Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 08-Apr-2022 from the annotated genome of Acholeplasma laidlawii DSM 23060, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_QRDS010000011,0701,0383021,122,426RefSeq:NZ_QRDS01000001
NZ_QRDS0100000234934081364,210RefSeq:NZ_QRDS01000002
NZ_QRDS0100000330305,002RefSeq:NZ_QRDS01000003
Total:1,4221,3784131,491,638
Ortholog data available?No
Database Contents
Genes1,420
Pathways105
Enzymatic Reactions611
Transport Reactions25
Polypeptides1,381
Protein Complexes1
Enzymes336
Transporters161
Compounds405
Transcription Units707
tRNAs33
Protein Features1,737
GO Terms93
Database Version29.0
Sequence SourceGCF_003385765.1
Synonyms Asterococcus laidlawii
Mycoplasma laidlawii
Sapromyces laidlawi AB
"Types A and B" Laidlaw and Elford 1936
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Mycoplasmatota
Mollicutes
Acholeplasmatales
Acholeplasmataceae
Acholeplasma
Acholeplasma laidlawii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN08769264
NCBI BioProjectPRJNA224116
NCBI-Taxonomy2148
Annotation ProviderNCBI RefSeq
Annotation Date2021-04-21
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.1
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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