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 12-July-2021 from the annotated genome of Marinobacter oulmenensis DSM 22359, 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 25.0) [Karp16, Karp11] using MetaCyc version 25.0 [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_JACHFE01000000162562145702,384RefSeq:NZ_JACHFE010000001
NZ_JACHFE010000002615600154651,288RefSeq:NZ_JACHFE010000002
NZ_JACHFE01000000340039731450,228RefSeq:NZ_JACHFE010000003
NZ_JACHFE01000000438337852414,156RefSeq:NZ_JACHFE010000004
NZ_JACHFE01000000529929811349,287RefSeq:NZ_JACHFE010000005
NZ_JACHFE01000000628028003293,479RefSeq:NZ_JACHFE010000006
NZ_JACHFE01000000717617160186,717RefSeq:NZ_JACHFE010000007
NZ_JACHFE01000000817416861180,486RefSeq:NZ_JACHFE010000008
NZ_JACHFE01000000914814713169,021RefSeq:NZ_JACHFE010000009
NZ_JACHFE01000001011511150117,237RefSeq:NZ_JACHFE010000010
NZ_JACHFE01000001184814093,786RefSeq:NZ_JACHFE010000011
NZ_JACHFE01000001234331037,956RefSeq:NZ_JACHFE010000012
NZ_JACHFE01000001322220221,978RefSeq:NZ_JACHFE010000013
NZ_JACHFE01000001411110113,449RefSeq:NZ_JACHFE010000014
10 Undisplayed Contigs/Replicons23203033,159
Total:3,4123,33854233,714,611
Ortholog data available?No
Database Contents
Genes3,389
Pathways275
Enzymatic Reactions1,405
Transport Reactions72
Polypeptides3,353
Protein Complexes51
Enzymes836
Transporters409
Compounds980
Transcription Units1,985
tRNAs43
Protein Features4,682
GO Annotations2
Database Version29.6
Sequence SourceGCF_014201735.1
Synonyms Marinobacter sp. Set74
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Gammaproteobacteria
Pseudomonadales
Marinobacteraceae
Marinobacter
Marinobacter oulmenensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN14908463
NCBI BioProjectPRJNA224116
NCBI-Taxonomy643747
Annotation ProviderNCBI RefSeq
Annotation Date2020-08-16
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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