Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 25-Oct-2020 from the annotated genome of Methylomonas denitrificans FJG1, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0144764,5994,539601585,172,098RefSeq:NZ_CP014476
Ortholog data available?No
Database Contents
Genes4,757
Pathways255
Enzymatic Reactions1,270
Transport Reactions55
Polypeptides4,539
Protein Complexes42
Enzymes841
Transporters315
Compounds897
Transcription Units2,834
tRNAs47
Protein Features5,759
GO Terms18,179
Database Version29.1
Sequence SourceGCF_000785705.2
Synonyms Methylomonas sp. FJG1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Methylococcales
Methylococcaceae
Methylomonas
Methylomonas denitrificans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02997349
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1538553
EnvironmentNA
Geographic LocationNA
Annotation ProviderNCBI RefSeq
Annotation Date2020-08-30
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.12
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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