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 hippikon ATCC 29725, 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_JNJT01000009272251201256,550RefSeq:NZ_JNJT01000009
NZ_JNJT0100001015114911197,275RefSeq:NZ_JNJT01000010
NZ_JNJT0100001118818620192,087RefSeq:NZ_JNJT01000011
NZ_JNJT0100001217116821173,079RefSeq:NZ_JNJT01000012
NZ_JNJT0100001389890097,204RefSeq:NZ_JNJT01000013
NZ_JNJT0100001489860392,136RefSeq:NZ_JNJT01000014
NZ_JNJT0100001581773187,781RefSeq:NZ_JNJT01000015
NZ_JNJT0100001671673172,672RefSeq:NZ_JNJT01000016
NZ_JNJT0100001769653169,358RefSeq:NZ_JNJT01000017
NZ_JNJT0100000150500056,863RefSeq:NZ_JNJT01000001
NZ_JNJT0100000232320035,483RefSeq:NZ_JNJT01000002
NZ_JNJT0100000331300133,606RefSeq:NZ_JNJT01000003
NZ_JNJT0100000423220120,816RefSeq:NZ_JNJT01000004
NZ_JNJT0100000524231020,778RefSeq:NZ_JNJT01000005
NZ_JNJT0100000615104111,398RefSeq:NZ_JNJT01000006
NZ_JNJT01000007109108,155RefSeq:NZ_JNJT01000007
NZ_JNJT0100000865015,210RefSeq:NZ_JNJT01000008
Total:1,3721,31940131,430,451
Ortholog data available?No
Database Contents
Genes1,371
Pathways96
Enzymatic Reactions541
Transport Reactions22
Polypeptides1,340
Protein Complexes20
Enzymes298
Transporters112
Compounds357
Transcription Units738
tRNAs33
Protein Features1,617
Database Version29.0
Sequence SourceGCF_000702765.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Mycoplasmatota
Mollicutes
Acholeplasmatales
Acholeplasmataceae
Acholeplasma
Acholeplasma hippikon
Acholeplasma hippikon ATCC 29725
Genetic Code Number 4 -- Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
BIOSAMPLESAMN02841174
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1408416
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+

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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