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 multilocale ATCC 49900, 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_KI519557308290144325,127RefSeq:NZ_KI519557
NZ_AXXW0100000526325562284,263RefSeq:NZ_AXXW01000005
NZ_AXXW0100000616015721174,148RefSeq:NZ_AXXW01000006
NZ_AXXW0100000780737076,789RefSeq:NZ_AXXW01000007
NZ_AXXW0100000845377149,738RefSeq:NZ_AXXW01000008
6 Undisplayed Contigs/Replicons883014,928
Total:867820398924,993
Ortholog data available?Yes
Database Contents
Genes861
Pathways58
Enzymatic Reactions319
Transport Reactions16
Polypeptides823
Protein Complexes14
Enzymes183
Transporters71
Compounds264
Transcription Units505
tRNAs28
Protein Features905
Database Version29.0
Sequence SourceGCF_000483165.1
Synonyms Acholeplasma multilocale PN525
Acholeplasma multilocale ATCC 49900
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Mycoplasmatota
Mollicutes
Acholeplasmatales
Acholeplasmataceae
Acholeplasma
Acholeplasma multilocale
Acholeplasma multilocale ATCC 49900
Genetic Code Number 4 -- Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
BIOSAMPLESAMN02441097
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1278299
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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