Nitrosococcus watsonii C-113 plasmid pNWAT02, complete sequence.
type: Entry
definition: Nitrosococcus watsonii C-113 plasmid pNWAT02, complete sequence.
sequence version: NC_014317.1
sequence date: 2022-12-29
sequence: sequence
division: CON
label: NC_014317.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02598531
keyword: RefSeq
source: Nitrosococcus watsonii C-113
organism: Nitrosococcus watsonii C-113
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Chromatiales; Chromatiaceae; Nitrosococcus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP002088.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4082961\nSource DNA and organism available from Martin G. Klotz\n(martin.klotz@louisville.edu)\nContacts: Martin G. Klotz (martin.klotz@louisville.edu)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-PGF\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. it is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Metadata-START##\ninvestigation_type :: bacteria_archaea\nproject_name :: Nitrosococcus watsoni C-113\ncollection_date :: N/A\ndepth :: N/A\nalt_elev :: N/A\ncountry :: N/A\nnum_replicons :: N/A\nref_biomaterial :: N/A\nbiotic_relationship :: Free living\nrel_to_oxygen :: Aerobe\nassembly :: N/A\nfinishing_strategy :: N/A\ntrophic_level :: Autotroph, Chemolithotroph\nenvironment :: Marine\nGOLD Stamp ID :: Gi05339\nrel_to_oxygen :: Aerobe\nMotility :: Motile\nTemperature Range :: Mesophile\nGram Staining :: gram-\nDiseases :: None\nPhenotypes :: Carbon sequestration\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/29/2022 00:58:29\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnot…

sequence
subclass of: SO_0000155
sequence length: 5611
topology: circular
so has quality: SO_0000988
location: 1..5611
location: region:1-5611:1
RO_0002162: 105559

NC_014317
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02598531
type: BioSample
SIO_000068: biosample

1
title: Complete sequence of plasmid2 of Nitrosococcus watsoni C-113
author: Lucas, S.
author: Copeland, A.
author: Lapidus, A.
author: Cheng, J.-F.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Malfatti, S.A.
author: Chain, P.S.G.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Ivanova, N.
author: Cambell, M.A.
author: Heidelberg, J.F.
author: Klotz, M.G.
author: Woyke, T.
journal: Unpublished

2
title: Direct Submission
author: Lucas, S.
author: Copeland, A.
author: Lapidus, A.
author: Cheng, J.-F.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Malfatti, S.A.
author: Chain, P.S.G.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Ivanova, N.
author: Cambell, M.A.
author: Heidelberg, J.F.
author: Klotz, M.G.
author: Woyke, T.
journal: Submitted (21-JUN-2010) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5611:1
position: 5611
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5611:1:source
so part of: sequence
organism: Nitrosococcus watsonii C-113
mol type: genomic DNA
strain: C-113
type material: type strain of Nitrosococcus watsonii
plasmid: pNWAT02

105559
type: Taxonomy
SIO_000068: taxonomy

NWAT_RS15485
type: Gene
subclass of: SO_0000704
RO_0002162: 105559
locus tag: NWAT_RS15485
old locus tag: Nwat_3188
so part of: sequence
location: complement(31..1059)
location: region:31-1059:-1
so has part: feature:31-1059:-1:exon
subclass of: SO_0000010

position:31:-1
position: 31
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1059:-1
position: 1059
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:31-1059:-1:exon

