Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Neptuniibacter marinus ATR 1.1, 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_LUTR0100000137136473414,555RefSeq:NZ_LUTR01000001
NZ_LUTR01000002372362104383,178RefSeq:NZ_LUTR01000002
NZ_LUTR0100000328227573313,066RefSeq:NZ_LUTR01000003
NZ_LUTR0100000413313301152,699RefSeq:NZ_LUTR01000004
NZ_LUTR0100000514814530148,212RefSeq:NZ_LUTR01000005
NZ_LUTR0100000611111012124,905RefSeq:NZ_LUTR01000006
NZ_LUTR0100000710910900119,813RefSeq:NZ_LUTR01000007
NZ_LUTR010000081019740108,465RefSeq:NZ_LUTR01000008
NZ_LUTR0100000910910902108,046RefSeq:NZ_LUTR01000009
NZ_LUTR01000010929021106,715RefSeq:NZ_LUTR01000010
NZ_LUTR0100001186815196,606RefSeq:NZ_LUTR01000011
NZ_LUTR0100001289872093,894RefSeq:NZ_LUTR01000012
NZ_LUTR0100001387852089,922RefSeq:NZ_LUTR01000013
NZ_LUTR0100001473712084,768RefSeq:NZ_LUTR01000014
NZ_LUTR0100001581765084,237RefSeq:NZ_LUTR01000015
NZ_LUTR0100001681801282,069RefSeq:NZ_LUTR01000016
NZ_LUTR0100001767625168,552RefSeq:NZ_LUTR01000017
NZ_LUTR0100001859590167,086RefSeq:NZ_LUTR01000018
NZ_LUTR0100001961610066,422RefSeq:NZ_LUTR01000019
NZ_LUTR0100002054522060,103RefSeq:NZ_LUTR01000020
NZ_LUTR0100002158562058,136RefSeq:NZ_LUTR01000021
NZ_LUTR0100002244440053,572RefSeq:NZ_LUTR01000022
NZ_LUTR0100002348480052,444RefSeq:NZ_LUTR01000023
NZ_LUTR0100002450500251,358RefSeq:NZ_LUTR01000024
NZ_LUTR0100002545441048,487RefSeq:NZ_LUTR01000025
NZ_LUTR0100002653530048,106RefSeq:NZ_LUTR01000026
NZ_LUTR0100002736360243,516RefSeq:NZ_LUTR01000027
NZ_LUTR0100002832320040,614RefSeq:NZ_LUTR01000028
NZ_LUTR0100002939390038,086RefSeq:NZ_LUTR01000029
NZ_LUTR0100003029290035,405RefSeq:NZ_LUTR01000030
NZ_LUTR0100003125250027,012RefSeq:NZ_LUTR01000031
NZ_LUTR0100003225232026,149RefSeq:NZ_LUTR01000032
NZ_LUTR0100003328271026,086RefSeq:NZ_LUTR01000033
NZ_LUTR0100003429290025,819RefSeq:NZ_LUTR01000034
NZ_LUTR0100003517152020,181RefSeq:NZ_LUTR01000035
NZ_LUTR0100003621210020,064RefSeq:NZ_LUTR01000036
NZ_LUTR0100003719190016,850RefSeq:NZ_LUTR01000037
80 Undisplayed Contigs/Replicons3824141448,993
Total:3,2413,12280393,454,191
Ortholog data available?No
Database Contents
Genes3,202
Pathways259
Enzymatic Reactions1,355
Transport Reactions48
Polypeptides3,170
Protein Complexes3
Enzymes791
Transporters312
Compounds940
Transcription Units2,082
tRNAs69
Protein Features4,200
GO Annotations204
Database Version29.6
Sequence SourceGCF_001597725.1
Synonyms Neptuniibacter sp. ATR 1.1
Neptuniibacter sp. ATR 1.2
Neptuniibacter sp. ATR 1.5
Neptuniibacter sp. BFR 2.2
Neptuniibacter sp. BFR 3.3
Neptuniibacter sp. CECT 8938
Neptuniibacter sp. CECT 8939
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Gammaproteobacteria
Oceanospirillales
Oceanospirillaceae
Neptuniibacter
Neptuniibacter marinus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04506967
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1806670
Environmentwater
Geographic LocationNorway
Collection Date2011-01-27
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-14
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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