Komagataeibacter medellinensis NBRC 3288 plasmid pGXY040, complete sequence.
type: Entry
definition: Komagataeibacter medellinensis NBRC 3288 plasmid pGXY040, complete sequence.
sequence version: NC_016022.1
sequence date: 2022-12-24
sequence: sequence
division: CON
label: NC_016022.1
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\nAP012163.1.\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: 4776
topology: circular
so has quality: SO_0000988
location: 1..4776
location: region:1-4776:1
RO_0002162: 634177

NC_016022
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:4776:1
position: 4776
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4776:1: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: pGXY040

3288
type: NBRC
SIO_000068: nbrc

634177
type: Taxonomy
SIO_000068: taxonomy

GLX_RS16315
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS16315
old locus tag: GLX_31800
so part of: sequence
location: 1..882
location: region:1-882:1
so has part: feature:1-882:1:exon
subclass of: SO_0000010

position:882:1
position: 882
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-882:1:exon

GLX_RS16315
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS16315
old locus tag: GLX_31800
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006741876.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helicase RepA family protein
translation: MAAVTSTINDSALPRLDIRSAFVTAPEPLDFVLPGMLAGTVGALIAPGGTGKSWFALELAMAVAGGPDLLEMSVDDKYGGVLYLAAEDPALAITHRLHSVGYVVRDSIGMLAENLEIIPLMGRPVNLLLPAWAEALKRMGTGKRLIILDTLRRFHVADENNGGDMAALLSVLEDIAQVTGASIMFLHHAAKGASLNGSGDVQQASRGSSVLVDNVRGGQINLVGMTDAEAQTYGVTDRRQFVRSVQSKVNFGCGNSDRWYRRDTGGVLVPAHLERQEPTPTTRRPTGRARGNA
SIO_010081: GLX_RS16315
subclass of: SO_0000673
so part of: GLX_RS16315
location: 1..882
location: region:1-882:1
so has part: feature:1-882:1:exon

WP_014095398.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-882:1:exon

GLX_RS16320
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
gene: repC
locus tag: GLX_RS16320
old locus tag: GLX_31810
so part of: sequence
location: 875..1720
location: region:875-1720:1
so has part: feature:875-1720:1:exon
subclass of: SO_0000010

position:875:1
position: 875
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1720:1
position: 1720
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:875-1720:1:exon

GLX_RS16320
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
gene: repC
locus tag: GLX_RS16320
old locus tag: GLX_31810
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014003864.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication protein C, IncQ-type
translation: MRNNKALTHARHDPGHVLAHGLFRSLASGDYKRLKLDVAYEIGNERLEFGAKEPLGTDEMRVLQGLVALAGPKGLILKADTQSSDARQLFLDLFAPASEFVAATDQPESLVVRGSFRRLAREIGMNESGPNITRIRQAIERLFAVTIFIQSGRRRVGCRLISSYASDEGVGDLYVALNPRLTEAILGQGQHVRIDMEEVRGLKSDPARLMHQRLSGWINPGMRREVSIDTLCSYVWPDAGSDAAMRKRRQRIRSALAELRKVGWFADVQEGVVTVGRPKIA
SIO_010081: GLX_RS16320
subclass of: SO_0000673
so part of: GLX_RS16320
location: 875..1720
location: region:875-1720:1
so has part: feature:875-1720:1:exon

WP_014095399.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:875-1720:1:exon

GLX_RS18340
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS18340
so part of: sequence
location: 2134..2520
location: region:2134-2520:1
so has part: feature:2134-2520:1:exon
subclass of: SO_0000010

position:2134:1
position: 2134
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2520:1
position: 2520
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2134-2520:1:exon

GLX_RS18340
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS18340
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013123520.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid mobilization relaxosome protein MobC
translation: MEQSSPSPKKRRYGPTPKASSDRRWHSVSCRLTDDELALVDARRGKVRRGEWLRLSALGKPPRIVPELNRVAWVDLARSASNLNQIAHAVNCGEVPAGGDLASVLDALRADLDALRLAMIGGGDEGEG
SIO_010081: GLX_RS18340
subclass of: SO_0000673
so part of: GLX_RS18340
location: 2134..2520
location: region:2134-2520:1
so has part: feature:2134-2520:1:exon

WP_148268693.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2134-2520:1:exon

GLX_RS19120
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS19120
so part of: sequence
location: 3249..3734
location: region:3249-3734:1
so has part: feature:3249-3734:1:exon
subclass of: SO_0000010

position:3249:1
position: 3249
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3734:1
position: 3734
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3249-3734:1:exon

GLX_RS19120
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS19120
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: MSKIETVRRLSQEQTEASRRAVTSTTEAQMLLIETLDRLATDQSRLTVEYRAAAVSLIETLTKAAEASEAMILGAHGEAQSVLMSATAAVSKADSAAAKTADLLKSAETAARDQHREMKRLVERQTALSRRLMTCAIIVAVSAAGTLLGAGLVILRVMHPL
SIO_010081: GLX_RS19120
subclass of: SO_0000673
so part of: GLX_RS19120
location: 3249..3734
location: region:3249-3734:1
so has part: feature:3249-3734:1:exon

WP_041247991.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3249-3734:1:exon

GLX_RS19125
type: Gene
subclass of: SO_0000704
RO_0002162: 634177
locus tag: GLX_RS19125
so part of: sequence
location: 3650..4684
location: region:3650-4684:1
so has part: feature:3650-4684:1:exon
subclass of: SO_0000010

position:3650:1
position: 3650
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4684:1
position: 4684
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3650-4684:1:exon

GLX_RS19125
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 634177
locus tag: GLX_RS19125
inference: COORDINATES: protein motif:HMM:NF028103.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DNA-primase RepB domain-containing protein
translation: MRDHRRRIGGWNALGRRVGDLASDAPALTTKPVTAAVRAKMEAWSVQAGALSSPLYRLTLKSRRDALPSFNIGKGRGADGAEQFYSASDVAALIPYLSAQNMKGRDIYLTPIDAAHHYLVVDDMTPDTLTAMTGQGWSPAIVQESSAGNRQAVLKVPRIDGPNEQRVANALVVSLNREFGDPNFSGAIHPFRMAGFANKKPGRDNAFTRIITAAGVICEKAASALAELRAAFRPTPLPVSASAPSPGRIIRPAVSGGEFSRARGMILGLAIKHGWTVDESRLDFQAARLMSAEGMSVDEVAAGIVAESPNLTARHRDPHGYAVRTAENAAAQGAKRPSPDDMEP
SIO_010081: GLX_RS19125
subclass of: SO_0000673
so part of: GLX_RS19125
location: 3650..4684
location: region:3650-4684:1
so has part: feature:3650-4684:1:exon

WP_231850475.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3650-4684:1:exon