Database Authors
Pallavi Subhraveti1, Anamika Kothari1, Peter Midford1, Ron Caspi1, Lisa Moore1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 05-Nov-2025 from the annotated genome of Marinobacter zhejiangensis CGMCC 1.7061, as obtained from RefSeq (annotation date: 03-MAY-2025). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 29.5) [Karp11, Karp16] using MetaCyc version 29.5 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_FOUE010000011,0981,092631,236,377RefSeq:NZ_FOUE01000001
NZ_FOUE01000002882862202990,617RefSeq:NZ_FOUE01000002
NZ_FOUE0100000359058642641,018RefSeq:NZ_FOUE01000003
NZ_FOUE01000004426416113460,905RefSeq:NZ_FOUE01000004
NZ_FOUE0100000523423310236,936RefSeq:NZ_FOUE01000005
NZ_FOUE0100000622222200228,815RefSeq:NZ_FOUE01000006
NZ_FOUE0100000712912641128,856RefSeq:NZ_FOUE01000007
NZ_FOUE0100000875741173,881RefSeq:NZ_FOUE01000008
NZ_FOUE0100000912111115,571RefSeq:NZ_FOUE01000009
NZ_FOUE01000010127609,245RefSeq:NZ_FOUE01000010
NZ_FOUE0100001140405,229RefSeq:NZ_FOUE01000011
NZ_FOUE0100001211021,806RefSeq:NZ_FOUE01000012
Total:3,7003,63058154,029,256
Ortholog data available?Yes
Database Contents
Genes3,685
Pathways284
Enzymatic Reactions1,628
Transport Reactions87
Polypeptides3,703
Protein Complexes90
Enzymes873
Transporters326
Compounds1,353
Transcription Units2,506
tRNAs46
GO Annotations6,053
Database Version29.6
Sequence SourceGCF_900114775.1
Synonyms Marinobacter sp. CN74
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Gammaproteobacteria
Pseudomonadales
Marinobacteraceae
Marinobacter
Marinobacter zhejiangensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04487963
NCBI BioProjectPRJNA224116
NCBI-Taxonomy488535
Annotation ProviderNCBI RefSeq
Annotation Date2025-05-3
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.10
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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Page generated by Pathway Tools version 29.5 (software by SRI International) on Tue Jun 9, 2026, BIOCYC18.