Methylobacterium currus strain PR1016A plasmid unnamed2.
type: Entry
definition: Methylobacterium currus strain PR1016A plasmid unnamed2.
sequence version: NZ_CP028846.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP028846.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN08828928
keyword: RefSeq
source: Methylobacterium currus
organism: Methylobacterium currus
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Methylobacteriaceae; Methylobacterium.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP028846.1.\nBacteria and source DNA available from Woojun Park, Department of\nEnvironmental Science and Ecological Engineering. Korea University\nAnam-Dong, Seungbuk-Ku, Seoul 02841, Republic of Korea.\nGenome assembly not circularized.\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##\nAssembly Method :: PacBio SMRT Analysis v. 2.3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 93.64x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/24/2023 23:26:05\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) :: 7,243\nCDSs (total) :: 7,112\nGenes (coding) :: 6,899\nCDSs (with protein) :: 6,899\nGenes (RNA) :: 131\nrRNAs :: 12, 12, 12 (5S, 16S, 23S)\ncomplete rRNAs :: 12, 12, 12 (5S, 16S, 23S)\ntRNAs :: 91\nncRNAs :: 4\nPseudo Genes (total) :: 213\nCDSs (without protein) :: 213\nPseudo Genes (ambiguous residues) :: 0 of 213\nPseudo Genes (frameshifted) :: 82 of 213\nPseudo Genes (incomplete) :: 161 of 213\nPseudo Genes (internal stop) :: 33 of 213\nPseudo Genes (multiple problems) :: 56 of 213\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##

sequence
subclass of: SO_0000155
sequence length: 4473
topology: circular
so has quality: SO_0000988
location: 1..4473
location: region:1-4473:1
RO_0002162: 2051553

NZ_CP028846
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN08828928
type: BioSample
SIO_000068: biosample

1
title: Methylobacterium sp. PR1016A genome
author: Park, W.
journal: Unpublished

2
title: Direct Submission
author: Park, W.
journal: Submitted (04-APR-2018) Laboratory of Molecular Environmental Microbiology, Korea university, Anam-ro, Seoul 02841, Korea, Republic of

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

position:4473:1
position: 4473
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4473:1:source
so part of: sequence
organism: Methylobacterium currus
mol type: genomic DNA
strain: PR1016A
isolation source: Automobile air-conditioning evaporator
type material: type strain of Methylobacterium currus
plasmid: unnamed2
country: Korea:Seoul
collection date: 2015-09

2051553
type: Taxonomy
SIO_000068: taxonomy

DA075_RS37280
type: Gene
subclass of: SO_0000704
RO_0002162: 2051553
locus tag: DA075_RS37280
old locus tag: DA075_35410
pseudo: true
so part of: sequence
location: <1..118
location: region:1-118:1
so has part: feature:1-118:1:exon
subclass of: SO_0000010

position:118:1
position: 118
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-118:1:exon

DA075_RS37280
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2051553
locus tag: DA075_RS37280
old locus tag: DA075_35410
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003602200.1
note: incomplete; too short partial abutting assembly gap; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 2
transl table: 11
product: AAA family ATPase
SIO_010081: DA075_RS37280
subclass of: SO_0000673
so part of: DA075_RS37280
location: <1..118
location: region:1-118:1
so has part: feature:1-118:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:1-118:1:exon

DA075_RS35420
type: Gene
subclass of: SO_0000704
RO_0002162: 2051553
gene: tnpB
locus tag: DA075_RS35420
old locus tag: DA075_35415
so part of: sequence
location: 190..486
location: region:190-486:1
so has part: feature:190-486:1:exon
subclass of: SO_0000010

position:190:1
position: 190
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:486:1
position: 486
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:190-486:1:exon

DA075_RS35420
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2051553
gene: tnpB
locus tag: DA075_RS35420
old locus tag: DA075_35415
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008554466.1
note: TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase.; TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: IS66 family insertion sequence element accessory protein TnpB
translation: MTRKGFDGLAALVQDHLARDPFSGQAFVFRGRQGHLIKVLWWDGQGLCLFAKRLEKGRFVWPSTAGAAAALTPAQLAMLLEGIDWRAPLRTDRPTIAG
SIO_010081: DA075_RS35420
subclass of: SO_0000673
so part of: DA075_RS35420
location: 190..486
location: region:190-486:1
so has part: feature:190-486:1:exon

WP_244936724.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:190-486:1:exon

DA075_RS35425
type: Gene
subclass of: SO_0000704
RO_0002162: 2051553
locus tag: DA075_RS35425
old locus tag: DA075_35420
so part of: sequence
location: 566..2122
location: region:566-2122:1
so has part: feature:566-2122:1:exon
subclass of: SO_0000010

position:566:1
position: 566
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2122:1
position: 2122
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:566-2122:1:exon