NWAT_RS15485
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 105559
locus tag: NWAT_RS15485
old locus tag: Nwat_3188
inference: COORDINATES: protein motif:HMM:NF015354.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobQ family relaxase
translation: MGRSAGRSATAAAAYRAGLEITDTRTGETHDYRNRHGVLDHAILTPARAPDWAKESARLWNAAEQAENRKDSRVARENIVALPHELTLEQNRSLLHRFVEENYIRRGMAAQVDIHGADEKGDSRNIHAHILLTTRPLTRNGFKAQKPQSWNDKATLAQWRENWAQCVNQALERHGFKDRIDSRTLQAQGIFREATRHLGPAVTAMERRGQSTRAGDHNRAVERGNRALSWLEQQRATVEEALAAEQTRQRADPSRLKVAEFRENMAAQRRPTLPQPPPTPARQAGPAFNWEAPPQGPPESPAQEQAQAERRAALVEEFRQAQEKARKQAREWGRDDGPELER
SIO_010081: NWAT_RS15485
subclass of: SO_0000673
so part of: NWAT_RS15485
location: complement(31..1059)
location: region:31-1059:-1
so has part: feature:31-1059:-1:exon

WP_083781481.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:31-1059:-1:exon

NWAT_RS15490
type: Gene
subclass of: SO_0000704
RO_0002162: 105559
locus tag: NWAT_RS15490
old locus tag: Nwat_3189
so part of: sequence
location: 1459..1935
location: region:1459-1935:1
so has part: feature:1459-1935:1:exon
subclass of: SO_0000010

position:1459:1
position: 1459
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1935:1
position: 1935
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1459-1935:1:exon

NWAT_RS15490
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 105559
locus tag: NWAT_RS15490
old locus tag: Nwat_3189
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKDPTKLKQKFWQAVEATPEDRREELLQLVQTFAVNAKQQPAHPLPTNLKEMRKLGIKLYPEFKQETGSTDSEKCLRQNWGEWLKAYNPKLDRDYMSLADIRKLDPQLLGRLKKQYKTDELHKFLPSLPLVNKQIANNMTDDERREIGRLNALYYTHV
SIO_010081: NWAT_RS15490
subclass of: SO_0000673
so part of: NWAT_RS15490
location: 1459..1935
location: region:1459-1935:1
so has part: feature:1459-1935:1:exon

WP_013221949.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1459-1935:1:exon

NWAT_RS15495
type: Gene
subclass of: SO_0000704
RO_0002162: 105559
locus tag: NWAT_RS15495
old locus tag: Nwat_3190
so part of: sequence
location: 2022..2333
location: region:2022-2333:1
so has part: feature:2022-2333:1:exon
subclass of: SO_0000010

position:2022:1
position: 2022
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2333:1
position: 2333
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2022-2333:1:exon

NWAT_RS15495
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 105559
locus tag: NWAT_RS15495
old locus tag: Nwat_3190
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKTFWTDKEIENFLTRETRTVQLPEGRRRTVNCFHLTWRQLDGLLHYNIFSEEWYADHAEKIAQESRRFDFAQCFAWVIAYSFSDMKLLAYGGGIPSARAPLI
SIO_010081: NWAT_RS15495
subclass of: SO_0000673
so part of: NWAT_RS15495
location: 2022..2333
location: region:2022-2333:1
so has part: feature:2022-2333:1:exon

WP_013221950.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2022-2333:1:exon

NWAT_RS15500
type: Gene
subclass of: SO_0000704
RO_0002162: 105559
locus tag: NWAT_RS15500
old locus tag: Nwat_3191
so part of: sequence
location: complement(2559..2840)
location: region:2559-2840:-1
so has part: feature:2559-2840:-1:exon
subclass of: SO_0000010

position:2559:-1
position: 2559
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2840:-1
position: 2840
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2559-2840:-1:exon

NWAT_RS15500
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 105559
locus tag: NWAT_RS15500
old locus tag: Nwat_3191
inference: COORDINATES: similar to AA sequence:RefSeq:WP_015279222.1
GO function: GO:0003677 - DNA binding [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: HigA family addiction module antitoxin
translation: MSMKNPPHPGHCVKLDCLDPLGLSVTEGAKVLGVTRQALSNVINGKAGISAEMAIRLSQAFGGTPDVWLRMQTAYALAQAKQKNIQVERFEHA
SIO_010081: NWAT_RS15500
subclass of: SO_0000673
so part of: NWAT_RS15500
location: complement(2559..2840)
location: region:2559-2840:-1
so has part: feature:2559-2840:-1:exon

