Database Authors
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Acholeplasma modicum ATCC 29102, 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_JHYB01000002526506155540,049RefSeq:NZ_JHYB01000002
NZ_JHYB0100000320119362238,812RefSeq:NZ_JHYB01000003
NZ_JHYB01000004157139162156,061RefSeq:NZ_JHYB01000004
NZ_JHYB0100000511911702132,509RefSeq:NZ_JHYB01000005
NZ_JHYB010000061141113097,543RefSeq:NZ_JHYB01000006
NZ_JHYB0100000746451048,321RefSeq:NZ_JHYB01000007
NZ_JHYB0100000821011,697RefSeq:NZ_JHYB01000008
NZ_JHYB0100000910101,509RefSeq:NZ_JHYB01000009
NZ_JHYB0100001010101,435RefSeq:NZ_JHYB01000010
NZ_JHYB0100000110101,244RefSeq:NZ_JHYB01000001
Total:1,1681,11244121,219,180
Ortholog data available?Yes
Database Contents
Genes1,162
Pathways89
Enzymatic Reactions512
Transport Reactions25
Polypeptides1,116
Protein Complexes16
Enzymes263
Transporters109
Compounds345
Transcription Units589
tRNAs33
Protein Features1,435
Database Version29.0
Sequence SourceGCF_000687835.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Mycoplasmatota
Mollicutes
Acholeplasmatales
Acholeplasmataceae
Acholeplasma
Acholeplasma modicum
Acholeplasma modicum ATCC 29102
Genetic Code Number 4 -- Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
BIOSAMPLESAMN02743893
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1408417
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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