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 Methylomarinum vadi IT-4, 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_JPON010000014,0663,829611764,335,162RefSeq:NZ_JPON01000001
Ortholog data available?Yes
Database Contents
Genes4,066
Pathways254
Enzymatic Reactions1,213
Transport Reactions53
Polypeptides3,831
Protein Complexes38
Enzymes796
Transporters296
Compounds855
Transcription Units2,489
tRNAs48
Protein Features4,921
Database Version29.0
Sequence SourceGCF_000733935.1
Synonyms Methylococcaceae bacterium IT-4
Methylococcaceae bacterium T2-1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Methylococcales
Methylococcaceae
Methylomarinum
Methylomarinum vadi
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02745036
NCBI BioProjectPRJNA224116
NCBI-Taxonomy438855
EnvironmentHydrothermal sediment
Geographic LocationJapan
Annotation ProviderNCBI
Annotation Date2017-04-16
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+
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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