Candidatus Profftella armatura plasmid unnamed, complete sequence.
type: Entry
definition: Candidatus Profftella armatura plasmid unnamed, complete sequence.
sequence version: NC_021886.1
sequence date: 2023-02-23
sequence: sequence
division: CON
label: NC_021886.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02603760
keyword: RefSeq
source: Candidatus Profftella armatura
organism: Candidatus Profftella armatura
taxonomy: Bacteria; Pseudomonadota; Betaproteobacteria; Candidatus Profftella.
reference: 1
references: 23850282
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP003469.1.\nGenome was manually curated based on annotation generated by the\nNCBI Prokaryotic Genomes Automatic Annotation Pipeline Group.\nInformation about the Pipeline can be found here:\nhttp://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html.\nSource DNA is available from Atsushi Nakabachi, Toyohashi\nUniversity of Technology.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/23/2023 03:51:14\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) :: 403\nCDSs (total) :: 363\nGenes (coding) :: 351\nCDSs (with protein) :: 351\nGenes (RNA) :: 40\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 34\nncRNAs :: 3\nPseudo Genes (total) :: 12\nCDSs (without protein) :: 12\nPseudo Genes (ambiguous residues) :: 0 of 12\nPseudo Genes (frameshifted) :: 1 of 12\nPseudo Genes (incomplete) :: 11 of 12\nPseudo Genes (internal stop) :: 0 of 12\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 5458
topology: circular
so has quality: SO_0000988
location: 1..5458
location: region:1-5458:1
RO_0002162: 669502

NC_021886
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02603760
type: BioSample
SIO_000068: biosample

1
title: Defensive bacteriome symbiont with a drastically reduced genome
author: Nakabachi, A.
author: Ueoka, R.
author: Oshima, K.
author: Teta, R.
author: Mangoni, A.
author: Gurgui, M.
author: Oldham, N.J.
author: van Echten-Deckert, G.
author: Okamura, K.
author: Yamamoto, K.
author: Inoue, H.
author: Ohkuma, M.
author: Hongoh, Y.
author: Miyagishima, S.Y.
author: Hattori, M.
author: Piel, J.
author: Fukatsu, T.
journal: Curr Biol
volume: 23
issue: 15
pages: 1478-1484
year: 2013
pubmed: 23850282

23850282
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Nakabachi, A.
journal: Submitted (03-APR-2012) Electronics-Inspired Interdisciplinary Research Institute, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan

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

position:5458:1
position: 5458
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5458:1:source
so part of: sequence
organism: Candidatus Profftella armatura
mol type: genomic DNA
strain: DC
host: Diaphorina citri
plasmid: unnamed
country: Japan

669502
type: Taxonomy
SIO_000068: taxonomy

SSDC_RS01985
type: Gene
subclass of: SO_0000704
RO_0002162: 669502
locus tag: SSDC_RS01985
old locus tag: SSDC_01974
so part of: sequence
location: 1..897
location: region:1-897:1
so has part: feature:1-897:1:exon
subclass of: SO_0000010

position:897:1
position: 897
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-897:1:exon

SSDC_RS01985
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 669502
locus tag: SSDC_RS01985
old locus tag: SSDC_01974
inference: COORDINATES: protein motif:HMM:NF016670.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication protein RepA
translation: MFFRYNKLIKYALRIKKKDVKKVNTLGCITKTLAQATLPHTNPKLPIGTLYSRSTGQLIFSIIPTSPNYGIPYGSIPRLILAWICSEVIKTKKRILFLGKSQSDFLKQINLHNNGRDIARFREQALRLFKSVISIEYNDEKKNNFSSRLLISESSHIFWNTKTRKKKWESSLELSDGFFREIIDASVPIDIRIFHALSKSPLAMDIYTWLVYRIFILQKSKLSSVFISWINLKFQFGVGYPNTNQGFRDFKKRFRLRLKEVLFFYKKAKRHVRENKIGLIITSCDLHISKLNSKNKND
SIO_010081: SSDC_RS01985
subclass of: SO_0000673
so part of: SSDC_RS01985
location: 1..897
location: region:1-897:1
so has part: feature:1-897:1:exon

WP_020915267.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-897:1:exon

SSDC_RS01990
type: Gene
subclass of: SO_0000704
RO_0002162: 669502
locus tag: SSDC_RS01990
old locus tag: SSDC_01979
so part of: sequence
location: 988..1236
location: region:988-1236:1
so has part: feature:988-1236:1:exon
subclass of: SO_0000010

position:988:1
position: 988
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1236:1
position: 1236
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:988-1236:1:exon

SSDC_RS01990
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 669502
locus tag: SSDC_RS01990
old locus tag: SSDC_01979
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: MIVKNRKIKLLSWINLKFQFGVGYPNTNQGFRDFKKRFRLRLKEVLFFYKKAKRHVRENKIGLIITSCDLHISKLNSKNKND
SIO_010081: SSDC_RS01990
subclass of: SO_0000673
so part of: SSDC_RS01990
location: 988..1236
location: region:988-1236:1
so has part: feature:988-1236:1:exon

WP_020915268.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:988-1236:1:exon

SSDC_RS01995
type: Gene
subclass of: SO_0000704
RO_0002162: 669502
gene: crtY
locus tag: SSDC_RS01995
old locus tag: SSDC_01989
so part of: sequence
location: 1807..2967
location: region:1807-2967:1
so has part: feature:1807-2967:1:exon
subclass of: SO_0000010

position:1807:1
position: 1807
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2967:1
position: 2967
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1807-2967:1:exon

