Komagataeibacter medellinensis NBRC 3288 plasmid pGXY050, complete sequence.
type: Entry
definition: Komagataeibacter medellinensis NBRC 3288 plasmid pGXY050, complete sequence.
sequence version: NC_016029.1
sequence date: 2022-12-24
sequence: sequence
division: CON
label: NC_016029.1
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\nAP012164.1.\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: 4615
topology: circular
so has quality: SO_0000988
location: 1..4615
location: region:1-4615:1
RO_0002162: 634177

NC_016029
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:4615:1
position: 4615
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4615:1: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: pGXY050

3288
type: NBRC
SIO_000068: nbrc

634177
type: Taxonomy
SIO_000068: taxonomy

GLX_RS16340
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS16340
old locus tag: GLX_31830
so part of: sequence
location: 1..948
location: region:1-948:1
so has part: feature:1-948:1:exon
subclass of: SO_0000010

position:948:1
position: 948
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-948:1:exon

GLX_RS16340
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS16340
old locus tag: GLX_31830
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014106735.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: site-specific integrase
translation: MLLTPRCSDPALSEADRERITSYLMASLSPATRAAYATDWQSFTVWCAEHDVLALQATPAQIASWLSSLAEAGRKASGITRARAALSHAFQGQEHNPVKAPGVERVMAGIRRTLGTAPTRKQAATAEIVRDMLAHCPSSLSGQRDKALLALGFAGALRRSELVALTTDDLLFQERGLLVTIRRSKTDQDGSGQTIGIPNGRRLRPVDAIRSWLAASGITQGPVFRSITRHGHLSAQPLSDRSVATIVKTYAHAAGYDPRGFSGHSLRAGFVTSGAQTGQDALALARVTRHKNLSVLQTYVRDDAPFLNHPGEAFL
SIO_010081: GLX_RS16340
subclass of: SO_0000673
so part of: GLX_RS16340
location: 1..948
location: region:1-948:1
so has part: feature:1-948:1:exon

WP_014106735.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-948:1:exon

GLX_RS17875
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS17875
so part of: sequence
location: complement(924..1211)
location: region:924-1211:-1
so has part: feature:924-1211:-1:exon
subclass of: SO_0000010

position:924:-1
position: 924
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1211:-1
position: 1211
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:924-1211:-1:exon

GLX_RS17875
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS17875
inference: COORDINATES: similar to AA sequence:RefSeq:WP_019092405.1
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: MARHSDRTPTHPGALLREDLLPAMGQSVTDLAARLALSEADLLDLLAERTPVTPELALRLGAVFGNGAAFWNRLQAAHDGRSHPPSGSYRNASPG
SIO_010081: GLX_RS17875
subclass of: SO_0000673
so part of: GLX_RS17875
location: complement(924..1211)
location: region:924-1211:-1
so has part: feature:924-1211:-1:exon

WP_081477960.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:924-1211:-1:exon

GLX_RS16350
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS16350
old locus tag: GLX_31840
so part of: sequence
location: 1330..1686
location: region:1330-1686:1
so has part: feature:1330-1686:1:exon
subclass of: SO_0000010

position:1330:1
position: 1330
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1686:1
position: 1686
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1330-1686:1:exon

GLX_RS16350
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS16350
old locus tag: GLX_31840
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003631001.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MTDEPKPWSIRGVHPEVRNAALAAAKREGVTIGEWLDRAIRSHVKNGRNPTENLSDVPVKQTPDLSDAERLVSMIAQLSEAGAPVPKSVSSKAYALIRDSLKGVQQQHRAALPSPEQD
SIO_010081: GLX_RS16350
subclass of: SO_0000673
so part of: GLX_RS16350
location: 1330..1686
location: region:1330-1686:1
so has part: feature:1330-1686:1:exon

WP_014106736.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1330-1686:1:exon

GLX_RS16355
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS16355
old locus tag: GLX_31850
so part of: sequence
location: complement(2131..2643)
location: region:2131-2643:-1
so has part: feature:2131-2643:-1:exon
subclass of: SO_0000010

position:2131:-1
position: 2131
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2643:-1
position: 2643
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2131-2643:-1:exon

GLX_RS16355
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS16355
old locus tag: GLX_31850
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010505713.1
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: MSQTFSSQLWTLTQSRMISGKTHLVLQALASFEGPHGLFPSHEAIAARAGCSARTVIRSLEKAYLLGLVERTRRRVKRQGRMVSGSNLYRLVLKPLEQAKVAARHYAQQLREALARRKQRFLQTDIFTAETYSKNINQPYPRHTKDEWLEILTRMQSGQTPQEAGYRGKT
SIO_010081: GLX_RS16355
subclass of: SO_0000673
so part of: GLX_RS16355
location: complement(2131..2643)
location: region:2131-2643:-1
so has part: feature:2131-2643:-1:exon

WP_231850476.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2131-2643:-1:exon

GLX_RS17880
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS17880
old locus tag: GLX_31860
so part of: sequence
location: complement(2928..3314)
location: region:2928-3314:-1
so has part: feature:2928-3314:-1:exon
subclass of: SO_0000010

position:2928:-1
position: 2928
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3314:-1
position: 3314
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2928-3314:-1:exon

GLX_RS17880
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS17880
old locus tag: GLX_31860
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: MKDNSTIEDNRVVTEFLSNKLKEIDSELSRLKKERDVTYGMLRDLNFGLLKINNINPTEKRIDIKILRSYIIDYLKFRNGKPTKSCFIYDYLNSKYKNLNKSSFRTHLLKMKKEGLIYPTYKKGYWKI
SIO_010081: GLX_RS17880
subclass of: SO_0000673
so part of: GLX_RS17880
location: complement(2928..3314)
location: region:2928-3314:-1
so has part: feature:2928-3314:-1:exon

WP_014106738.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2928-3314:-1:exon

GLX_RS16360
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS16360
old locus tag: GLX_31870
so part of: sequence
location: complement(3915..4244)
location: region:3915-4244:-1
so has part: feature:3915-4244:-1:exon
subclass of: SO_0000010

position:3915:-1
position: 3915
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4244:-1
position: 4244
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3915-4244:-1:exon

GLX_RS16360
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS16360
old locus tag: GLX_31870
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003630731.1
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: MAKLTLADIKRRGGRVDRARVQATTAAEIDQQAREDGTQSDLPGPAYPSPATVRRQLKLTQTDIAALAGVPVATWRNWEQGRVSLDPAVRTLLRVLWREPDAVRRAMVA
SIO_010081: GLX_RS16360
subclass of: SO_0000673
so part of: GLX_RS16360
location: complement(3915..4244)
location: region:3915-4244:-1
so has part: feature:3915-4244:-1:exon

WP_014106739.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3915-4244:-1:exon

GLX_RS16365
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS16365
so part of: sequence
location: complement(4232..4510)
location: region:4232-4510:-1
so has part: feature:4232-4510:-1:exon
subclass of: SO_0000010

position:4232:-1
position: 4232
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4510:-1
position: 4510
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4232-4510:-1:exon

GLX_RS16365
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS16365
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003630730.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: BrnT family toxin
translation: MTGPEIEFEWDDAKSDACFEERGFDFEYAAQIFLGPVLQKPDDRKDYGEPRIRAAGLIEGIPFMVVYTVRGTCLRIISARKMHRKEWIKWQN
SIO_010081: GLX_RS16365
subclass of: SO_0000673
so part of: GLX_RS16365
location: complement(4232..4510)
location: region:4232-4510:-1
so has part: feature:4232-4510:-1:exon

WP_041247997.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4232-4510:-1:exon