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 Acetanaerobacterium elongatum CGMCC 1.5012, 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_FNID0100000111511320137,627RefSeq:NZ_FNID01000001
NZ_FNID0100000212312012131,307RefSeq:NZ_FNID01000002
NZ_FNID0100000311410554112,398RefSeq:NZ_FNID01000003
NZ_FNID01000004999504108,937RefSeq:NZ_FNID01000004
NZ_FNID01000005949310103,865RefSeq:NZ_FNID01000005
NZ_FNID0100000683811193,586RefSeq:NZ_FNID01000006
NZ_FNID0100000786830393,475RefSeq:NZ_FNID01000007
NZ_FNID010000081011001092,662RefSeq:NZ_FNID01000008
NZ_FNID0100000993867092,168RefSeq:NZ_FNID01000009
NZ_FNID0100001089872091,420RefSeq:NZ_FNID01000010
NZ_FNID0100001187842190,421RefSeq:NZ_FNID01000011
NZ_FNID010000121061051085,377RefSeq:NZ_FNID01000012
NZ_FNID0100001388862081,730RefSeq:NZ_FNID01000013
NZ_FNID0100001469670281,345RefSeq:NZ_FNID01000014
NZ_FNID0100001576731272,541RefSeq:NZ_FNID01000015
NZ_FNID0100001659581068,228RefSeq:NZ_FNID01000016
NZ_FNID0100001764620266,509RefSeq:NZ_FNID01000017
NZ_FNID0100001859562164,977RefSeq:NZ_FNID01000018
NZ_FNID0100001970636164,622RefSeq:NZ_FNID01000019
NZ_FNID0100002059581062,985RefSeq:NZ_FNID01000020
NZ_FNID0100002151473160,390RefSeq:NZ_FNID01000021
NZ_FNID0100002243402150,080RefSeq:NZ_FNID01000022
NZ_FNID0100002342400247,721RefSeq:NZ_FNID01000023
NZ_FNID0100002436350145,372RefSeq:NZ_FNID01000024
NZ_FNID0100002538371043,166RefSeq:NZ_FNID01000025
NZ_FNID0100002634331043,102RefSeq:NZ_FNID01000026
NZ_FNID0100002739390041,335RefSeq:NZ_FNID01000027
NZ_FNID0100002837370041,100RefSeq:NZ_FNID01000028
NZ_FNID0100002941401039,712RefSeq:NZ_FNID01000029
NZ_FNID0100003036331236,449RefSeq:NZ_FNID01000030
NZ_FNID0100003144422036,420RefSeq:NZ_FNID01000031
NZ_FNID0100003244430133,823RefSeq:NZ_FNID01000032
NZ_FNID0100003322220032,879RefSeq:NZ_FNID01000033
NZ_FNID0100003437370031,287RefSeq:NZ_FNID01000034
NZ_FNID0100003525240131,275RefSeq:NZ_FNID01000035
NZ_FNID0100003634285130,837RefSeq:NZ_FNID01000036
NZ_FNID0100003730282030,431RefSeq:NZ_FNID01000037
NZ_FNID0100003829290029,434RefSeq:NZ_FNID01000038
NZ_FNID0100003922220027,191RefSeq:NZ_FNID01000039
NZ_FNID0100004022220024,169RefSeq:NZ_FNID01000040
NZ_FNID0100004124240024,059RefSeq:NZ_FNID01000041
NZ_FNID0100004220190122,165RefSeq:NZ_FNID01000042
NZ_FNID0100004315140120,399RefSeq:NZ_FNID01000043
NZ_FNID0100004413130019,194RefSeq:NZ_FNID01000044
NZ_FNID0100004517170018,548RefSeq:NZ_FNID01000045
NZ_FNID0100004613130018,173RefSeq:NZ_FNID01000046
NZ_FNID0100004717170017,904RefSeq:NZ_FNID01000047
NZ_FNID0100004818171017,649RefSeq:NZ_FNID01000048
NZ_FNID0100004919190017,298RefSeq:NZ_FNID01000049
NZ_FNID0100005016150117,047RefSeq:NZ_FNID01000050
NZ_FNID0100005117152016,570RefSeq:NZ_FNID01000051
NZ_FNID0100005214140016,345RefSeq:NZ_FNID01000052
NZ_FNID0100005312120014,983RefSeq:NZ_FNID01000053
NZ_FNID0100005516160014,429RefSeq:NZ_FNID01000055
NZ_FNID0100005611110011,890RefSeq:NZ_FNID01000056
NZ_FNID010000611111008,662RefSeq:NZ_FNID01000061
NZ_FNID010000621010007,338RefSeq:NZ_FNID01000062
16 Undisplayed Contigs/Replicons60582281,209
Total:2,7652,66859382,916,215
Ortholog data available?Yes
Database Contents
Genes2,764
Pathways133
Enzymatic Reactions808
Transport Reactions39
Polypeptides2,748
Protein Complexes72
Enzymes532
Transporters204
Compounds594
Transcription Units1,934
tRNAs51
Protein Features3,270
GO Terms182
Database Version29.0
Sequence SourceGCF_900103835.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Clostridia
Eubacteriales
Oscillospiraceae
Acetanaerobacterium
Acetanaerobacterium elongatum
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05192585
NCBI BioProjectPRJNA224116
NCBI-Taxonomy258515
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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