Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Acholeplasma equifetale ATCC 29724, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_JHXL0100000133232057337,208RefSeq:NZ_JHXL01000001
NZ_JHXL0100000213413211187,654RefSeq:NZ_JHXL01000002
NZ_JHXL0100000312512023124,644RefSeq:NZ_JHXL01000003
NZ_JHXL0100000476732192,308RefSeq:NZ_JHXL01000004
NZ_JHXL0100000594911287,007RefSeq:NZ_JHXL01000005
NZ_JHXL0100000671710077,699RefSeq:NZ_JHXL01000006
NZ_JHXL0100000763602169,992RefSeq:NZ_JHXL01000007
NZ_JHXL0100000859553160,107RefSeq:NZ_JHXL01000008
NZ_JHXL0100000954520257,773RefSeq:NZ_JHXL01000009
NZ_JHXL01000010867214056,899RefSeq:NZ_JHXL01000010
NZ_JHXL0100001126224029,615RefSeq:NZ_JHXL01000011
NZ_JHXL0100001213110216,457RefSeq:NZ_JHXL01000012
NZ_JHXL0100001314130115,241RefSeq:NZ_JHXL01000013
NZ_JHXL0100001413130014,584RefSeq:NZ_JHXL01000014
NZ_JHXL010000151477011,688RefSeq:NZ_JHXL01000015
NZ_JHXL0100001614130110,589RefSeq:NZ_JHXL01000016
10 Undisplayed Contigs/Replicons23222332,907
Total:1,2151,14743251,282,372
Ortholog data available?Yes
Database Contents
Genes1,210
Pathways85
Enzymatic Reactions507
Transport Reactions19
Polypeptides1,166
Protein Complexes15
Enzymes272
Transporters84
Compounds336
Transcription Units638
tRNAs33
Protein Features1,467
GO Terms3
Database Version29.0
Sequence SourceGCF_000687735.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Mycoplasmatota
Mollicutes
Acholeplasmatales
Acholeplasmataceae
Acholeplasma
Acholeplasma equifetale
Acholeplasma equifetale ATCC 29724
Genetic Code Number 4 -- Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
BIOSAMPLESAMN02743882
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1408415
EnvironmentHost
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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