DA075_RS35425
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2051553
locus tag: DA075_RS35425
old locus tag: DA075_35420
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017980713.1
GO function: GO:0004803 - transposase activity [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: IS66 family transposase
translation: MALDLATLPDDVNALKRLIVGLAREAVHASTLIEKLRGELARLKRARFGTSSEKFGPRLEQLELAIEALEVDEAERLAGALVVAEAREAARLKPARRDLPAHLPRESVVHAGPCACPACGGSLRRIGEDVTESLDYVPGRFKVVRHIREAFACRACEQVVQAPAPHHAVPRGRAGPGLLAHIAVAKFDDHLPLYRQAEIYARDGVDLATSTLSGWLGATAATLQPLTELLRREVIGGSDVLHGDDTPIPVLAPGTGKTSTGRLWTYVRDERPHGGARPPAAVFFASPDRRGERPLAHLAAFSGVLVADGYAGFNGLYEAGRAGGALTEAACWAHVRRKIFDVHAATGSALAAEALERIGALYGVERDLHGKPPDARTRERQMRSKPLAEALKAFAETSLAQVPGRSDLAKALRYMLARWPALMRTFDDGRLTLDNNAAERALRCVAVGRKNYLFAGSELGAERAAAFYTLIETAKMNGLDPEGYLRDVLTRIADHPAKRLADLLPWNWMPTGRAEQAA
SIO_010081: DA075_RS35425
subclass of: SO_0000673
so part of: DA075_RS35425
location: 566..2122
location: region:566-2122:1
so has part: feature:566-2122:1:exon

WP_099957694.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:566-2122:1:exon

DA075_RS35430
type: Gene
subclass of: SO_0000704
RO_0002162: 2051553
locus tag: DA075_RS35430
old locus tag: DA075_35425
so part of: sequence
location: complement(2135..2293)
location: region:2135-2293:-1
so has part: feature:2135-2293:-1:exon
subclass of: SO_0000010

position:2135:-1
position: 2135
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2293:-1
position: 2293
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2135-2293:-1:exon

DA075_RS35430
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2051553
locus tag: DA075_RS35430
old locus tag: DA075_35425
inference: COORDINATES: protein motif:HMM:NF018168.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: flagellar basal body rod C-terminal domain-containing protein
translation: MSGNLEMPNVYPVTEMAGLRAAMGTYEFDLKVIATLDDLNRRTIDLLKVSAR
SIO_010081: DA075_RS35430
subclass of: SO_0000673
so part of: DA075_RS35430
location: complement(2135..2293)
location: region:2135-2293:-1
so has part: feature:2135-2293:-1:exon

WP_276330954.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2135-2293:-1:exon

DA075_RS35435
type: Gene
subclass of: SO_0000704
RO_0002162: 2051553
gene: flgB
locus tag: DA075_RS35435
old locus tag: DA075_35430
so part of: sequence
location: complement(2392..2775)
location: region:2392-2775:-1
so has part: feature:2392-2775:-1:exon
subclass of: SO_0000010

position:2392:-1
position: 2392
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2775:-1
position: 2775
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2392-2775:-1:exon

DA075_RS35435
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2051553
gene: flgB
locus tag: DA075_RS35435
old locus tag: DA075_35430
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012252379.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: flagellar basal body rod protein FlgB
translation: MTEVYLFDLASKQARYLAVRQATIAGNVANANTPGYKARDVVPFSQVMAQTHLELAVTASAHTSILASDAPVRTMQSREGWDVLETSSAVSLEQEMLKANDVSRQHNLNIGVTKAFDRMLSLAIRGA
SIO_010081: DA075_RS35435
subclass of: SO_0000673
so part of: DA075_RS35435
location: complement(2392..2775)
location: region:2392-2775:-1
so has part: feature:2392-2775:-1:exon

WP_099957696.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2392-2775:-1:exon

DA075_RS35440
type: Gene
subclass of: SO_0000704
RO_0002162: 2051553
locus tag: DA075_RS35440
old locus tag: DA075_35435
so part of: sequence
location: complement(3508..>4373)
location: region:3508-4373:-1
so has part: feature:3508-4373:-1:exon
subclass of: SO_0000010

position:3508:-1
position: 3508
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4373:-1
position: 4373
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3508-4373:-1:exon

DA075_RS35440
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2051553
locus tag: DA075_RS35440
old locus tag: DA075_35435
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017485366.1
GO component: GO:0016020 - membrane [Evidence IEA]
GO function: GO:0015288 - porin activity [Evidence IEA]
GO process: GO:0008643 - carbohydrate transport [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 3
transl table: 11
product: carbohydrate porin
translation: VAGKFAMGDFFDGNVYAHDPRVDFFNWALWASSAWDFPANLAGYTQGVVVEYNRKEFAVRAAYAQVPKEPSSNVLDPRILQKGGLNVELEVRYSVLDQAGRLRFGAFSNEGRSANYREAVTLTGLDPVAFPDANTAALANRKNRNKSGGYINLEQALSPTLGMFARISASDGRNESLSFADIDRSASGGFSLKGTTWGRSDDAVGIGAAINGISRSHREFFAKGGLGLVIGEGQLRYRPETILETYYSVSLTRDVALSLDYQFVANPGYNRDRGPAHFFSARLHTDF
SIO_010081: DA075_RS35440
subclass of: SO_0000673
so part of: DA075_RS35440
location: complement(3508..>4373)
location: region:3508-4373:-1
so has part: feature:3508-4373:-1:exon

WP_164712609.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3508-4373:-1:exon