WP_013221951.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2559-2840:-1:exon

NWAT_RS15505
type: Gene
subclass of: SO_0000704
RO_0002162: 105559
locus tag: NWAT_RS15505
old locus tag: Nwat_3192
so part of: sequence
location: complement(2858..3136)
location: region:2858-3136:-1
so has part: feature:2858-3136:-1:exon
subclass of: SO_0000010

position:2858:-1
position: 2858
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3136:-1
position: 3136
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2858-3136:-1:exon

NWAT_RS15505
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 105559
locus tag: NWAT_RS15505
old locus tag: Nwat_3192
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009613268.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system RelE/ParE family toxin
translation: MIENFKDRRLKRLYERADRSKIQADLVDKVERILARLEQALVIEDMDLPGYRLHSLKGDLKGFWSVSISGNWRVIFRFENGKARDVEMIDYH
SIO_010081: NWAT_RS15505
subclass of: SO_0000673
so part of: NWAT_RS15505
location: complement(2858..3136)
location: region:2858-3136:-1
so has part: feature:2858-3136:-1:exon

WP_013221952.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2858-3136:-1:exon

NWAT_RS15515
type: Gene
subclass of: SO_0000704
RO_0002162: 105559
gene: trfA
locus tag: NWAT_RS15515
old locus tag: Nwat_3193
so part of: sequence
location: complement(4185..5066)
location: region:4185-5066:-1
so has part: feature:4185-5066:-1:exon
subclass of: SO_0000010

position:4185:-1
position: 4185
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5066:-1
position: 5066
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4185-5066:-1:exon

NWAT_RS15515
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 105559
gene: trfA
locus tag: NWAT_RS15515
old locus tag: Nwat_3193
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012972314.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid replication initiator TrfA
translation: MDTYDPALQRRLESLEEAAKARQWKQTAEQPKSADIIQLPLWPEPARGVPNSTLRGALFAAIQGKNRQALKRAVLSAQNGIEIRFTGWQLDQSDLDVWEQVLHLARQHPLGTRCDFTAHAFLKSLGRSAGKPMHEWLKDVFARLAGAVVEITHNRKTYFGPLIEGGVRDEASGLYTLKLNPELVKLYGAGMWTAIDWKERQKLRRKPLALWLHGFYASHAESYPMKLETLRLLSGSRTRDLWKFKQNLVKAFQELKAVGVIRNFEIRDGLVYVVNVPSASQQKHLRKPKPRKK
SIO_010081: NWAT_RS15515
subclass of: SO_0000673
so part of: NWAT_RS15515
location: complement(4185..5066)
location: region:4185-5066:-1
so has part: feature:4185-5066:-1:exon

WP_013221953.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4185-5066:-1:exon

NWAT_RS15520
type: Gene
subclass of: SO_0000704
RO_0002162: 105559
locus tag: NWAT_RS15520
old locus tag: Nwat_3194
so part of: sequence
location: complement(5102..5542)
location: region:5102-5542:-1
so has part: feature:5102-5542:-1:exon
subclass of: SO_0000010

position:5102:-1
position: 5102
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5542:-1
position: 5542
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5102-5542:-1:exon

NWAT_RS15520
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 105559
locus tag: NWAT_RS15520
old locus tag: Nwat_3194
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSYTLGEAAKAAGKSKTTIKRALDKGRISGKKNEIGEWEIEPVELHRVYPKIEPGTVTAGIPESTPGNGALQARLDAAEREAALLREQHDRERRQLESTIEDLRADRDQWRQQATALLPDQREKEARQQPTGGRIARAWAALTGKA
SIO_010081: NWAT_RS15520
subclass of: SO_0000673
so part of: NWAT_RS15520
location: complement(5102..5542)
location: region:5102-5542:-1
so has part: feature:5102-5542:-1:exon

WP_013221954.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5102-5542:-1:exon