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 axanthum ATCC 25176, 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_AUAL0100000116716223193,864RefSeq:NZ_AUAL01000001
NZ_KE38678812412211125,255RefSeq:NZ_KE386788
NZ_AUAL0100000410010000111,234RefSeq:NZ_AUAL01000004
NZ_AUAL0100000595950097,568RefSeq:NZ_AUAL01000005
NZ_AUAL0100000672693085,444RefSeq:NZ_AUAL01000006
NZ_AUAL0100000764620268,835RefSeq:NZ_AUAL01000007
NZ_AUAL0100000853483267,757RefSeq:NZ_AUAL01000008
NZ_AUAL0100000958580066,286RefSeq:NZ_AUAL01000009
NZ_AUAL0100001042400255,109RefSeq:NZ_AUAL01000010
NZ_AUAL0100001142400249,854RefSeq:NZ_AUAL01000011
NZ_AUAL0100001236350148,700RefSeq:NZ_AUAL01000012
NZ_AUAL0100001543430047,846RefSeq:NZ_AUAL01000015
NZ_KE38678941400147,804RefSeq:NZ_KE386789
NZ_AUAL0100001649490047,034RefSeq:NZ_AUAL01000016
NZ_AUAL01000017533815046,434RefSeq:NZ_AUAL01000017
NZ_AUAL0100001838380043,644RefSeq:NZ_AUAL01000018
NZ_AUAL0100001957560142,649RefSeq:NZ_AUAL01000019
NZ_AUAL0100002032320041,126RefSeq:NZ_AUAL01000020
NZ_KE38679036330340,389RefSeq:NZ_KE386790
NZ_AUAL0100002340380235,666RefSeq:NZ_AUAL01000023
NZ_AUAL0100002436324035,554RefSeq:NZ_AUAL01000024
NZ_AUAL0100002527250233,065RefSeq:NZ_AUAL01000025
NZ_AUAL0100002633257132,795RefSeq:NZ_AUAL01000026
NZ_AUAL0100002725240129,416RefSeq:NZ_AUAL01000027
NZ_AUAL0100002831291128,895RefSeq:NZ_AUAL01000028
NZ_AUAL0100002931292028,624RefSeq:NZ_AUAL01000029
NZ_AUAL0100003021210026,270RefSeq:NZ_AUAL01000030
NZ_AUAL0100003123220120,423RefSeq:NZ_AUAL01000031
NZ_AUAL0100003219180119,801RefSeq:NZ_AUAL01000032
NZ_AUAL0100003322201119,521RefSeq:NZ_AUAL01000033
NZ_AUAL0100003417151117,645RefSeq:NZ_AUAL01000034
NZ_AUAL0100003516160016,522RefSeq:NZ_AUAL01000035
NZ_AUAL0100003615141012,084RefSeq:NZ_AUAL01000036
NZ_AUAL010000391817109,739RefSeq:NZ_AUAL01000039
23 Undisplayed Contigs/Replicons838127114,271
Total:1,6661,58644361,807,123
Ortholog data available?No
Database Contents
Genes1,665
Pathways95
Enzymatic Reactions527
Transport Reactions24
Polypeptides1,603
Protein Complexes25
Enzymes283
Transporters146
Compounds354
Transcription Units889
tRNAs36
Protein Features1,944
GO Terms2
Database Version29.0
Sequence SourceGCF_000428705.1
Synonyms Acholeplasma axanthum S-743
Acholeplasma axanthum ATCC 25176
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Mycoplasmatota
Mollicutes
Acholeplasmatales
Acholeplasmataceae
Acholeplasma
Acholeplasma axanthum
Acholeplasma axanthum ATCC 25176
Genetic Code Number 4 -- Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
BIOSAMPLESAMN02441544
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1278311
EnvironmentMurine leukemia tissue culture
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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