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 granularum ATCC 19168, 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_JAFR0100000628828341326,094RefSeq:NZ_JAFR01000006
NZ_JAFR0100000719419211211,086RefSeq:NZ_JAFR01000007
NZ_JAFR0100000816215741165,065RefSeq:NZ_JAFR01000008
NZ_JAFR0100000913513131150,806RefSeq:NZ_JAFR01000009
NZ_JAFR0100001011811341116,037RefSeq:NZ_JAFR01000010
NZ_JAFR0100001110110001111,671RefSeq:NZ_JAFR01000011
NZ_JAFR01000012100991099,194RefSeq:NZ_JAFR01000012
NZ_JAFR0100001382756182,505RefSeq:NZ_JAFR01000013
NZ_JAFR01000014938013071,094RefSeq:NZ_JAFR01000014
NZ_JAFR0100000141400161,884RefSeq:NZ_JAFR01000001
NZ_JAFR0100000249408147,159RefSeq:NZ_JAFR01000002
NZ_JAFR0100000344006,117RefSeq:NZ_JAFR01000003
NZ_JAFR0100000453113,785RefSeq:NZ_JAFR01000004
NZ_JAFR0100000500001,042RefSeq:NZ_JAFR01000005
Total:1,3721,31745101,453,539
Ortholog data available?Yes
Database Contents
Genes1,370
Pathways98
Enzymatic Reactions566
Transport Reactions23
Polypeptides1,325
Protein Complexes16
Enzymes304
Transporters123
Compounds374
Transcription Units699
tRNAs36
Protein Features1,637
Database Version29.0
Sequence SourceGCF_000526235.1
Synonyms Acholeplasma granularum BTS-39
Acholeplasma granularum ATCC 19168
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Mycoplasmatota
Mollicutes
Acholeplasmatales
Acholeplasmataceae
Acholeplasma
Acholeplasma granularum
Acholeplasma granularum ATCC 19168
Genetic Code Number 4 -- Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
BIOSAMPLESAMN02584924
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1278304
EnvironmentNasal cavity of pig
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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