Komagataeibacter medellinensis NBRC 3288 plasmid pGXY060, complete sequence.
type: Entry
definition: Komagataeibacter medellinensis NBRC 3288 plasmid pGXY060, complete sequence.
sequence version: NC_016900.1
sequence date: 2022-12-24
sequence: sequence
division: CON
label: NC_016900.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMD00060987
keyword: RefSeq
source: Komagataeibacter medellinensis NBRC 3288
organism: Komagataeibacter medellinensis NBRC 3288
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodospirillales; Acetobacteraceae; Komagataeibacter.
reference: 1
references: 22123756
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nAP012165.1.\n\n\nThis work was done by Gluconacetobacter xylinus genome sequencing\nconsortium\nincluding Department of Microbiology and Immunology, Yamaguchi\nUniversity School of Medicine,\nNational Institute of Technology and Evaluation,\nGenetic Resources Technology, Faculty of Agriculture, Kyushu\nUniversity,\nDepartment of Biological Chemistry, Faculty of Agriculture,\nYamaguchi University and\nMizkan Group Corporation Central Research Institute.\n\nPlease visit our web site.\nURL:http://www.bio.nite.go.jp/\n\nDOGAN ; Database of Genomes Analyzed at NITE\nThe database contains genome sequence data, physical maps and the\ngenomic and proteomic data of the microorganisms analyzed.\nURL:http://www.bio.nite.go.jp/dogan/Top.\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##Genome-Assembly-Data-START##\nGenome Coverage :: 8x\nSequencing Technology :: Sanger ABI3730\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/24/2022 02:25:10\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,378\nCDSs (total) :: 3,302\nGenes (coding) :: 3,172\nCDSs (with protein) :: 3,172\nGenes (RNA) :: 76\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 57\nncRNAs :: 4\nPseudo Genes (total) :: 130\nCDSs (without protein) :: 130\nPseudo Genes (ambiguous residues) :: 0 of 130\nPseudo Genes (frameshifted) :: 54 of 130\nPseudo Genes (incomplete) :: 105 of 130\nPseudo Genes (internal stop) :: 39 of 130\nPseudo Genes (multiple problems) :: 50 of 130\nCRISPR Arrays :: 3\n##Genome-Annotation-D…

sequence
subclass of: SO_0000155
sequence length: 4255
topology: circular
so has quality: SO_0000988
location: 1..4255
location: region:1-4255:1
RO_0002162: 634177

NC_016900
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMD00060987
type: BioSample
SIO_000068: biosample

1
title: Complete genome sequence of NBRC 3288, a unique cellulose-nonproducing strain of Gluconacetobacter xylinus isolated from vinegar
author: Ogino, H.
author: Azuma, Y.
author: Hosoyama, A.
author: Nakazawa, H.
author: Matsutani, M.
author: Hasegawa, A.
author: Otsuyama, K.
author: Matsushita, K.
author: Fujita, N.
author: Shirai, M.
journal: J Bacteriol
volume: 193
issue: 24
pages: 6997-6998
year: 2011
pubmed: 22123756

22123756
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
journal: Submitted (13-APR-2011) Contact:Director-General Department of Biotechnology National Institute of Technology and Evaluation, NITE Bioresource Information Center (NBIC), Department of Biotechnology; 2-49-10 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan URL :http://www.bio.nite.go.jp/

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

position:4255:1
position: 4255
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4255:1:source
so part of: sequence
organism: Komagataeibacter medellinensis NBRC 3288
mol type: genomic DNA
strain: NBRC 3288
type material: type strain of Komagataeibacter medellinensis
plasmid: pGXY060

3288
type: NBRC
SIO_000068: nbrc

634177
type: Taxonomy
SIO_000068: taxonomy

GLX_RS16370
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS16370
old locus tag: GLX_31880
so part of: sequence
location: 1..1044
location: region:1-1044:1
so has part: feature:1-1044:1:exon
subclass of: SO_0000010

position:1044:1
position: 1044
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-1044:1:exon

GLX_RS16370
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS16370
old locus tag: GLX_31880
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003627465.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobQ family relaxase
translation: MAIYHLSVKSISRSAGRSVVAAAAYRAGQELTDERQGLTHDYTRKQGVEDAFIVAPDGADWAQDRNALWNAAEAAEKRKDAKTGREYELALPAELDAGARKELARDFARELVARYGVVADVAMHEPGREGDNRNHHAHILTTTRTVGENGLGAKTRVLDVASTASTEIEHMRGVWARQVNMALERHQVEQRVDHRSFERQGREQEPTRHMGVSATAMERQAAREIPGREPVTDLGKQNAEIRERNRVLETARKAVEKAQELFSGLEKRARQAVGLARKIGQRMEREREAERQRKELARQAEIRRQQDIRAAEEARKAAEKDRQKQLAKEIDEPTFRRSRDRGPSIGF
SIO_010081: GLX_RS16370
subclass of: SO_0000673
so part of: GLX_RS16370
location: 1..1044
location: region:1-1044:1
so has part: feature:1-1044:1:exon

WP_014357864.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-1044:1:exon

GLX_RS17890
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS17890
old locus tag: GLX_31890
so part of: sequence
location: complement(1281..1589)
location: region:1281-1589:-1
so has part: feature:1281-1589:-1:exon
subclass of: SO_0000010

position:1281:-1
position: 1281
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1589:-1
position: 1589
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1281-1589:-1:exon