SSDC_RS01995
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 669502
gene: crtY
locus tag: SSDC_RS01995
old locus tag: SSDC_01989
EC number: 5.5.1.19
inference: COORDINATES: protein motif:HMM:TIGR01789.1
GO function: GO:0045436 - lycopene beta cyclase activity [Evidence IEA]
GO process: GO:0016117 - carotenoid biosynthetic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: lycopene beta-cyclase CrtY
translation: MNFEKNYYWDFILIGAGLWNSIIAWYLKQYNPKLNVLLLELSSSVKNHIWSFHQNDISSSQYMLIKPLITYSWPSYQVKFPKFNRKIFSGYYSICSKHLNSYLIRALGINNFLFNNKTVEIITPTSIRINNKKIINANCIIDGRGLKNSQFDGIYQIFLGQQWNLSSPHGLDIPIIMDATVNQKNDEYHFIYTLPLTPNSLMIEDTRYTKKPFLKIDMLKKSIKDYAIKNRWKLKNIEREEIGSIPIALKNEKIIKFKKIICVGLRANLLHATTGYSLPIAIQLAENIAKYSITTNQINSTVLFKLVKKFIINHQKKQRFFCMLNRLFFLSNSRCHLDIMQYFYTLPDKIIRNFYANKLSFFDKIRIFSGKPPISLFQALYAFLNL
SIO_010081: SSDC_RS01995
subclass of: SO_0000673
so part of: SSDC_RS01995
location: 1807..2967
location: region:1807-2967:1
so has part: feature:1807-2967:1:exon

WP_020915270.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1807-2967:1:exon

SSDC_RS02000
type: Gene
subclass of: SO_0000704
RO_0002162: 669502
locus tag: SSDC_RS02000
old locus tag: SSDC_01994
so part of: sequence
location: 2970..4451
location: region:2970-4451:1
so has part: feature:2970-4451:1:exon
subclass of: SO_0000010

position:2970:1
position: 2970
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4451:1
position: 4451
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2970-4451:1:exon

SSDC_RS02000
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 669502
locus tag: SSDC_RS02000
old locus tag: SSDC_01994
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017373878.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: phytoene desaturase
translation: MKKAIIIGAGIGGIALAIRLQTAGISTIILEQRDKPGGRAYVYKQDGFIFDAGPTVITDPNSIKLLFDLSKNRMENYVNLLPIKPFYRLYWGKEKFLNYEDNIKDLEKQIAKFNLNDIKGYRLFLNYSKKVFKEGYLSFASKSFLTINDMLFILPKLIKIKAWKSVYSIVSQFIKNDYLKQAFSFNSLFIGGNPFSTSSIYTLIHALEYEWGIWFPKGGVGALIKALIKLFQNLGGNLILNSQVISIYVNNNKVNKVHLKNGQIFDADIIVSNADIINTYRNLLGQYAFGKKKYMNLIKKKMSNSLFVIYFGLSEQYTHLAHHTIFFPSNYKKSIENIFGKNFSRDNLSIYLHSPSVTDLSLAPTGCSTFYALIPVPNLSNSSINWSEESIKLKNIVFMYLEQYCIPNLRKKLITQRIFTPNDFKDVLGSYLGSAFSFAPLLTQSAWFRPHNRDKNLTNLYFVGAGTHPGAGIPGVIASANITAEIIFNDINL
SIO_010081: SSDC_RS02000
subclass of: SO_0000673
so part of: SSDC_RS02000
location: 2970..4451
location: region:2970-4451:1
so has part: feature:2970-4451:1:exon

WP_020915271.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2970-4451:1:exon

SSDC_RS02005
type: Gene
subclass of: SO_0000704
RO_0002162: 669502
locus tag: SSDC_RS02005
old locus tag: SSDC_01999
so part of: sequence
location: 4448..5398
location: region:4448-5398:1
so has part: feature:4448-5398:1:exon
subclass of: SO_0000010

position:4448:1
position: 4448
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5398:1
position: 5398
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4448-5398:1:exon

SSDC_RS02005
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 669502
locus tag: SSDC_RS02005
old locus tag: SSDC_01999
EC number: 2.5.1.-
inference: COORDINATES: protein motif:HMM:NF012705.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: phytoene/squalene synthase family protein
translation: MIDDSILKLANKIIKAGSKSFSSAIKLFDPVIRYKVLMLYAWCRYCDDVIDNQICGNRSKFLKKNVSMKHKLKILRIKTKRACIGFKMKEPAFLALQKIISIHSFPVHLLFEHLDGFEMDVMERTYITLDETLGYCYHVAGTIGLIIAHLIGVKEKDTLNCARNLGIAFQLTNISRDVIDDFYVGRCYLPLDWLRNEGLNKSNFVLAENRKKLFKVVTRILDIAEFYYSSSLVKLNTLPLRSTLAIVTSWSIYREIGIKIRKYKHKAWNKRQHTNFFEKLKIFLTIFFKLIISRIAISLNIYKKNFFKKFKKIFKK
SIO_010081: SSDC_RS02005
subclass of: SO_0000673
so part of: SSDC_RS02005
location: 4448..5398
location: region:4448-5398:1
so has part: feature:4448-5398:1:exon

WP_020915272.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4448-5398:1:exon