB0100004818180015,879RefSeq:NZ_ACGB01000048
NZ_ACGB0100005018143115,083RefSeq:NZ_ACGB01000050
NZ_ACGB0100005113120112,855RefSeq:NZ_ACGB01000051
NZ_ACGB0100005212120012,044RefSeq:NZ_ACGB01000052
NZ_ACGB0100005311100111,956RefSeq:NZ_ACGB01000053
27 Undisplayed Contigs/Replicons11511238150,267
Total:2,0831,99957272,238,973
Ortholog data available?No
Database Contents
Genes2,083
Pathways154
Enzymatic Reactions890
Transport Reactions36
Polypeptides2,041
Protein Complexes47
Enzymes485
Transporters221
Compounds653
Transcription Units1,141
tRNAs50
Protein Features2,677
GO Terms193
Database Version29.0
Sequence SourceGCF_000174215.1
Synonyms Acidaminococcus sp. ADV 255.99
Acidaminococcus sp. D21
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Negativicutes
Acidaminococcales
Acidaminococcaceae
Acidaminococcus
Acidaminococcus intestini
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02595304
NCBI BioProjectPRJNA224116
NCBI-Taxonomy187327
Annotation ProviderNCBI RefSeq
Annotation Date2022-03-29
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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17A.