GLX_RS17890
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS17890
old locus tag: GLX_31890
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: MLKRFEDSLAQRIDAVAWKGFSFIEWWELKSWYEKDRIGKGVWRDIYDRFKSIADDDEAELYLYQSDSGVMLIHSDGLNRIPSTGIWESISGSKTQEDDDNE
SIO_010081: GLX_RS17890
subclass of: SO_0000673
so part of: GLX_RS17890
location: complement(1281..1589)
location: region:1281-1589:-1
so has part: feature:1281-1589:-1:exon

WP_148268695.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1281-1589:-1:exon

GLX_RS16375
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS16375
old locus tag: GLX_31900
so part of: sequence
location: complement(1691..1966)
location: region:1691-1966:-1
so has part: feature:1691-1966:-1:exon
subclass of: SO_0000010

position:1691:-1
position: 1691
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1966:-1
position: 1966
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1691-1966:-1:exon

GLX_RS16375
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS16375
old locus tag: GLX_31900
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010518138.1
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: MRVEWSDEALTDRAAIVDYLLPRNPHAAKRILLRLIDATTDLAMFPNIGREGEDGTREWVIVHPYVLLYEVDNAAKSVRVLRVWHMSQDRL
SIO_010081: GLX_RS16375
subclass of: SO_0000673
so part of: GLX_RS16375
location: complement(1691..1966)
location: region:1691-1966:-1
so has part: feature:1691-1966:-1:exon

WP_014357866.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1691-1966:-1:exon

GLX_RS18680
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS18680
so part of: sequence
location: complement(1956..2129)
location: region:1956-2129:-1
so has part: feature:1956-2129:-1:exon
subclass of: SO_0000010

position:1956:-1
position: 1956
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2129:-1
position: 2129
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1956-2129:-1:exon

GLX_RS18680
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS18680
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010518137.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MTDLSDELAAKRAAIRKARNSTKPAVPAEQVLTILKADLARVQAAIDALPHEERRAG
SIO_010081: GLX_RS18680
subclass of: SO_0000673
so part of: GLX_RS18680
location: complement(1956..2129)
location: region:1956-2129:-1
so has part: feature:1956-2129:-1:exon

WP_167537207.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1956-2129:-1:exon

GLX_RS16380
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS16380
old locus tag: GLX_31910
so part of: sequence
location: complement(2320..2919)
location: region:2320-2919:-1
so has part: feature:2320-2919:-1:exon
subclass of: SO_0000010

position:2320:-1
position: 2320
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2919:-1
position: 2919
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2320-2919:-1:exon

GLX_RS16380
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS16380
old locus tag: GLX_31910
inference: COORDINATES: similar to AA sequence:RefSeq:WP_019089581.1
GO function: GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix domain-containing protein
translation: MAQIVRLTTKQQRSGQEEAAQAAEQLSLLSEELLKHLPGEARIAISRATHALQKAARPDTTEGLWPGGFTMLSRMQTATIWDAIRALPSDDRPNQVRHAFDLVLLNLRQDTGEVLLTRDQLAEEIDCAPRSVSTIMGTLEKMGVIRRERRKIEGVRGPGMAVYFINPHVAWNGSLDVRKAQAAETRPPMQLELLHGGVR
SIO_010081: GLX_RS16380
subclass of: SO_0000673
so part of: GLX_RS16380
location: complement(2320..2919)
location: region:2320-2919:-1
so has part: feature:2320-2919:-1:exon

WP_014357867.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2320-2919:-1:exon

GLX_RS16385
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS16385
so part of: sequence
location: complement(3249..3785)
location: region:3249-3785:-1
so has part: feature:3249-3785:-1:exon
subclass of: SO_0000010

position:3249:-1
position: 3249
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3785:-1
position: 3785
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3249-3785:-1:exon

GLX_RS16385
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS16385
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006560191.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication protein
translation: MIDERELDDGLAAFDQLGREMAETNRLLRAVRSDQAIRNQQEHALSAEMQTTLRQATGASQEALQASQTEIRSSLLWTGLTALLIVLVAFGGGYFVGQRAGWDTGHADGYQKARNQEAAASWANTPAGQRAYGLDRQGSLDLLTMCRGNGWTTERQKGGTVCFPYADAKGNVTGWYLP
SIO_010081: GLX_RS16385
subclass of: SO_0000673
so part of: GLX_RS16385
location: complement(3249..3785)
location: region:3249-3785:-1
so has part: feature:3249-3785:-1:exon

WP_041248003.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3249-3785:-1:exon

GLX_RS16390
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS16390
old locus tag: GLX_31920
so part of: sequence
location: complement(3782..4039)
location: region:3782-4039:-1
so has part: feature:3782-4039:-1:exon
subclass of: SO_0000010

position:3782:-1
position: 3782
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4039:-1
position: 4039
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3782-4039:-1:exon

GLX_RS16390
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS16390
old locus tag: GLX_31920
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006560192.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: mobilization protein
translation: MTPIEKAKQQVEQAKARYQALLARQNAEERKLDTRRKVILGGLLIGAAGKDERFGRVIDELMKRITRDHDHKAFEGWQKPEPDRS
SIO_010081: GLX_RS16390
subclass of: SO_0000673
so part of: GLX_RS16390
location: complement(3782..4039)
location: region:3782-4039:-1
so has part: feature:3782-4039:-1:exon

WP_014357868.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3782-4039:-1:exon